Notebook

In [1]:

%%bash
echo "TODAY'S DATE"
date
echo "------------"
echo ""
lsb_release -a
echo ""
echo "------------"
echo "HOSTNAME: "
hostname
echo ""
echo "------------"
echo "Computer Specs:"
echo ""
lscpu
echo ""
echo "------------"
echo ""
echo "Memory Specs"
echo ""
free -mh

TODAY'S DATE
Thu Jan 25 08:57:57 PST 2018
------------

Distributor ID:	Ubuntu
Description:	Ubuntu 16.04.3 LTS
Release:	16.04
Codename:	xenial

------------
HOSTNAME: 
roadrunner

------------
Computer Specs:

Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                16
On-line CPU(s) list:   0-15
Thread(s) per core:    2
Core(s) per socket:    4
Socket(s):             2
NUMA node(s):          1
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 26
Model name:            Intel(R) Xeon(R) CPU           E5520  @ 2.27GHz
Stepping:              5
CPU MHz:               1596.000
CPU max MHz:           2394.0000
CPU min MHz:           1596.0000
BogoMIPS:              4521.75
Virtualization:        VT-x
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              8192K
NUMA node0 CPU(s):     0-15
Flags:                 fpu vme de pse tsc msr pae mce cx8 apic sep mtrr pge mca cmov pat pse36 clflush dts acpi mmx fxsr sse sse2 ss ht tm pbe syscall nx rdtscp lm constant_tsc arch_perfmon pebs bts nopl xtopology nonstop_tsc aperfmperf pni dtes64 monitor ds_cpl vmx est tm2 ssse3 cx16 xtpr pdcm dca sse4_1 sse4_2 popcnt lahf_lm kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida

------------

Memory Specs

              total        used        free      shared  buff/cache   available
Mem:            47G        556M         18G         77M         28G         46G
Swap:           47G          0B         47G

No LSB modules are available.

In [2]:

%%bash
time cp /home/sam/owl/nightingales/P_generosa/[AN][DR]0*.gz /home/sam/data/geoduck_illumina/

real	149m27.558s
user	0m6.264s
sys	10m11.356s

In [3]:

%%bash
source /etc/environment
source ~/.bashrc
source ~/.bash_aliases
emailme

bash: line 3: emailme: command not found

Steven previously ran these through MultiQC and they failed the adapter sequence contamination check. See his results here: http://owl.fish.washington.edu/halfshell/bu-alanine-wd/17-09-15b/multiqc_report.html#fastqc_adapter_content

That means we need to trim them. Will use trim_galore for this; it has built-in adapter sequences for standar Illumina libraries, as well as Nextera libraries (will probably need to trim for both).

In [4]:

%%bash
ls -lh /home/sam/data/geoduck_illumina/

total 541G
-rwxr-xr-x 1 sam sam  15G Jan 25 09:05 AD002_S9_L001_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam  15G Jan 25 09:08 AD002_S9_L001_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam  17G Jan 25 09:13 AD002_S9_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam  18G Jan 25 09:17 AD002_S9_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam 3.4M Jan 25 09:17 NR005_S4_L001_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam 3.5M Jan 25 09:17 NR005_S4_L001_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam 2.8M Jan 25 09:17 NR005_S4_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam 2.9M Jan 25 09:17 NR005_S4_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam 262M Jan 25 09:17 NR006_S3_L001_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam 271M Jan 25 09:17 NR006_S3_L001_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam 217M Jan 25 09:17 NR006_S3_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam 226M Jan 25 09:17 NR006_S3_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam  25M Jan 25 09:17 NR012_S1_L001_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam  27M Jan 25 09:17 NR012_S1_L001_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam  28M Jan 25 09:17 NR012_S1_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam  29M Jan 25 09:17 NR012_S1_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam  26G Jan 25 09:23 NR013_AD013_S2_L001_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam  28G Jan 25 09:30 NR013_AD013_S2_L001_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam  30G Jan 25 09:37 NR013_AD013_S2_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam  32G Jan 25 09:44 NR013_AD013_S2_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam  64G Jan 25 10:02 NR014_AD014_S5_L001_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam  66G Jan 25 10:20 NR014_AD014_S5_L001_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam  70G Jan 25 10:39 NR014_AD014_S5_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam  73G Jan 25 11:01 NR014_AD014_S5_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam  22G Jan 25 11:07 NR015_AD015_S6_L001_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam  23G Jan 25 11:15 NR015_AD015_S6_L001_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam  23G Jan 25 11:23 NR015_AD015_S6_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam  24G Jan 25 11:31 NR015_AD015_S6_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam 4.5M Jan 25 11:31 NR019_S7_L001_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam 4.5M Jan 25 11:31 NR019_S7_L001_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam 2.5M Jan 25 11:31 NR019_S7_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam 2.5M Jan 25 11:31 NR019_S7_L002_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam 319M Jan 25 11:31 NR021_S8_L001_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam 333M Jan 25 11:31 NR021_S8_L001_R2_001.fastq.gz
-rwxr-xr-x 1 sam sam 265M Jan 25 11:31 NR021_S8_L002_R1_001.fastq.gz
-rwxr-xr-x 1 sam sam 276M Jan 25 11:31 NR021_S8_L002_R2_001.fastq.gz

Restarted notebook to load in fixes for email notifications.

In [1]:

%%bash
date

Thu Jan 25 11:52:01 PST 2018

In [2]:

%%bash
mkdir /home/sam/data/geoduck_illumina/trimmed

In [3]:

%%bash
time /home/shared/trimgalore/trim_galore \
--paired \
--output_dir /home/sam/data/geoduck_illumina/trimmed/
emailme

No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)


Please provide the filename(s) of one or more FastQ file(s) to launch Trim Galore!

USAGE:  'trim_galore [options] <filename(s)>'    or    'trim_galore --help'    for more options


real	0m1.499s
user	0m0.036s
sys	0m0.012s
bash: line 4: emailme: command not found

In [4]:

%%bash
echo $EMAIL

samwhite@uw.edu

In [5]:

%%bash
echo "testing"; emailme

testing

bash: line 1: emailme: command not found

In [6]:

%%bash
source /home/sam/.bash_aliases

In [7]:

%%bash
echo "testing"; emailme

testing

bash: line 1: emailme: command not found

In [8]:

%%bash
source /home/sam/.bash_aliases
echo "testing"; emailme

testing

bash: line 2: emailme: command not found

In [9]:

%%bash
cat /home/sam/.bash_aliases

# Alias for emailing with default email sender/subject
alias emailme='cat ~/.default_subject.mail | msmtp "$EMAIL"'

In [10]:

%%bash
cat /home/sam/.bash_aliases

# Alias for emailing with default email sender/subject
alias emailme='cat ~/.default-subject.mail | msmtp "$EMAIL"'

In [11]:

%%bash
source /home/sam/.bash_aliases
echo "testing"; emailme

testing

bash: line 2: emailme: command not found

In [12]:

%%bash
for file in /home/sam/data/geoduck_illumina/*.gz
do
printf %s/n "$file \"
done

bash: line 3: unexpected EOF while looking for matching `"'
bash: line 5: syntax error: unexpected end of file

In [13]:

%%bash
for file in /home/sam/data/geoduck_illumina/*.gz
do
printf ""%s\n"" "$file \"
done

bash: line 3: unexpected EOF while looking for matching `"'
bash: line 5: syntax error: unexpected end of file

In [14]:

%%bash
for file in /home/sam/data/geoduck_illumina/*.gz
do
printf "%s\n" "$file \"
done

bash: line 3: unexpected EOF while looking for matching `"'
bash: line 5: syntax error: unexpected end of file

In [15]:

%%bash
for file in /home/sam/data/geoduck_illumina/*.gz
do
printf "%s\n" "$file \\"
done

/home/sam/data/geoduck_illumina/AD002_S9_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/AD002_S9_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/AD002_S9_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/AD002_S9_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR005_S4_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR005_S4_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR005_S4_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR005_S4_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR006_S3_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR006_S3_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR006_S3_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR006_S3_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR012_S1_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR012_S1_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR012_S1_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR012_S1_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR019_S7_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR019_S7_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR019_S7_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR019_S7_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR021_S8_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR021_S8_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR021_S8_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR021_S8_L002_R2_001.fastq.gz \

In [16]:

%%bash
for file in /home/sam/data/geoduck_illumina/*.gz
do
filename=${file##*/}
printf "%s\n" "$filename \\"
done

AD002_S9_L001_R1_001.fastq.gz \
AD002_S9_L001_R2_001.fastq.gz \
AD002_S9_L002_R1_001.fastq.gz \
AD002_S9_L002_R2_001.fastq.gz \
NR005_S4_L001_R1_001.fastq.gz \
NR005_S4_L001_R2_001.fastq.gz \
NR005_S4_L002_R1_001.fastq.gz \
NR005_S4_L002_R2_001.fastq.gz \
NR006_S3_L001_R1_001.fastq.gz \
NR006_S3_L001_R2_001.fastq.gz \
NR006_S3_L002_R1_001.fastq.gz \
NR006_S3_L002_R2_001.fastq.gz \
NR012_S1_L001_R1_001.fastq.gz \
NR012_S1_L001_R2_001.fastq.gz \
NR012_S1_L002_R1_001.fastq.gz \
NR012_S1_L002_R2_001.fastq.gz \
NR013_AD013_S2_L001_R1_001.fastq.gz \
NR013_AD013_S2_L001_R2_001.fastq.gz \
NR013_AD013_S2_L002_R1_001.fastq.gz \
NR013_AD013_S2_L002_R2_001.fastq.gz \
NR014_AD014_S5_L001_R1_001.fastq.gz \
NR014_AD014_S5_L001_R2_001.fastq.gz \
NR014_AD014_S5_L002_R1_001.fastq.gz \
NR014_AD014_S5_L002_R2_001.fastq.gz \
NR015_AD015_S6_L001_R1_001.fastq.gz \
NR015_AD015_S6_L001_R2_001.fastq.gz \
NR015_AD015_S6_L002_R1_001.fastq.gz \
NR015_AD015_S6_L002_R2_001.fastq.gz \
NR019_S7_L001_R1_001.fastq.gz \
NR019_S7_L001_R2_001.fastq.gz \
NR019_S7_L002_R1_001.fastq.gz \
NR019_S7_L002_R2_001.fastq.gz \
NR021_S8_L001_R1_001.fastq.gz \
NR021_S8_L001_R2_001.fastq.gz \
NR021_S8_L002_R1_001.fastq.gz \
NR021_S8_L002_R2_001.fastq.gz \

In [17]:

%%bash
time /home/shared/trimgalore/trim_galore \
--paired \
--output_dir /home/sam/data/geoduck_illumina/trimmed/ \
AD002_S9_L001_R1_001.fastq.gz \
AD002_S9_L001_R2_001.fastq.gz \
AD002_S9_L002_R1_001.fastq.gz \
AD002_S9_L002_R2_001.fastq.gz \
NR005_S4_L001_R1_001.fastq.gz \
NR005_S4_L001_R2_001.fastq.gz \
NR005_S4_L002_R1_001.fastq.gz \
NR005_S4_L002_R2_001.fastq.gz \
NR006_S3_L001_R1_001.fastq.gz \
NR006_S3_L001_R2_001.fastq.gz \
NR006_S3_L002_R1_001.fastq.gz \
NR006_S3_L002_R2_001.fastq.gz \
NR012_S1_L001_R1_001.fastq.gz \
NR012_S1_L001_R2_001.fastq.gz \
NR012_S1_L002_R1_001.fastq.gz \
NR012_S1_L002_R2_001.fastq.gz \
NR013_AD013_S2_L001_R1_001.fastq.gz \
NR013_AD013_S2_L001_R2_001.fastq.gz \
NR013_AD013_S2_L002_R1_001.fastq.gz \
NR013_AD013_S2_L002_R2_001.fastq.gz \
NR014_AD014_S5_L001_R1_001.fastq.gz \
NR014_AD014_S5_L001_R2_001.fastq.gz \
NR014_AD014_S5_L002_R1_001.fastq.gz \
NR014_AD014_S5_L002_R2_001.fastq.gz \
NR015_AD015_S6_L001_R1_001.fastq.gz \
NR015_AD015_S6_L001_R2_001.fastq.gz \
NR015_AD015_S6_L002_R1_001.fastq.gz \
NR015_AD015_S6_L002_R2_001.fastq.gz \
NR019_S7_L001_R1_001.fastq.gz \
NR019_S7_L001_R2_001.fastq.gz \
NR019_S7_L002_R1_001.fastq.gz \
NR019_S7_L002_R2_001.fastq.gz \
NR021_S8_L001_R1_001.fastq.gz \
NR021_S8_L001_R2_001.fastq.gz \
NR021_S8_L002_R1_001.fastq.gz \
NR021_S8_L002_R2_001.fastq.gz

1.9.1

No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

gzip: AD002_S9_L001_R1_001.fastq.gz: No such file or directory
Input file 'AD002_S9_L001_R1_001.fastq.gz' seems to be completely empty. Consider respecifying!

Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> AD002_S9_L001_R1_001.fastq.gz <<)

gzip: AD002_S9_L001_R1_001.fastq.gz: No such file or directory
Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
Illegal division by zero at /home/shared/trimgalore/trim_galore line 1229.

real	0m1.615s
user	0m0.112s
sys	0m0.024s

In [18]:

cat ~/.default-subject.mail | msmtp "$EMAIL"

In [19]:

%%bash
time /home/shared/trimgalore/trim_galore \
--paired \
--output_dir /home/sam/data/geoduck_illumina/trimmed/ \
/home/sam/data/geoduck_illumina/AD002_S9_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/AD002_S9_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/AD002_S9_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/AD002_S9_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR005_S4_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR005_S4_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR005_S4_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR005_S4_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR006_S3_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR006_S3_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR006_S3_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR006_S3_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR012_S1_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR012_S1_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR012_S1_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR012_S1_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR019_S7_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR019_S7_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR019_S7_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR019_S7_L002_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR021_S8_L001_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR021_S8_L001_R2_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR021_S8_L002_R1_001.fastq.gz \
/home/sam/data/geoduck_illumina/NR021_S8_L002_R2_001.fastq.gz

1.9.1

No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> /home/sam/data/geoduck_illumina/AD002_S9_L001_R1_001.fastq.gz <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
Nextera	373733	CTGTCTCTTATA	1000000	37.37
Illumina	15621	AGATCGGAAGAGC	1000000	1.56
smallRNA	4	TGGAATTCTCGG	1000000	0.00
Using Nextera adapter for trimming (count: 373733). Second best hit was Illumina (count: 15621)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/AD002_S9_L001_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to AD002_S9_L001_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/AD002_S9_L001_R1_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/AD002_S9_L001_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 4482.08 s (24 us/read; 2.51 M reads/minute).

=== Summary ===

Total reads processed:             187,796,434
Reads with adapters:               108,648,810 (57.9%)
Reads written (passing filters):   187,796,434 (100.0%)

Total basepairs processed: 28,357,261,534 bp
Quality-trimmed:              69,695,707 bp (0.2%)
Total written (filtered):  21,758,478,183 bp (76.7%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 108648810 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 17.6%
  C: 35.0%
  G: 20.6%
  T: 26.7%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	19862890	46949108.5	0	19862890
2	5913069	11737277.1	0	5913069
3	2045500	2934319.3	0	2045500
4	923646	733579.8	0	923646
5	581270	183395.0	0	581270
6	473952	45848.7	0	473952
7	477046	11462.2	0	477046
8	506207	2865.5	0	506207
9	429336	716.4	0	425000 4336
10	477601	179.1	1	446591 31010
11	496442	44.8	1	467811 28631
12	470709	11.2	1	439639 31070
13	485921	11.2	1	457188 28733
14	445391	11.2	1	418393 26998
15	536842	11.2	1	502591 34251
16	578317	11.2	1	543340 34977
17	347969	11.2	1	327499 20470
18	491372	11.2	1	463777 27595
19	504486	11.2	1	478695 25791
20	446679	11.2	1	419960 26719
21	493397	11.2	1	467370 26027
22	545771	11.2	1	515112 30659
23	404368	11.2	1	380754 23614
24	504717	11.2	1	478368 26349
25	438793	11.2	1	416645 22148
26	518329	11.2	1	488120 30209
27	491943	11.2	1	466877 25066
28	464468	11.2	1	440682 23786
29	481248	11.2	1	458288 22960
30	528107	11.2	1	500993 27114
31	489811	11.2	1	464264 25547
32	474388	11.2	1	451937 22451
33	478470	11.2	1	454082 24388
34	480220	11.2	1	457224 22996
35	488796	11.2	1	463539 25257
36	528715	11.2	1	504098 24617
37	468294	11.2	1	443393 24901
38	516389	11.2	1	491239 25150
39	504166	11.2	1	479708 24458
40	504772	11.2	1	480743 24029
41	497388	11.2	1	472917 24471
42	503256	11.2	1	479203 24053
43	500098	11.2	1	476330 23768
44	499772	11.2	1	476045 23727
45	502817	11.2	1	479398 23419
46	499435	11.2	1	475501 23934
47	508746	11.2	1	485077 23669
48	504236	11.2	1	480644 23592
49	510124	11.2	1	486308 23816
50	507278	11.2	1	483978 23300
51	509992	11.2	1	486588 23404
52	510956	11.2	1	488137 22819
53	513247	11.2	1	490293 22954
54	511277	11.2	1	488419 22858
55	512173	11.2	1	489481 22692
56	514152	11.2	1	491750 22402
57	516243	11.2	1	493679 22564
58	516952	11.2	1	494663 22289
59	520137	11.2	1	497533 22604
60	521470	11.2	1	499230 22240
61	523017	11.2	1	500690 22327
62	521644	11.2	1	499715 21929
63	522362	11.2	1	500517 21845
64	521660	11.2	1	500073 21587
65	523669	11.2	1	501771 21898
66	523555	11.2	1	501965 21590
67	525958	11.2	1	504466 21492
68	527930	11.2	1	506663 21267
69	531548	11.2	1	510020 21528
70	531427	11.2	1	509837 21590
71	535318	11.2	1	513792 21526
72	533752	11.2	1	512805 20947
73	535054	11.2	1	513827 21227
74	534874	11.2	1	513683 21191
75	534350	11.2	1	513385 20965
76	537816	11.2	1	516778 21038
77	538471	11.2	1	517588 20883
78	540612	11.2	1	519613 20999
79	544380	11.2	1	523348 21032
80	546669	11.2	1	525727 20942
81	547518	11.2	1	526685 20833
82	548135	11.2	1	527694 20441
83	548870	11.2	1	528385 20485
84	548717	11.2	1	528375 20342
85	549117	11.2	1	528665 20452
86	549211	11.2	1	528761 20450
87	552056	11.2	1	531833 20223
88	553878	11.2	1	533813 20065
89	558989	11.2	1	539020 19969
90	560248	11.2	1	539997 20251
91	564403	11.2	1	544171 20232
92	565138	11.2	1	545285 19853
93	563567	11.2	1	543638 19929
94	562873	11.2	1	543490 19383
95	564022	11.2	1	544851 19171
96	565332	11.2	1	546247 19085
97	565694	11.2	1	546817 18877
98	567802	11.2	1	549213 18589
99	571052	11.2	1	551955 19097
100	578310	11.2	1	559322 18988
101	579982	11.2	1	560847 19135
102	581851	11.2	1	562931 18920
103	582338	11.2	1	563504 18834
104	581897	11.2	1	563677 18220
105	582162	11.2	1	563575 18587
106	584452	11.2	1	565201 19251
107	585199	11.2	1	566128 19071
108	585585	11.2	1	566374 19211
109	590983	11.2	1	572016 18967
110	597596	11.2	1	578755 18841
111	602875	11.2	1	583907 18968
112	604774	11.2	1	585834 18940
113	606458	11.2	1	587404 19054
114	603940	11.2	1	585325 18615
115	602671	11.2	1	584245 18426
116	603098	11.2	1	584684 18414
117	601322	11.2	1	583229 18093
118	602874	11.2	1	585432 17442
119	607469	11.2	1	589940 17529
120	614394	11.2	1	597046 17348
121	621318	11.2	1	603834 17484
122	627635	11.2	1	610100 17535
123	628652	11.2	1	611112 17540
124	623745	11.2	1	606579 17166
125	623213	11.2	1	605905 17308
126	621191	11.2	1	604400 16791
127	623732	11.2	1	607347 16385
128	627258	11.2	1	611387 15871
129	629912	11.2	1	614647 15265
130	639245	11.2	1	624973 14272
131	647229	11.2	1	633032 14197
132	650488	11.2	1	636946 13542
133	648379	11.2	1	635925 12454
134	623141	11.2	1	611943 11198
135	618297	11.2	1	607766 10531
136	606623	11.2	1	596528 10095
137	596508	11.2	1	587014 9494
138	576880	11.2	1	567742 9138
139	578999	11.2	1	569999 9000
140	604758	11.2	1	595394 9364
141	631799	11.2	1	622180 9619
142	562420	11.2	1	553470 8950
143	560808	11.2	1	552100 8708
144	607571	11.2	1	598417 9154
145	618301	11.2	1	608953 9348
146	692057	11.2	1	681341 10716
147	606471	11.2	1	596463 10008
148	616191	11.2	1	605739 10452
149	535095	11.2	1	525226 9869
150	470574	11.2	1	460819 9755
151	129846	11.2	1	118414 11432


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/AD002_S9_L001_R1_001.fastq.gz
=============================================
187796434 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/AD002_S9_L001_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to AD002_S9_L001_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/AD002_S9_L001_R2_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/AD002_S9_L001_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 4531.42 s (24 us/read; 2.49 M reads/minute).

=== Summary ===

Total reads processed:             187,796,434
Reads with adapters:               100,915,965 (53.7%)
Reads written (passing filters):   187,796,434 (100.0%)

Total basepairs processed: 28,357,261,534 bp
Quality-trimmed:              94,931,330 bp (0.3%)
Total written (filtered):  22,585,496,126 bp (79.6%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 100915965 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 18.4%
  C: 33.9%
  G: 20.7%
  T: 26.9%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	20650020	46949108.5	0	20650020
2	6146591	11737277.1	0	6146591
3	2063660	2934319.3	0	2063660
4	928498	733579.8	0	928498
5	556966	183395.0	0	556966
6	447817	45848.7	0	447817
7	447043	11462.2	0	447043
8	483777	2865.5	0	483777
9	396818	716.4	0	391992 4826
10	450848	179.1	1	409394 41454
11	475250	44.8	1	433221 42029
12	431724	11.2	1	391413 40311
13	464934	11.2	1	421617 43317
14	408441	11.2	1	373001 35440
15	511046	11.2	1	461934 49112
16	519299	11.2	1	474033 45266
17	344217	11.2	1	314891 29326
18	462589	11.2	1	422724 39865
19	480574	11.2	1	442349 38225
20	419028	11.2	1	385224 33804
21	460933	11.2	1	421638 39295
22	500587	11.2	1	458801 41786
23	390996	11.2	1	358743 32253
24	465914	11.2	1	425972 39942
25	423719	11.2	1	391596 32123
26	485401	11.2	1	441113 44288
27	468114	11.2	1	430294 37820
28	434335	11.2	1	400519 33816
29	455764	11.2	1	420992 34772
30	486842	11.2	1	449922 36920
31	448704	11.2	1	415257 33447
32	448446	11.2	1	413280 35166
33	448111	11.2	1	415051 33060
34	456901	11.2	1	421409 35492
35	439833	11.2	1	407311 32522
36	509049	11.2	1	472481 36568
37	424417	11.2	1	394152 30265
38	486419	11.2	1	450966 35453
39	471960	11.2	1	437628 34332
40	471765	11.2	1	439658 32107
41	462077	11.2	1	430652 31425
42	472140	11.2	1	440570 31570
43	465706	11.2	1	434911 30795
44	464453	11.2	1	433263 31190
45	469081	11.2	1	437985 31096
46	459298	11.2	1	429257 30041
47	474981	11.2	1	443732 31249
48	469209	11.2	1	439383 29826
49	473557	11.2	1	442818 30739
50	470041	11.2	1	440425 29616
51	473783	11.2	1	443509 30274
52	474757	11.2	1	444462 30295
53	475307	11.2	1	445128 30179
54	472071	11.2	1	442640 29431
55	475395	11.2	1	445582 29813
56	475724	11.2	1	445975 29749
57	476269	11.2	1	446159 30110
58	476959	11.2	1	447093 29866
59	478099	11.2	1	448834 29265
60	478576	11.2	1	449612 28964
61	479282	11.2	1	450016 29266
62	481457	11.2	1	452783 28674
63	478247	11.2	1	449894 28353
64	478841	11.2	1	450466 28375
65	478549	11.2	1	450611 27938
66	479979	11.2	1	451904 28075
67	481071	11.2	1	453308 27763
68	482818	11.2	1	455896 26922
69	484993	11.2	1	457915 27078
70	486889	11.2	1	460560 26329
71	487578	11.2	1	461120 26458
72	485738	11.2	1	459656 26082
73	488282	11.2	1	461838 26444
74	487590	11.2	1	461697 25893
75	487303	11.2	1	461346 25957
76	486311	11.2	1	460232 26079
77	488979	11.2	1	463045 25934
78	490213	11.2	1	464154 26059
79	492178	11.2	1	466091 26087
80	492827	11.2	1	466797 26030
81	492482	11.2	1	467029 25453
82	491966	11.2	1	466587 25379
83	493081	11.2	1	467963 25118
84	491190	11.2	1	466462 24728
85	492594	11.2	1	468151 24443
86	490583	11.2	1	465975 24608
87	493010	11.2	1	469115 23895
88	493945	11.2	1	470101 23844
89	497734	11.2	1	473992 23742
90	501831	11.2	1	478080 23751
91	503337	11.2	1	479396 23941
92	501925	11.2	1	478668 23257
93	501448	11.2	1	478337 23111
94	501486	11.2	1	478357 23129
95	502017	11.2	1	478999 23018
96	500520	11.2	1	477575 22945
97	499635	11.2	1	477000 22635
98	501649	11.2	1	479271 22378
99	505010	11.2	1	482347 22663
100	509609	11.2	1	486981 22628
101	511840	11.2	1	489583 22257
102	511708	11.2	1	489794 21914
103	510594	11.2	1	488660 21934
104	507823	11.2	1	486170 21653
105	508658	11.2	1	486649 22009
106	507271	11.2	1	485790 21481
107	509055	11.2	1	487589 21466
108	510254	11.2	1	489106 21148
109	514493	11.2	1	492907 21586
110	520231	11.2	1	498699 21532
111	522522	11.2	1	500937 21585
112	523991	11.2	1	502802 21189
113	523643	11.2	1	502433 21210
114	520343	11.2	1	499062 21281
115	517356	11.2	1	496367 20989
116	517419	11.2	1	496877 20542
117	516465	11.2	1	496247 20218
118	516238	11.2	1	496476 19762
119	518995	11.2	1	498684 20311
120	523000	11.2	1	502330 20670
121	529423	11.2	1	508680 20743
122	533679	11.2	1	513238 20441
123	532550	11.2	1	513115 19435
124	529611	11.2	1	510522 19089
125	525244	11.2	1	505674 19570
126	524042	11.2	1	505297 18745
127	523692	11.2	1	505543 18149
128	524364	11.2	1	506458 17906
129	527599	11.2	1	509650 17949
130	535228	11.2	1	517692 17536
131	539486	11.2	1	521571 17915
132	540903	11.2	1	523267 17636
133	538194	11.2	1	521637 16557
134	518674	11.2	1	502197 16477
135	510992	11.2	1	495319 15673
136	498733	11.2	1	483585 15148
137	485446	11.2	1	470312 15134
138	466869	11.2	1	452108 14761
139	468212	11.2	1	453288 14924
140	490235	11.2	1	475108 15127
141	508536	11.2	1	493732 14804
142	459703	11.2	1	446002 13701
143	463847	11.2	1	449849 13998
144	504000	11.2	1	488925 15075
145	519512	11.2	1	504195 15317
146	567962	11.2	1	551637 16325
147	502594	11.2	1	488956 13638
148	499738	11.2	1	487156 12582
149	408142	11.2	1	397294 10848
150	360984	11.2	1	350911 10073
151	96862	11.2	1	86400 10462


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/AD002_S9_L001_R2_001.fastq.gz
=============================================
187796434 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files AD002_S9_L001_R1_001_trimmed.fq.gz and AD002_S9_L001_R2_001_trimmed.fq.gz
file_1: AD002_S9_L001_R1_001_trimmed.fq.gz, file_2: AD002_S9_L001_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: AD002_S9_L001_R1_001_trimmed.fq.gz and AD002_S9_L001_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to AD002_S9_L001_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to AD002_S9_L001_R2_001_val_2.fq.gz

Total number of sequences analysed: 187796434

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 21276885 (11.33%)

Deleting both intermediate output files AD002_S9_L001_R1_001_trimmed.fq.gz and AD002_S9_L001_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/AD002_S9_L002_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to AD002_S9_L002_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/AD002_S9_L002_R1_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/AD002_S9_L002_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 5604.32 s (24 us/read; 2.54 M reads/minute).

=== Summary ===

Total reads processed:             236,917,763
Reads with adapters:               130,979,298 (55.3%)
Reads written (passing filters):   236,917,763 (100.0%)

Total basepairs processed: 35,774,582,213 bp
Quality-trimmed:              88,859,002 bp (0.2%)
Total written (filtered):  28,048,913,479 bp (78.4%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 130979298 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 18.0%
  C: 34.6%
  G: 20.6%
  T: 26.7%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	26072283	59229440.8	0	26072283
2	7754424	14807360.2	0	7754424
3	2615393	3701840.0	0	2615393
4	1158233	925460.0	0	1158233
5	687215	231365.0	0	687215
6	571963	57841.3	0	571963
7	562880	14460.3	0	562880
8	589858	3615.1	0	589858
9	515603	903.8	0	510820 4783
10	558528	225.9	1	533113 25415
11	579007	56.5	1	556144 22863
12	550249	14.1	1	527149 23100
13	569428	14.1	1	547481 21947
14	530109	14.1	1	510052 20057
15	609273	14.1	1	583556 25717
16	669393	14.1	1	643174 26219
17	420062	14.1	1	404987 15075
18	572732	14.1	1	552523 20209
19	584470	14.1	1	565824 18646
20	527803	14.1	1	508276 19527
21	579340	14.1	1	559307 20033
22	634357	14.1	1	611402 22955
23	476587	14.1	1	459153 17434
24	590952	14.1	1	569969 20983
25	523353	14.1	1	506915 16438
26	603228	14.1	1	578877 24351
27	574554	14.1	1	555345 19209
28	549718	14.1	1	531929 17789
29	564848	14.1	1	547635 17213
30	603054	14.1	1	583440 19614
31	572748	14.1	1	553819 18929
32	561827	14.1	1	544923 16904
33	555924	14.1	1	537944 17980
34	567520	14.1	1	549405 18115
35	570660	14.1	1	551916 18744
36	606452	14.1	1	588048 18404
37	551655	14.1	1	533363 18292
38	601494	14.1	1	582405 19089
39	589056	14.1	1	570060 18996
40	587735	14.1	1	569593 18142
41	579628	14.1	1	561509 18119
42	586109	14.1	1	568279 17830
43	584440	14.1	1	566783 17657
44	584969	14.1	1	566818 18151
45	586075	14.1	1	568309 17766
46	582480	14.1	1	564331 18149
47	592528	14.1	1	574820 17708
48	590483	14.1	1	572804 17679
49	593997	14.1	1	576332 17665
50	593229	14.1	1	575839 17390
51	596082	14.1	1	578259 17823
52	595558	14.1	1	578372 17186
53	598320	14.1	1	580967 17353
54	595790	14.1	1	578760 17030
55	597323	14.1	1	580229 17094
56	599762	14.1	1	582868 16894
57	602795	14.1	1	585705 17090
58	604365	14.1	1	587139 17226
59	605710	14.1	1	588517 17193
60	606801	14.1	1	588958 17843
61	609421	14.1	1	591688 17733
62	608612	14.1	1	591172 17440
63	608648	14.1	1	591196 17452
64	608196	14.1	1	590905 17291
65	609725	14.1	1	592600 17125
66	609413	14.1	1	592260 17153
67	612898	14.1	1	595333 17565
68	616938	14.1	1	599377 17561
69	617724	14.1	1	600854 16870
70	619077	14.1	1	601734 17343
71	624176	14.1	1	607084 17092
72	622177	14.1	1	605239 16938
73	622519	14.1	1	605669 16850
74	623572	14.1	1	606594 16978
75	624251	14.1	1	607245 17006
76	625248	14.1	1	608642 16606
77	627801	14.1	1	611028 16773
78	630419	14.1	1	613444 16975
79	634153	14.1	1	617371 16782
80	635881	14.1	1	618818 17063
81	638379	14.1	1	621561 16818
82	637956	14.1	1	621092 16864
83	640101	14.1	1	623416 16685
84	637670	14.1	1	621708 15962
85	639728	14.1	1	623623 16105
86	640254	14.1	1	624253 16001
87	643421	14.1	1	627535 15886
88	644225	14.1	1	628545 15680
89	651062	14.1	1	635406 15656
90	652219	14.1	1	636697 15522
91	658193	14.1	1	642736 15457
92	659828	14.1	1	644294 15534
93	656037	14.1	1	640796 15241
94	658274	14.1	1	642974 15300
95	658259	14.1	1	643337 14922
96	656656	14.1	1	641988 14668
97	660650	14.1	1	645915 14735
98	662431	14.1	1	647874 14557
99	668276	14.1	1	653707 14569
100	671359	14.1	1	656857 14502
101	677681	14.1	1	663080 14601
102	679269	14.1	1	664931 14338
103	679433	14.1	1	665364 14069
104	679108	14.1	1	665031 14077
105	679269	14.1	1	665256 14013
106	679618	14.1	1	665694 13924
107	682355	14.1	1	668119 14236
108	684217	14.1	1	670229 13988
109	691454	14.1	1	677286 14168
110	697612	14.1	1	683244 14368
111	703722	14.1	1	689434 14288
112	707554	14.1	1	693554 14000
113	709388	14.1	1	695376 14012
114	705346	14.1	1	691737 13609
115	706472	14.1	1	692603 13869
116	703507	14.1	1	689984 13523
117	703149	14.1	1	689920 13229
118	705069	14.1	1	691583 13486
119	709943	14.1	1	696568 13375
120	719130	14.1	1	705483 13647
121	726635	14.1	1	712989 13646
122	730601	14.1	1	716906 13695
123	733595	14.1	1	720128 13467
124	730327	14.1	1	716993 13334
125	726890	14.1	1	713700 13190
126	726378	14.1	1	713447 12931
127	726914	14.1	1	714379 12535
128	728880	14.1	1	716716 12164
129	733607	14.1	1	722057 11550
130	743886	14.1	1	732788 11098
131	750672	14.1	1	739882 10790
132	755266	14.1	1	745280 9986
133	754441	14.1	1	744908 9533
134	725363	14.1	1	716616 8747
135	720274	14.1	1	712044 8230
136	704731	14.1	1	697012 7719
137	694080	14.1	1	686893 7187
138	669855	14.1	1	663062 6793
139	671478	14.1	1	664565 6913
140	701689	14.1	1	694670 7019
141	738780	14.1	1	731568 7212
142	658836	14.1	1	652082 6754
143	659728	14.1	1	653259 6469
144	714783	14.1	1	708059 6724
145	730774	14.1	1	723961 6813
146	825298	14.1	1	817454 7844
147	722526	14.1	1	715234 7292
148	735852	14.1	1	728488 7364
149	635235	14.1	1	627859 7376
150	572343	14.1	1	564528 7815
151	160046	14.1	1	147090 12956


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/AD002_S9_L002_R1_001.fastq.gz
=============================================
236917763 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/AD002_S9_L002_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to AD002_S9_L002_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/AD002_S9_L002_R2_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/AD002_S9_L002_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 5672.61 s (24 us/read; 2.51 M reads/minute).

=== Summary ===

Total reads processed:             236,917,763
Reads with adapters:               119,760,324 (50.5%)
Reads written (passing filters):   236,917,763 (100.0%)

Total basepairs processed: 35,774,582,213 bp
Quality-trimmed:             122,766,404 bp (0.3%)
Total written (filtered):  29,261,997,335 bp (81.8%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 119760324 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 18.9%
  C: 33.4%
  G: 20.7%
  T: 26.9%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	27184123	59229440.8	0	27184123
2	8041586	14807360.2	0	8041586
3	2666576	3701840.0	0	2666576
4	1168313	925460.0	0	1168313
5	667985	231365.0	0	667985
6	538222	57841.3	0	538222
7	530151	14460.3	0	530151
8	564228	3615.1	0	564228
9	475542	903.8	0	470308 5234
10	522966	225.9	1	487785 35181
11	553066	56.5	1	517586 35480
12	498888	14.1	1	466969 31919
13	543535	14.1	1	507568 35967
14	480829	14.1	1	452490 28339
15	587923	14.1	1	546194 41729
16	601689	14.1	1	565659 36030
17	400438	14.1	1	377348 23090
18	539995	14.1	1	506401 33594
19	553585	14.1	1	523066 30519
20	480346	14.1	1	454275 26071
21	543014	14.1	1	507807 35207
22	582207	14.1	1	547563 34644
23	438809	14.1	1	413367 25442
24	551698	14.1	1	516672 35026
25	484624	14.1	1	459539 25085
26	573140	14.1	1	532542 40598
27	543672	14.1	1	512212 31460
28	502380	14.1	1	474888 27492
29	525406	14.1	1	496963 28443
30	555686	14.1	1	524310 31376
31	507209	14.1	1	481126 26083
32	532674	14.1	1	500832 31842
33	506897	14.1	1	480620 26277
34	538904	14.1	1	506428 32476
35	510614	14.1	1	483465 27149
36	581646	14.1	1	550317 31329
37	486866	14.1	1	462566 24300
38	562896	14.1	1	531710 31186
39	546810	14.1	1	515949 30861
40	542171	14.1	1	514164 28007
41	531228	14.1	1	503089 28139
42	541915	14.1	1	514053 27862
43	534303	14.1	1	507549 26754
44	533769	14.1	1	506552 27217
45	538343	14.1	1	510751 27592
46	526920	14.1	1	500509 26411
47	546871	14.1	1	518567 28304
48	537810	14.1	1	511582 26228
49	544217	14.1	1	516812 27405
50	538442	14.1	1	512132 26310
51	543023	14.1	1	516151 26872
52	542906	14.1	1	516336 26570
53	543461	14.1	1	516903 26558
54	540855	14.1	1	514609 26246
55	542847	14.1	1	516385 26462
56	544020	14.1	1	517541 26479
57	544660	14.1	1	518095 26565
58	545208	14.1	1	518699 26509
59	547713	14.1	1	521458 26255
60	546919	14.1	1	520881 26038
61	546617	14.1	1	520845 25772
62	546592	14.1	1	521095 25497
63	544423	14.1	1	518758 25665
64	547012	14.1	1	521324 25688
65	545326	14.1	1	519438 25888
66	545967	14.1	1	520268 25699
67	548645	14.1	1	523426 25219
68	550206	14.1	1	525275 24931
69	552617	14.1	1	528189 24428
70	553674	14.1	1	529313 24361
71	555862	14.1	1	531442 24420
72	552489	14.1	1	528475 24014
73	552862	14.1	1	528692 24170
74	553292	14.1	1	529511 23781
75	553465	14.1	1	529439 24026
76	553976	14.1	1	530186 23790
77	553197	14.1	1	529355 23842
78	555113	14.1	1	531602 23511
79	558745	14.1	1	535383 23362
80	558122	14.1	1	534714 23408
81	559044	14.1	1	535496 23548
82	557981	14.1	1	534901 23080
83	557826	14.1	1	534758 23068
84	555966	14.1	1	533296 22670
85	554929	14.1	1	532240 22689
86	554125	14.1	1	531736 22389
87	556244	14.1	1	534083 22161
88	557437	14.1	1	535075 22362
89	563161	14.1	1	540630 22531
90	564419	14.1	1	542124 22295
91	568529	14.1	1	546368 22161
92	566760	14.1	1	544580 22180
93	566536	14.1	1	544341 22195
94	565746	14.1	1	543984 21762
95	564054	14.1	1	542487 21567
96	563055	14.1	1	541337 21718
97	563442	14.1	1	541848 21594
98	564578	14.1	1	542893 21685
99	569033	14.1	1	547266 21767
100	571529	14.1	1	550147 21382
101	572792	14.1	1	551940 20852
102	574962	14.1	1	554356 20606
103	574068	14.1	1	553643 20425
104	570390	14.1	1	550099 20291
105	570644	14.1	1	550442 20202
106	570156	14.1	1	550276 19880
107	568786	14.1	1	549037 19749
108	571635	14.1	1	551875 19760
109	576550	14.1	1	556970 19580
110	580922	14.1	1	561141 19781
111	583973	14.1	1	564217 19756
112	586948	14.1	1	567436 19512
113	586672	14.1	1	567094 19578
114	579669	14.1	1	560557 19112
115	578056	14.1	1	559029 19027
116	576319	14.1	1	557223 19096
117	575447	14.1	1	556765 18682
118	575524	14.1	1	557025 18499
119	577752	14.1	1	558883 18869
120	584731	14.1	1	565703 19028
121	592424	14.1	1	573182 19242
122	593492	14.1	1	574808 18684
123	595523	14.1	1	577343 18180
124	588624	14.1	1	570955 17669
125	586601	14.1	1	568934 17667
126	583242	14.1	1	565959 17283
127	583398	14.1	1	566484 16914
128	585615	14.1	1	568906 16709
129	586789	14.1	1	570207 16582
130	595337	14.1	1	579228 16109
131	599699	14.1	1	583358 16341
132	602201	14.1	1	586199 16002
133	598589	14.1	1	583429 15160
134	576993	14.1	1	562472 14521
135	568948	14.1	1	555235 13713
136	553101	14.1	1	540371 12730
137	540774	14.1	1	528222 12552
138	517048	14.1	1	505103 11945
139	519527	14.1	1	507776 11751
140	542939	14.1	1	530762 12177
141	560987	14.1	1	549293 11694
142	508971	14.1	1	497610 11361
143	511483	14.1	1	500236 11247
144	555570	14.1	1	543422 12148
145	575167	14.1	1	562620 12547
146	629380	14.1	1	616367 13013
147	552383	14.1	1	540777 11606
148	552853	14.1	1	541802 11051
149	451659	14.1	1	442111 9548
150	399813	14.1	1	390507 9306
151	109863	14.1	1	98224 11639


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/AD002_S9_L002_R2_001.fastq.gz
=============================================
236917763 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files AD002_S9_L002_R1_001_trimmed.fq.gz and AD002_S9_L002_R2_001_trimmed.fq.gz
file_1: AD002_S9_L002_R1_001_trimmed.fq.gz, file_2: AD002_S9_L002_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: AD002_S9_L002_R1_001_trimmed.fq.gz and AD002_S9_L002_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to AD002_S9_L002_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to AD002_S9_L002_R2_001_val_2.fq.gz

Total number of sequences analysed: 236917763

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 24346749 (10.28%)

Deleting both intermediate output files AD002_S9_L002_R1_001_trimmed.fq.gz and AD002_S9_L002_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR005_S4_L001_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR005_S4_L001_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR005_S4_L001_R1_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR005_S4_L001_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.14 s (27 us/read; 2.19 M reads/minute).

=== Summary ===

Total reads processed:                  41,570
Reads with adapters:                    12,428 (29.9%)
Reads written (passing filters):        41,570 (100.0%)

Total basepairs processed:     6,277,070 bp
Quality-trimmed:                   7,538 bp (0.1%)
Total written (filtered):      6,243,003 bp (99.5%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 12428 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 31.0%
  C: 14.7%
  G: 14.9%
  T: 39.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	9041	10392.5	0	9041
2	2328	2598.1	0	2328
3	716	649.5	0	716
4	170	162.4	0	170
5	33	40.6	0	33
6	10	10.1	0	10
7	5	2.5	0	5
9	2	0.2	0	0 2
10	2	0.0	1	1 1
11	1	0.0	1	0 1
12	1	0.0	1	1
14	1	0.0	1	1
16	3	0.0	1	2 1
19	1	0.0	1	1
21	1	0.0	1	1
23	1	0.0	1	1
24	1	0.0	1	0 1
25	1	0.0	1	1
29	2	0.0	1	1 1
30	1	0.0	1	0 1
31	3	0.0	1	1 2
32	1	0.0	1	0 1
34	3	0.0	1	1 2
36	3	0.0	1	1 2
38	3	0.0	1	3
40	1	0.0	1	0 1
41	3	0.0	1	1 2
42	1	0.0	1	0 1
44	1	0.0	1	1
45	1	0.0	1	0 1
46	1	0.0	1	0 1
47	1	0.0	1	0 1
49	1	0.0	1	1
51	2	0.0	1	1 1
54	2	0.0	1	1 1
58	1	0.0	1	0 1
62	1	0.0	1	0 1
63	2	0.0	1	0 2
65	3	0.0	1	1 2
67	1	0.0	1	0 1
70	2	0.0	1	2
76	2	0.0	1	2
78	1	0.0	1	1
81	1	0.0	1	1
82	3	0.0	1	2 1
86	1	0.0	1	0 1
87	1	0.0	1	0 1
88	1	0.0	1	0 1
89	3	0.0	1	1 2
90	1	0.0	1	0 1
92	1	0.0	1	1
93	3	0.0	1	2 1
94	2	0.0	1	0 2
96	2	0.0	1	0 2
97	1	0.0	1	1
98	1	0.0	1	0 1
99	1	0.0	1	0 1
101	4	0.0	1	3 1
102	2	0.0	1	1 1
103	2	0.0	1	2
105	1	0.0	1	0 1
106	1	0.0	1	0 1
107	2	0.0	1	0 2
108	1	0.0	1	0 1
111	1	0.0	1	1
112	1	0.0	1	1
113	1	0.0	1	0 1
114	1	0.0	1	0 1
116	1	0.0	1	0 1
117	1	0.0	1	1
118	4	0.0	1	3 1
119	2	0.0	1	2
121	1	0.0	1	1
122	2	0.0	1	0 2
124	1	0.0	1	1
127	1	0.0	1	1
128	1	0.0	1	1
130	1	0.0	1	1
131	1	0.0	1	1
132	1	0.0	1	1
135	2	0.0	1	1 1
141	1	0.0	1	1
142	1	0.0	1	1
143	1	0.0	1	0 1
144	1	0.0	1	1
146	1	0.0	1	0 1
147	1	0.0	1	1
148	1	0.0	1	0 1
149	1	0.0	1	1
151	1	0.0	1	0 1


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR005_S4_L001_R1_001.fastq.gz
=============================================
41570 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR005_S4_L001_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR005_S4_L001_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR005_S4_L001_R2_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR005_S4_L001_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.05 s (25 us/read; 2.38 M reads/minute).

=== Summary ===

Total reads processed:                  41,570
Reads with adapters:                     7,910 (19.0%)
Reads written (passing filters):        41,570 (100.0%)

Total basepairs processed:     6,277,070 bp
Quality-trimmed:                  37,349 bp (0.6%)
Total written (filtered):      6,222,043 bp (99.1%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 7910 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 28.6%
  C: 15.8%
  G: 21.2%
  T: 34.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	5880	10392.5	0	5880
2	1384	2598.1	0	1384
3	385	649.5	0	385
4	143	162.4	0	143
5	20	40.6	0	20
6	9	10.1	0	9
7	2	2.5	0	2
10	1	0.0	1	1
14	1	0.0	1	1
15	1	0.0	1	0 1
16	1	0.0	1	0 1
18	1	0.0	1	1
26	1	0.0	1	1
27	1	0.0	1	1
28	2	0.0	1	2
29	1	0.0	1	1
30	1	0.0	1	0 1
33	1	0.0	1	1
37	1	0.0	1	0 1
38	2	0.0	1	2
43	1	0.0	1	1
44	2	0.0	1	1 1
51	1	0.0	1	0 1
52	1	0.0	1	0 1
53	1	0.0	1	1
55	1	0.0	1	0 1
56	1	0.0	1	0 1
57	1	0.0	1	1
62	1	0.0	1	1
63	1	0.0	1	1
64	2	0.0	1	2
65	1	0.0	1	1
66	1	0.0	1	1
69	1	0.0	1	0 1
70	1	0.0	1	0 1
73	1	0.0	1	1
74	2	0.0	1	1 1
76	1	0.0	1	1
77	1	0.0	1	1
78	2	0.0	1	0 2
79	1	0.0	1	1
80	2	0.0	1	2
81	2	0.0	1	2
85	2	0.0	1	2
87	1	0.0	1	1
88	1	0.0	1	1
89	1	0.0	1	1
92	1	0.0	1	1
93	1	0.0	1	0 1
94	2	0.0	1	1 1
95	1	0.0	1	0 1
97	1	0.0	1	1
98	1	0.0	1	0 1
99	1	0.0	1	0 1
100	1	0.0	1	0 1
101	1	0.0	1	1
106	1	0.0	1	0 1
107	1	0.0	1	1
108	2	0.0	1	2
110	1	0.0	1	1
111	1	0.0	1	1
113	2	0.0	1	1 1
114	1	0.0	1	1
115	2	0.0	1	2
116	1	0.0	1	0 1
118	1	0.0	1	1
120	2	0.0	1	2
126	1	0.0	1	1
129	2	0.0	1	1 1
130	1	0.0	1	1
131	2	0.0	1	2
134	2	0.0	1	1 1
137	1	0.0	1	1
138	1	0.0	1	0 1
141	1	0.0	1	1
143	1	0.0	1	1
145	1	0.0	1	1


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR005_S4_L001_R2_001.fastq.gz
=============================================
41570 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR005_S4_L001_R1_001_trimmed.fq.gz and NR005_S4_L001_R2_001_trimmed.fq.gz
file_1: NR005_S4_L001_R1_001_trimmed.fq.gz, file_2: NR005_S4_L001_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR005_S4_L001_R1_001_trimmed.fq.gz and NR005_S4_L001_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR005_S4_L001_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR005_S4_L001_R2_001_val_2.fq.gz

Total number of sequences analysed: 41570

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 110 (0.26%)

Deleting both intermediate output files NR005_S4_L001_R1_001_trimmed.fq.gz and NR005_S4_L001_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR005_S4_L002_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR005_S4_L002_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR005_S4_L002_R1_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR005_S4_L002_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.96 s (26 us/read; 2.30 M reads/minute).

=== Summary ===

Total reads processed:                  36,577
Reads with adapters:                    11,175 (30.6%)
Reads written (passing filters):        36,577 (100.0%)

Total basepairs processed:     5,523,127 bp
Quality-trimmed:                   4,381 bp (0.1%)
Total written (filtered):      5,492,464 bp (99.4%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 11175 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 29.9%
  C: 15.0%
  G: 15.2%
  T: 39.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	8079	9144.2	0	8079
2	2102	2286.1	0	2102
3	665	571.5	0	665
4	132	142.9	0	132
5	37	35.7	0	37
6	8	8.9	0	8
7	7	2.2	0	7
8	1	0.6	0	1
10	1	0.0	1	0 1
11	1	0.0	1	1
20	1	0.0	1	1
21	2	0.0	1	1 1
22	1	0.0	1	0 1
25	2	0.0	1	2
26	1	0.0	1	0 1
27	1	0.0	1	1
28	1	0.0	1	0 1
29	2	0.0	1	1 1
31	2	0.0	1	2
32	2	0.0	1	2
33	3	0.0	1	3
35	1	0.0	1	1
37	2	0.0	1	1 1
38	2	0.0	1	2
39	4	0.0	1	3 1
41	2	0.0	1	0 2
42	1	0.0	1	0 1
44	3	0.0	1	2 1
45	5	0.0	1	3 2
46	3	0.0	1	1 2
47	2	0.0	1	1 1
49	2	0.0	1	0 2
50	1	0.0	1	1
52	2	0.0	1	2
54	3	0.0	1	2 1
57	2	0.0	1	2
58	2	0.0	1	1 1
59	2	0.0	1	2
60	1	0.0	1	1
62	2	0.0	1	1 1
65	2	0.0	1	1 1
66	1	0.0	1	0 1
67	1	0.0	1	0 1
69	3	0.0	1	3
70	1	0.0	1	1
71	1	0.0	1	1
72	3	0.0	1	3
73	1	0.0	1	1
74	1	0.0	1	1
75	2	0.0	1	1 1
76	2	0.0	1	1 1
77	2	0.0	1	2
80	1	0.0	1	0 1
81	4	0.0	1	4
83	2	0.0	1	1 1
86	1	0.0	1	1
87	1	0.0	1	1
94	2	0.0	1	1 1
95	1	0.0	1	1
96	1	0.0	1	1
97	2	0.0	1	0 2
98	2	0.0	1	2
102	1	0.0	1	1
106	2	0.0	1	0 2
107	1	0.0	1	1
110	1	0.0	1	1
111	3	0.0	1	3
112	3	0.0	1	0 3
114	1	0.0	1	0 1
115	1	0.0	1	1
116	3	0.0	1	2 1
118	2	0.0	1	1 1
122	1	0.0	1	0 1
125	1	0.0	1	0 1
126	1	0.0	1	1
127	1	0.0	1	0 1
129	2	0.0	1	2
130	1	0.0	1	1
131	2	0.0	1	2
134	2	0.0	1	1 1
137	1	0.0	1	0 1
138	2	0.0	1	1 1
139	2	0.0	1	1 1
142	1	0.0	1	1
143	1	0.0	1	0 1
145	4	0.0	1	3 1
147	2	0.0	1	2
148	3	0.0	1	3


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR005_S4_L002_R1_001.fastq.gz
=============================================
36577 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR005_S4_L002_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR005_S4_L002_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR005_S4_L002_R2_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR005_S4_L002_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.93 s (25 us/read; 2.37 M reads/minute).

=== Summary ===

Total reads processed:                  36,577
Reads with adapters:                     6,876 (18.8%)
Reads written (passing filters):        36,577 (100.0%)

Total basepairs processed:     5,523,127 bp
Quality-trimmed:                  34,645 bp (0.6%)
Total written (filtered):      5,471,904 bp (99.1%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 6876 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 29.6%
  C: 16.2%
  G: 21.3%
  T: 33.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	5020	9144.2	0	5020
2	1245	2286.1	0	1245
3	388	571.5	0	388
4	104	142.9	0	104
5	19	35.7	0	19
6	9	8.9	0	9
8	2	0.6	0	2
10	1	0.0	1	0 1
16	2	0.0	1	1 1
18	1	0.0	1	1
20	4	0.0	1	3 1
21	1	0.0	1	1
22	1	0.0	1	1
26	1	0.0	1	1
27	1	0.0	1	1
28	1	0.0	1	0 1
32	1	0.0	1	1
36	2	0.0	1	2
37	1	0.0	1	1
46	1	0.0	1	1
48	1	0.0	1	1
50	3	0.0	1	2 1
51	2	0.0	1	2
52	1	0.0	1	1
53	1	0.0	1	0 1
55	1	0.0	1	1
56	1	0.0	1	0 1
57	1	0.0	1	1
58	1	0.0	1	1
61	2	0.0	1	2
63	1	0.0	1	1
64	2	0.0	1	2
66	1	0.0	1	0 1
67	3	0.0	1	2 1
70	1	0.0	1	1
75	1	0.0	1	1
81	1	0.0	1	0 1
82	1	0.0	1	1
84	1	0.0	1	1
86	1	0.0	1	1
87	2	0.0	1	1 1
89	1	0.0	1	1
90	2	0.0	1	2
91	2	0.0	1	2
95	1	0.0	1	1
96	1	0.0	1	1
97	1	0.0	1	1
102	1	0.0	1	1
107	2	0.0	1	2
110	1	0.0	1	1
111	1	0.0	1	1
112	1	0.0	1	0 1
113	1	0.0	1	0 1
114	1	0.0	1	0 1
115	1	0.0	1	1
117	1	0.0	1	1
120	2	0.0	1	2
121	3	0.0	1	3
122	1	0.0	1	1
123	2	0.0	1	2
125	1	0.0	1	1
126	1	0.0	1	1
128	1	0.0	1	1
129	1	0.0	1	0 1
130	2	0.0	1	1 1
132	2	0.0	1	2
135	1	0.0	1	1
142	1	0.0	1	1
144	1	0.0	1	1
146	1	0.0	1	1
147	2	0.0	1	1 1
148	1	0.0	1	1
150	1	0.0	1	1


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR005_S4_L002_R2_001.fastq.gz
=============================================
36577 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR005_S4_L002_R1_001_trimmed.fq.gz and NR005_S4_L002_R2_001_trimmed.fq.gz
file_1: NR005_S4_L002_R1_001_trimmed.fq.gz, file_2: NR005_S4_L002_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR005_S4_L002_R1_001_trimmed.fq.gz and NR005_S4_L002_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR005_S4_L002_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR005_S4_L002_R2_001_val_2.fq.gz

Total number of sequences analysed: 36577

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 121 (0.33%)

Deleting both intermediate output files NR005_S4_L002_R1_001_trimmed.fq.gz and NR005_S4_L002_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR006_S3_L001_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR006_S3_L001_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR006_S3_L001_R1_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR006_S3_L001_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 88.92 s (26 us/read; 2.31 M reads/minute).

=== Summary ===

Total reads processed:               3,427,897
Reads with adapters:                   993,908 (29.0%)
Reads written (passing filters):     3,427,897 (100.0%)

Total basepairs processed:   517,612,447 bp
Quality-trimmed:                 649,955 bp (0.1%)
Total written (filtered):    515,115,749 bp (99.5%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 993908 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 30.6%
  C: 15.9%
  G: 15.8%
  T: 37.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	729743	856974.2	0	729743
2	182904	214243.6	0	182904
3	59512	53560.9	0	59512
4	12113	13390.2	0	12113
5	2394	3347.6	0	2394
6	759	836.9	0	759
7	197	209.2	0	197
8	84	52.3	0	84
9	67	13.1	0	14 53
10	95	3.3	1	8 87
11	68	0.8	1	11 57
12	24	0.2	1	9 15
13	29	0.2	1	9 20
14	31	0.2	1	12 19
15	22	0.2	1	10 12
16	36	0.2	1	11 25
17	8	0.2	1	4 4
18	38	0.2	1	10 28
19	30	0.2	1	6 24
20	36	0.2	1	9 27
21	36	0.2	1	14 22
22	32	0.2	1	10 22
23	32	0.2	1	4 28
24	51	0.2	1	18 33
25	42	0.2	1	5 37
26	30	0.2	1	13 17
27	36	0.2	1	11 25
28	35	0.2	1	7 28
29	49	0.2	1	11 38
30	37	0.2	1	13 24
31	48	0.2	1	15 33
32	72	0.2	1	13 59
33	55	0.2	1	14 41
34	33	0.2	1	5 28
35	34	0.2	1	7 27
36	59	0.2	1	13 46
37	46	0.2	1	11 35
38	41	0.2	1	11 30
39	33	0.2	1	10 23
40	55	0.2	1	15 40
41	66	0.2	1	13 53
42	46	0.2	1	13 33
43	42	0.2	1	14 28
44	51	0.2	1	17 34
45	68	0.2	1	12 56
46	51	0.2	1	11 40
47	30	0.2	1	8 22
48	29	0.2	1	11 18
49	33	0.2	1	9 24
50	33	0.2	1	11 22
51	29	0.2	1	12 17
52	44	0.2	1	14 30
53	23	0.2	1	9 14
54	41	0.2	1	17 24
55	25	0.2	1	12 13
56	49	0.2	1	9 40
57	38	0.2	1	18 20
58	31	0.2	1	13 18
59	20	0.2	1	13 7
60	25	0.2	1	17 8
61	22	0.2	1	11 11
62	25	0.2	1	10 15
63	34	0.2	1	10 24
64	62	0.2	1	20 42
65	61	0.2	1	17 44
66	43	0.2	1	17 26
67	36	0.2	1	17 19
68	42	0.2	1	20 22
69	32	0.2	1	13 19
70	25	0.2	1	15 10
71	34	0.2	1	15 19
72	29	0.2	1	11 18
73	20	0.2	1	13 7
74	46	0.2	1	20 26
75	35	0.2	1	9 26
76	37	0.2	1	20 17
77	36	0.2	1	10 26
78	32	0.2	1	16 16
79	23	0.2	1	12 11
80	37	0.2	1	25 12
81	28	0.2	1	8 20
82	73	0.2	1	19 54
83	37	0.2	1	19 18
84	36	0.2	1	19 17
85	51	0.2	1	16 35
86	35	0.2	1	16 19
87	44	0.2	1	17 27
88	43	0.2	1	15 28
89	57	0.2	1	22 35
90	60	0.2	1	15 45
91	47	0.2	1	26 21
92	46	0.2	1	17 29
93	45	0.2	1	25 20
94	55	0.2	1	19 36
95	58	0.2	1	17 41
96	87	0.2	1	18 69
97	44	0.2	1	19 25
98	39	0.2	1	17 22
99	33	0.2	1	15 18
100	44	0.2	1	18 26
101	54	0.2	1	12 42
102	76	0.2	1	18 58
103	49	0.2	1	22 27
104	53	0.2	1	25 28
105	52	0.2	1	18 34
106	125	0.2	1	10 115
107	71	0.2	1	25 46
108	86	0.2	1	10 76
109	71	0.2	1	25 46
110	40	0.2	1	20 20
111	69	0.2	1	19 50
112	43	0.2	1	17 26
113	53	0.2	1	13 40
114	66	0.2	1	27 39
115	55	0.2	1	15 40
116	37	0.2	1	18 19
117	45	0.2	1	12 33
118	41	0.2	1	14 27
119	41	0.2	1	12 29
120	44	0.2	1	22 22
121	45	0.2	1	12 33
122	37	0.2	1	12 25
123	41	0.2	1	23 18
124	35	0.2	1	18 17
125	40	0.2	1	22 18
126	45	0.2	1	27 18
127	35	0.2	1	20 15
128	43	0.2	1	26 17
129	42	0.2	1	25 17
130	37	0.2	1	18 19
131	35	0.2	1	26 9
132	37	0.2	1	18 19
133	39	0.2	1	24 15
134	28	0.2	1	14 14
135	43	0.2	1	20 23
136	33	0.2	1	24 9
137	42	0.2	1	19 23
138	56	0.2	1	24 32
139	33	0.2	1	19 14
140	69	0.2	1	27 42
141	40	0.2	1	17 23
142	30	0.2	1	15 15
143	52	0.2	1	21 31
144	42	0.2	1	17 25
145	55	0.2	1	28 27
146	48	0.2	1	16 32
147	54	0.2	1	22 32
148	33	0.2	1	17 16
149	20	0.2	1	11 9
150	36	0.2	1	12 24
151	19	0.2	1	3 16


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR006_S3_L001_R1_001.fastq.gz
=============================================
3427897 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR006_S3_L001_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR006_S3_L001_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR006_S3_L001_R2_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR006_S3_L001_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 84.08 s (25 us/read; 2.45 M reads/minute).

=== Summary ===

Total reads processed:               3,427,897
Reads with adapters:                   655,420 (19.1%)
Reads written (passing filters):     3,427,897 (100.0%)

Total basepairs processed:   517,612,447 bp
Quality-trimmed:               4,287,079 bp (0.8%)
Total written (filtered):    512,054,481 bp (98.9%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 655420 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 28.9%
  C: 16.1%
  G: 19.6%
  T: 35.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	484728	856974.2	0	484728
2	116897	214243.6	0	116897
3	35120	53560.9	0	35120
4	11002	13390.2	0	11002
5	1997	3347.6	0	1997
6	692	836.9	0	692
7	182	209.2	0	182
8	67	52.3	0	67
9	51	13.1	0	12 39
10	99	3.3	1	12 87
11	44	0.8	1	7 37
12	26	0.2	1	12 14
13	42	0.2	1	10 32
14	23	0.2	1	7 16
15	25	0.2	1	9 16
16	27	0.2	1	9 18
17	18	0.2	1	4 14
18	23	0.2	1	11 12
19	29	0.2	1	7 22
20	17	0.2	1	6 11
21	27	0.2	1	9 18
22	30	0.2	1	8 22
23	23	0.2	1	7 16
24	31	0.2	1	11 20
25	36	0.2	1	9 27
26	39	0.2	1	15 24
27	38	0.2	1	15 23
28	35	0.2	1	12 23
29	22	0.2	1	2 20
30	44	0.2	1	17 27
31	22	0.2	1	10 12
32	51	0.2	1	15 36
33	31	0.2	1	5 26
34	24	0.2	1	8 16
35	18	0.2	1	6 12
36	34	0.2	1	15 19
37	32	0.2	1	9 23
38	32	0.2	1	12 20
39	30	0.2	1	16 14
40	42	0.2	1	14 28
41	22	0.2	1	11 11
42	27	0.2	1	10 17
43	29	0.2	1	12 17
44	40	0.2	1	12 28
45	39	0.2	1	13 26
46	23	0.2	1	9 14
47	21	0.2	1	15 6
48	25	0.2	1	12 13
49	35	0.2	1	11 24
50	26	0.2	1	12 14
51	31	0.2	1	16 15
52	33	0.2	1	12 21
53	31	0.2	1	14 17
54	27	0.2	1	15 12
55	33	0.2	1	15 18
56	25	0.2	1	13 12
57	21	0.2	1	14 7
58	18	0.2	1	9 9
59	24	0.2	1	18 6
60	33	0.2	1	9 24
61	25	0.2	1	9 16
62	19	0.2	1	12 7
63	28	0.2	1	14 14
64	37	0.2	1	17 20
65	36	0.2	1	10 26
66	23	0.2	1	12 11
67	34	0.2	1	16 18
68	35	0.2	1	15 20
69	34	0.2	1	13 21
70	30	0.2	1	17 13
71	26	0.2	1	16 10
72	31	0.2	1	19 12
73	25	0.2	1	13 12
74	20	0.2	1	11 9
75	23	0.2	1	9 14
76	34	0.2	1	15 19
77	30	0.2	1	16 14
78	30	0.2	1	12 18
79	33	0.2	1	15 18
80	33	0.2	1	8 25
81	24	0.2	1	13 11
82	29	0.2	1	10 19
83	30	0.2	1	8 22
84	29	0.2	1	9 20
85	35	0.2	1	11 24
86	31	0.2	1	16 15
87	27	0.2	1	10 17
88	30	0.2	1	13 17
89	33	0.2	1	11 22
90	33	0.2	1	10 23
91	26	0.2	1	12 14
92	51	0.2	1	19 32
93	38	0.2	1	10 28
94	30	0.2	1	17 13
95	46	0.2	1	13 33
96	31	0.2	1	14 17
97	23	0.2	1	12 11
98	48	0.2	1	16 32
99	36	0.2	1	16 20
100	36	0.2	1	14 22
101	54	0.2	1	18 36
102	53	0.2	1	18 35
103	39	0.2	1	20 19
104	35	0.2	1	14 21
105	33	0.2	1	10 23
106	61	0.2	1	19 42
107	43	0.2	1	20 23
108	52	0.2	1	16 36
109	39	0.2	1	17 22
110	38	0.2	1	18 20
111	40	0.2	1	19 21
112	28	0.2	1	14 14
113	35	0.2	1	22 13
114	36	0.2	1	18 18
115	36	0.2	1	18 18
116	36	0.2	1	9 27
117	29	0.2	1	13 16
118	39	0.2	1	17 22
119	37	0.2	1	16 21
120	46	0.2	1	25 21
121	32	0.2	1	22 10
122	33	0.2	1	10 23
123	33	0.2	1	17 16
124	20	0.2	1	7 13
125	31	0.2	1	14 17
126	33	0.2	1	19 14
127	22	0.2	1	11 11
128	21	0.2	1	11 10
129	32	0.2	1	13 19
130	39	0.2	1	21 18
131	34	0.2	1	18 16
132	42	0.2	1	15 27
133	43	0.2	1	22 21
134	30	0.2	1	12 18
135	39	0.2	1	16 23
136	23	0.2	1	13 10
137	38	0.2	1	16 22
138	24	0.2	1	12 12
139	38	0.2	1	25 13
140	54	0.2	1	11 43
141	45	0.2	1	22 23
142	35	0.2	1	16 19
143	43	0.2	1	16 27
144	48	0.2	1	19 29
145	30	0.2	1	10 20
146	55	0.2	1	13 42
147	34	0.2	1	11 23
148	28	0.2	1	15 13
149	17	0.2	1	8 9
150	38	0.2	1	13 25
151	12	0.2	1	4 8


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR006_S3_L001_R2_001.fastq.gz
=============================================
3427897 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR006_S3_L001_R1_001_trimmed.fq.gz and NR006_S3_L001_R2_001_trimmed.fq.gz
file_1: NR006_S3_L001_R1_001_trimmed.fq.gz, file_2: NR006_S3_L001_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR006_S3_L001_R1_001_trimmed.fq.gz and NR006_S3_L001_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR006_S3_L001_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR006_S3_L001_R2_001_val_2.fq.gz

Total number of sequences analysed: 3427897

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 13219 (0.39%)

Deleting both intermediate output files NR006_S3_L001_R1_001_trimmed.fq.gz and NR006_S3_L001_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR006_S3_L002_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR006_S3_L002_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR006_S3_L002_R1_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR006_S3_L002_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 77.02 s (25 us/read; 2.37 M reads/minute).

=== Summary ===

Total reads processed:               3,045,976
Reads with adapters:                   866,851 (28.5%)
Reads written (passing filters):     3,045,976 (100.0%)

Total basepairs processed:   459,942,376 bp
Quality-trimmed:                 610,758 bp (0.1%)
Total written (filtered):    457,563,475 bp (99.5%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 866851 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 30.0%
  C: 16.1%
  G: 16.1%
  T: 37.9%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	633365	761494.0	0	633365
2	160558	190373.5	0	160558
3	52444	47593.4	0	52444
4	10136	11898.3	0	10136
5	2116	2974.6	0	2116
6	771	743.6	0	771
7	216	185.9	0	216
8	70	46.5	0	70
9	62	11.6	0	16 46
10	99	2.9	1	21 78
11	83	0.7	1	25 58
12	18	0.2	1	8 10
13	34	0.2	1	20 14
14	28	0.2	1	14 14
15	40	0.2	1	21 19
16	39	0.2	1	18 21
17	31	0.2	1	17 14
18	46	0.2	1	24 22
19	38	0.2	1	14 24
20	36	0.2	1	18 18
21	51	0.2	1	23 28
22	44	0.2	1	25 19
23	30	0.2	1	17 13
24	55	0.2	1	21 34
25	31	0.2	1	15 16
26	38	0.2	1	23 15
27	36	0.2	1	15 21
28	45	0.2	1	21 24
29	36	0.2	1	22 14
30	42	0.2	1	17 25
31	59	0.2	1	25 34
32	78	0.2	1	28 50
33	51	0.2	1	16 35
34	47	0.2	1	30 17
35	38	0.2	1	17 21
36	62	0.2	1	9 53
37	40	0.2	1	19 21
38	56	0.2	1	26 30
39	51	0.2	1	26 25
40	46	0.2	1	16 30
41	40	0.2	1	12 28
42	39	0.2	1	20 19
43	52	0.2	1	18 34
44	47	0.2	1	12 35
45	62	0.2	1	18 44
46	47	0.2	1	18 29
47	37	0.2	1	16 21
48	54	0.2	1	23 31
49	34	0.2	1	20 14
50	41	0.2	1	14 27
51	40	0.2	1	19 21
52	63	0.2	1	28 35
53	33	0.2	1	21 12
54	46	0.2	1	27 19
55	39	0.2	1	25 14
56	52	0.2	1	28 24
57	32	0.2	1	15 17
58	37	0.2	1	26 11
59	23	0.2	1	19 4
60	30	0.2	1	19 11
61	44	0.2	1	21 23
62	48	0.2	1	32 16
63	32	0.2	1	26 6
64	51	0.2	1	24 27
65	48	0.2	1	16 32
66	38	0.2	1	24 14
67	42	0.2	1	24 18
68	46	0.2	1	29 17
69	40	0.2	1	24 16
70	35	0.2	1	24 11
71	40	0.2	1	21 19
72	40	0.2	1	27 13
73	42	0.2	1	27 15
74	49	0.2	1	19 30
75	39	0.2	1	28 11
76	36	0.2	1	18 18
77	42	0.2	1	28 14
78	42	0.2	1	31 11
79	54	0.2	1	41 13
80	21	0.2	1	16 5
81	36	0.2	1	23 13
82	74	0.2	1	30 44
83	34	0.2	1	18 16
84	44	0.2	1	28 16
85	49	0.2	1	23 26
86	29	0.2	1	16 13
87	52	0.2	1	28 24
88	57	0.2	1	43 14
89	59	0.2	1	26 33
90	59	0.2	1	27 32
91	51	0.2	1	24 27
92	50	0.2	1	20 30
93	40	0.2	1	25 15
94	76	0.2	1	29 47
95	49	0.2	1	25 24
96	102	0.2	1	34 68
97	56	0.2	1	34 22
98	49	0.2	1	27 22
99	45	0.2	1	25 20
100	57	0.2	1	31 26
101	66	0.2	1	34 32
102	82	0.2	1	23 59
103	53	0.2	1	24 29
104	48	0.2	1	31 17
105	68	0.2	1	26 42
106	125	0.2	1	28 97
107	68	0.2	1	33 35
108	76	0.2	1	26 50
109	58	0.2	1	28 30
110	53	0.2	1	38 15
111	60	0.2	1	32 28
112	63	0.2	1	31 32
113	85	0.2	1	45 40
114	51	0.2	1	30 21
115	70	0.2	1	28 42
116	63	0.2	1	41 22
117	87	0.2	1	34 53
118	54	0.2	1	30 24
119	64	0.2	1	38 26
120	47	0.2	1	31 16
121	71	0.2	1	36 35
122	49	0.2	1	26 23
123	64	0.2	1	45 19
124	47	0.2	1	30 17
125	70	0.2	1	43 27
126	41	0.2	1	24 17
127	45	0.2	1	34 11
128	36	0.2	1	28 8
129	64	0.2	1	34 30
130	58	0.2	1	38 20
131	53	0.2	1	37 16
132	59	0.2	1	37 22
133	49	0.2	1	37 12
134	50	0.2	1	39 11
135	68	0.2	1	36 32
136	43	0.2	1	28 15
137	44	0.2	1	32 12
138	49	0.2	1	29 20
139	44	0.2	1	33 11
140	62	0.2	1	29 33
141	50	0.2	1	28 22
142	41	0.2	1	31 10
143	58	0.2	1	30 28
144	59	0.2	1	38 21
145	55	0.2	1	39 16
146	67	0.2	1	36 31
147	49	0.2	1	31 18
148	62	0.2	1	38 24
149	31	0.2	1	23 8
150	44	0.2	1	20 24
151	17	0.2	1	5 12


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR006_S3_L002_R1_001.fastq.gz
=============================================
3045976 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR006_S3_L002_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR006_S3_L002_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR006_S3_L002_R2_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR006_S3_L002_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 73.98 s (24 us/read; 2.47 M reads/minute).

=== Summary ===

Total reads processed:               3,045,976
Reads with adapters:                   565,031 (18.6%)
Reads written (passing filters):     3,045,976 (100.0%)

Total basepairs processed:   459,942,376 bp
Quality-trimmed:               4,313,218 bp (0.9%)
Total written (filtered):    454,437,558 bp (98.8%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 565031 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 28.3%
  C: 16.5%
  G: 20.0%
  T: 35.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	417639	761494.0	0	417639
2	100209	190373.5	0	100209
3	29961	47593.4	0	29961
4	9506	11898.3	0	9506
5	1704	2974.6	0	1704
6	588	743.6	0	588
7	164	185.9	0	164
8	37	46.5	0	37
9	68	11.6	0	22 46
10	73	2.9	1	18 55
11	50	0.7	1	12 38
12	24	0.2	1	15 9
13	44	0.2	1	19 25
14	23	0.2	1	14 9
15	25	0.2	1	12 13
16	37	0.2	1	21 16
17	23	0.2	1	13 10
18	33	0.2	1	19 14
19	31	0.2	1	13 18
20	32	0.2	1	20 12
21	22	0.2	1	9 13
22	27	0.2	1	18 9
23	26	0.2	1	11 15
24	34	0.2	1	22 12
25	36	0.2	1	14 22
26	24	0.2	1	16 8
27	31	0.2	1	14 17
28	34	0.2	1	13 21
29	31	0.2	1	21 10
30	37	0.2	1	14 23
31	38	0.2	1	21 17
32	38	0.2	1	11 27
33	43	0.2	1	19 24
34	16	0.2	1	12 4
35	43	0.2	1	23 20
36	38	0.2	1	19 19
37	36	0.2	1	20 16
38	41	0.2	1	23 18
39	26	0.2	1	12 14
40	29	0.2	1	16 13
41	20	0.2	1	12 8
42	33	0.2	1	17 16
43	32	0.2	1	19 13
44	30	0.2	1	15 15
45	35	0.2	1	11 24
46	27	0.2	1	14 13
47	24	0.2	1	16 8
48	24	0.2	1	20 4
49	37	0.2	1	22 15
50	41	0.2	1	22 19
51	29	0.2	1	20 9
52	35	0.2	1	17 18
53	33	0.2	1	13 20
54	31	0.2	1	17 14
55	30	0.2	1	22 8
56	28	0.2	1	12 16
57	23	0.2	1	13 10
58	29	0.2	1	18 11
59	23	0.2	1	19 4
60	39	0.2	1	22 17
61	33	0.2	1	18 15
62	34	0.2	1	22 12
63	29	0.2	1	17 12
64	29	0.2	1	18 11
65	51	0.2	1	18 33
66	27	0.2	1	11 16
67	45	0.2	1	27 18
68	38	0.2	1	18 20
69	40	0.2	1	16 24
70	25	0.2	1	17 8
71	29	0.2	1	19 10
72	36	0.2	1	23 13
73	29	0.2	1	19 10
74	36	0.2	1	20 16
75	37	0.2	1	22 15
76	33	0.2	1	20 13
77	35	0.2	1	26 9
78	38	0.2	1	14 24
79	33	0.2	1	23 10
80	33	0.2	1	17 16
81	29	0.2	1	20 9
82	44	0.2	1	17 27
83	38	0.2	1	19 19
84	41	0.2	1	24 17
85	29	0.2	1	17 12
86	24	0.2	1	18 6
87	36	0.2	1	22 14
88	29	0.2	1	17 12
89	33	0.2	1	24 9
90	37	0.2	1	21 16
91	42	0.2	1	29 13
92	35	0.2	1	17 18
93	42	0.2	1	25 17
94	31	0.2	1	19 12
95	44	0.2	1	21 23
96	46	0.2	1	25 21
97	40	0.2	1	22 18
98	45	0.2	1	19 26
99	42	0.2	1	19 23
100	42	0.2	1	23 19
101	37	0.2	1	16 21
102	52	0.2	1	29 23
103	55	0.2	1	33 22
104	35	0.2	1	20 15
105	41	0.2	1	20 21
106	50	0.2	1	15 35
107	65	0.2	1	29 36
108	45	0.2	1	24 21
109	41	0.2	1	24 17
110	38	0.2	1	26 12
111	48	0.2	1	32 16
112	32	0.2	1	24 8
113	45	0.2	1	25 20
114	43	0.2	1	26 17
115	40	0.2	1	20 20
116	45	0.2	1	24 21
117	33	0.2	1	23 10
118	42	0.2	1	24 18
119	35	0.2	1	22 13
120	60	0.2	1	34 26
121	50	0.2	1	35 15
122	34	0.2	1	20 14
123	33	0.2	1	14 19
124	28	0.2	1	20 8
125	34	0.2	1	24 10
126	32	0.2	1	20 12
127	40	0.2	1	28 12
128	28	0.2	1	18 10
129	37	0.2	1	21 16
130	59	0.2	1	31 28
131	46	0.2	1	25 21
132	48	0.2	1	30 18
133	41	0.2	1	28 13
134	38	0.2	1	21 17
135	45	0.2	1	22 23
136	25	0.2	1	13 12
137	30	0.2	1	21 9
138	27	0.2	1	17 10
139	32	0.2	1	20 12
140	59	0.2	1	32 27
141	30	0.2	1	22 8
142	36	0.2	1	25 11
143	47	0.2	1	31 16
144	48	0.2	1	30 18
145	40	0.2	1	23 17
146	66	0.2	1	33 33
147	35	0.2	1	19 16
148	33	0.2	1	14 19
149	25	0.2	1	17 8
150	46	0.2	1	19 27
151	14	0.2	1	5 9


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR006_S3_L002_R2_001.fastq.gz
=============================================
3045976 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR006_S3_L002_R1_001_trimmed.fq.gz and NR006_S3_L002_R2_001_trimmed.fq.gz
file_1: NR006_S3_L002_R1_001_trimmed.fq.gz, file_2: NR006_S3_L002_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR006_S3_L002_R1_001_trimmed.fq.gz and NR006_S3_L002_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR006_S3_L002_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR006_S3_L002_R2_001_val_2.fq.gz

Total number of sequences analysed: 3045976

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 14951 (0.49%)

Deleting both intermediate output files NR006_S3_L002_R1_001_trimmed.fq.gz and NR006_S3_L002_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR012_S1_L001_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR012_S1_L001_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR012_S1_L001_R1_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR012_S1_L001_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 7.64 s (25 us/read; 2.44 M reads/minute).

=== Summary ===

Total reads processed:                 310,937
Reads with adapters:                   165,260 (53.1%)
Reads written (passing filters):       310,937 (100.0%)

Total basepairs processed:    46,951,487 bp
Quality-trimmed:                 110,996 bp (0.2%)
Total written (filtered):     37,726,449 bp (80.4%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 165260 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 19.2%
  C: 33.1%
  G: 19.9%
  T: 27.7%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	38006	77734.2	0	38006
2	11189	19433.6	0	11189
3	3721	4858.4	0	3721
4	1394	1214.6	0	1394
5	833	303.6	0	833
6	691	75.9	0	691
7	644	19.0	0	644
8	689	4.7	0	689
9	629	1.2	0	624 5
10	647	0.3	1	617 30
11	630	0.1	1	598 32
12	636	0.0	1	598 38
13	650	0.0	1	617 33
14	609	0.0	1	570 39
15	727	0.0	1	687 40
16	756	0.0	1	716 40
17	504	0.0	1	478 26
18	642	0.0	1	613 29
19	650	0.0	1	624 26
20	603	0.0	1	562 41
21	622	0.0	1	586 36
22	753	0.0	1	705 48
23	583	0.0	1	545 38
24	673	0.0	1	640 33
25	582	0.0	1	550 32
26	721	0.0	1	692 29
27	658	0.0	1	617 41
28	630	0.0	1	599 31
29	651	0.0	1	631 20
30	684	0.0	1	655 29
31	668	0.0	1	641 27
32	616	0.0	1	587 29
33	643	0.0	1	628 15
34	624	0.0	1	596 28
35	673	0.0	1	631 42
36	695	0.0	1	669 26
37	651	0.0	1	615 36
38	666	0.0	1	632 34
39	697	0.0	1	673 24
40	730	0.0	1	695 35
41	679	0.0	1	648 31
42	669	0.0	1	639 30
43	697	0.0	1	655 42
44	718	0.0	1	684 34
45	703	0.0	1	678 25
46	669	0.0	1	637 32
47	724	0.0	1	699 25
48	659	0.0	1	618 41
49	758	0.0	1	727 31
50	701	0.0	1	682 19
51	701	0.0	1	670 31
52	699	0.0	1	667 32
53	704	0.0	1	673 31
54	728	0.0	1	710 18
55	693	0.0	1	672 21
56	736	0.0	1	701 35
57	701	0.0	1	678 23
58	692	0.0	1	663 29
59	690	0.0	1	663 27
60	712	0.0	1	678 34
61	759	0.0	1	723 36
62	749	0.0	1	723 26
63	761	0.0	1	737 24
64	764	0.0	1	734 30
65	750	0.0	1	718 32
66	729	0.0	1	705 24
67	774	0.0	1	742 32
68	741	0.0	1	710 31
69	734	0.0	1	699 35
70	708	0.0	1	684 24
71	762	0.0	1	740 22
72	782	0.0	1	760 22
73	783	0.0	1	763 20
74	729	0.0	1	699 30
75	736	0.0	1	711 25
76	763	0.0	1	729 34
77	780	0.0	1	743 37
78	749	0.0	1	716 33
79	778	0.0	1	752 26
80	804	0.0	1	771 33
81	758	0.0	1	738 20
82	752	0.0	1	723 29
83	749	0.0	1	725 24
84	761	0.0	1	740 21
85	801	0.0	1	771 30
86	826	0.0	1	799 27
87	783	0.0	1	752 31
88	803	0.0	1	777 26
89	831	0.0	1	803 28
90	796	0.0	1	773 23
91	789	0.0	1	767 22
92	768	0.0	1	739 29
93	780	0.0	1	751 29
94	757	0.0	1	738 19
95	797	0.0	1	771 26
96	815	0.0	1	783 32
97	779	0.0	1	754 25
98	810	0.0	1	796 14
99	872	0.0	1	848 24
100	826	0.0	1	799 27
101	858	0.0	1	833 25
102	846	0.0	1	826 20
103	819	0.0	1	798 21
104	818	0.0	1	802 16
105	806	0.0	1	786 20
106	789	0.0	1	768 21
107	843	0.0	1	817 26
108	876	0.0	1	846 30
109	841	0.0	1	815 26
110	823	0.0	1	796 27
111	824	0.0	1	802 22
112	883	0.0	1	863 20
113	884	0.0	1	846 38
114	798	0.0	1	780 18
115	802	0.0	1	780 22
116	815	0.0	1	794 21
117	872	0.0	1	844 28
118	846	0.0	1	821 25
119	875	0.0	1	850 25
120	856	0.0	1	840 16
121	842	0.0	1	818 24
122	866	0.0	1	844 22
123	820	0.0	1	788 32
124	825	0.0	1	804 21
125	930	0.0	1	912 18
126	879	0.0	1	864 15
127	929	0.0	1	906 23
128	865	0.0	1	848 17
129	919	0.0	1	896 23
130	891	0.0	1	870 21
131	976	0.0	1	960 16
132	857	0.0	1	839 18
133	908	0.0	1	884 24
134	836	0.0	1	823 13
135	781	0.0	1	772 9
136	771	0.0	1	758 13
137	828	0.0	1	819 9
138	807	0.0	1	794 13
139	809	0.0	1	802 7
140	873	0.0	1	862 11
141	908	0.0	1	897 11
142	778	0.0	1	766 12
143	765	0.0	1	753 12
144	850	0.0	1	840 10
145	802	0.0	1	795 7
146	901	0.0	1	887 14
147	797	0.0	1	782 15
148	843	0.0	1	826 17
149	686	0.0	1	670 16
150	675	0.0	1	663 12
151	178	0.0	1	159 19


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR012_S1_L001_R1_001.fastq.gz
=============================================
310937 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR012_S1_L001_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR012_S1_L001_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR012_S1_L001_R2_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR012_S1_L001_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 7.84 s (25 us/read; 2.38 M reads/minute).

=== Summary ===

Total reads processed:                 310,937
Reads with adapters:                   148,571 (47.8%)
Reads written (passing filters):       310,937 (100.0%)

Total basepairs processed:    46,951,487 bp
Quality-trimmed:                 185,152 bp (0.4%)
Total written (filtered):     38,811,744 bp (82.7%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 148571 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 19.2%
  C: 32.6%
  G: 20.8%
  T: 27.3%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	35513	77734.2	0	35513
2	9836	19433.6	0	9836
3	3265	4858.4	0	3265
4	1404	1214.6	0	1404
5	753	303.6	0	753
6	576	75.9	0	576
7	551	19.0	0	551
8	641	4.7	0	641
9	580	1.2	0	570 10
10	609	0.3	1	544 65
11	588	0.1	1	527 61
12	603	0.0	1	558 45
13	631	0.0	1	575 56
14	520	0.0	1	472 48
15	654	0.0	1	576 78
16	708	0.0	1	638 70
17	453	0.0	1	419 34
18	629	0.0	1	583 46
19	675	0.0	1	636 39
20	567	0.0	1	509 58
21	651	0.0	1	586 65
22	705	0.0	1	647 58
23	509	0.0	1	459 50
24	603	0.0	1	558 45
25	620	0.0	1	574 46
26	675	0.0	1	608 67
27	649	0.0	1	607 42
28	559	0.0	1	512 47
29	649	0.0	1	605 44
30	677	0.0	1	626 51
31	577	0.0	1	536 41
32	609	0.0	1	550 59
33	566	0.0	1	508 58
34	630	0.0	1	573 57
35	563	0.0	1	518 45
36	696	0.0	1	647 49
37	551	0.0	1	506 45
38	672	0.0	1	612 60
39	661	0.0	1	613 48
40	628	0.0	1	586 42
41	627	0.0	1	573 54
42	676	0.0	1	641 35
43	616	0.0	1	578 38
44	579	0.0	1	547 32
45	645	0.0	1	603 42
46	601	0.0	1	556 45
47	652	0.0	1	610 42
48	669	0.0	1	627 42
49	600	0.0	1	544 56
50	679	0.0	1	625 54
51	618	0.0	1	570 48
52	611	0.0	1	557 54
53	601	0.0	1	574 27
54	646	0.0	1	596 50
55	637	0.0	1	594 43
56	658	0.0	1	618 40
57	611	0.0	1	576 35
58	652	0.0	1	613 39
59	670	0.0	1	624 46
60	658	0.0	1	619 39
61	645	0.0	1	611 34
62	678	0.0	1	641 37
63	714	0.0	1	668 46
64	617	0.0	1	581 36
65	669	0.0	1	634 35
66	673	0.0	1	633 40
67	624	0.0	1	585 39
68	650	0.0	1	606 44
69	650	0.0	1	610 40
70	725	0.0	1	679 46
71	662	0.0	1	628 34
72	691	0.0	1	652 39
73	701	0.0	1	670 31
74	693	0.0	1	657 36
75	709	0.0	1	679 30
76	682	0.0	1	637 45
77	749	0.0	1	706 43
78	674	0.0	1	635 39
79	685	0.0	1	654 31
80	646	0.0	1	613 33
81	697	0.0	1	665 32
82	690	0.0	1	651 39
83	714	0.0	1	671 43
84	686	0.0	1	657 29
85	692	0.0	1	657 35
86	688	0.0	1	660 28
87	657	0.0	1	618 39
88	700	0.0	1	668 32
89	724	0.0	1	689 35
90	655	0.0	1	624 31
91	740	0.0	1	700 40
92	671	0.0	1	641 30
93	724	0.0	1	691 33
94	738	0.0	1	715 23
95	703	0.0	1	671 32
96	737	0.0	1	700 37
97	685	0.0	1	648 37
98	685	0.0	1	655 30
99	731	0.0	1	702 29
100	744	0.0	1	717 27
101	726	0.0	1	690 36
102	738	0.0	1	718 20
103	713	0.0	1	690 23
104	722	0.0	1	680 42
105	700	0.0	1	675 25
106	703	0.0	1	674 29
107	731	0.0	1	696 35
108	783	0.0	1	744 39
109	724	0.0	1	694 30
110	696	0.0	1	672 24
111	802	0.0	1	768 34
112	737	0.0	1	719 18
113	752	0.0	1	722 30
114	742	0.0	1	717 25
115	715	0.0	1	691 24
116	732	0.0	1	701 31
117	743	0.0	1	697 46
118	745	0.0	1	705 40
119	726	0.0	1	703 23
120	752	0.0	1	730 22
121	723	0.0	1	701 22
122	779	0.0	1	745 34
123	787	0.0	1	760 27
124	720	0.0	1	689 31
125	752	0.0	1	731 21
126	723	0.0	1	689 34
127	719	0.0	1	689 30
128	714	0.0	1	682 32
129	788	0.0	1	750 38
130	737	0.0	1	714 23
131	796	0.0	1	771 25
132	770	0.0	1	739 31
133	755	0.0	1	735 20
134	760	0.0	1	739 21
135	705	0.0	1	688 17
136	652	0.0	1	632 20
137	687	0.0	1	669 18
138	664	0.0	1	641 23
139	658	0.0	1	632 26
140	686	0.0	1	670 16
141	742	0.0	1	721 21
142	638	0.0	1	615 23
143	663	0.0	1	636 27
144	719	0.0	1	700 19
145	746	0.0	1	737 9
146	766	0.0	1	748 18
147	737	0.0	1	720 17
148	632	0.0	1	619 13
149	536	0.0	1	527 9
150	507	0.0	1	492 15
151	118	0.0	1	104 14


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR012_S1_L001_R2_001.fastq.gz
=============================================
310937 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR012_S1_L001_R1_001_trimmed.fq.gz and NR012_S1_L001_R2_001_trimmed.fq.gz
file_1: NR012_S1_L001_R1_001_trimmed.fq.gz, file_2: NR012_S1_L001_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR012_S1_L001_R1_001_trimmed.fq.gz and NR012_S1_L001_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR012_S1_L001_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR012_S1_L001_R2_001_val_2.fq.gz

Total number of sequences analysed: 310937

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 29465 (9.48%)

Deleting both intermediate output files NR012_S1_L001_R1_001_trimmed.fq.gz and NR012_S1_L001_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR012_S1_L002_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR012_S1_L002_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR012_S1_L002_R1_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR012_S1_L002_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 8.82 s (25 us/read; 2.44 M reads/minute).

=== Summary ===

Total reads processed:                 358,756
Reads with adapters:                   186,719 (52.0%)
Reads written (passing filters):       358,756 (100.0%)

Total basepairs processed:    54,172,156 bp
Quality-trimmed:                 132,160 bp (0.2%)
Total written (filtered):     43,801,446 bp (80.9%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 186719 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 19.2%
  C: 33.2%
  G: 20.2%
  T: 27.3%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	43381	89689.0	0	43381
2	12814	22422.2	0	12814
3	4159	5605.6	0	4159
4	1624	1401.4	0	1624
5	948	350.3	0	948
6	706	87.6	0	706
7	729	21.9	0	729
8	787	5.5	0	787
9	700	1.4	0	694 6
10	769	0.3	1	729 40
11	713	0.1	1	687 26
12	671	0.0	1	648 23
13	690	0.0	1	668 22
14	669	0.0	1	637 32
15	754	0.0	1	725 29
16	907	0.0	1	870 37
17	503	0.0	1	488 15
18	788	0.0	1	770 18
19	765	0.0	1	749 16
20	744	0.0	1	716 28
21	734	0.0	1	715 19
22	834	0.0	1	810 24
23	630	0.0	1	608 22
24	727	0.0	1	705 22
25	685	0.0	1	664 21
26	823	0.0	1	794 29
27	776	0.0	1	750 26
28	785	0.0	1	758 27
29	776	0.0	1	759 17
30	763	0.0	1	738 25
31	734	0.0	1	711 23
32	759	0.0	1	740 19
33	708	0.0	1	686 22
34	712	0.0	1	696 16
35	821	0.0	1	793 28
36	796	0.0	1	767 29
37	726	0.0	1	703 23
38	817	0.0	1	797 20
39	766	0.0	1	738 28
40	788	0.0	1	766 22
41	751	0.0	1	726 25
42	779	0.0	1	757 22
43	750	0.0	1	721 29
44	816	0.0	1	793 23
45	746	0.0	1	724 22
46	780	0.0	1	749 31
47	825	0.0	1	802 23
48	798	0.0	1	781 17
49	790	0.0	1	771 19
50	791	0.0	1	781 10
51	804	0.0	1	780 24
52	790	0.0	1	765 25
53	755	0.0	1	738 17
54	805	0.0	1	780 25
55	739	0.0	1	723 16
56	802	0.0	1	776 26
57	779	0.0	1	747 32
58	837	0.0	1	809 28
59	823	0.0	1	802 21
60	813	0.0	1	796 17
61	816	0.0	1	796 20
62	845	0.0	1	829 16
63	802	0.0	1	779 23
64	770	0.0	1	739 31
65	845	0.0	1	822 23
66	766	0.0	1	744 22
67	834	0.0	1	804 30
68	905	0.0	1	879 26
69	789	0.0	1	771 18
70	851	0.0	1	829 22
71	871	0.0	1	850 21
72	844	0.0	1	821 23
73	860	0.0	1	839 21
74	856	0.0	1	845 11
75	838	0.0	1	812 26
76	900	0.0	1	874 26
77	870	0.0	1	854 16
78	917	0.0	1	881 36
79	820	0.0	1	807 13
80	844	0.0	1	821 23
81	875	0.0	1	850 25
82	886	0.0	1	865 21
83	842	0.0	1	817 25
84	872	0.0	1	850 22
85	857	0.0	1	839 18
86	803	0.0	1	784 19
87	880	0.0	1	856 24
88	926	0.0	1	902 24
89	882	0.0	1	860 22
90	973	0.0	1	953 20
91	893	0.0	1	874 19
92	873	0.0	1	858 15
93	846	0.0	1	834 12
94	851	0.0	1	832 19
95	867	0.0	1	848 19
96	914	0.0	1	898 16
97	920	0.0	1	898 22
98	895	0.0	1	872 23
99	918	0.0	1	906 12
100	932	0.0	1	918 14
101	945	0.0	1	925 20
102	914	0.0	1	901 13
103	906	0.0	1	891 15
104	889	0.0	1	873 16
105	927	0.0	1	911 16
106	960	0.0	1	946 14
107	958	0.0	1	948 10
108	934	0.0	1	917 17
109	917	0.0	1	892 25
110	928	0.0	1	908 20
111	998	0.0	1	975 23
112	930	0.0	1	903 27
113	966	0.0	1	952 14
114	997	0.0	1	982 15
115	917	0.0	1	892 25
116	893	0.0	1	875 18
117	956	0.0	1	941 15
118	963	0.0	1	943 20
119	931	0.0	1	908 23
120	1010	0.0	1	998 12
121	1004	0.0	1	992 12
122	964	0.0	1	953 11
123	964	0.0	1	943 21
124	988	0.0	1	971 17
125	986	0.0	1	970 16
126	958	0.0	1	950 8
127	1019	0.0	1	1003 16
128	944	0.0	1	930 14
129	1032	0.0	1	1014 18
130	970	0.0	1	956 14
131	1060	0.0	1	1050 10
132	1003	0.0	1	998 5
133	989	0.0	1	980 9
134	966	0.0	1	955 11
135	977	0.0	1	972 5
136	954	0.0	1	945 9
137	886	0.0	1	871 15
138	886	0.0	1	877 9
139	850	0.0	1	842 8
140	898	0.0	1	892 6
141	943	0.0	1	933 10
142	864	0.0	1	851 13
143	889	0.0	1	883 6
144	1000	0.0	1	997 3
145	936	0.0	1	928 8
146	1039	0.0	1	1025 14
147	934	0.0	1	927 7
148	944	0.0	1	939 5
149	754	0.0	1	746 8
150	776	0.0	1	765 11
151	201	0.0	1	181 20


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR012_S1_L002_R1_001.fastq.gz
=============================================
358756 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR012_S1_L002_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR012_S1_L002_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR012_S1_L002_R2_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR012_S1_L002_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 8.62 s (24 us/read; 2.50 M reads/minute).

=== Summary ===

Total reads processed:                 358,756
Reads with adapters:                   168,067 (46.8%)
Reads written (passing filters):       358,756 (100.0%)

Total basepairs processed:    54,172,156 bp
Quality-trimmed:                 213,647 bp (0.4%)
Total written (filtered):     45,232,988 bp (83.5%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 168067 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 19.6%
  C: 32.2%
  G: 20.8%
  T: 27.2%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	41199	89689.0	0	41199
2	12173	22422.2	0	12173
3	3946	5605.6	0	3946
4	1645	1401.4	0	1645
5	906	350.3	0	906
6	713	87.6	0	713
7	700	21.9	0	700
8	706	5.5	0	706
9	594	1.4	0	584 10
10	660	0.3	1	611 49
11	689	0.1	1	642 47
12	649	0.0	1	604 45
13	754	0.0	1	699 55
14	629	0.0	1	597 32
15	819	0.0	1	771 48
16	829	0.0	1	770 59
17	469	0.0	1	443 26
18	684	0.0	1	634 50
19	702	0.0	1	661 41
20	591	0.0	1	556 35
21	736	0.0	1	690 46
22	768	0.0	1	735 33
23	566	0.0	1	539 27
24	693	0.0	1	642 51
25	595	0.0	1	561 34
26	741	0.0	1	680 61
27	748	0.0	1	705 43
28	660	0.0	1	627 33
29	757	0.0	1	718 39
30	710	0.0	1	678 32
31	701	0.0	1	666 35
32	714	0.0	1	667 47
33	669	0.0	1	633 36
34	711	0.0	1	675 36
35	693	0.0	1	660 33
36	793	0.0	1	754 39
37	680	0.0	1	653 27
38	755	0.0	1	715 40
39	716	0.0	1	680 36
40	696	0.0	1	665 31
41	739	0.0	1	699 40
42	681	0.0	1	640 41
43	737	0.0	1	700 37
44	696	0.0	1	656 40
45	742	0.0	1	706 36
46	697	0.0	1	652 45
47	723	0.0	1	684 39
48	680	0.0	1	656 24
49	695	0.0	1	670 25
50	705	0.0	1	664 41
51	708	0.0	1	677 31
52	715	0.0	1	680 35
53	715	0.0	1	682 33
54	710	0.0	1	684 26
55	701	0.0	1	674 27
56	736	0.0	1	691 45
57	705	0.0	1	680 25
58	746	0.0	1	712 34
59	692	0.0	1	656 36
60	699	0.0	1	665 34
61	732	0.0	1	702 30
62	766	0.0	1	730 36
63	697	0.0	1	670 27
64	749	0.0	1	719 30
65	798	0.0	1	765 33
66	735	0.0	1	701 34
67	791	0.0	1	756 35
68	804	0.0	1	757 47
69	751	0.0	1	724 27
70	711	0.0	1	680 31
71	750	0.0	1	712 38
72	785	0.0	1	758 27
73	803	0.0	1	762 41
74	759	0.0	1	728 31
75	730	0.0	1	698 32
76	765	0.0	1	737 28
77	768	0.0	1	729 39
78	715	0.0	1	683 32
79	812	0.0	1	775 37
80	771	0.0	1	732 39
81	731	0.0	1	707 24
82	719	0.0	1	695 24
83	771	0.0	1	730 41
84	737	0.0	1	708 29
85	816	0.0	1	784 32
86	794	0.0	1	765 29
87	763	0.0	1	732 31
88	736	0.0	1	719 17
89	764	0.0	1	726 38
90	720	0.0	1	684 36
91	792	0.0	1	770 22
92	802	0.0	1	774 28
93	770	0.0	1	731 39
94	799	0.0	1	772 27
95	757	0.0	1	727 30
96	771	0.0	1	744 27
97	746	0.0	1	715 31
98	803	0.0	1	782 21
99	794	0.0	1	764 30
100	799	0.0	1	775 24
101	798	0.0	1	766 32
102	755	0.0	1	728 27
103	803	0.0	1	779 24
104	765	0.0	1	740 25
105	745	0.0	1	723 22
106	814	0.0	1	788 26
107	793	0.0	1	767 26
108	778	0.0	1	755 23
109	858	0.0	1	825 33
110	813	0.0	1	785 28
111	823	0.0	1	797 26
112	777	0.0	1	760 17
113	790	0.0	1	768 22
114	797	0.0	1	777 20
115	880	0.0	1	840 40
116	775	0.0	1	758 17
117	792	0.0	1	772 20
118	789	0.0	1	769 20
119	839	0.0	1	816 23
120	825	0.0	1	799 26
121	818	0.0	1	789 29
122	776	0.0	1	758 18
123	883	0.0	1	858 25
124	744	0.0	1	722 22
125	857	0.0	1	834 23
126	805	0.0	1	787 18
127	783	0.0	1	763 20
128	815	0.0	1	798 17
129	805	0.0	1	788 17
130	845	0.0	1	820 25
131	862	0.0	1	843 19
132	816	0.0	1	803 13
133	823	0.0	1	802 21
134	824	0.0	1	804 20
135	785	0.0	1	767 18
136	734	0.0	1	714 20
137	712	0.0	1	697 15
138	704	0.0	1	687 17
139	695	0.0	1	678 17
140	723	0.0	1	706 17
141	737	0.0	1	723 14
142	696	0.0	1	683 13
143	711	0.0	1	696 15
144	799	0.0	1	788 11
145	804	0.0	1	786 18
146	815	0.0	1	794 21
147	716	0.0	1	695 21
148	703	0.0	1	688 15
149	592	0.0	1	574 18
150	572	0.0	1	560 12
151	147	0.0	1	134 13


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR012_S1_L002_R2_001.fastq.gz
=============================================
358756 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR012_S1_L002_R1_001_trimmed.fq.gz and NR012_S1_L002_R2_001_trimmed.fq.gz
file_1: NR012_S1_L002_R1_001_trimmed.fq.gz, file_2: NR012_S1_L002_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR012_S1_L002_R1_001_trimmed.fq.gz and NR012_S1_L002_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR012_S1_L002_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR012_S1_L002_R2_001_val_2.fq.gz

Total number of sequences analysed: 358756

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 32504 (9.06%)

Deleting both intermediate output files NR012_S1_L002_R1_001_trimmed.fq.gz and NR012_S1_L002_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR013_AD013_S2_L001_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R1_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
330000000 sequences processed
340000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 8220.39 s (24 us/read; 2.50 M reads/minute).

=== Summary ===

Total reads processed:             342,277,558
Reads with adapters:               183,891,810 (53.7%)
Reads written (passing filters):   342,277,558 (100.0%)

Total basepairs processed: 51,683,911,258 bp
Quality-trimmed:             177,870,597 bp (0.3%)
Total written (filtered):  41,309,193,256 bp (79.9%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 183891810 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 19.7%
  C: 32.7%
  G: 20.4%
  T: 27.0%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	40388880	85569389.5	0	40388880
2	11683799	21392347.4	0	11683799
3	4010339	5348086.8	0	4010339
4	1712947	1337021.7	0	1712947
5	995397	334255.4	0	995397
6	786526	83563.9	0	786526
7	784662	20891.0	0	784662
8	827819	5222.7	0	827819
9	695311	1305.7	0	686951 8360
10	779196	326.4	1	723277 55919
11	806919	81.6	1	755613 51306
12	763544	20.4	1	709569 53975
13	779656	20.4	1	731038 48618
14	727535	20.4	1	680076 47459
15	852162	20.4	1	793739 58423
16	927854	20.4	1	865786 62068
17	595097	20.4	1	559071 36026
18	793308	20.4	1	745158 48150
19	820813	20.4	1	774999 45814
20	726618	20.4	1	680830 45788
21	797575	20.4	1	751754 45821
22	875656	20.4	1	822159 53497
23	670794	20.4	1	629734 41060
24	815418	20.4	1	769524 45894
25	718144	20.4	1	679059 39085
26	838493	20.4	1	785154 53339
27	796979	20.4	1	753147 43832
28	752459	20.4	1	710800 41659
29	779708	20.4	1	739042 40666
30	846865	20.4	1	800159 46706
31	789467	20.4	1	745353 44114
32	766285	20.4	1	726684 39601
33	775956	20.4	1	732627 43329
34	777116	20.4	1	735561 41555
35	789816	20.4	1	744671 45145
36	847851	20.4	1	804739 43112
37	758734	20.4	1	715110 43624
38	832663	20.4	1	788304 44359
39	812276	20.4	1	768737 43539
40	810942	20.4	1	768401 42541
41	800677	20.4	1	757743 42934
42	808457	20.4	1	766837 41620
43	801371	20.4	1	760095 41276
44	805830	20.4	1	764204 41626
45	810657	20.4	1	769292 41365
46	803540	20.4	1	761439 42101
47	817900	20.4	1	776415 41485
48	813316	20.4	1	772060 41256
49	818804	20.4	1	777318 41486
50	815442	20.4	1	774692 40750
51	818321	20.4	1	777259 41062
52	818382	20.4	1	778490 39892
53	823951	20.4	1	783815 40136
54	818968	20.4	1	779047 39921
55	822143	20.4	1	781895 40248
56	823609	20.4	1	784267 39342
57	825029	20.4	1	785368 39661
58	827704	20.4	1	788128 39576
59	833104	20.4	1	793259 39845
60	831235	20.4	1	792380 38855
61	832657	20.4	1	793431 39226
62	831832	20.4	1	793357 38475
63	833288	20.4	1	794795 38493
64	833485	20.4	1	795306 38179
65	834389	20.4	1	796142 38247
66	837347	20.4	1	799230 38117
67	840684	20.4	1	802647 38037
68	845216	20.4	1	807252 37964
69	847361	20.4	1	809367 37994
70	848360	20.4	1	810649 37711
71	851310	20.4	1	813436 37874
72	849201	20.4	1	811832 37369
73	848981	20.4	1	811750 37231
74	848610	20.4	1	811471 37139
75	851947	20.4	1	814603 37344
76	851151	20.4	1	814602 36549
77	855712	20.4	1	818946 36766
78	857694	20.4	1	820917 36777
79	867771	20.4	1	830904 36867
80	868545	20.4	1	831831 36714
81	870150	20.4	1	833875 36275
82	869271	20.4	1	832978 36293
83	868005	20.4	1	832273 35732
84	865449	20.4	1	829813 35636
85	868387	20.4	1	832417 35970
86	866211	20.4	1	830618 35593
87	870208	20.4	1	835273 34935
88	874875	20.4	1	839361 35514
89	881784	20.4	1	846527 35257
90	886150	20.4	1	851230 34920
91	893644	20.4	1	858759 34885
92	887519	20.4	1	853104 34415
93	888386	20.4	1	854265 34121
94	886135	20.4	1	852195 33940
95	886285	20.4	1	853201 33084
96	884044	20.4	1	851257 32787
97	887292	20.4	1	854429 32863
98	893376	20.4	1	860471 32905
99	901175	20.4	1	868374 32801
100	907164	20.4	1	874405 32759
101	913618	20.4	1	880838 32780
102	913959	20.4	1	881754 32205
103	911739	20.4	1	879647 32092
104	905964	20.4	1	874314 31650
105	905993	20.4	1	874258 31735
106	906182	20.4	1	873559 32623
107	908110	20.4	1	876186 31924
108	913564	20.4	1	881156 32408
109	925991	20.4	1	893692 32299
110	931480	20.4	1	899357 32123
111	941940	20.4	1	910234 31706
112	946848	20.4	1	915100 31748
113	944143	20.4	1	912658 31485
114	937208	20.4	1	905801 31407
115	931563	20.4	1	901242 30321
116	929805	20.4	1	899326 30479
117	928394	20.4	1	898673 29721
118	929624	20.4	1	901129 28495
119	936256	20.4	1	907871 28385
120	947616	20.4	1	918957 28659
121	961453	20.4	1	932789 28664
122	970862	20.4	1	942499 28363
123	968427	20.4	1	939973 28454
124	963612	20.4	1	935591 28021
125	957482	20.4	1	929511 27971
126	953436	20.4	1	926550 26886
127	954852	20.4	1	928741 26111
128	962979	20.4	1	938243 24736
129	971364	20.4	1	947262 24102
130	991716	20.4	1	968746 22970
131	1010119	20.4	1	987255 22864
132	1017220	20.4	1	996130 21090
133	1015734	20.4	1	995762 19972
134	965026	20.4	1	946900 18126
135	947123	20.4	1	930865 16258
136	919019	20.4	1	903569 15450
137	895405	20.4	1	881112 14293
138	860977	20.4	1	847091 13886
139	851175	20.4	1	837420 13755
140	918814	20.4	1	904007 14807
141	977689	20.4	1	962530 15159
142	886262	20.4	1	872083 14179
143	919381	20.4	1	905178 14203
144	975731	20.4	1	960540 15191
145	945359	20.4	1	930332 15027
146	990217	20.4	1	973971 16246
147	834988	20.4	1	820525 14463
148	851341	20.4	1	835999 15342
149	716897	20.4	1	702235 14662
150	690547	20.4	1	673848 16699
151	315536	20.4	1	286994 28542


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R1_001.fastq.gz
=============================================
342277558 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR013_AD013_S2_L001_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R2_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
330000000 sequences processed
340000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 8511.76 s (25 us/read; 2.41 M reads/minute).

=== Summary ===

Total reads processed:             342,277,558
Reads with adapters:               169,073,071 (49.4%)
Reads written (passing filters):   342,277,558 (100.0%)

Total basepairs processed: 51,683,911,258 bp
Quality-trimmed:             235,733,156 bp (0.5%)
Total written (filtered):  42,650,220,228 bp (82.5%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 169073071 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 20.3%
  C: 31.7%
  G: 20.6%
  T: 27.2%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	40820229	85569389.5	0	40820229
2	11782648	21392347.4	0	11782648
3	4020450	5348086.8	0	4020450
4	1715428	1337021.7	0	1715428
5	935513	334255.4	0	935513
6	719155	83563.9	0	719155
7	714435	20891.0	0	714435
8	756165	5222.7	0	756165
9	624028	1305.7	0	614695 9333
10	706778	326.4	1	624616 82162
11	759782	81.6	1	674567 85215
12	671199	20.4	1	593380 77819
13	736821	20.4	1	651009 85812
14	633841	20.4	1	564162 69679
15	820538	20.4	1	722627 97911
16	806259	20.4	1	718905 87354
17	536268	20.4	1	477709 58559
18	735258	20.4	1	655106 80152
19	758719	20.4	1	682265 76454
20	635894	20.4	1	571100 64794
21	742006	20.4	1	661359 80647
22	782074	20.4	1	701445 80629
23	605414	20.4	1	541973 63441
24	744945	20.4	1	664620 80325
25	655255	20.4	1	591736 63519
26	776270	20.4	1	686776 89494
27	741583	20.4	1	665113 76470
28	677788	20.4	1	611417 66371
29	718819	20.4	1	648277 70542
30	764766	20.4	1	691730 73036
31	682123	20.4	1	617636 64487
32	719464	20.4	1	647349 72115
33	691777	20.4	1	627625 64152
34	729627	20.4	1	656813 72814
35	687137	20.4	1	621884 65253
36	805068	20.4	1	731891 73177
37	655611	20.4	1	595685 59926
38	768117	20.4	1	696101 72016
39	748806	20.4	1	678859 69947
40	741903	20.4	1	676610 65293
41	725713	20.4	1	661915 63798
42	741386	20.4	1	677245 64141
43	729434	20.4	1	666505 62929
44	728751	20.4	1	665841 62910
45	737282	20.4	1	673834 63448
46	722712	20.4	1	661574 61138
47	753002	20.4	1	688608 64394
48	732571	20.4	1	672457 60114
49	745387	20.4	1	683334 62053
50	737709	20.4	1	677391 60318
51	742692	20.4	1	681024 61668
52	743725	20.4	1	682869 60856
53	747773	20.4	1	686419 61354
54	741385	20.4	1	681898 59487
55	744573	20.4	1	684320 60253
56	746636	20.4	1	686510 60126
57	747951	20.4	1	687440 60511
58	750971	20.4	1	690584 60387
59	751688	20.4	1	692024 59664
60	752003	20.4	1	692912 59091
61	753403	20.4	1	694485 58918
62	749599	20.4	1	691886 57713
63	750095	20.4	1	692505 57590
64	751757	20.4	1	694286 57471
65	748781	20.4	1	691588 57193
66	751316	20.4	1	694429 56887
67	755739	20.4	1	699092 56647
68	757346	20.4	1	702379 54967
69	761461	20.4	1	706811 54650
70	763474	20.4	1	709206 54268
71	762579	20.4	1	708069 54510
72	761282	20.4	1	708276 53006
73	760388	20.4	1	706805 53583
74	760282	20.4	1	707097 53185
75	760919	20.4	1	708085 52834
76	761360	20.4	1	708364 52996
77	765345	20.4	1	712241 53104
78	765972	20.4	1	712751 53221
79	769659	20.4	1	716379 53280
80	771993	20.4	1	719829 52164
81	772403	20.4	1	720381 52022
82	770945	20.4	1	719545 51400
83	766876	20.4	1	715360 51516
84	766959	20.4	1	716014 50945
85	765578	20.4	1	715552 50026
86	765398	20.4	1	715395 50003
87	769546	20.4	1	719845 49701
88	770661	20.4	1	722014 48647
89	779324	20.4	1	730585 48739
90	782440	20.4	1	733139 49301
91	785621	20.4	1	736955 48666
92	784128	20.4	1	735042 49086
93	783323	20.4	1	735462 47861
94	777276	20.4	1	729989 47287
95	776780	20.4	1	729845 46935
96	775301	20.4	1	728847 46454
97	778120	20.4	1	731379 46741
98	782054	20.4	1	735883 46171
99	787491	20.4	1	741122 46369
100	792380	20.4	1	746352 46028
101	797343	20.4	1	751323 46020
102	793873	20.4	1	749291 44582
103	791473	20.4	1	747107 44366
104	786531	20.4	1	742401 44130
105	784956	20.4	1	741447 43509
106	784602	20.4	1	741267 43335
107	785094	20.4	1	741639 43455
108	788685	20.4	1	746409 42276
109	798037	20.4	1	754775 43262
110	805426	20.4	1	762153 43273
111	810956	20.4	1	767929 43027
112	813814	20.4	1	771545 42269
113	811795	20.4	1	769721 42074
114	801975	20.4	1	760023 41952
115	798716	20.4	1	757606 41110
116	793490	20.4	1	753519 39971
117	792405	20.4	1	752759 39646
118	792182	20.4	1	752956 39226
119	798086	20.4	1	759124 38962
120	807653	20.4	1	768894 38759
121	818403	20.4	1	778685 39718
122	819793	20.4	1	780823 38970
123	820755	20.4	1	782414 38341
124	813872	20.4	1	775571 38301
125	805064	20.4	1	767871 37193
126	801000	20.4	1	764847 36153
127	804159	20.4	1	768491 35668
128	808143	20.4	1	773386 34757
129	816192	20.4	1	781321 34871
130	834445	20.4	1	799613 34832
131	847004	20.4	1	812141 34863
132	848895	20.4	1	815313 33582
133	841281	20.4	1	808989 32292
134	799405	20.4	1	768827 30578
135	783067	20.4	1	753818 29249
136	757259	20.4	1	728681 28578
137	733223	20.4	1	705331 27892
138	701751	20.4	1	674466 27285
139	697866	20.4	1	671317 26549
140	750187	20.4	1	722013 28174
141	791694	20.4	1	763209 28485
142	729754	20.4	1	702984 26770
143	760344	20.4	1	733107 27237
144	802331	20.4	1	774018 28313
145	791346	20.4	1	764886 26460
146	804731	20.4	1	777907 26824
147	686659	20.4	1	664329 22330
148	686872	20.4	1	665692 21180
149	550444	20.4	1	532595 17849
150	529171	20.4	1	510636 18535
151	234210	20.4	1	208660 25550


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR013_AD013_S2_L001_R2_001.fastq.gz
=============================================
342277558 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR013_AD013_S2_L001_R1_001_trimmed.fq.gz and NR013_AD013_S2_L001_R2_001_trimmed.fq.gz
file_1: NR013_AD013_S2_L001_R1_001_trimmed.fq.gz, file_2: NR013_AD013_S2_L001_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR013_AD013_S2_L001_R1_001_trimmed.fq.gz and NR013_AD013_S2_L001_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR013_AD013_S2_L001_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR013_AD013_S2_L001_R2_001_val_2.fq.gz

Total number of sequences analysed: 342277558

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 32399854 (9.47%)

Deleting both intermediate output files NR013_AD013_S2_L001_R1_001_trimmed.fq.gz and NR013_AD013_S2_L001_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR013_AD013_S2_L002_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R1_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
330000000 sequences processed
340000000 sequences processed
350000000 sequences processed
360000000 sequences processed
370000000 sequences processed
380000000 sequences processed
390000000 sequences processed
400000000 sequences processed
410000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 9950.16 s (24 us/read; 2.51 M reads/minute).

=== Summary ===

Total reads processed:             415,822,852
Reads with adapters:               214,614,887 (51.6%)
Reads written (passing filters):   415,822,852 (100.0%)

Total basepairs processed: 62,789,250,652 bp
Quality-trimmed:             237,916,547 bp (0.4%)
Total written (filtered):  50,986,157,920 bp (81.2%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 214614887 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 20.0%
  C: 32.4%
  G: 20.4%
  T: 27.1%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	50386724	103955713.0	0	50386724
2	14542061	25988928.2	0	14542061
3	4910218	6497232.1	0	4910218
4	2070214	1624308.0	0	2070214
5	1141353	406077.0	0	1141353
6	914915	101519.3	0	914915
7	892217	25379.8	0	892217
8	927453	6345.0	0	927453
9	808460	1586.2	0	799470 8990
10	881043	396.6	1	835188 45855
11	910256	99.1	1	869754 40502
12	863077	24.8	1	822517 40560
13	884312	24.8	1	847815 36497
14	833437	24.8	1	797878 35559
15	943139	24.8	1	899833 43306
16	1031643	24.8	1	985067 46576
17	693776	24.8	1	666899 26877
18	890739	24.8	1	856113 34626
19	919240	24.8	1	886166 33074
20	830740	24.8	1	797012 33728
21	904625	24.8	1	869090 35535
22	980608	24.8	1	940157 40451
23	758414	24.8	1	727750 30664
24	922246	24.8	1	886504 35742
25	821687	24.8	1	792410 29277
26	940516	24.8	1	898312 42204
27	895290	24.8	1	862092 33198
28	861508	24.8	1	829893 31615
29	878923	24.8	1	848680 30243
30	935661	24.8	1	900959 34702
31	890427	24.8	1	856911 33516
32	876170	24.8	1	845708 30462
33	871818	24.8	1	839349 32469
34	888056	24.8	1	855472 32584
35	893985	24.8	1	860462 33523
36	941283	24.8	1	908816 32467
37	866803	24.8	1	833795 33008
38	938084	24.8	1	903662 34422
39	917384	24.8	1	883803 33581
40	915553	24.8	1	883357 32196
41	903529	24.8	1	871137 32392
42	912337	24.8	1	880927 31410
43	903619	24.8	1	872819 30800
44	908618	24.8	1	876636 31982
45	913382	24.8	1	881338 32044
46	904794	24.8	1	872879 31915
47	921905	24.8	1	889613 32292
48	917471	24.8	1	885935 31536
49	925145	24.8	1	892957 32188
50	917758	24.8	1	886669 31089
51	923602	24.8	1	892274 31328
52	922737	24.8	1	892327 30410
53	927239	24.8	1	896380 30859
54	924549	24.8	1	894108 30441
55	927519	24.8	1	897253 30266
56	926828	24.8	1	896613 30215
57	930704	24.8	1	900241 30463
58	933679	24.8	1	903258 30421
59	937434	24.8	1	907011 30423
60	938844	24.8	1	906975 31869
61	941495	24.8	1	910132 31363
62	937993	24.8	1	906915 31078
63	939883	24.8	1	909197 30686
64	938737	24.8	1	907708 31029
65	941343	24.8	1	910953 30390
66	941832	24.8	1	911016 30816
67	948012	24.8	1	917423 30589
68	952097	24.8	1	920730 31367
69	954987	24.8	1	924503 30484
70	957511	24.8	1	926593 30918
71	960740	24.8	1	929915 30825
72	957389	24.8	1	927925 29464
73	956968	24.8	1	927378 29590
74	957044	24.8	1	926974 30070
75	958262	24.8	1	928562 29700
76	960471	24.8	1	930347 30124
77	962961	24.8	1	933258 29703
78	967356	24.8	1	937373 29983
79	975461	24.8	1	945341 30120
80	978503	24.8	1	948386 30117
81	980057	24.8	1	950376 29681
82	977649	24.8	1	947985 29664
83	979192	24.8	1	949570 29622
84	976875	24.8	1	948299 28576
85	975691	24.8	1	947442 28249
86	977587	24.8	1	949341 28246
87	980919	24.8	1	952844 28075
88	984578	24.8	1	956968 27610
89	997379	24.8	1	969773 27606
90	1000000	24.8	1	972394 27606
91	1003424	24.8	1	976109 27315
92	1004385	24.8	1	977118 27267
93	1003119	24.8	1	976170 26949
94	999184	24.8	1	972804 26380
95	998306	24.8	1	972314 25992
96	998683	24.8	1	973128 25555
97	1002572	24.8	1	976999 25573
98	1006682	24.8	1	981162 25520
99	1016517	24.8	1	991004 25513
100	1022183	24.8	1	996830 25353
101	1031521	24.8	1	1006155 25366
102	1030657	24.8	1	1005449 25208
103	1027733	24.8	1	1003218 24515
104	1025713	24.8	1	1000982 24731
105	1023390	24.8	1	999444 23946
106	1024626	24.8	1	1000157 24469
107	1026709	24.8	1	1002684 24025
108	1031646	24.8	1	1007518 24128
109	1044142	24.8	1	1020064 24078
110	1054697	24.8	1	1030442 24255
111	1066868	24.8	1	1042597 24271
112	1071797	24.8	1	1048108 23689
113	1068927	24.8	1	1045243 23684
114	1061437	24.8	1	1038079 23358
115	1057880	24.8	1	1034973 22907
116	1053289	24.8	1	1030728 22561
117	1050856	24.8	1	1028684 22172
118	1053560	24.8	1	1031621 21939
119	1061908	24.8	1	1039826 22082
120	1075671	24.8	1	1053660 22011
121	1088488	24.8	1	1066958 21530
122	1099624	24.8	1	1077807 21817
123	1100307	24.8	1	1078581 21726
124	1093196	24.8	1	1071906 21290
125	1088872	24.8	1	1067782 21090
126	1080913	24.8	1	1060665 20248
127	1082559	24.8	1	1062971 19588
128	1091522	24.8	1	1072804 18718
129	1099304	24.8	1	1081305 17999
130	1123433	24.8	1	1106053 17380
131	1143425	24.8	1	1126843 16582
132	1152356	24.8	1	1136746 15610
133	1150847	24.8	1	1136490 14357
134	1092790	24.8	1	1079514 13276
135	1077084	24.8	1	1064836 12248
136	1041814	24.8	1	1030419 11395
137	1020805	24.8	1	1010103 10702
138	975771	24.8	1	965638 10133
139	963770	24.8	1	953785 9985
140	1038313	24.8	1	1027735 10578
141	1114144	24.8	1	1103362 10782
142	1011252	24.8	1	1001043 10209
143	1051290	24.8	1	1041028 10262
144	1119587	24.8	1	1109095 10492
145	1088092	24.8	1	1077647 10445
146	1146022	24.8	1	1135202 10820
147	965267	24.8	1	955299 9968
148	985875	24.8	1	974918 10957
149	829994	24.8	1	819882 10112
150	809616	24.8	1	796770 12846
151	375750	24.8	1	344451 31299


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R1_001.fastq.gz
=============================================
415822852 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR013_AD013_S2_L002_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R2_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
330000000 sequences processed
340000000 sequences processed
350000000 sequences processed
360000000 sequences processed
370000000 sequences processed
380000000 sequences processed
390000000 sequences processed
400000000 sequences processed
410000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 10000.93 s (24 us/read; 2.49 M reads/minute).

=== Summary ===

Total reads processed:             415,822,852
Reads with adapters:               195,051,478 (46.9%)
Reads written (passing filters):   415,822,852 (100.0%)

Total basepairs processed: 62,789,250,652 bp
Quality-trimmed:             300,902,002 bp (0.5%)
Total written (filtered):  52,776,478,423 bp (84.1%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 195051478 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 20.6%
  C: 31.4%
  G: 20.7%
  T: 27.1%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	50376644	103955713.0	0	50376644
2	14530385	25988928.2	0	14530385
3	4919981	6497232.1	0	4919981
4	2063073	1624308.0	0	2063073
5	1089623	406077.0	0	1089623
6	846907	101519.3	0	846907
7	828973	25379.8	0	828973
8	871760	6345.0	0	871760
9	733129	1586.2	0	723427 9702
10	805998	396.6	1	740838 65160
11	866553	99.1	1	798189 68364
12	766453	24.8	1	707500 58953
13	842509	24.8	1	775794 66715
14	738722	24.8	1	685925 52797
15	919245	24.8	1	842448 76797
16	922621	24.8	1	856628 65993
17	611188	24.8	1	567954 43234
18	840028	24.8	1	777999 62029
19	855634	24.8	1	798944 56690
20	721068	24.8	1	673814 47254
21	848419	24.8	1	782227 66192
22	891577	24.8	1	829103 62474
23	672434	24.8	1	625447 46987
24	856230	24.8	1	790616 65614
25	738811	24.8	1	691994 46817
26	893273	24.8	1	817121 76152
27	840898	24.8	1	781937 58961
28	770808	24.8	1	720250 50558
29	809273	24.8	1	755595 53678
30	853030	24.8	1	796489 56541
31	764530	24.8	1	716938 47592
32	825283	24.8	1	765344 59939
33	770499	24.8	1	722594 47905
34	839651	24.8	1	777504 62147
35	783513	24.8	1	732634 50879
36	897953	24.8	1	840382 57571
37	742736	24.8	1	698140 44596
38	869146	24.8	1	809777 59369
39	846334	24.8	1	788617 57717
40	835033	24.8	1	782357 52676
41	819318	24.8	1	766923 52395
42	832665	24.8	1	780899 51766
43	818450	24.8	1	768055 50395
44	820542	24.8	1	769251 51291
45	831004	24.8	1	779335 51669
46	811273	24.8	1	761779 49494
47	846143	24.8	1	793562 52581
48	822612	24.8	1	773646 48966
49	838768	24.8	1	787145 51623
50	829239	24.8	1	779651 49588
51	835080	24.8	1	784644 50436
52	837242	24.8	1	787293 49949
53	837448	24.8	1	787925 49523
54	832022	24.8	1	782853 49169
55	835247	24.8	1	785871 49376
56	835097	24.8	1	785426 49671
57	837995	24.8	1	788349 49646
58	840020	24.8	1	790213 49807
59	838925	24.8	1	789775 49150
60	838163	24.8	1	789473 48690
61	840633	24.8	1	792371 48262
62	836051	24.8	1	788239 47812
63	836058	24.8	1	787238 48820
64	836865	24.8	1	788863 48002
65	836861	24.8	1	788598 48263
66	837232	24.8	1	789580 47652
67	843818	24.8	1	795801 48017
68	843955	24.8	1	797710 46245
69	850044	24.8	1	804229 45815
70	850165	24.8	1	804166 45999
71	850458	24.8	1	804615 45843
72	845184	24.8	1	800242 44942
73	844426	24.8	1	799306 45120
74	844512	24.8	1	800028 44484
75	844998	24.8	1	800235 44763
76	845256	24.8	1	800467 44789
77	849297	24.8	1	804447 44850
78	851261	24.8	1	806903 44358
79	853746	24.8	1	809400 44346
80	855327	24.8	1	811613 43714
81	854922	24.8	1	811331 43591
82	852487	24.8	1	809322 43165
83	849815	24.8	1	807066 42749
84	847575	24.8	1	804804 42771
85	847253	24.8	1	804749 42504
86	845785	24.8	1	804397 41388
87	851200	24.8	1	809416 41784
88	853308	24.8	1	811548 41760
89	860452	24.8	1	818777 41675
90	862644	24.8	1	820913 41731
91	866608	24.8	1	824895 41713
92	862286	24.8	1	821023 41263
93	859686	24.8	1	818521 41165
94	855080	24.8	1	814910 40170
95	854072	24.8	1	813903 40169
96	854289	24.8	1	814606 39683
97	858145	24.8	1	818021 40124
98	859297	24.8	1	819787 39510
99	868611	24.8	1	828295 40316
100	870352	24.8	1	830927 39425
101	874720	24.8	1	835812 38908
102	872775	24.8	1	834595 38180
103	868011	24.8	1	830697 37314
104	862209	24.8	1	824704 37505
105	860907	24.8	1	824179 36728
106	857830	24.8	1	821703 36127
107	861400	24.8	1	824886 36514
108	865493	24.8	1	829437 36056
109	874548	24.8	1	838358 36190
110	881911	24.8	1	846025 35886
111	889032	24.8	1	852858 36174
112	891732	24.8	1	855803 35929
113	887699	24.8	1	852625 35074
114	879159	24.8	1	844446 34713
115	873492	24.8	1	839178 34314
116	867474	24.8	1	833590 33884
117	867596	24.8	1	834348 33248
118	867927	24.8	1	835268 32659
119	872419	24.8	1	839444 32975
120	882790	24.8	1	850657 32133
121	893102	24.8	1	860255 32847
122	897101	24.8	1	864400 32701
123	896660	24.8	1	864496 32164
124	889027	24.8	1	857300 31727
125	882687	24.8	1	851900 30787
126	875583	24.8	1	845434 30149
127	878522	24.8	1	848723 29799
128	880624	24.8	1	851524 29100
129	891696	24.8	1	862630 29066
130	909308	24.8	1	880950 28358
131	924788	24.8	1	896377 28411
132	928656	24.8	1	901311 27345
133	923575	24.8	1	897579 25996
134	875339	24.8	1	851275 24064
135	859221	24.8	1	836132 23089
136	827125	24.8	1	805178 21947
137	803333	24.8	1	782677 20656
138	764232	24.8	1	744812 19420
139	761529	24.8	1	742327 19202
140	818179	24.8	1	798006 20173
141	864027	24.8	1	843726 20301
142	793172	24.8	1	774186 18986
143	825833	24.8	1	806330 19503
144	873372	24.8	1	853791 19581
145	863405	24.8	1	843829 19576
146	882008	24.8	1	862794 19214
147	746019	24.8	1	728926 17093
148	750025	24.8	1	733057 16968
149	601951	24.8	1	587440 14511
150	581023	24.8	1	565019 16004
151	264040	24.8	1	236618 27422


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR013_AD013_S2_L002_R2_001.fastq.gz
=============================================
415822852 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR013_AD013_S2_L002_R1_001_trimmed.fq.gz and NR013_AD013_S2_L002_R2_001_trimmed.fq.gz
file_1: NR013_AD013_S2_L002_R1_001_trimmed.fq.gz, file_2: NR013_AD013_S2_L002_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR013_AD013_S2_L002_R1_001_trimmed.fq.gz and NR013_AD013_S2_L002_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR013_AD013_S2_L002_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR013_AD013_S2_L002_R2_001_val_2.fq.gz

Total number of sequences analysed: 415822852

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 36287376 (8.73%)

Deleting both intermediate output files NR013_AD013_S2_L002_R1_001_trimmed.fq.gz and NR013_AD013_S2_L002_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR014_AD014_S5_L001_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R1_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
330000000 sequences processed
340000000 sequences processed
350000000 sequences processed
360000000 sequences processed
370000000 sequences processed
380000000 sequences processed
390000000 sequences processed
400000000 sequences processed
410000000 sequences processed
420000000 sequences processed
430000000 sequences processed
440000000 sequences processed
450000000 sequences processed
460000000 sequences processed
470000000 sequences processed
480000000 sequences processed
490000000 sequences processed
500000000 sequences processed
510000000 sequences processed
520000000 sequences processed
530000000 sequences processed
540000000 sequences processed
550000000 sequences processed
560000000 sequences processed
570000000 sequences processed
580000000 sequences processed
590000000 sequences processed
600000000 sequences processed
610000000 sequences processed
620000000 sequences processed
630000000 sequences processed
640000000 sequences processed
650000000 sequences processed
660000000 sequences processed
670000000 sequences processed
680000000 sequences processed
690000000 sequences processed
700000000 sequences processed
710000000 sequences processed
720000000 sequences processed
730000000 sequences processed
740000000 sequences processed
750000000 sequences processed
760000000 sequences processed
770000000 sequences processed
780000000 sequences processed
790000000 sequences processed
800000000 sequences processed
810000000 sequences processed
820000000 sequences processed
830000000 sequences processed
840000000 sequences processed
850000000 sequences processed
860000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 20359.64 s (24 us/read; 2.54 M reads/minute).

=== Summary ===

Total reads processed:             862,125,010
Reads with adapters:               533,204,383 (61.8%)
Reads written (passing filters):   862,125,010 (100.0%)

Total basepairs processed: 130,180,876,510 bp
Quality-trimmed:             334,776,299 bp (0.3%)
Total written (filtered):  95,709,543,010 bp (73.5%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 533204383 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 17.6%
  C: 35.0%
  G: 21.0%
  T: 26.2%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	87080155	215531252.5	0	87080155
2	25292498	53882813.1	0	25292498
3	9084426	13470703.3	0	9084426
4	3966676	3367675.8	0	3966676
5	2555848	841919.0	0	2555848
6	2088422	210479.7	0	2088422
7	2118728	52619.9	0	2118728
8	2261416	13155.0	0	2261416
9	1886696	3288.7	0	1867679 19017
10	2147259	822.2	1	2004833 142426
11	2203344	205.5	1	2075356 127988
12	2108294	51.4	1	1968257 140037
13	2169915	51.4	1	2041590 128325
14	2021464	51.4	1	1897261 124203
15	2393307	51.4	1	2240058 153249
16	2633473	51.4	1	2468212 165261
17	1606055	51.4	1	1514305 91750
18	2244922	51.4	1	2117650 127272
19	2287131	51.4	1	2169631 117500
20	2080994	51.4	1	1956165 124829
21	2250052	51.4	1	2131462 118590
22	2488161	51.4	1	2345857 142304
23	1936361	51.4	1	1824356 112005
24	2320736	51.4	1	2200479 120257
25	2080551	51.4	1	1974444 106107
26	2398126	51.4	1	2261532 136594
27	2282553	51.4	1	2167217 115336
28	2203983	51.4	1	2090981 113002
29	2265578	51.4	1	2158870 106708
30	2459124	51.4	1	2334870 124254
31	2336574	51.4	1	2214330 122244
32	2241450	51.4	1	2137849 103601
33	2300131	51.4	1	2182495 117636
34	2276939	51.4	1	2169620 107319
35	2342900	51.4	1	2222984 119916
36	2497021	51.4	1	2381268 115753
37	2287522	51.4	1	2167544 119978
38	2470408	51.4	1	2352984 117424
39	2425490	51.4	1	2310420 115070
40	2439284	51.4	1	2323810 115474
41	2414344	51.4	1	2297988 116356
42	2448239	51.4	1	2334656 113583
43	2437622	51.4	1	2324780 112842
44	2456618	51.4	1	2341773 114845
45	2462796	51.4	1	2350224 112572
46	2462042	51.4	1	2346814 115228
47	2500349	51.4	1	2387065 113284
48	2496001	51.4	1	2382375 113626
49	2521603	51.4	1	2407901 113702
50	2513138	51.4	1	2401474 111664
51	2534183	51.4	1	2421520 112663
52	2540436	51.4	1	2430240 110196
53	2565999	51.4	1	2455494 110505
54	2555806	51.4	1	2445598 110208
55	2572280	51.4	1	2462609 109671
56	2574683	51.4	1	2465802 108881
57	2594847	51.4	1	2485833 109014
58	2610567	51.4	1	2501646 108921
59	2627272	51.4	1	2517701 109571
60	2635121	51.4	1	2526668 108453
61	2654719	51.4	1	2545287 109432
62	2657073	51.4	1	2549708 107365
63	2667257	51.4	1	2560316 106941
64	2670252	51.4	1	2563309 106943
65	2680079	51.4	1	2573975 106104
66	2688354	51.4	1	2581832 106522
67	2705663	51.4	1	2600297 105366
68	2720740	51.4	1	2614255 106485
69	2733983	51.4	1	2628177 105806
70	2750706	51.4	1	2644823 105883
71	2768728	51.4	1	2662313 106415
72	2763810	51.4	1	2659284 104526
73	2779320	51.4	1	2674617 104703
74	2780824	51.4	1	2676963 103861
75	2790976	51.4	1	2687019 103957
76	2798570	51.4	1	2695245 103325
77	2816231	51.4	1	2713058 103173
78	2829212	51.4	1	2725782 103430
79	2853748	51.4	1	2749834 103914
80	2869560	51.4	1	2766239 103321
81	2890251	51.4	1	2786754 103497
82	2891288	51.4	1	2788604 102684
83	2902158	51.4	1	2799792 102366
84	2896361	51.4	1	2794399 101962
85	2905313	51.4	1	2803625 101688
86	2909616	51.4	1	2809255 100361
87	2923807	51.4	1	2824179 99628
88	2936907	51.4	1	2836420 100487
89	2973776	51.4	1	2873815 99961
90	2990303	51.4	1	2890819 99484
91	3017239	51.4	1	2917249 99990
92	3018303	51.4	1	2919523 98780
93	3014708	51.4	1	2916507 98201
94	3007926	51.4	1	2910368 97558
95	3009371	51.4	1	2913587 95784
96	3014847	51.4	1	2919837 95010
97	3019027	51.4	1	2925475 93552
98	3028470	51.4	1	2935414 93056
99	3062728	51.4	1	2968036 94692
100	3090295	51.4	1	2996430 93865
101	3124072	51.4	1	3029715 94357
102	3134236	51.4	1	3040238 93998
103	3138432	51.4	1	3045501 92931
104	3128789	51.4	1	3036751 92038
105	3133332	51.4	1	3041492 91840
106	3137813	51.4	1	3042358 95455
107	3150614	51.4	1	3056704 93910
108	3161119	51.4	1	3066820 94299
109	3198509	51.4	1	3103458 95051
110	3227579	51.4	1	3132921 94658
111	3260459	51.4	1	3166715 93744
112	3279500	51.4	1	3185425 94075
113	3277782	51.4	1	3184045 93737
114	3261944	51.4	1	3169228 92716
115	3254278	51.4	1	3163286 90992
116	3240928	51.4	1	3150610 90318
117	3242700	51.4	1	3153325 89375
118	3250451	51.4	1	3165383 85068
119	3273347	51.4	1	3188209 85138
120	3318878	51.4	1	3232818 86060
121	3362073	51.4	1	3275743 86330
122	3385722	51.4	1	3299424 86298
123	3391280	51.4	1	3305843 85437
124	3368401	51.4	1	3283712 84689
125	3350159	51.4	1	3266191 83968
126	3337400	51.4	1	3255357 82043
127	3346478	51.4	1	3267373 79105
128	3365912	51.4	1	3290370 75542
129	3392332	51.4	1	3319468 72864
130	3456596	51.4	1	3386811 69785
131	3512135	51.4	1	3443703 68432
132	3534163	51.4	1	3470024 64139
133	3527032	51.4	1	3467795 59237
134	3366546	51.4	1	3313043 53503
135	3314373	51.4	1	3264902 49471
136	3232974	51.4	1	3185864 47110
137	3169126	51.4	1	3125121 44005
138	3051003	51.4	1	3008768 42235
139	3031240	51.4	1	2989648 41592
140	3206007	51.4	1	3161792 44215
141	3388074	51.4	1	3342324 45750
142	3064860	51.4	1	3021913 42947
143	3112107	51.4	1	3069853 42254
144	3282636	51.4	1	3237661 44975
145	3229456	51.4	1	3184052 45404
146	3411642	51.4	1	3362254 49388
147	2895283	51.4	1	2850748 44535
148	2936412	51.4	1	2889423 46989
149	2482511	51.4	1	2437084 45427
150	2322797	51.4	1	2273335 49462
151	642479	51.4	1	558867 83612


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R1_001.fastq.gz
=============================================
862125010 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR014_AD014_S5_L001_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R2_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
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810000000 sequences processed
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830000000 sequences processed
840000000 sequences processed
850000000 sequences processed
860000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 20481.41 s (24 us/read; 2.53 M reads/minute).

=== Summary ===

Total reads processed:             862,125,010
Reads with adapters:               487,764,267 (56.6%)
Reads written (passing filters):   862,125,010 (100.0%)

Total basepairs processed: 130,180,876,510 bp
Quality-trimmed:             491,072,754 bp (0.4%)
Total written (filtered):  99,751,113,723 bp (76.6%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 487764267 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 18.2%
  C: 34.2%
  G: 21.3%
  T: 26.2%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	87028076	215531252.5	0	87028076
2	25005929	53882813.1	0	25005929
3	8757729	13470703.3	0	8757729
4	3927470	3367675.8	0	3927470
5	2400919	841919.0	0	2400919
6	1921020	210479.7	0	1921020
7	1926124	52619.9	0	1926124
8	2100507	13155.0	0	2100507
9	1691346	3288.7	0	1670888 20458
10	1983842	822.2	1	1799270 184572
11	2049425	205.5	1	1872211 177214
12	1908398	51.4	1	1732610 175788
13	2013760	51.4	1	1833479 180281
14	1820806	51.4	1	1662157 158649
15	2236287	51.4	1	2029086 207201
16	2336471	51.4	1	2135777 200694
17	1529610	51.4	1	1404488 125122
18	2075483	51.4	1	1901684 173799
19	2125493	51.4	1	1964773 160720
20	1889054	51.4	1	1738034 151020
21	2065453	51.4	1	1899037 166416
22	2264900	51.4	1	2083297 181603
23	1792766	51.4	1	1648943 143823
24	2116890	51.4	1	1946592 170298
25	1937600	51.4	1	1796850 140750
26	2211197	51.4	1	2022651 188546
27	2119858	51.4	1	1959552 160306
28	2017289	51.4	1	1868078 149211
29	2092915	51.4	1	1941839 151076
30	2230433	51.4	1	2069250 161183
31	2116272	51.4	1	1964321 151951
32	2074805	51.4	1	1926024 148781
33	2112018	51.4	1	1965296 146722
34	2126005	51.4	1	1974863 151142
35	2086790	51.4	1	1941610 145180
36	2349700	51.4	1	2193950 155750
37	2043605	51.4	1	1903729 139876
38	2281250	51.4	1	2127512 153738
39	2232758	51.4	1	2083895 148863
40	2246748	51.4	1	2105177 141571
41	2215186	51.4	1	2075304 139882
42	2256580	51.4	1	2119006 137574
43	2236822	51.4	1	2100470 136352
44	2247188	51.4	1	2109839 137349
45	2264335	51.4	1	2127647 136688
46	2239179	51.4	1	2104091 135088
47	2311919	51.4	1	2173517 138402
48	2282704	51.4	1	2150238 132466
49	2314448	51.4	1	2179692 134756
50	2306588	51.4	1	2174950 131638
51	2334353	51.4	1	2200395 133958
52	2341092	51.4	1	2208567 132525
53	2361761	51.4	1	2228645 133116
54	2353318	51.4	1	2223325 129993
55	2371829	51.4	1	2239474 132355
56	2377716	51.4	1	2245731 131985
57	2382829	51.4	1	2250386 132443
58	2401828	51.4	1	2269156 132672
59	2404005	51.4	1	2272998 131007
60	2411636	51.4	1	2282859 128777
61	2420325	51.4	1	2291354 128971
62	2409011	51.4	1	2282853 126158
63	2412489	51.4	1	2287903 124586
64	2422442	51.4	1	2298046 124396
65	2430842	51.4	1	2306564 124278
66	2441731	51.4	1	2318398 123333
67	2462080	51.4	1	2338880 123200
68	2477727	51.4	1	2358116 119611
69	2494630	51.4	1	2375510 119120
70	2514500	51.4	1	2396752 117748
71	2538019	51.4	1	2419844 118175
72	2535544	51.4	1	2419572 115972
73	2547911	51.4	1	2430295 117616
74	2551576	51.4	1	2436283 115293
75	2564161	51.4	1	2448581 115580
76	2568464	51.4	1	2451468 116996
77	2574669	51.4	1	2459014 115655
78	2576573	51.4	1	2460550 116023
79	2586971	51.4	1	2471587 115384
80	2601956	51.4	1	2487255 114701
81	2604089	51.4	1	2490316 113773
82	2598946	51.4	1	2486257 112689
83	2597111	51.4	1	2484667 112444
84	2596091	51.4	1	2484893 111198
85	2600808	51.4	1	2491003 109805
86	2602017	51.4	1	2492772 109245
87	2617675	51.4	1	2509804 107871
88	2628059	51.4	1	2522908 105151
89	2656556	51.4	1	2550977 105579
90	2678549	51.4	1	2572181 106368
91	2711992	51.4	1	2605720 106272
92	2709747	51.4	1	2604331 105416
93	2720802	51.4	1	2616590 104212
94	2715438	51.4	1	2612666 102772
95	2715878	51.4	1	2613599 102279
96	2717943	51.4	1	2616783 101160
97	2727126	51.4	1	2626685 100441
98	2729717	51.4	1	2630179 99538
99	2750261	51.4	1	2650773 99488
100	2769128	51.4	1	2669279 99849
101	2784074	51.4	1	2685552 98522
102	2779256	51.4	1	2682293 96963
103	2774652	51.4	1	2677750 96902
104	2764015	51.4	1	2668058 95957
105	2763579	51.4	1	2667341 96238
106	2760893	51.4	1	2666635 94258
107	2771229	51.4	1	2676722 94507
108	2778417	51.4	1	2684624 93793
109	2808111	51.4	1	2714040 94071
110	2835428	51.4	1	2741756 93672
111	2859636	51.4	1	2765558 94078
112	2867098	51.4	1	2773415 93683
113	2871085	51.4	1	2778831 92254
114	2848747	51.4	1	2754596 94151
115	2836727	51.4	1	2745064 91663
116	2822508	51.4	1	2733691 88817
117	2822178	51.4	1	2734575 87603
118	2820961	51.4	1	2733877 87084
119	2840487	51.4	1	2755127 85360
120	2872604	51.4	1	2786743 85861
121	2905072	51.4	1	2817025 88047
122	2918926	51.4	1	2831786 87140
123	2918551	51.4	1	2832810 85741
124	2893447	51.4	1	2808747 84700
125	2876293	51.4	1	2792744 83549
126	2860089	51.4	1	2780036 80053
127	2863069	51.4	1	2784561 78508
128	2873015	51.4	1	2795738 77277
129	2897555	51.4	1	2819879 77676
130	2950723	51.4	1	2873723 77000
131	2987708	51.4	1	2910728 76980
132	3006128	51.4	1	2931330 74798
133	2987603	51.4	1	2915914 71689
134	2858781	51.4	1	2791363 67418
135	2810253	51.4	1	2744333 65920
136	2729398	51.4	1	2663657 65741
137	2657428	51.4	1	2594103 63325
138	2554440	51.4	1	2491392 63048
139	2535549	51.4	1	2473600 61949
140	2693635	51.4	1	2628959 64676
141	2807944	51.4	1	2741639 66305
142	2574701	51.4	1	2512666 62035
143	2623685	51.4	1	2562540 61145
144	2760564	51.4	1	2696845 63719
145	2746186	51.4	1	2684250 61936
146	2833928	51.4	1	2770612 63316
147	2428426	51.4	1	2375426 53000
148	2415547	51.4	1	2366272 49275
149	1965341	51.4	1	1923068 42273
150	1809700	51.4	1	1764804 44896
151	497026	51.4	1	420224 76802


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR014_AD014_S5_L001_R2_001.fastq.gz
=============================================
862125010 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR014_AD014_S5_L001_R1_001_trimmed.fq.gz and NR014_AD014_S5_L001_R2_001_trimmed.fq.gz
file_1: NR014_AD014_S5_L001_R1_001_trimmed.fq.gz, file_2: NR014_AD014_S5_L001_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR014_AD014_S5_L001_R1_001_trimmed.fq.gz and NR014_AD014_S5_L001_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR014_AD014_S5_L001_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR014_AD014_S5_L001_R2_001_val_2.fq.gz

Total number of sequences analysed: 862125010

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 111554567 (12.94%)

Deleting both intermediate output files NR014_AD014_S5_L001_R1_001_trimmed.fq.gz and NR014_AD014_S5_L001_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR014_AD014_S5_L002_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R1_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
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This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 23581.69 s (24 us/read; 2.55 M reads/minute).

=== Summary ===

Total reads processed:           1,001,146,597
Reads with adapters:               591,796,332 (59.1%)
Reads written (passing filters): 1,001,146,597 (100.0%)

Total basepairs processed: 151,173,136,147 bp
Quality-trimmed:             401,721,818 bp (0.3%)
Total written (filtered):  114,053,730,623 bp (75.4%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 591796332 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 18.0%
  C: 34.6%
  G: 21.0%
  T: 26.3%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	106033455	250286649.2	0	106033455
2	30932237	62571662.3	0	30932237
3	10827392	15642915.6	0	10827392
4	4701997	3910728.9	0	4701997
5	2851053	977682.2	0	2851053
6	2372352	244420.6	0	2372352
7	2341225	61105.1	0	2341225
8	2467049	15276.3	0	2467049
9	2128322	3819.1	0	2108774 19548
10	2353039	954.8	1	2243274 109765
11	2416142	238.7	1	2320919 95223
12	2311432	59.7	1	2212214 99218
13	2380798	59.7	1	2289511 91287
14	2252041	59.7	1	2163098 88943
15	2555705	59.7	1	2446445 109260
16	2850726	59.7	1	2733034 117692
17	1817016	59.7	1	1753007 64009
18	2442218	59.7	1	2355110 87108
19	2486262	59.7	1	2405860 80402
20	2298798	59.7	1	2212615 86183
21	2462281	59.7	1	2376944 85337
22	2693256	59.7	1	2591580 101676
23	2117201	59.7	1	2038877 78324
24	2529069	59.7	1	2441475 87594
25	2300578	59.7	1	2226358 74220
26	2596745	59.7	1	2494708 102037
27	2478522	59.7	1	2396674 81848
28	2424775	59.7	1	2344388 80387
29	2468561	59.7	1	2392313 76248
30	2625645	59.7	1	2538195 87450
31	2534062	59.7	1	2448131 85931
32	2463975	59.7	1	2389974 74001
33	2485864	59.7	1	2403092 82772
34	2500312	59.7	1	2422559 77753
35	2541533	59.7	1	2457377 84156
36	2669327	59.7	1	2588129 81198
37	2498773	59.7	1	2414488 84285
38	2672991	59.7	1	2588709 84282
39	2621845	59.7	1	2539402 82443
40	2638822	59.7	1	2557832 80990
41	2612895	59.7	1	2531898 80997
42	2637743	59.7	1	2557749 79994
43	2632806	59.7	1	2553076 79730
44	2647914	59.7	1	2566441 81473
45	2658677	59.7	1	2578375 80302
46	2654614	59.7	1	2572937 81677
47	2696968	59.7	1	2615932 81036
48	2692360	59.7	1	2612005 80355
49	2718504	59.7	1	2638142 80362
50	2713258	59.7	1	2634426 78832
51	2734828	59.7	1	2655686 79142
52	2736621	59.7	1	2659002 77619
53	2761328	59.7	1	2683593 77735
54	2750340	59.7	1	2673319 77021
55	2766771	59.7	1	2689905 76866
56	2771458	59.7	1	2695068 76390
57	2788435	59.7	1	2711265 77170
58	2797577	59.7	1	2720254 77323
59	2818435	59.7	1	2739863 78572
60	2828457	59.7	1	2747028 81429
61	2850147	59.7	1	2769784 80363
62	2849460	59.7	1	2769623 79837
63	2860655	59.7	1	2781562 79093
64	2864719	59.7	1	2785496 79223
65	2874706	59.7	1	2796483 78223
66	2877715	59.7	1	2799029 78686
67	2894761	59.7	1	2815535 79226
68	2916632	59.7	1	2836622 80010
69	2930076	59.7	1	2851903 78173
70	2943178	59.7	1	2864631 78547
71	2960700	59.7	1	2881553 79147
72	2959836	59.7	1	2882947 76889
73	2972005	59.7	1	2895233 76772
74	2972897	59.7	1	2896091 76806
75	2984527	59.7	1	2907091 77436
76	2990507	59.7	1	2913466 77041
77	3009208	59.7	1	2932000 77208
78	3021368	59.7	1	2944757 76611
79	3047385	59.7	1	2970350 77035
80	3064830	59.7	1	2987317 77513
81	3084135	59.7	1	3007723 76412
82	3087131	59.7	1	3009868 77263
83	3098954	59.7	1	3022614 76340
84	3093141	59.7	1	3020085 73056
85	3102656	59.7	1	3029977 72679
86	3111762	59.7	1	3038627 73135
87	3116552	59.7	1	3045030 71522
88	3138573	59.7	1	3066619 71954
89	3171353	59.7	1	3099692 71661
90	3187992	59.7	1	3117359 70633
91	3222803	59.7	1	3151511 71292
92	3227079	59.7	1	3156589 70490
93	3229980	59.7	1	3160347 69633
94	3222379	59.7	1	3154099 68280
95	3220966	59.7	1	3153222 67744
96	3221695	59.7	1	3155035 66660
97	3229784	59.7	1	3163740 66044
98	3242698	59.7	1	3177003 65695
99	3271604	59.7	1	3206202 65402
100	3300569	59.7	1	3234765 65804
101	3334886	59.7	1	3269446 65440
102	3346942	59.7	1	3281672 65270
103	3351934	59.7	1	3287666 64268
104	3343578	59.7	1	3279884 63694
105	3345122	59.7	1	3281513 63609
106	3352183	59.7	1	3288738 63445
107	3367566	59.7	1	3304077 63489
108	3378354	59.7	1	3315190 63164
109	3420686	59.7	1	3357714 62972
110	3449826	59.7	1	3386281 63545
111	3487365	59.7	1	3423872 63493
112	3508368	59.7	1	3445495 62873
113	3507180	59.7	1	3445383 61797
114	3494159	59.7	1	3432618 61541
115	3484932	59.7	1	3424522 60410
116	3476413	59.7	1	3416442 59971
117	3475301	59.7	1	3415502 59799
118	3482407	59.7	1	3423675 58732
119	3508843	59.7	1	3449512 59331
120	3547443	59.7	1	3488043 59400
121	3601402	59.7	1	3542591 58811
122	3631504	59.7	1	3572349 59155
123	3636265	59.7	1	3577504 58761
124	3617049	59.7	1	3558907 58142
125	3595969	59.7	1	3538341 57628
126	3584447	59.7	1	3528276 56171
127	3588428	59.7	1	3534270 54158
128	3609387	59.7	1	3557382 52005
129	3632653	59.7	1	3582960 49693
130	3703568	59.7	1	3655789 47779
131	3760631	59.7	1	3714652 45979
132	3784172	59.7	1	3741312 42860
133	3781183	59.7	1	3741281 39902
134	3607068	59.7	1	3570649 36419
135	3565429	59.7	1	3532081 33348
136	3471060	59.7	1	3439177 31883
137	3403980	59.7	1	3374394 29586
138	3273300	59.7	1	3244828 28472
139	3246174	59.7	1	3218100 28074
140	3438033	59.7	1	3408723 29310
141	3653904	59.7	1	3624269 29635
142	3305687	59.7	1	3277694 27993
143	3365594	59.7	1	3337863 27731
144	3572185	59.7	1	3543480 28705
145	3520268	59.7	1	3492330 27938
146	3747209	59.7	1	3716610 30599
147	3171755	59.7	1	3143829 27926
148	3229065	59.7	1	3199486 29579
149	2726822	59.7	1	2698510 28312
150	2602798	59.7	1	2568461 34337
151	715352	59.7	1	625610 89742


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R1_001.fastq.gz
=============================================
1001146597 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR014_AD014_S5_L002_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R2_001.fastq.gz <<< 
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This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 23633.95 s (24 us/read; 2.54 M reads/minute).

=== Summary ===

Total reads processed:           1,001,146,597
Reads with adapters:               540,115,126 (53.9%)
Reads written (passing filters): 1,001,146,597 (100.0%)

Total basepairs processed: 151,173,136,147 bp
Quality-trimmed:             591,626,564 bp (0.4%)
Total written (filtered):  118,805,814,263 bp (78.6%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 540115126 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 18.6%
  C: 33.8%
  G: 21.3%
  T: 26.2%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	106085948	250286649.2	0	106085948
2	30545591	62571662.3	0	30545591
3	10550586	15642915.6	0	10550586
4	4664851	3910728.9	0	4664851
5	2730219	977682.2	0	2730219
6	2212374	244420.6	0	2212374
7	2182387	61105.1	0	2182387
8	2342229	15276.3	0	2342229
9	1941104	3819.1	0	1920265 20839
10	2193387	954.8	1	2050691 142696
11	2286146	238.7	1	2148338 137808
12	2106924	59.7	1	1977364 129560
13	2244772	59.7	1	2109049 135723
14	2045749	59.7	1	1931101 114648
15	2439558	59.7	1	2281814 157744
16	2565286	59.7	1	2417982 147304
17	1703369	59.7	1	1613204 90165
18	2294530	59.7	1	2165029 129501
19	2338286	59.7	1	2222577 115709
20	2066198	59.7	1	1958793 107405
21	2299627	59.7	1	2166870 132757
22	2489525	59.7	1	2352703 136822
23	1931407	59.7	1	1829181 102226
24	2354926	59.7	1	2222838 132088
25	2119895	59.7	1	2018624 101271
26	2446505	59.7	1	2295144 151361
27	2329182	59.7	1	2209792 119390
28	2215355	59.7	1	2106158 109197
29	2288397	59.7	1	2177986 110411
30	2411852	59.7	1	2291226 120626
31	2280500	59.7	1	2173162 107338
32	2315968	59.7	1	2197426 118542
33	2269381	59.7	1	2163038 106343
34	2364664	59.7	1	2241517 123147
35	2283233	59.7	1	2174730 108503
36	2532452	59.7	1	2413990 118462
37	2228870	59.7	1	2127630 101240
38	2492963	59.7	1	2372371 120592
39	2436639	59.7	1	2319409 117230
40	2434599	59.7	1	2325313 109286
41	2397752	59.7	1	2288471 109281
42	2443026	59.7	1	2334096 108930
43	2418021	59.7	1	2313093 104928
44	2426060	59.7	1	2318750 107310
45	2450430	59.7	1	2343658 106772
46	2419646	59.7	1	2314974 104672
47	2495511	59.7	1	2386452 109059
48	2462435	59.7	1	2359933 102502
49	2497544	59.7	1	2390867 106677
50	2486318	59.7	1	2382721 103597
51	2511781	59.7	1	2406493 105288
52	2516552	59.7	1	2413543 103009
53	2536624	59.7	1	2433362 103262
54	2526890	59.7	1	2424609 102281
55	2550150	59.7	1	2447125 103025
56	2554177	59.7	1	2450023 104154
57	2563613	59.7	1	2459640 103973
58	2573415	59.7	1	2470076 103339
59	2576096	59.7	1	2472977 103119
60	2585802	59.7	1	2483898 101904
61	2593413	59.7	1	2492734 100679
62	2580047	59.7	1	2480538 99509
63	2585329	59.7	1	2484750 100579
64	2589823	59.7	1	2489860 99963
65	2598352	59.7	1	2497953 100399
66	2604715	59.7	1	2506764 97951
67	2633277	59.7	1	2534640 98637
68	2646868	59.7	1	2550522 96346
69	2664167	59.7	1	2568169 95998
70	2684490	59.7	1	2589178 95312
71	2711492	59.7	1	2615749 95743
72	2700448	59.7	1	2606191 94257
73	2718039	59.7	1	2623903 94136
74	2724997	59.7	1	2631281 93716
75	2730017	59.7	1	2636608 93409
76	2733638	59.7	1	2640868 92770
77	2741293	59.7	1	2648922 92371
78	2742165	59.7	1	2649675 92490
79	2748939	59.7	1	2656849 92090
80	2762857	59.7	1	2672290 90567
81	2758435	59.7	1	2667298 91137
82	2751060	59.7	1	2661259 89801
83	2749612	59.7	1	2660092 89520
84	2749708	59.7	1	2661184 88524
85	2755076	59.7	1	2667316 87760
86	2760271	59.7	1	2673075 87196
87	2775417	59.7	1	2688980 86437
88	2785855	59.7	1	2700066 85789
89	2816661	59.7	1	2730237 86424
90	2835228	59.7	1	2748725 86503
91	2875858	59.7	1	2789532 86326
92	2875642	59.7	1	2789932 85710
93	2880444	59.7	1	2794772 85672
94	2869719	59.7	1	2785410 84309
95	2877087	59.7	1	2793123 83964
96	2871155	59.7	1	2788195 82960
97	2883832	59.7	1	2800983 82849
98	2881604	59.7	1	2799707 81897
99	2907764	59.7	1	2825768 81996
100	2923615	59.7	1	2842173 81442
101	2937759	59.7	1	2857065 80694
102	2934449	59.7	1	2855607 78842
103	2929161	59.7	1	2851529 77632
104	2916318	59.7	1	2839154 77164
105	2913070	59.7	1	2836950 76120
106	2912618	59.7	1	2837416 75202
107	2922490	59.7	1	2847436 75054
108	2930126	59.7	1	2855625 74501
109	2963369	59.7	1	2888878 74491
110	2989674	59.7	1	2915613 74061
111	3014074	59.7	1	2939976 74098
112	3024627	59.7	1	2950972 73655
113	3020183	59.7	1	2946755 73428
114	2999238	59.7	1	2926933 72305
115	2986885	59.7	1	2914692 72193
116	2972850	59.7	1	2902526 70324
117	2970432	59.7	1	2900649 69783
118	2973151	59.7	1	2904782 68369
119	2991872	59.7	1	2923437 68435
120	3021460	59.7	1	2953417 68043
121	3060676	59.7	1	2992459 68217
122	3070719	59.7	1	3003092 67627
123	3071679	59.7	1	3004456 67223
124	3050603	59.7	1	2984437 66166
125	3030367	59.7	1	2965802 64565
126	3009064	59.7	1	2945744 63320
127	3015770	59.7	1	2953622 62148
128	3033521	59.7	1	2972488 61033
129	3054558	59.7	1	2993596 60962
130	3109911	59.7	1	3049821 60090
131	3152250	59.7	1	3092703 59547
132	3166216	59.7	1	3108855 57361
133	3151380	59.7	1	3096855 54525
134	3013295	59.7	1	2961818 51477
135	2959648	59.7	1	2910572 49076
136	2878218	59.7	1	2831405 46813
137	2804192	59.7	1	2759721 44471
138	2689723	59.7	1	2646720 43003
139	2674202	59.7	1	2631616 42586
140	2833434	59.7	1	2789250 44184
141	2954295	59.7	1	2909824 44471
142	2703519	59.7	1	2661904 41615
143	2758010	59.7	1	2716272 41738
144	2902059	59.7	1	2858855 43204
145	2888745	59.7	1	2846765 41980
146	2988648	59.7	1	2945061 43587
147	2547900	59.7	1	2508323 39577
148	2553590	59.7	1	2515877 37713
149	2071172	59.7	1	2038481 32691
150	1925273	59.7	1	1888267 37006
151	532997	59.7	1	452276 80721


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR014_AD014_S5_L002_R2_001.fastq.gz
=============================================
1001146597 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR014_AD014_S5_L002_R1_001_trimmed.fq.gz and NR014_AD014_S5_L002_R2_001_trimmed.fq.gz
file_1: NR014_AD014_S5_L002_R1_001_trimmed.fq.gz, file_2: NR014_AD014_S5_L002_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR014_AD014_S5_L002_R1_001_trimmed.fq.gz and NR014_AD014_S5_L002_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR014_AD014_S5_L002_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR014_AD014_S5_L002_R2_001_val_2.fq.gz

Total number of sequences analysed: 1001146597

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 119117389 (11.90%)

Deleting both intermediate output files NR014_AD014_S5_L002_R1_001_trimmed.fq.gz and NR014_AD014_S5_L002_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR015_AD015_S6_L001_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R1_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 6775.87 s (24 us/read; 2.53 M reads/minute).

=== Summary ===

Total reads processed:             285,533,287
Reads with adapters:               169,989,862 (59.5%)
Reads written (passing filters):   285,533,287 (100.0%)

Total basepairs processed: 43,115,526,337 bp
Quality-trimmed:             123,865,249 bp (0.3%)
Total written (filtered):  32,523,865,323 bp (75.4%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 169989862 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 18.2%
  C: 34.5%
  G: 20.8%
  T: 26.4%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	29792576	71383321.8	0	29792576
2	8699292	17845830.4	0	8699292
3	3016802	4461457.6	0	3016802
4	1352424	1115364.4	0	1352424
5	851917	278841.1	0	851917
6	697513	69710.3	0	697513
7	702213	17427.6	0	702213
8	750289	4356.9	0	750289
9	625043	1089.2	0	618654 6389
10	710461	272.3	1	665107 45354
11	725783	68.1	1	686258 39525
12	700592	17.0	1	656441 44151
13	712703	17.0	1	672993 39710
14	670584	17.0	1	631337 39247
15	779929	17.0	1	732943 46986
16	867361	17.0	1	815669 51692
17	530622	17.0	1	501640 28982
18	734140	17.0	1	694490 39650
19	744592	17.0	1	707856 36736
20	696416	17.0	1	656510 39906
21	728429	17.0	1	692715 35714
22	808117	17.0	1	763635 44482
23	647819	17.0	1	612348 35471
24	752409	17.0	1	715569 36840
25	683072	17.0	1	649761 33311
26	774130	17.0	1	732740 41390
27	742658	17.0	1	707216 35442
28	716799	17.0	1	681752 35047
29	736131	17.0	1	703087 33044
30	796547	17.0	1	758064 38483
31	767477	17.0	1	728669 38808
32	719213	17.0	1	687765 31448
33	748944	17.0	1	711909 37035
34	731523	17.0	1	699463 32060
35	757281	17.0	1	720415 36866
36	802097	17.0	1	767134 34963
37	740131	17.0	1	702594 37537
38	796013	17.0	1	760533 35480
39	776981	17.0	1	741938 35043
40	783824	17.0	1	748737 35087
41	775402	17.0	1	739845 35557
42	785913	17.0	1	751294 34619
43	782239	17.0	1	747571 34668
44	786684	17.0	1	751988 34696
45	788745	17.0	1	754358 34387
46	788331	17.0	1	753040 35291
47	798012	17.0	1	763567 34445
48	797453	17.0	1	762868 34585
49	803305	17.0	1	768798 34507
50	799982	17.0	1	766197 33785
51	807707	17.0	1	773712 33995
52	807355	17.0	1	774426 32929
53	815077	17.0	1	781495 33582
54	812082	17.0	1	778651 33431
55	816296	17.0	1	783180 33116
56	817488	17.0	1	784641 32847
57	822263	17.0	1	789225 33038
58	825639	17.0	1	792905 32734
59	828745	17.0	1	796040 32705
60	832287	17.0	1	799618 32669
61	837921	17.0	1	805204 32717
62	838305	17.0	1	806051 32254
63	838900	17.0	1	806855 32045
64	842185	17.0	1	810266 31919
65	844056	17.0	1	811848 32208
66	844356	17.0	1	812113 32243
67	852383	17.0	1	820642 31741
68	859922	17.0	1	827933 31989
69	868210	17.0	1	836120 32090
70	880306	17.0	1	848423 31883
71	897985	17.0	1	865875 32110
72	897151	17.0	1	865344 31807
73	904164	17.0	1	872200 31964
74	903736	17.0	1	871795 31941
75	897498	17.0	1	866324 31174
76	899288	17.0	1	868223 31065
77	894824	17.0	1	863925 30899
78	890599	17.0	1	859591 31008
79	893370	17.0	1	862677 30693
80	893795	17.0	1	863349 30446
81	892345	17.0	1	861685 30660
82	892131	17.0	1	861405 30726
83	893349	17.0	1	863083 30266
84	892497	17.0	1	862117 30380
85	894637	17.0	1	864073 30564
86	897308	17.0	1	867437 29871
87	906289	17.0	1	876604 29685
88	912437	17.0	1	882447 29990
89	922804	17.0	1	892965 29839
90	928225	17.0	1	898763 29462
91	937247	17.0	1	907461 29786
92	935078	17.0	1	905771 29307
93	934982	17.0	1	905742 29240
94	934844	17.0	1	905790 29054
95	933821	17.0	1	905633 28188
96	934157	17.0	1	906041 28116
97	938472	17.0	1	910612 27860
98	940550	17.0	1	912752 27798
99	950446	17.0	1	922495 27951
100	956684	17.0	1	929074 27610
101	967262	17.0	1	938911 28351
102	967365	17.0	1	939406 27959
103	970501	17.0	1	943032 27469
104	964843	17.0	1	937746 27097
105	968357	17.0	1	940882 27475
106	966090	17.0	1	937744 28346
107	969058	17.0	1	940982 28076
108	972508	17.0	1	944372 28136
109	981904	17.0	1	953344 28560
110	990718	17.0	1	962403 28315
111	999198	17.0	1	971471 27727
112	999684	17.0	1	971418 28266
113	1002254	17.0	1	974645 27609
114	995071	17.0	1	967646 27425
115	991423	17.0	1	964462 26961
116	987577	17.0	1	961122 26455
117	986621	17.0	1	960218 26403
118	988469	17.0	1	963274 25195
119	996353	17.0	1	971324 25029
120	1006116	17.0	1	981048 25068
121	1019944	17.0	1	994255 25689
122	1024438	17.0	1	999173 25265
123	1024449	17.0	1	998959 25490
124	1015450	17.0	1	990480 24970
125	1011230	17.0	1	986267 24963
126	1004233	17.0	1	979906 24327
127	1006617	17.0	1	982982 23635
128	1014744	17.0	1	992132 22612
129	1019618	17.0	1	997952 21666
130	1037145	17.0	1	1016488 20657
131	1048705	17.0	1	1028160 20545
132	1052244	17.0	1	1033111 19133
133	1045541	17.0	1	1027553 17988
134	993870	17.0	1	977559 16311
135	972700	17.0	1	958081 14619
136	947762	17.0	1	933670 14092
137	933281	17.0	1	920281 13000
138	896741	17.0	1	884207 12534
139	884462	17.0	1	871784 12678
140	934731	17.0	1	921566 13165
141	987796	17.0	1	974351 13445
142	895519	17.0	1	882888 12631
143	907679	17.0	1	894977 12702
144	954227	17.0	1	940736 13491
145	934549	17.0	1	921308 13241
146	984637	17.0	1	970166 14471
147	863134	17.0	1	849593 13541
148	877344	17.0	1	863127 14217
149	754291	17.0	1	740309 13982
150	703851	17.0	1	688503 15348
151	198449	17.0	1	173946 24503


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R1_001.fastq.gz
=============================================
285533287 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR015_AD015_S6_L001_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R2_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 7088.25 s (25 us/read; 2.42 M reads/minute).

=== Summary ===

Total reads processed:             285,533,287
Reads with adapters:               157,006,761 (55.0%)
Reads written (passing filters):   285,533,287 (100.0%)

Total basepairs processed: 43,115,526,337 bp
Quality-trimmed:             157,457,656 bp (0.4%)
Total written (filtered):  33,761,528,513 bp (78.3%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 157006761 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 18.8%
  C: 33.4%
  G: 21.1%
  T: 26.6%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	30892934	71383321.8	0	30892934
2	8842653	17845830.4	0	8842653
3	3036633	4461457.6	0	3036633
4	1352553	1115364.4	0	1352553
5	804188	278841.1	0	804188
6	627405	69710.3	0	627405
7	637710	17427.6	0	637710
8	679417	4356.9	0	679417
9	561170	1089.2	0	553764 7406
10	640071	272.3	1	570312 69759
11	684928	68.1	1	614828 70100
12	610934	17.0	1	544462 66472
13	672166	17.0	1	598467 73699
14	580697	17.0	1	520155 60542
15	751250	17.0	1	667039 84211
16	749114	17.0	1	672504 76610
17	488364	17.0	1	439322 49042
18	681948	17.0	1	612562 69386
19	697953	17.0	1	632882 65071
20	595572	17.0	1	537606 57966
21	687290	17.0	1	620331 66959
22	733249	17.0	1	662668 70581
23	560944	17.0	1	505838 55106
24	695222	17.0	1	627539 67683
25	612818	17.0	1	557862 54956
26	723686	17.0	1	649351 74335
27	694756	17.0	1	630424 64332
28	640582	17.0	1	582597 57985
29	677477	17.0	1	617223 60254
30	725168	17.0	1	661387 63781
31	654432	17.0	1	597087 57345
32	681756	17.0	1	621111 60645
33	662584	17.0	1	606062 56522
34	692497	17.0	1	632868 59629
35	660621	17.0	1	604658 55963
36	769018	17.0	1	706367 62651
37	634494	17.0	1	581405 53089
38	733662	17.0	1	673564 60098
39	720096	17.0	1	661670 58426
40	714845	17.0	1	660111 54734
41	706121	17.0	1	651362 54759
42	722037	17.0	1	667239 54798
43	711500	17.0	1	658400 53100
44	712712	17.0	1	658774 53938
45	719585	17.0	1	665912 53673
46	708603	17.0	1	656187 52416
47	738664	17.0	1	683959 54705
48	722752	17.0	1	670419 52333
49	732813	17.0	1	680151 52662
50	730494	17.0	1	679130 51364
51	737398	17.0	1	684817 52581
52	738925	17.0	1	687162 51763
53	743924	17.0	1	691508 52416
54	739480	17.0	1	688344 51136
55	745511	17.0	1	693777 51734
56	746772	17.0	1	695270 51502
57	748412	17.0	1	697011 51401
58	753350	17.0	1	701736 51614
59	755770	17.0	1	704763 51007
60	756077	17.0	1	705375 50702
61	760081	17.0	1	709780 50301
62	757352	17.0	1	708067 49285
63	759930	17.0	1	711067 48863
64	760333	17.0	1	712053 48280
65	760289	17.0	1	711908 48381
66	763657	17.0	1	715196 48461
67	769671	17.0	1	721880 47791
68	772301	17.0	1	725793 46508
69	777565	17.0	1	731201 46364
70	783273	17.0	1	737515 45758
71	787444	17.0	1	741603 45841
72	788184	17.0	1	742881 45303
73	789988	17.0	1	744238 45750
74	791860	17.0	1	746876 44984
75	792960	17.0	1	748415 44545
76	793783	17.0	1	748863 44920
77	795542	17.0	1	750482 45060
78	799402	17.0	1	754179 45223
79	802797	17.0	1	757870 44927
80	805167	17.0	1	760666 44501
81	805524	17.0	1	760846 44678
82	804535	17.0	1	760571 43964
83	804385	17.0	1	760840 43545
84	803261	17.0	1	760237 43024
85	804198	17.0	1	761656 42542
86	804501	17.0	1	762184 42317
87	807766	17.0	1	765356 42410
88	811546	17.0	1	770568 40978
89	820574	17.0	1	779074 41500
90	825523	17.0	1	784488 41035
91	833927	17.0	1	792409 41518
92	832224	17.0	1	791378 40846
93	833467	17.0	1	792752 40715
94	831332	17.0	1	791581 39751
95	832656	17.0	1	793259 39397
96	831820	17.0	1	792267 39553
97	833384	17.0	1	794027 39357
98	835416	17.0	1	796598 38818
99	843521	17.0	1	804367 39154
100	848434	17.0	1	809375 39059
101	852409	17.0	1	813970 38439
102	849342	17.0	1	811821 37521
103	848756	17.0	1	811258 37498
104	843868	17.0	1	806569 37299
105	844315	17.0	1	807043 37272
106	844170	17.0	1	807095 37075
107	846389	17.0	1	809347 37042
108	849244	17.0	1	812412 36832
109	861743	17.0	1	824734 37009
110	866612	17.0	1	830068 36544
111	874546	17.0	1	837664 36882
112	876108	17.0	1	839587 36521
113	875074	17.0	1	838844 36230
114	869212	17.0	1	832999 36213
115	863094	17.0	1	827066 36028
116	859690	17.0	1	824407 35283
117	862067	17.0	1	827437 34630
118	860516	17.0	1	826211 34305
119	867871	17.0	1	833540 34331
120	876210	17.0	1	842324 33886
121	886066	17.0	1	850955 35111
122	886757	17.0	1	851867 34890
123	886389	17.0	1	852753 33636
124	878836	17.0	1	845123 33713
125	874740	17.0	1	841597 33143
126	870295	17.0	1	838143 32152
127	874572	17.0	1	842967 31605
128	874859	17.0	1	843781 31078
129	882170	17.0	1	851081 31089
130	897136	17.0	1	866112 31024
131	907722	17.0	1	876284 31438
132	909859	17.0	1	879421 30438
133	898530	17.0	1	869510 29020
134	860975	17.0	1	833133 27842
135	840928	17.0	1	814542 26386
136	815616	17.0	1	789219 26397
137	796809	17.0	1	771242 25567
138	766737	17.0	1	741069 25668
139	758657	17.0	1	733464 25193
140	802927	17.0	1	776681 26246
141	833980	17.0	1	807836 26144
142	768328	17.0	1	743356 24972
143	781148	17.0	1	756777 24371
144	823246	17.0	1	797509 25737
145	819014	17.0	1	794209 24805
146	840558	17.0	1	815823 24735
147	740025	17.0	1	718959 21066
148	736002	17.0	1	715942 20060
149	602840	17.0	1	585965 16875
150	551937	17.0	1	534926 17011
151	154537	17.0	1	131184 23353


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR015_AD015_S6_L001_R2_001.fastq.gz
=============================================
285533287 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR015_AD015_S6_L001_R1_001_trimmed.fq.gz and NR015_AD015_S6_L001_R2_001_trimmed.fq.gz
file_1: NR015_AD015_S6_L001_R1_001_trimmed.fq.gz, file_2: NR015_AD015_S6_L001_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR015_AD015_S6_L001_R1_001_trimmed.fq.gz and NR015_AD015_S6_L001_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR015_AD015_S6_L001_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR015_AD015_S6_L001_R2_001_val_2.fq.gz

Total number of sequences analysed: 285533287

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 33572503 (11.76%)

Deleting both intermediate output files NR015_AD015_S6_L001_R1_001_trimmed.fq.gz and NR015_AD015_S6_L001_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR015_AD015_S6_L002_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R1_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 7582.12 s (24 us/read; 2.54 M reads/minute).

=== Summary ===

Total reads processed:             321,498,091
Reads with adapters:               184,340,232 (57.3%)
Reads written (passing filters):   321,498,091 (100.0%)

Total basepairs processed: 48,546,211,741 bp
Quality-trimmed:             137,293,336 bp (0.3%)
Total written (filtered):  37,358,729,319 bp (77.0%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 184340232 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 18.4%
  C: 34.2%
  G: 20.8%
  T: 26.4%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	34790084	80374522.8	0	34790084
2	10150781	20093630.7	0	10150781
3	3455870	5023407.7	0	3455870
4	1550491	1255851.9	0	1550491
5	927725	313963.0	0	927725
6	770794	78490.7	0	770794
7	754425	19622.7	0	754425
8	797832	4905.7	0	797832
9	691341	1226.4	0	684878 6463
10	758798	306.6	1	725268 33530
11	778225	76.7	1	750138 28087
12	748512	19.2	1	718530 29982
13	765827	19.2	1	738763 27064
14	726721	19.2	1	700221 26500
15	815459	19.2	1	783705 31754
16	915524	19.2	1	880213 35311
17	587101	19.2	1	567780 19321
18	781893	19.2	1	755981 25912
19	792509	19.2	1	769002 23507
20	748975	19.2	1	722729 26246
21	782165	19.2	1	757504 24661
22	852780	19.2	1	822725 30055
23	691805	19.2	1	668119 23686
24	805558	19.2	1	779970 25588
25	736868	19.2	1	714887 21981
26	822137	19.2	1	792880 29257
27	789184	19.2	1	764765 24419
28	772352	19.2	1	748395 23957
29	784069	19.2	1	761850 22219
30	833009	19.2	1	807070 25939
31	815747	19.2	1	789965 25782
32	776719	19.2	1	755157 21562
33	789052	19.2	1	764505 24547
34	789460	19.2	1	766973 22487
35	805768	19.2	1	780985 24783
36	842970	19.2	1	819287 23683
37	792247	19.2	1	766918 25329
38	843554	19.2	1	819153 24401
39	824158	19.2	1	800485 23673
40	831040	19.2	1	807572 23468
41	822263	19.2	1	798414 23849
42	831352	19.2	1	808055 23297
43	826580	19.2	1	803164 23416
44	833919	19.2	1	810469 23450
45	835277	19.2	1	811727 23550
46	832389	19.2	1	808710 23679
47	842958	19.2	1	819635 23323
48	842970	19.2	1	819646 23324
49	850579	19.2	1	827435 23144
50	847871	19.2	1	825067 22804
51	852432	19.2	1	829531 22901
52	854212	19.2	1	832043 22169
53	860708	19.2	1	837881 22827
54	856600	19.2	1	834068 22532
55	863103	19.2	1	840716 22387
56	864778	19.2	1	842629 22149
57	867713	19.2	1	845061 22652
58	870823	19.2	1	848482 22341
59	876055	19.2	1	853340 22715
60	876721	19.2	1	853334 23387
61	882393	19.2	1	858988 23405
62	882089	19.2	1	859480 22609
63	884924	19.2	1	862269 22655
64	885825	19.2	1	862985 22840
65	887968	19.2	1	865206 22762
66	890524	19.2	1	867695 22829
67	898610	19.2	1	875470 23140
68	906335	19.2	1	883040 23295
69	913024	19.2	1	889966 23058
70	927209	19.2	1	904215 22994
71	945175	19.2	1	922060 23115
72	943361	19.2	1	920516 22845
73	946895	19.2	1	924212 22683
74	947759	19.2	1	925234 22525
75	942196	19.2	1	919565 22631
76	943335	19.2	1	921008 22327
77	937755	19.2	1	915504 22251
78	934875	19.2	1	912853 22022
79	938131	19.2	1	915986 22145
80	936987	19.2	1	914620 22367
81	938329	19.2	1	916438 21891
82	935782	19.2	1	913692 22090
83	938343	19.2	1	916585 21758
84	935073	19.2	1	914475 20598
85	940035	19.2	1	919229 20806
86	939880	19.2	1	919261 20619
87	951772	19.2	1	930974 20798
88	960541	19.2	1	939850 20691
89	969723	19.2	1	949268 20455
90	977212	19.2	1	956989 20223
91	984873	19.2	1	964532 20341
92	984415	19.2	1	964253 20162
93	984826	19.2	1	964857 19969
94	983629	19.2	1	963927 19702
95	983271	19.2	1	964083 19188
96	984818	19.2	1	965656 19162
97	987744	19.2	1	968976 18768
98	991585	19.2	1	972448 19137
99	998782	19.2	1	980063 18719
100	1006929	19.2	1	988098 18831
101	1016236	19.2	1	997457 18779
102	1015347	19.2	1	996839 18508
103	1015941	19.2	1	997618 18323
104	1016174	19.2	1	998126 18048
105	1016223	19.2	1	998200 18023
106	1015283	19.2	1	997204 18079
107	1020440	19.2	1	1002559 17881
108	1022949	19.2	1	1004987 17962
109	1033100	19.2	1	1014919 18181
110	1040647	19.2	1	1022755 17892
111	1049931	19.2	1	1031961 17970
112	1052388	19.2	1	1034485 17903
113	1053965	19.2	1	1036714 17251
114	1045382	19.2	1	1028126 17256
115	1042613	19.2	1	1025509 17104
116	1039537	19.2	1	1022507 17030
117	1042085	19.2	1	1024968 17117
118	1043803	19.2	1	1027074 16729
119	1048392	19.2	1	1031467 16925
120	1061976	19.2	1	1044853 17123
121	1073203	19.2	1	1056386 16817
122	1080326	19.2	1	1063446 16880
123	1081603	19.2	1	1064743 16860
124	1072872	19.2	1	1056325 16547
125	1067458	19.2	1	1051113 16345
126	1059117	19.2	1	1043275 15842
127	1061594	19.2	1	1045828 15766
128	1066420	19.2	1	1051515 14905
129	1075741	19.2	1	1061136 14605
130	1089148	19.2	1	1075527 13621
131	1102866	19.2	1	1089562 13304
132	1104828	19.2	1	1092300 12528
133	1096746	19.2	1	1085225 11521
134	1045190	19.2	1	1034410 10780
135	1025762	19.2	1	1015987 9775
136	997219	19.2	1	987974 9245
137	981054	19.2	1	972263 8791
138	942063	19.2	1	933525 8538
139	926620	19.2	1	918413 8207
140	980179	19.2	1	971584 8595
141	1041953	19.2	1	1033445 8508
142	945000	19.2	1	936861 8139
143	959076	19.2	1	950894 8182
144	1014659	19.2	1	1006353 8306
145	994434	19.2	1	986281 8153
146	1056592	19.2	1	1047615 8977
147	923683	19.2	1	915307 8376
148	942012	19.2	1	933183 8829
149	808997	19.2	1	800351 8646
150	765587	19.2	1	755202 10385
151	214054	19.2	1	188464 25590


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R1_001.fastq.gz
=============================================
321498091 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR015_AD015_S6_L002_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R2_001.fastq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 7687.78 s (24 us/read; 2.51 M reads/minute).

=== Summary ===

Total reads processed:             321,498,091
Reads with adapters:               170,243,880 (53.0%)
Reads written (passing filters):   321,498,091 (100.0%)

Total basepairs processed: 48,546,211,741 bp
Quality-trimmed:             172,654,465 bp (0.4%)
Total written (filtered):  38,758,510,378 bp (79.8%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 170243880 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 19.0%
  C: 33.2%
  G: 21.1%
  T: 26.5%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	35821180	80374522.8	0	35821180
2	10345651	20093630.7	0	10345651
3	3515062	5023407.7	0	3515062
4	1546659	1255851.9	0	1546659
5	892628	313963.0	0	892628
6	713202	78490.7	0	713202
7	707245	19622.7	0	707245
8	750011	4905.7	0	750011
9	632023	1226.4	0	624891 7132
10	701720	306.6	1	651564 50156
11	744375	76.7	1	694721 49654
12	667399	19.2	1	622330 45069
13	732507	19.2	1	681942 50565
14	645906	19.2	1	605175 40731
15	800653	19.2	1	741958 58695
16	814227	19.2	1	762292 51935
17	536472	19.2	1	503877 32595
18	739124	19.2	1	691178 47946
19	755959	19.2	1	713097 42862
20	645905	19.2	1	608312 37593
21	747401	19.2	1	698218 49183
22	798672	19.2	1	749309 49363
23	599746	19.2	1	563392 36354
24	762430	19.2	1	713620 48810
25	663609	19.2	1	627610 35999
26	785312	19.2	1	730745 54567
27	750778	19.2	1	706726 44052
28	696938	19.2	1	657507 39431
29	727087	19.2	1	686935 40152
30	770953	19.2	1	727314 43639
31	702681	19.2	1	664825 37856
32	745054	19.2	1	701250 43804
33	707859	19.2	1	670315 37544
34	753535	19.2	1	709190 44345
35	716629	19.2	1	678511 38118
36	814526	19.2	1	770511 44015
37	685832	19.2	1	650690 35142
38	786295	19.2	1	743333 42962
39	770800	19.2	1	728209 42591
40	764857	19.2	1	725735 39122
41	753964	19.2	1	714760 39204
42	768953	19.2	1	729810 39143
43	758528	19.2	1	720874 37654
44	759904	19.2	1	721620 38284
45	768252	19.2	1	729692 38560
46	755252	19.2	1	717957 37295
47	782949	19.2	1	743701 39248
48	769278	19.2	1	732606 36672
49	780986	19.2	1	742971 38015
50	776196	19.2	1	739070 37126
51	783018	19.2	1	745627 37391
52	784834	19.2	1	747752 37082
53	789080	19.2	1	752048 37032
54	785314	19.2	1	749220 36094
55	791960	19.2	1	755134 36826
56	793510	19.2	1	756398 37112
57	794491	19.2	1	757625 36866
58	797753	19.2	1	760954 36799
59	801924	19.2	1	765216 36708
60	800898	19.2	1	764777 36121
61	803365	19.2	1	767413 35952
62	800610	19.2	1	764766 35844
63	802117	19.2	1	766527 35590
64	804521	19.2	1	768700 35821
65	803126	19.2	1	767444 35682
66	806034	19.2	1	770918 35116
67	811835	19.2	1	776898 34937
68	814695	19.2	1	780709 33986
69	820961	19.2	1	786981 33980
70	824379	19.2	1	790486 33893
71	830072	19.2	1	796500 33572
72	828652	19.2	1	795351 33301
73	829785	19.2	1	796449 33336
74	832733	19.2	1	799938 32795
75	834898	19.2	1	801697 33201
76	835677	19.2	1	802839 32838
77	838829	19.2	1	805994 32835
78	839114	19.2	1	806367 32747
79	842308	19.2	1	809848 32460
80	844389	19.2	1	811913 32476
81	842812	19.2	1	810541 32271
82	841902	19.2	1	809792 32110
83	839941	19.2	1	808430 31511
84	841472	19.2	1	810158 31314
85	842893	19.2	1	811724 31169
86	841634	19.2	1	810482 31152
87	847141	19.2	1	816486 30655
88	847988	19.2	1	817691 30297
89	856838	19.2	1	826335 30503
90	861767	19.2	1	831031 30736
91	870130	19.2	1	839396 30734
92	870519	19.2	1	840098 30421
93	872720	19.2	1	842532 30188
94	867199	19.2	1	837299 29900
95	870431	19.2	1	840294 30137
96	866119	19.2	1	836550 29569
97	871655	19.2	1	842197 29458
98	871196	19.2	1	841756 29440
99	879050	19.2	1	849774 29276
100	882429	19.2	1	852996 29433
101	886488	19.2	1	857813 28675
102	885709	19.2	1	857702 28007
103	883041	19.2	1	855308 27733
104	880615	19.2	1	853348 27267
105	878156	19.2	1	851201 26955
106	876813	19.2	1	849997 26816
107	879870	19.2	1	853114 26756
108	882817	19.2	1	856362 26455
109	893851	19.2	1	866929 26922
110	900868	19.2	1	873583 27285
111	906883	19.2	1	880097 26786
112	908725	19.2	1	882462 26263
113	908170	19.2	1	881831 26339
114	900204	19.2	1	874110 26094
115	896826	19.2	1	870861 25965
116	892341	19.2	1	867266 25075
117	891351	19.2	1	866163 25188
118	893358	19.2	1	868532 24826
119	899627	19.2	1	874913 24714
120	907557	19.2	1	882938 24619
121	917517	19.2	1	892645 24872
122	919984	19.2	1	895291 24693
123	919027	19.2	1	894358 24669
124	912068	19.2	1	887701 24367
125	905685	19.2	1	882228 23457
126	899775	19.2	1	876705 23070
127	905322	19.2	1	882419 22903
128	907214	19.2	1	884900 22314
129	914551	19.2	1	892583 21968
130	931316	19.2	1	908862 22454
131	939671	19.2	1	917402 22269
132	942016	19.2	1	920419 21597
133	932673	19.2	1	912159 20514
134	886972	19.2	1	867900 19072
135	869322	19.2	1	850867 18455
136	845098	19.2	1	827564 17534
137	826006	19.2	1	809330 16676
138	792349	19.2	1	776217 16132
139	784638	19.2	1	768588 16050
140	828483	19.2	1	812017 16466
141	862129	19.2	1	845560 16569
142	793137	19.2	1	777344 15793
143	806747	19.2	1	791137 15610
144	846238	19.2	1	830018 16220
145	844949	19.2	1	828902 16047
146	874514	19.2	1	858356 16158
147	765041	19.2	1	750640 14401
148	762653	19.2	1	748529 14124
149	624227	19.2	1	612024 12203
150	578109	19.2	1	564908 13201
151	163297	19.2	1	139818 23479


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR015_AD015_S6_L002_R2_001.fastq.gz
=============================================
321498091 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR015_AD015_S6_L002_R1_001_trimmed.fq.gz and NR015_AD015_S6_L002_R2_001_trimmed.fq.gz
file_1: NR015_AD015_S6_L002_R1_001_trimmed.fq.gz, file_2: NR015_AD015_S6_L002_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR015_AD015_S6_L002_R1_001_trimmed.fq.gz and NR015_AD015_S6_L002_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR015_AD015_S6_L002_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR015_AD015_S6_L002_R2_001_val_2.fq.gz

Total number of sequences analysed: 321498091

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 35152577 (10.93%)

Deleting both intermediate output files NR015_AD015_S6_L002_R1_001_trimmed.fq.gz and NR015_AD015_S6_L002_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR019_S7_L001_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR019_S7_L001_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR019_S7_L001_R1_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR019_S7_L001_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.16 s (26 us/read; 2.28 M reads/minute).

=== Summary ===

Total reads processed:                  44,316
Reads with adapters:                    18,312 (41.3%)
Reads written (passing filters):        44,316 (100.0%)

Total basepairs processed:     6,691,716 bp
Quality-trimmed:                  48,533 bp (0.7%)
Total written (filtered):      5,823,503 bp (87.0%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 18312 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 28.3%
  C: 27.4%
  G: 16.4%
  T: 27.8%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	5941	11079.0	0	5941
2	1800	2769.8	0	1800
3	410	692.4	0	410
4	164	173.1	0	164
5	87	43.3	0	87
6	54	10.8	0	54
7	64	2.7	0	64
8	55	0.7	0	55
9	42	0.2	0	39 3
10	44	0.0	1	32 12
11	73	0.0	1	44 29
12	68	0.0	1	39 29
13	45	0.0	1	30 15
14	53	0.0	1	33 20
15	60	0.0	1	33 27
16	81	0.0	1	50 31
17	43	0.0	1	27 16
18	60	0.0	1	28 32
19	65	0.0	1	37 28
20	49	0.0	1	29 20
21	40	0.0	1	28 12
22	60	0.0	1	36 24
23	52	0.0	1	29 23
24	72	0.0	1	47 25
25	51	0.0	1	27 24
26	63	0.0	1	41 22
27	72	0.0	1	46 26
28	62	0.0	1	36 26
29	52	0.0	1	35 17
30	48	0.0	1	35 13
31	54	0.0	1	36 18
32	63	0.0	1	40 23
33	73	0.0	1	43 30
34	59	0.0	1	47 12
35	63	0.0	1	40 23
36	63	0.0	1	46 17
37	75	0.0	1	46 29
38	53	0.0	1	32 21
39	70	0.0	1	52 18
40	61	0.0	1	34 27
41	67	0.0	1	43 24
42	57	0.0	1	37 20
43	66	0.0	1	42 24
44	64	0.0	1	38 26
45	59	0.0	1	36 23
46	76	0.0	1	45 31
47	56	0.0	1	47 9
48	61	0.0	1	41 20
49	66	0.0	1	42 24
50	69	0.0	1	39 30
51	50	0.0	1	32 18
52	64	0.0	1	41 23
53	59	0.0	1	39 20
54	73	0.0	1	49 24
55	71	0.0	1	47 24
56	69	0.0	1	40 29
57	65	0.0	1	38 27
58	62	0.0	1	40 22
59	62	0.0	1	31 31
60	64	0.0	1	42 22
61	62	0.0	1	38 24
62	64	0.0	1	43 21
63	61	0.0	1	41 20
64	45	0.0	1	34 11
65	68	0.0	1	48 20
66	76	0.0	1	51 25
67	71	0.0	1	41 30
68	64	0.0	1	43 21
69	54	0.0	1	37 17
70	70	0.0	1	47 23
71	69	0.0	1	45 24
72	73	0.0	1	54 19
73	62	0.0	1	39 23
74	69	0.0	1	45 24
75	63	0.0	1	39 24
76	81	0.0	1	52 29
77	72	0.0	1	44 28
78	58	0.0	1	37 21
79	85	0.0	1	54 31
80	65	0.0	1	43 22
81	73	0.0	1	53 20
82	73	0.0	1	52 21
83	87	0.0	1	64 23
84	67	0.0	1	44 23
85	65	0.0	1	43 22
86	61	0.0	1	42 19
87	82	0.0	1	65 17
88	93	0.0	1	58 35
89	78	0.0	1	55 23
90	74	0.0	1	49 25
91	76	0.0	1	55 21
92	80	0.0	1	51 29
93	69	0.0	1	43 26
94	69	0.0	1	48 21
95	67	0.0	1	48 19
96	76	0.0	1	48 28
97	60	0.0	1	42 18
98	72	0.0	1	44 28
99	82	0.0	1	62 20
100	85	0.0	1	58 27
101	85	0.0	1	58 27
102	78	0.0	1	47 31
103	81	0.0	1	57 24
104	66	0.0	1	41 25
105	86	0.0	1	64 22
106	77	0.0	1	50 27
107	78	0.0	1	52 26
108	96	0.0	1	65 31
109	84	0.0	1	61 23
110	87	0.0	1	66 21
111	76	0.0	1	52 24
112	72	0.0	1	55 17
113	94	0.0	1	71 23
114	62	0.0	1	39 23
115	83	0.0	1	54 29
116	80	0.0	1	54 26
117	77	0.0	1	54 23
118	73	0.0	1	50 23
119	88	0.0	1	63 25
120	66	0.0	1	47 19
121	97	0.0	1	69 28
122	94	0.0	1	57 37
123	81	0.0	1	60 21
124	87	0.0	1	55 32
125	77	0.0	1	53 24
126	64	0.0	1	43 21
127	86	0.0	1	64 22
128	75	0.0	1	50 25
129	68	0.0	1	43 25
130	80	0.0	1	65 15
131	75	0.0	1	57 18
132	76	0.0	1	64 12
133	96	0.0	1	69 27
134	60	0.0	1	44 16
135	76	0.0	1	61 15
136	60	0.0	1	49 11
137	70	0.0	1	57 13
138	56	0.0	1	37 19
139	62	0.0	1	51 11
140	73	0.0	1	55 18
141	75	0.0	1	52 23
142	72	0.0	1	57 15
143	65	0.0	1	54 11
144	68	0.0	1	53 15
145	67	0.0	1	55 12
146	65	0.0	1	51 14
147	53	0.0	1	41 12
148	69	0.0	1	55 14
149	61	0.0	1	52 9
150	38	0.0	1	32 6
151	12	0.0	1	9 3


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR019_S7_L001_R1_001.fastq.gz
=============================================
44316 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR019_S7_L001_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR019_S7_L001_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR019_S7_L001_R2_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR019_S7_L001_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.16 s (26 us/read; 2.30 M reads/minute).

=== Summary ===

Total reads processed:                  44,316
Reads with adapters:                    18,561 (41.9%)
Reads written (passing filters):        44,316 (100.0%)

Total basepairs processed:     6,691,716 bp
Quality-trimmed:                  61,028 bp (0.9%)
Total written (filtered):      5,736,985 bp (85.7%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 18561 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 26.6%
  C: 27.0%
  G: 18.1%
  T: 28.1%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	6053	11079.0	0	6053
2	1568	2769.8	0	1568
3	484	692.4	0	484
4	164	173.1	0	164
5	78	43.3	0	78
6	42	10.8	0	42
7	48	2.7	0	48
8	38	0.7	0	38
9	32	0.2	0	28 4
10	56	0.0	1	32 24
11	44	0.0	1	25 19
12	43	0.0	1	24 19
13	62	0.0	1	38 24
14	39	0.0	1	21 18
15	61	0.0	1	35 26
16	55	0.0	1	29 26
17	42	0.0	1	23 19
18	56	0.0	1	28 28
19	44	0.0	1	25 19
20	45	0.0	1	27 18
21	46	0.0	1	30 16
22	58	0.0	1	36 22
23	45	0.0	1	27 18
24	40	0.0	1	29 11
25	51	0.0	1	30 21
26	57	0.0	1	33 24
27	61	0.0	1	40 21
28	45	0.0	1	28 17
29	75	0.0	1	48 27
30	55	0.0	1	26 29
31	66	0.0	1	39 27
32	43	0.0	1	25 18
33	42	0.0	1	29 13
34	53	0.0	1	37 16
35	45	0.0	1	21 24
36	70	0.0	1	40 30
37	61	0.0	1	41 20
38	56	0.0	1	39 17
39	58	0.0	1	36 22
40	55	0.0	1	33 22
41	69	0.0	1	42 27
42	82	0.0	1	57 25
43	57	0.0	1	26 31
44	44	0.0	1	23 21
45	53	0.0	1	35 18
46	55	0.0	1	36 19
47	64	0.0	1	43 21
48	57	0.0	1	34 23
49	58	0.0	1	33 25
50	64	0.0	1	39 25
51	55	0.0	1	37 18
52	59	0.0	1	40 19
53	50	0.0	1	38 12
54	73	0.0	1	46 27
55	61	0.0	1	41 20
56	55	0.0	1	37 18
57	58	0.0	1	37 21
58	76	0.0	1	49 27
59	54	0.0	1	37 17
60	72	0.0	1	47 25
61	64	0.0	1	40 24
62	63	0.0	1	37 26
63	63	0.0	1	31 32
64	55	0.0	1	40 15
65	62	0.0	1	44 18
66	76	0.0	1	48 28
67	76	0.0	1	54 22
68	71	0.0	1	47 24
69	55	0.0	1	37 18
70	74	0.0	1	40 34
71	85	0.0	1	61 24
72	70	0.0	1	49 21
73	67	0.0	1	46 21
74	67	0.0	1	41 26
75	70	0.0	1	48 22
76	73	0.0	1	45 28
77	73	0.0	1	53 20
78	73	0.0	1	53 20
79	78	0.0	1	48 30
80	77	0.0	1	45 32
81	61	0.0	1	47 14
82	61	0.0	1	35 26
83	82	0.0	1	71 11
84	70	0.0	1	48 22
85	78	0.0	1	59 19
86	59	0.0	1	37 22
87	76	0.0	1	47 29
88	55	0.0	1	34 21
89	84	0.0	1	62 22
90	68	0.0	1	44 24
91	69	0.0	1	44 25
92	74	0.0	1	49 25
93	79	0.0	1	60 19
94	87	0.0	1	61 26
95	83	0.0	1	60 23
96	83	0.0	1	58 25
97	77	0.0	1	50 27
98	87	0.0	1	70 17
99	87	0.0	1	57 30
100	85	0.0	1	60 25
101	95	0.0	1	64 31
102	87	0.0	1	61 26
103	65	0.0	1	41 24
104	72	0.0	1	57 15
105	65	0.0	1	48 17
106	70	0.0	1	52 18
107	76	0.0	1	49 27
108	81	0.0	1	53 28
109	69	0.0	1	48 21
110	75	0.0	1	57 18
111	78	0.0	1	55 23
112	93	0.0	1	65 28
113	86	0.0	1	62 24
114	87	0.0	1	50 37
115	91	0.0	1	70 21
116	89	0.0	1	62 27
117	92	0.0	1	70 22
118	100	0.0	1	76 24
119	91	0.0	1	65 26
120	84	0.0	1	57 27
121	93	0.0	1	73 20
122	87	0.0	1	59 28
123	96	0.0	1	74 22
124	106	0.0	1	80 26
125	98	0.0	1	75 23
126	91	0.0	1	65 26
127	88	0.0	1	61 27
128	87	0.0	1	62 25
129	90	0.0	1	61 29
130	95	0.0	1	68 27
131	102	0.0	1	70 32
132	94	0.0	1	71 23
133	104	0.0	1	76 28
134	93	0.0	1	67 26
135	94	0.0	1	75 19
136	83	0.0	1	60 23
137	77	0.0	1	63 14
138	87	0.0	1	59 28
139	81	0.0	1	55 26
140	75	0.0	1	61 14
141	100	0.0	1	81 19
142	88	0.0	1	71 17
143	93	0.0	1	62 31
144	96	0.0	1	75 21
145	95	0.0	1	71 24
146	92	0.0	1	73 19
147	73	0.0	1	64 9
148	71	0.0	1	59 12
149	58	0.0	1	44 14
150	60	0.0	1	42 18
151	19	0.0	1	16 3


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR019_S7_L001_R2_001.fastq.gz
=============================================
44316 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR019_S7_L001_R1_001_trimmed.fq.gz and NR019_S7_L001_R2_001_trimmed.fq.gz
file_1: NR019_S7_L001_R1_001_trimmed.fq.gz, file_2: NR019_S7_L001_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR019_S7_L001_R1_001_trimmed.fq.gz and NR019_S7_L001_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR019_S7_L001_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR019_S7_L001_R2_001_val_2.fq.gz

Total number of sequences analysed: 44316

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3072 (6.93%)

Deleting both intermediate output files NR019_S7_L001_R1_001_trimmed.fq.gz and NR019_S7_L001_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR019_S7_L002_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR019_S7_L002_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR019_S7_L002_R1_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR019_S7_L002_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.63 s (26 us/read; 2.31 M reads/minute).

=== Summary ===

Total reads processed:                  24,171
Reads with adapters:                    10,315 (42.7%)
Reads written (passing filters):        24,171 (100.0%)

Total basepairs processed:     3,649,821 bp
Quality-trimmed:                  26,203 bp (0.7%)
Total written (filtered):      3,156,842 bp (86.5%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 10315 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 26.5%
  C: 27.8%
  G: 18.1%
  T: 27.5%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	3268	6042.8	0	3268
2	983	1510.7	0	983
3	276	377.7	0	276
4	91	94.4	0	91
5	45	23.6	0	45
6	35	5.9	0	35
7	26	1.5	0	26
8	32	0.4	0	32
9	22	0.1	0	22
10	43	0.0	1	37 6
11	43	0.0	1	30 13
12	35	0.0	1	22 13
13	29	0.0	1	21 8
14	29	0.0	1	23 6
15	43	0.0	1	29 14
16	49	0.0	1	42 7
17	29	0.0	1	18 11
18	37	0.0	1	28 9
19	32	0.0	1	25 7
20	39	0.0	1	29 10
21	31	0.0	1	22 9
22	39	0.0	1	28 11
23	24	0.0	1	15 9
24	26	0.0	1	17 9
25	34	0.0	1	25 9
26	35	0.0	1	29 6
27	40	0.0	1	31 9
28	26	0.0	1	20 6
29	39	0.0	1	24 15
30	27	0.0	1	21 6
31	36	0.0	1	27 9
32	33	0.0	1	23 10
33	33	0.0	1	20 13
34	38	0.0	1	30 8
35	50	0.0	1	33 17
36	45	0.0	1	34 11
37	24	0.0	1	19 5
38	36	0.0	1	21 15
39	37	0.0	1	23 14
40	46	0.0	1	32 14
41	39	0.0	1	22 17
42	30	0.0	1	22 8
43	34	0.0	1	26 8
44	35	0.0	1	19 16
45	40	0.0	1	34 6
46	38	0.0	1	22 16
47	31	0.0	1	23 8
48	35	0.0	1	22 13
49	39	0.0	1	30 9
50	40	0.0	1	29 11
51	29	0.0	1	19 10
52	32	0.0	1	25 7
53	31	0.0	1	24 7
54	32	0.0	1	18 14
55	36	0.0	1	32 4
56	44	0.0	1	34 10
57	37	0.0	1	29 8
58	39	0.0	1	30 9
59	24	0.0	1	19 5
60	37	0.0	1	29 8
61	26	0.0	1	18 8
62	31	0.0	1	29 2
63	38	0.0	1	34 4
64	35	0.0	1	26 9
65	37	0.0	1	30 7
66	37	0.0	1	27 10
67	33	0.0	1	23 10
68	36	0.0	1	28 8
69	45	0.0	1	36 9
70	40	0.0	1	33 7
71	44	0.0	1	36 8
72	42	0.0	1	27 15
73	43	0.0	1	37 6
74	44	0.0	1	38 6
75	43	0.0	1	41 2
76	38	0.0	1	32 6
77	34	0.0	1	25 9
78	38	0.0	1	34 4
79	48	0.0	1	40 8
80	47	0.0	1	33 14
81	45	0.0	1	25 20
82	29	0.0	1	24 5
83	36	0.0	1	30 6
84	26	0.0	1	22 4
85	41	0.0	1	34 7
86	41	0.0	1	30 11
87	37	0.0	1	31 6
88	27	0.0	1	23 4
89	35	0.0	1	30 5
90	48	0.0	1	40 8
91	39	0.0	1	30 9
92	59	0.0	1	46 13
93	39	0.0	1	32 7
94	53	0.0	1	44 9
95	51	0.0	1	42 9
96	46	0.0	1	34 12
97	42	0.0	1	32 10
98	40	0.0	1	29 11
99	45	0.0	1	38 7
100	33	0.0	1	26 7
101	50	0.0	1	43 7
102	48	0.0	1	39 9
103	35	0.0	1	25 10
104	39	0.0	1	28 11
105	33	0.0	1	26 7
106	49	0.0	1	41 8
107	56	0.0	1	47 9
108	55	0.0	1	45 10
109	40	0.0	1	33 7
110	42	0.0	1	33 9
111	39	0.0	1	36 3
112	55	0.0	1	46 9
113	39	0.0	1	30 9
114	49	0.0	1	37 12
115	44	0.0	1	30 14
116	30	0.0	1	25 5
117	45	0.0	1	35 10
118	36	0.0	1	27 9
119	49	0.0	1	35 14
120	44	0.0	1	34 10
121	46	0.0	1	37 9
122	42	0.0	1	32 10
123	43	0.0	1	37 6
124	43	0.0	1	27 16
125	55	0.0	1	42 13
126	36	0.0	1	34 2
127	41	0.0	1	38 3
128	41	0.0	1	32 9
129	44	0.0	1	35 9
130	53	0.0	1	47 6
131	53	0.0	1	47 6
132	56	0.0	1	49 7
133	40	0.0	1	30 10
134	33	0.0	1	29 4
135	43	0.0	1	34 9
136	34	0.0	1	27 7
137	46	0.0	1	40 6
138	47	0.0	1	38 9
139	33	0.0	1	29 4
140	37	0.0	1	31 6
141	32	0.0	1	27 5
142	39	0.0	1	34 5
143	39	0.0	1	33 6
144	51	0.0	1	43 8
145	40	0.0	1	35 5
146	50	0.0	1	43 7
147	38	0.0	1	33 5
148	33	0.0	1	31 2
149	31	0.0	1	30 1
150	35	0.0	1	28 7
151	6	0.0	1	6


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR019_S7_L002_R1_001.fastq.gz
=============================================
24171 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR019_S7_L002_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR019_S7_L002_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR019_S7_L002_R2_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR019_S7_L002_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.62 s (26 us/read; 2.32 M reads/minute).

=== Summary ===

Total reads processed:                  24,171
Reads with adapters:                    10,641 (44.0%)
Reads written (passing filters):        24,171 (100.0%)

Total basepairs processed:     3,649,821 bp
Quality-trimmed:                  30,593 bp (0.8%)
Total written (filtered):      3,064,527 bp (84.0%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 10641 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 23.8%
  C: 29.4%
  G: 19.7%
  T: 26.9%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	3115	6042.8	0	3115
2	786	1510.7	0	786
3	254	377.7	0	254
4	83	94.4	0	83
5	45	23.6	0	45
6	39	5.9	0	39
7	25	1.5	0	25
8	41	0.4	0	41
9	21	0.1	0	21
10	28	0.0	1	18 10
11	30	0.0	1	22 8
12	34	0.0	1	26 8
13	32	0.0	1	22 10
14	25	0.0	1	21 4
15	30	0.0	1	19 11
16	32	0.0	1	23 9
17	15	0.0	1	11 4
18	39	0.0	1	23 16
19	29	0.0	1	20 9
20	24	0.0	1	15 9
21	35	0.0	1	20 15
22	42	0.0	1	30 12
23	32	0.0	1	22 10
24	25	0.0	1	16 9
25	33	0.0	1	23 10
26	39	0.0	1	28 11
27	34	0.0	1	28 6
28	28	0.0	1	23 5
29	26	0.0	1	18 8
30	38	0.0	1	28 10
31	33	0.0	1	20 13
32	33	0.0	1	22 11
33	26	0.0	1	18 8
34	29	0.0	1	24 5
35	45	0.0	1	32 13
36	32	0.0	1	22 10
37	40	0.0	1	30 10
38	43	0.0	1	34 9
39	28	0.0	1	24 4
40	40	0.0	1	28 12
41	31	0.0	1	22 9
42	40	0.0	1	25 15
43	36	0.0	1	24 12
44	44	0.0	1	33 11
45	48	0.0	1	37 11
46	28	0.0	1	22 6
47	34	0.0	1	26 8
48	35	0.0	1	22 13
49	39	0.0	1	26 13
50	51	0.0	1	36 15
51	31	0.0	1	21 10
52	39	0.0	1	23 16
53	30	0.0	1	20 10
54	50	0.0	1	36 14
55	41	0.0	1	33 8
56	35	0.0	1	27 8
57	32	0.0	1	24 8
58	34	0.0	1	22 12
59	42	0.0	1	36 6
60	39	0.0	1	30 9
61	39	0.0	1	29 10
62	46	0.0	1	34 12
63	43	0.0	1	31 12
64	37	0.0	1	27 10
65	32	0.0	1	24 8
66	45	0.0	1	36 9
67	34	0.0	1	27 7
68	51	0.0	1	40 11
69	38	0.0	1	29 9
70	56	0.0	1	39 17
71	47	0.0	1	35 12
72	43	0.0	1	36 7
73	40	0.0	1	30 10
74	38	0.0	1	30 8
75	34	0.0	1	24 10
76	42	0.0	1	38 4
77	42	0.0	1	31 11
78	48	0.0	1	39 9
79	33	0.0	1	26 7
80	49	0.0	1	40 9
81	37	0.0	1	26 11
82	43	0.0	1	35 8
83	48	0.0	1	40 8
84	36	0.0	1	28 8
85	50	0.0	1	38 12
86	33	0.0	1	27 6
87	41	0.0	1	34 7
88	59	0.0	1	52 7
89	46	0.0	1	38 8
90	37	0.0	1	35 2
91	35	0.0	1	29 6
92	46	0.0	1	38 8
93	44	0.0	1	33 11
94	46	0.0	1	33 13
95	48	0.0	1	38 10
96	52	0.0	1	42 10
97	52	0.0	1	39 13
98	53	0.0	1	46 7
99	55	0.0	1	46 9
100	48	0.0	1	35 13
101	67	0.0	1	56 11
102	59	0.0	1	44 15
103	41	0.0	1	32 9
104	58	0.0	1	44 14
105	63	0.0	1	44 19
106	46	0.0	1	36 10
107	62	0.0	1	54 8
108	45	0.0	1	35 10
109	51	0.0	1	44 7
110	45	0.0	1	37 8
111	49	0.0	1	44 5
112	47	0.0	1	38 9
113	55	0.0	1	46 9
114	68	0.0	1	53 15
115	49	0.0	1	42 7
116	40	0.0	1	32 8
117	62	0.0	1	52 10
118	51	0.0	1	40 11
119	51	0.0	1	37 14
120	58	0.0	1	47 11
121	52	0.0	1	45 7
122	69	0.0	1	55 14
123	65	0.0	1	48 17
124	55	0.0	1	47 8
125	47	0.0	1	43 4
126	65	0.0	1	57 8
127	60	0.0	1	52 8
128	56	0.0	1	41 15
129	49	0.0	1	45 4
130	63	0.0	1	56 7
131	64	0.0	1	52 12
132	61	0.0	1	56 5
133	60	0.0	1	49 11
134	51	0.0	1	42 9
135	59	0.0	1	51 8
136	42	0.0	1	39 3
137	53	0.0	1	42 11
138	60	0.0	1	48 12
139	58	0.0	1	49 9
140	54	0.0	1	45 9
141	52	0.0	1	47 5
142	60	0.0	1	51 9
143	53	0.0	1	46 7
144	45	0.0	1	40 5
145	54	0.0	1	44 10
146	56	0.0	1	47 9
147	59	0.0	1	51 8
148	46	0.0	1	38 8
149	48	0.0	1	40 8
150	33	0.0	1	28 5
151	12	0.0	1	8 4


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR019_S7_L002_R2_001.fastq.gz
=============================================
24171 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR019_S7_L002_R1_001_trimmed.fq.gz and NR019_S7_L002_R2_001_trimmed.fq.gz
file_1: NR019_S7_L002_R1_001_trimmed.fq.gz, file_2: NR019_S7_L002_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR019_S7_L002_R1_001_trimmed.fq.gz and NR019_S7_L002_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR019_S7_L002_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR019_S7_L002_R2_001_val_2.fq.gz

Total number of sequences analysed: 24171

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1861 (7.70%)

Deleting both intermediate output files NR019_S7_L002_R1_001_trimmed.fq.gz and NR019_S7_L002_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR021_S8_L001_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR021_S8_L001_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR021_S8_L001_R1_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR021_S8_L001_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 103.81 s (26 us/read; 2.33 M reads/minute).

=== Summary ===

Total reads processed:               4,037,578
Reads with adapters:                 1,275,359 (31.6%)
Reads written (passing filters):     4,037,578 (100.0%)

Total basepairs processed:   609,674,278 bp
Quality-trimmed:               1,279,284 bp (0.2%)
Total written (filtered):    596,297,509 bp (97.8%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 1275359 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 29.7%
  C: 18.6%
  G: 15.4%
  T: 36.3%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	848241	1009394.5	0	848241
2	210630	252348.6	0	210630
3	69160	63087.2	0	69160
4	15786	15771.8	0	15786
5	4086	3942.9	0	4086
6	1638	985.7	0	1638
7	852	246.4	0	852
8	835	61.6	0	835
9	658	15.4	0	583 75
10	720	3.9	1	588 132
11	722	1.0	1	621 101
12	620	0.2	1	553 67
13	682	0.2	1	628 54
14	624	0.2	1	572 52
15	741	0.2	1	680 61
16	812	0.2	1	729 83
17	502	0.2	1	459 43
18	731	0.2	1	681 50
19	700	0.2	1	628 72
20	669	0.2	1	607 62
21	662	0.2	1	601 61
22	783	0.2	1	708 75
23	555	0.2	1	504 51
24	766	0.2	1	706 60
25	699	0.2	1	631 68
26	725	0.2	1	665 60
27	673	0.2	1	605 68
28	751	0.2	1	676 75
29	713	0.2	1	658 55
30	764	0.2	1	695 69
31	799	0.2	1	717 82
32	708	0.2	1	643 65
33	733	0.2	1	652 81
34	678	0.2	1	624 54
35	708	0.2	1	631 77
36	761	0.2	1	682 79
37	713	0.2	1	658 55
38	762	0.2	1	696 66
39	707	0.2	1	640 67
40	743	0.2	1	689 54
41	709	0.2	1	644 65
42	773	0.2	1	726 47
43	800	0.2	1	744 56
44	783	0.2	1	704 79
45	799	0.2	1	694 105
46	797	0.2	1	726 71
47	830	0.2	1	755 75
48	819	0.2	1	747 72
49	806	0.2	1	733 73
50	780	0.2	1	710 70
51	815	0.2	1	755 60
52	747	0.2	1	694 53
53	780	0.2	1	723 57
54	759	0.2	1	708 51
55	767	0.2	1	719 48
56	840	0.2	1	768 72
57	792	0.2	1	723 69
58	806	0.2	1	749 57
59	772	0.2	1	703 69
60	832	0.2	1	771 61
61	871	0.2	1	799 72
62	883	0.2	1	821 62
63	812	0.2	1	753 59
64	787	0.2	1	719 68
65	889	0.2	1	815 74
66	879	0.2	1	815 64
67	850	0.2	1	767 83
68	877	0.2	1	828 49
69	837	0.2	1	775 62
70	896	0.2	1	823 73
71	834	0.2	1	770 64
72	891	0.2	1	823 68
73	879	0.2	1	816 63
74	885	0.2	1	817 68
75	797	0.2	1	734 63
76	823	0.2	1	762 61
77	893	0.2	1	844 49
78	872	0.2	1	814 58
79	895	0.2	1	840 55
80	903	0.2	1	821 82
81	952	0.2	1	897 55
82	923	0.2	1	857 66
83	897	0.2	1	821 76
84	882	0.2	1	840 42
85	901	0.2	1	836 65
86	910	0.2	1	851 59
87	947	0.2	1	884 63
88	918	0.2	1	859 59
89	922	0.2	1	862 60
90	940	0.2	1	875 65
91	938	0.2	1	884 54
92	934	0.2	1	870 64
93	982	0.2	1	929 53
94	916	0.2	1	841 75
95	884	0.2	1	834 50
96	1010	0.2	1	930 80
97	1002	0.2	1	939 63
98	990	0.2	1	946 44
99	924	0.2	1	872 52
100	988	0.2	1	937 51
101	939	0.2	1	880 59
102	953	0.2	1	897 56
103	979	0.2	1	920 59
104	959	0.2	1	896 63
105	997	0.2	1	951 46
106	938	0.2	1	839 99
107	979	0.2	1	918 61
108	952	0.2	1	866 86
109	957	0.2	1	891 66
110	931	0.2	1	879 52
111	1011	0.2	1	942 69
112	1000	0.2	1	932 68
113	1038	0.2	1	977 61
114	1019	0.2	1	963 56
115	985	0.2	1	924 61
116	1024	0.2	1	957 67
117	1075	0.2	1	1011 64
118	956	0.2	1	896 60
119	999	0.2	1	942 57
120	1057	0.2	1	988 69
121	1001	0.2	1	948 53
122	1048	0.2	1	994 54
123	1019	0.2	1	960 59
124	1008	0.2	1	941 67
125	1009	0.2	1	938 71
126	984	0.2	1	930 54
127	1007	0.2	1	955 52
128	1017	0.2	1	964 53
129	1075	0.2	1	1014 61
130	1087	0.2	1	1045 42
131	1054	0.2	1	1014 40
132	1091	0.2	1	1036 55
133	1049	0.2	1	1000 49
134	1055	0.2	1	1011 44
135	1071	0.2	1	1021 50
136	1057	0.2	1	1006 51
137	905	0.2	1	867 38
138	919	0.2	1	886 33
139	937	0.2	1	889 48
140	1009	0.2	1	951 58
141	1090	0.2	1	1040 50
142	952	0.2	1	904 48
143	992	0.2	1	915 77
144	979	0.2	1	921 58
145	975	0.2	1	918 57
146	1085	0.2	1	1001 84
147	886	0.2	1	851 35
148	908	0.2	1	865 43
149	751	0.2	1	717 34
150	751	0.2	1	718 33
151	209	0.2	1	166 43


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR021_S8_L001_R1_001.fastq.gz
=============================================
4037578 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR021_S8_L001_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR021_S8_L001_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR021_S8_L001_R2_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR021_S8_L001_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 100.95 s (25 us/read; 2.40 M reads/minute).

=== Summary ===

Total reads processed:               4,037,578
Reads with adapters:                   905,282 (22.4%)
Reads written (passing filters):     4,037,578 (100.0%)

Total basepairs processed:   609,674,278 bp
Quality-trimmed:               3,103,799 bp (0.5%)
Total written (filtered):    596,405,354 bp (97.8%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 905282 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 26.9%
  C: 19.4%
  G: 20.9%
  T: 32.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	591315	1009394.5	0	591315
2	141381	252348.6	0	141381
3	44243	63087.2	0	44243
4	13764	15771.8	0	13764
5	3067	3942.9	0	3067
6	1349	985.7	0	1349
7	737	246.4	0	737
8	666	61.6	0	666
9	608	15.4	0	527 81
10	706	3.9	1	544 162
11	657	1.0	1	574 83
12	586	0.2	1	521 65
13	623	0.2	1	557 66
14	563	0.2	1	510 53
15	682	0.2	1	600 82
16	693	0.2	1	636 57
17	498	0.2	1	451 47
18	614	0.2	1	541 73
19	633	0.2	1	566 67
20	611	0.2	1	543 68
21	646	0.2	1	586 60
22	692	0.2	1	629 63
23	532	0.2	1	480 52
24	677	0.2	1	599 78
25	595	0.2	1	545 50
26	684	0.2	1	615 69
27	634	0.2	1	570 64
28	668	0.2	1	608 60
29	626	0.2	1	568 58
30	699	0.2	1	647 52
31	688	0.2	1	616 72
32	622	0.2	1	568 54
33	654	0.2	1	592 62
34	659	0.2	1	593 66
35	649	0.2	1	589 60
36	725	0.2	1	665 60
37	587	0.2	1	526 61
38	665	0.2	1	607 58
39	689	0.2	1	636 53
40	714	0.2	1	646 68
41	683	0.2	1	621 62
42	683	0.2	1	628 55
43	672	0.2	1	626 46
44	702	0.2	1	637 65
45	716	0.2	1	655 61
46	722	0.2	1	665 57
47	696	0.2	1	647 49
48	717	0.2	1	653 64
49	681	0.2	1	614 67
50	739	0.2	1	681 58
51	751	0.2	1	690 61
52	732	0.2	1	666 66
53	677	0.2	1	623 54
54	732	0.2	1	678 54
55	717	0.2	1	645 72
56	761	0.2	1	699 62
57	675	0.2	1	612 63
58	685	0.2	1	634 51
59	757	0.2	1	699 58
60	794	0.2	1	736 58
61	744	0.2	1	676 68
62	729	0.2	1	674 55
63	703	0.2	1	641 62
64	754	0.2	1	713 41
65	724	0.2	1	667 57
66	788	0.2	1	726 62
67	801	0.2	1	735 66
68	762	0.2	1	706 56
69	788	0.2	1	733 55
70	791	0.2	1	730 61
71	783	0.2	1	729 54
72	793	0.2	1	745 48
73	805	0.2	1	752 53
74	823	0.2	1	753 70
75	771	0.2	1	720 51
76	774	0.2	1	743 31
77	768	0.2	1	737 31
78	755	0.2	1	698 57
79	787	0.2	1	744 43
80	738	0.2	1	688 50
81	747	0.2	1	703 44
82	764	0.2	1	720 44
83	790	0.2	1	737 53
84	789	0.2	1	736 53
85	734	0.2	1	681 53
86	835	0.2	1	785 50
87	835	0.2	1	781 54
88	789	0.2	1	748 41
89	822	0.2	1	776 46
90	871	0.2	1	815 56
91	849	0.2	1	794 55
92	817	0.2	1	768 49
93	829	0.2	1	779 50
94	850	0.2	1	801 49
95	883	0.2	1	826 57
96	853	0.2	1	798 55
97	851	0.2	1	798 53
98	838	0.2	1	783 55
99	882	0.2	1	828 54
100	859	0.2	1	813 46
101	910	0.2	1	876 34
102	818	0.2	1	769 49
103	850	0.2	1	807 43
104	818	0.2	1	776 42
105	816	0.2	1	759 57
106	856	0.2	1	820 36
107	773	0.2	1	716 57
108	861	0.2	1	804 57
109	867	0.2	1	822 45
110	867	0.2	1	818 49
111	881	0.2	1	833 48
112	864	0.2	1	828 36
113	839	0.2	1	807 32
114	888	0.2	1	832 56
115	890	0.2	1	846 44
116	900	0.2	1	865 35
117	854	0.2	1	810 44
118	839	0.2	1	803 36
119	836	0.2	1	804 32
120	898	0.2	1	843 55
121	869	0.2	1	833 36
122	885	0.2	1	832 53
123	883	0.2	1	838 45
124	863	0.2	1	813 50
125	847	0.2	1	817 30
126	802	0.2	1	771 31
127	875	0.2	1	827 48
128	860	0.2	1	814 46
129	893	0.2	1	850 43
130	847	0.2	1	802 45
131	926	0.2	1	890 36
132	938	0.2	1	893 45
133	928	0.2	1	874 54
134	829	0.2	1	799 30
135	858	0.2	1	824 34
136	867	0.2	1	819 48
137	789	0.2	1	758 31
138	831	0.2	1	801 30
139	759	0.2	1	730 29
140	853	0.2	1	809 44
141	824	0.2	1	790 34
142	789	0.2	1	744 45
143	740	0.2	1	702 38
144	886	0.2	1	832 54
145	841	0.2	1	794 47
146	858	0.2	1	809 49
147	710	0.2	1	686 24
148	734	0.2	1	705 29
149	618	0.2	1	589 29
150	529	0.2	1	487 42
151	165	0.2	1	129 36


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR021_S8_L001_R2_001.fastq.gz
=============================================
4037578 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR021_S8_L001_R1_001_trimmed.fq.gz and NR021_S8_L001_R2_001_trimmed.fq.gz
file_1: NR021_S8_L001_R1_001_trimmed.fq.gz, file_2: NR021_S8_L001_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR021_S8_L001_R1_001_trimmed.fq.gz and NR021_S8_L001_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR021_S8_L001_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR021_S8_L001_R2_001_val_2.fq.gz

Total number of sequences analysed: 4037578

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 41263 (1.02%)

Deleting both intermediate output files NR021_S8_L001_R1_001_trimmed.fq.gz and NR021_S8_L001_R2_001_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R1_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR021_S8_L002_R1_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR021_S8_L002_R1_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR021_S8_L002_R1_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR021_S8_L002_R1_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 91.25 s (26 us/read; 2.35 M reads/minute).

=== Summary ===

Total reads processed:               3,575,592
Reads with adapters:                 1,134,870 (31.7%)
Reads written (passing filters):     3,575,592 (100.0%)

Total basepairs processed:   539,914,392 bp
Quality-trimmed:               1,205,207 bp (0.2%)
Total written (filtered):    526,158,055 bp (97.5%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 1134870 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 29.0%
  C: 19.1%
  G: 15.7%
  T: 36.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	737588	893898.0	0	737588
2	183929	223474.5	0	183929
3	60993	55868.6	0	60993
4	13612	13967.2	0	13612
5	3694	3491.8	0	3694
6	1512	872.9	0	1512
7	839	218.2	0	839
8	820	54.6	0	820
9	669	13.6	0	597 72
10	771	3.4	1	639 132
11	767	0.9	1	709 58
12	639	0.2	1	594 45
13	745	0.2	1	709 36
14	660	0.2	1	622 38
15	820	0.2	1	754 66
16	888	0.2	1	819 69
17	579	0.2	1	541 38
18	703	0.2	1	666 37
19	712	0.2	1	665 47
20	723	0.2	1	676 47
21	803	0.2	1	750 53
22	839	0.2	1	796 43
23	669	0.2	1	620 49
24	792	0.2	1	743 49
25	677	0.2	1	622 55
26	809	0.2	1	748 61
27	824	0.2	1	748 76
28	792	0.2	1	730 62
29	732	0.2	1	681 51
30	858	0.2	1	787 71
31	801	0.2	1	732 69
32	803	0.2	1	749 54
33	804	0.2	1	746 58
34	792	0.2	1	741 51
35	753	0.2	1	700 53
36	815	0.2	1	765 50
37	765	0.2	1	713 52
38	787	0.2	1	745 42
39	819	0.2	1	780 39
40	803	0.2	1	761 42
41	773	0.2	1	731 42
42	790	0.2	1	751 39
43	824	0.2	1	764 60
44	779	0.2	1	734 45
45	864	0.2	1	786 78
46	848	0.2	1	791 57
47	771	0.2	1	726 45
48	867	0.2	1	815 52
49	822	0.2	1	777 45
50	777	0.2	1	725 52
51	801	0.2	1	751 50
52	794	0.2	1	740 54
53	880	0.2	1	841 39
54	891	0.2	1	842 49
55	771	0.2	1	730 41
56	822	0.2	1	767 55
57	865	0.2	1	802 63
58	870	0.2	1	820 50
59	898	0.2	1	848 50
60	905	0.2	1	864 41
61	937	0.2	1	890 47
62	900	0.2	1	844 56
63	844	0.2	1	795 49
64	858	0.2	1	807 51
65	871	0.2	1	808 63
66	890	0.2	1	835 55
67	825	0.2	1	777 48
68	856	0.2	1	813 43
69	857	0.2	1	814 43
70	954	0.2	1	910 44
71	937	0.2	1	890 47
72	914	0.2	1	862 52
73	889	0.2	1	839 50
74	943	0.2	1	891 52
75	882	0.2	1	829 53
76	891	0.2	1	850 41
77	877	0.2	1	834 43
78	930	0.2	1	883 47
79	933	0.2	1	896 37
80	976	0.2	1	914 62
81	949	0.2	1	898 51
82	941	0.2	1	885 56
83	988	0.2	1	926 62
84	1007	0.2	1	963 44
85	947	0.2	1	885 62
86	965	0.2	1	913 52
87	953	0.2	1	906 47
88	1015	0.2	1	967 48
89	1010	0.2	1	946 64
90	955	0.2	1	895 60
91	1034	0.2	1	996 38
92	1010	0.2	1	980 30
93	971	0.2	1	921 50
94	999	0.2	1	947 52
95	966	0.2	1	918 48
96	947	0.2	1	884 63
97	1009	0.2	1	973 36
98	1061	0.2	1	1008 53
99	1027	0.2	1	981 46
100	1076	0.2	1	1034 42
101	1016	0.2	1	965 51
102	1009	0.2	1	953 56
103	978	0.2	1	946 32
104	1026	0.2	1	997 29
105	1086	0.2	1	1048 38
106	976	0.2	1	899 77
107	966	0.2	1	931 35
108	1087	0.2	1	1029 58
109	1087	0.2	1	1030 57
110	1058	0.2	1	1018 40
111	1092	0.2	1	1055 37
112	1090	0.2	1	1040 50
113	1034	0.2	1	988 46
114	1057	0.2	1	1021 36
115	1027	0.2	1	985 42
116	1067	0.2	1	1025 42
117	1129	0.2	1	1071 58
118	1083	0.2	1	1033 50
119	1097	0.2	1	1040 57
120	1119	0.2	1	1074 45
121	1090	0.2	1	1051 39
122	1096	0.2	1	1059 37
123	1168	0.2	1	1117 51
124	1147	0.2	1	1074 73
125	1113	0.2	1	1058 55
126	1099	0.2	1	1065 34
127	1092	0.2	1	1052 40
128	1091	0.2	1	1054 37
129	1107	0.2	1	1071 36
130	1090	0.2	1	1043 47
131	1141	0.2	1	1101 40
132	1145	0.2	1	1108 37
133	1159	0.2	1	1135 24
134	1086	0.2	1	1054 32
135	1084	0.2	1	1042 42
136	977	0.2	1	957 20
137	1030	0.2	1	1003 27
138	1018	0.2	1	977 41
139	1007	0.2	1	978 29
140	1075	0.2	1	1032 43
141	1106	0.2	1	1075 31
142	1113	0.2	1	1086 27
143	1085	0.2	1	1022 63
144	1030	0.2	1	984 46
145	1059	0.2	1	1022 37
146	1123	0.2	1	1066 57
147	925	0.2	1	899 26
148	918	0.2	1	883 35
149	805	0.2	1	784 21
150	758	0.2	1	733 25
151	243	0.2	1	195 48


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR021_S8_L002_R1_001.fastq.gz
=============================================
3575592 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R2_001.fastq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/NR021_S8_L002_R2_001.fastq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR021_S8_L002_R2_001_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file /home/sam/data/geoduck_illumina/NR021_S8_L002_R2_001.fastq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a CTGTCTCTTATA /home/sam/data/geoduck_illumina/NR021_S8_L002_R2_001.fastq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 89.37 s (25 us/read; 2.40 M reads/minute).

=== Summary ===

Total reads processed:               3,575,592
Reads with adapters:                   806,492 (22.6%)
Reads written (passing filters):     3,575,592 (100.0%)

Total basepairs processed:   539,914,392 bp
Quality-trimmed:               2,894,800 bp (0.5%)
Total written (filtered):    526,617,946 bp (97.5%)

=== Adapter 1 ===

Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 806492 times.

No. of allowed errors:
0-9 bp: 0; 10-12 bp: 1

Bases preceding removed adapters:
  A: 26.3%
  C: 20.1%
  G: 21.1%
  T: 32.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	513615	893898.0	0	513615
2	123311	223474.5	0	123311
3	38272	55868.6	0	38272
4	11752	13967.2	0	11752
5	2698	3491.8	0	2698
6	1276	872.9	0	1276
7	810	218.2	0	810
8	687	54.6	0	687
9	642	13.6	0	569 73
10	713	3.4	1	589 124
11	731	0.9	1	650 81
12	657	0.2	1	603 54
13	641	0.2	1	592 49
14	613	0.2	1	571 42
15	760	0.2	1	694 66
16	804	0.2	1	752 52
17	494	0.2	1	454 40
18	688	0.2	1	627 61
19	692	0.2	1	637 55
20	636	0.2	1	603 33
21	681	0.2	1	633 48
22	703	0.2	1	650 53
23	609	0.2	1	572 37
24	715	0.2	1	665 50
25	649	0.2	1	601 48
26	759	0.2	1	698 61
27	730	0.2	1	686 44
28	689	0.2	1	646 43
29	697	0.2	1	660 37
30	720	0.2	1	688 32
31	731	0.2	1	678 53
32	701	0.2	1	648 53
33	683	0.2	1	645 38
34	699	0.2	1	644 55
35	660	0.2	1	624 36
36	748	0.2	1	697 51
37	646	0.2	1	605 41
38	772	0.2	1	721 51
39	744	0.2	1	688 56
40	734	0.2	1	688 46
41	733	0.2	1	682 51
42	731	0.2	1	683 48
43	723	0.2	1	682 41
44	694	0.2	1	648 46
45	738	0.2	1	696 42
46	761	0.2	1	707 54
47	786	0.2	1	745 41
48	821	0.2	1	775 46
49	774	0.2	1	735 39
50	803	0.2	1	751 52
51	739	0.2	1	700 39
52	741	0.2	1	706 35
53	788	0.2	1	748 40
54	731	0.2	1	682 49
55	751	0.2	1	704 47
56	761	0.2	1	704 57
57	795	0.2	1	752 43
58	779	0.2	1	726 53
59	787	0.2	1	739 48
60	796	0.2	1	735 61
61	795	0.2	1	766 29
62	736	0.2	1	695 41
63	783	0.2	1	741 42
64	726	0.2	1	684 42
65	774	0.2	1	728 46
66	795	0.2	1	749 46
67	748	0.2	1	703 45
68	810	0.2	1	777 33
69	810	0.2	1	769 41
70	820	0.2	1	771 49
71	802	0.2	1	765 37
72	867	0.2	1	827 40
73	830	0.2	1	794 36
74	822	0.2	1	775 47
75	812	0.2	1	768 44
76	843	0.2	1	795 48
77	780	0.2	1	757 23
78	820	0.2	1	769 51
79	866	0.2	1	819 47
80	883	0.2	1	846 37
81	766	0.2	1	731 35
82	820	0.2	1	770 50
83	794	0.2	1	753 41
84	822	0.2	1	788 34
85	843	0.2	1	801 42
86	873	0.2	1	840 33
87	842	0.2	1	810 32
88	816	0.2	1	781 35
89	838	0.2	1	807 31
90	857	0.2	1	819 38
91	883	0.2	1	841 42
92	850	0.2	1	805 45
93	843	0.2	1	794 49
94	859	0.2	1	812 47
95	893	0.2	1	851 42
96	863	0.2	1	819 44
97	875	0.2	1	840 35
98	863	0.2	1	819 44
99	902	0.2	1	867 35
100	871	0.2	1	828 43
101	830	0.2	1	797 33
102	858	0.2	1	828 30
103	860	0.2	1	819 41
104	887	0.2	1	853 34
105	842	0.2	1	805 37
106	932	0.2	1	899 33
107	844	0.2	1	810 34
108	882	0.2	1	840 42
109	903	0.2	1	869 34
110	866	0.2	1	819 47
111	900	0.2	1	864 36
112	927	0.2	1	896 31
113	947	0.2	1	910 37
114	982	0.2	1	936 46
115	892	0.2	1	859 33
116	923	0.2	1	890 33
117	914	0.2	1	877 37
118	857	0.2	1	827 30
119	881	0.2	1	849 32
120	970	0.2	1	937 33
121	906	0.2	1	868 38
122	917	0.2	1	869 48
123	896	0.2	1	858 38
124	850	0.2	1	815 35
125	946	0.2	1	912 34
126	898	0.2	1	853 45
127	901	0.2	1	866 35
128	935	0.2	1	906 29
129	884	0.2	1	855 29
130	913	0.2	1	885 28
131	962	0.2	1	930 32
132	945	0.2	1	909 36
133	980	0.2	1	959 21
134	857	0.2	1	824 33
135	828	0.2	1	811 17
136	884	0.2	1	861 23
137	802	0.2	1	777 25
138	801	0.2	1	781 20
139	777	0.2	1	749 28
140	850	0.2	1	830 20
141	856	0.2	1	822 34
142	792	0.2	1	766 26
143	843	0.2	1	812 31
144	860	0.2	1	834 26
145	878	0.2	1	848 30
146	887	0.2	1	852 35
147	764	0.2	1	737 27
148	737	0.2	1	705 32
149	614	0.2	1	587 27
150	595	0.2	1	565 30
151	148	0.2	1	106 42


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/NR021_S8_L002_R2_001.fastq.gz
=============================================
3575592 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR021_S8_L002_R1_001_trimmed.fq.gz and NR021_S8_L002_R2_001_trimmed.fq.gz
file_1: NR021_S8_L002_R1_001_trimmed.fq.gz, file_2: NR021_S8_L002_R2_001_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR021_S8_L002_R1_001_trimmed.fq.gz and NR021_S8_L002_R2_001_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR021_S8_L002_R1_001_val_1.fq.gz
Writing validated paired-end read 2 reads to NR021_S8_L002_R2_001_val_2.fq.gz

Total number of sequences analysed: 3575592

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 43175 (1.21%)

Deleting both intermediate output files NR021_S8_L002_R1_001_trimmed.fq.gz and NR021_S8_L002_R2_001_trimmed.fq.gz

====================================================================================================


real	5246m24.934s
user	11047m42.956s
sys	242m23.672s

In [20]:

cat ~/.default-subject.mail | msmtp "$EMAIL"

In [21]:

%%bash
ls -lh /home/sam/data/geoduck_illumina/trimmed/

total 381G
-rw-rw-r-- 1 sam sam 6.2K Jan 25 14:07 AD002_S9_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 9.9G Jan 25 17:19 AD002_S9_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 6.4K Jan 25 17:19 AD002_S9_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  11G Jan 25 17:19 AD002_S9_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 6.2K Jan 25 19:11 AD002_S9_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  13G Jan 25 23:04 AD002_S9_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 6.4K Jan 25 23:04 AD002_S9_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  13G Jan 25 23:04 AD002_S9_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 3.0K Jan 25 23:04 NR005_S4_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 3.0M Jan 25 23:04 NR005_S4_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 3.0K Jan 25 23:04 NR005_S4_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 3.1M Jan 25 23:04 NR005_S4_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 3.0K Jan 25 23:04 NR005_S4_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 2.5M Jan 25 23:04 NR005_S4_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 2.9K Jan 25 23:04 NR005_S4_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 2.6M Jan 25 23:04 NR005_S4_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 4.4K Jan 25 23:06 NR006_S3_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 234M Jan 25 23:10 NR006_S3_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 4.6K Jan 25 23:10 NR006_S3_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 242M Jan 25 23:10 NR006_S3_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 4.4K Jan 25 23:12 NR006_S3_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 192M Jan 25 23:15 NR006_S3_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 4.6K Jan 25 23:15 NR006_S3_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 201M Jan 25 23:15 NR006_S3_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 4.7K Jan 25 23:15 NR012_S1_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  19M Jan 25 23:16 NR012_S1_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 4.9K Jan 25 23:16 NR012_S1_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  20M Jan 25 23:16 NR012_S1_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 4.7K Jan 25 23:16 NR012_S1_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  21M Jan 25 23:17 NR012_S1_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 4.9K Jan 25 23:17 NR012_S1_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  22M Jan 25 23:17 NR012_S1_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 6.2K Jan 26 02:10 NR013_AD013_S2_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  19G Jan 26 08:25 NR013_AD013_S2_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 6.4K Jan 26 08:25 NR013_AD013_S2_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  21G Jan 26 08:25 NR013_AD013_S2_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 6.3K Jan 26 11:46 NR013_AD013_S2_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  23G Jan 26 18:50 NR013_AD013_S2_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 6.4K Jan 26 18:50 NR013_AD013_S2_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  24G Jan 26 18:50 NR013_AD013_S2_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 6.6K Jan 27 01:21 NR014_AD014_S5_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  43G Jan 27 14:53 NR014_AD014_S5_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 6.8K Jan 27 14:53 NR014_AD014_S5_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  45G Jan 27 14:53 NR014_AD014_S5_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 6.5K Jan 27 22:11 NR014_AD014_S5_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  48G Jan 28 13:18 NR014_AD014_S5_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 6.8K Jan 28 13:18 NR014_AD014_S5_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  51G Jan 28 13:18 NR014_AD014_S5_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 6.2K Jan 28 15:32 NR015_AD015_S6_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  15G Jan 28 20:19 NR015_AD015_S6_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 6.4K Jan 28 20:19 NR015_AD015_S6_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  16G Jan 28 20:19 NR015_AD015_S6_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 6.3K Jan 28 22:43 NR015_AD015_S6_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  16G Jan 29 03:47 NR015_AD015_S6_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 6.4K Jan 29 03:48 NR015_AD015_S6_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam  18G Jan 29 03:47 NR015_AD015_S6_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 4.4K Jan 29 03:48 NR019_S7_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 3.6M Jan 29 03:48 NR019_S7_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 4.6K Jan 29 03:48 NR019_S7_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 3.6M Jan 29 03:48 NR019_S7_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 4.3K Jan 29 03:48 NR019_S7_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 1.9M Jan 29 03:48 NR019_S7_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 4.5K Jan 29 03:48 NR019_S7_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 1.9M Jan 29 03:48 NR019_S7_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 4.8K Jan 29 03:50 NR021_S8_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 280M Jan 29 03:55 NR021_S8_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 4.9K Jan 29 03:55 NR021_S8_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 295M Jan 29 03:55 NR021_S8_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam 4.8K Jan 29 03:57 NR021_S8_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 231M Jan 29 04:01 NR021_S8_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 4.9K Jan 29 04:02 NR021_S8_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 242M Jan 29 04:01 NR021_S8_L002_R2_001_val_2.fq.gz

In [22]:

%%bash
time /home/shared/MultiQC/multiqc/multiqc /home/sam/data/geoduck_illumina/trimmed/
cat ~/.default-subject.mail | msmtp "$EMAIL"

bash: line 1: /home/shared/MultiQC/multiqc/multiqc: No such file or directory

real	0m0.001s
user	0m0.000s
sys	0m0.000s

In [23]:

%%bash
time /home/shared/anaconda3/bin/multiqc /home/sam/data/geoduck_illumina/trimmed/
cat ~/.default-subject.mail | msmtp "$EMAIL"

Searching 72 files..

[INFO   ]         multiqc : This is MultiQC v1.5.dev0
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '/home/sam/data/geoduck_illumina/trimmed/'
/home/shared/anaconda3/lib/python3.6/site-packages/matplotlib/font_manager.py:279: UserWarning: Matplotlib is building the font cache using fc-list. This may take a moment.
  'Matplotlib is building the font cache using fc-list. '
[INFO   ]        cutadapt : Found 36 reports
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : multiqc_report.html
[INFO   ]         multiqc : Data        : multiqc_data
[INFO   ]         multiqc : MultiQC complete

real	0m44.957s
user	0m32.260s
sys	0m0.656s

In [24]:

%%bash
ls -ltr /home/sam/data/geoduck_illumina/trimmed/

total 398753364
-rw-rw-r-- 1 sam sam        6262 Jan 25 14:07 AD002_S9_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 10588237401 Jan 25 17:19 AD002_S9_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 11222294155 Jan 25 17:19 AD002_S9_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6479 Jan 25 17:19 AD002_S9_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6256 Jan 25 19:11 AD002_S9_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 13062478451 Jan 25 23:04 AD002_S9_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 13843776887 Jan 25 23:04 AD002_S9_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6480 Jan 25 23:04 AD002_S9_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        3027 Jan 25 23:04 NR005_S4_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam     3141496 Jan 25 23:04 NR005_S4_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam     3245747 Jan 25 23:04 NR005_S4_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        2992 Jan 25 23:04 NR005_S4_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        2970 Jan 25 23:04 NR005_S4_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam     2574088 Jan 25 23:04 NR005_S4_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam     2660195 Jan 25 23:04 NR005_S4_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        2925 Jan 25 23:04 NR005_S4_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4473 Jan 25 23:06 NR006_S3_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam   244698326 Jan 25 23:10 NR006_S3_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam   253711980 Jan 25 23:10 NR006_S3_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4663 Jan 25 23:10 NR006_S3_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4491 Jan 25 23:12 NR006_S3_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam   201301350 Jan 25 23:15 NR006_S3_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam   209991311 Jan 25 23:15 NR006_S3_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4673 Jan 25 23:15 NR006_S3_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4759 Jan 25 23:15 NR012_S1_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam    19050757 Jan 25 23:16 NR012_S1_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam    20357336 Jan 25 23:16 NR012_S1_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4961 Jan 25 23:16 NR012_S1_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4761 Jan 25 23:16 NR012_S1_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam    21014972 Jan 25 23:17 NR012_S1_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam    22380350 Jan 25 23:17 NR012_S1_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4965 Jan 25 23:17 NR012_S1_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6300 Jan 26 02:10 NR013_AD013_S2_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 20147543284 Jan 26 08:25 NR013_AD013_S2_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 21774947842 Jan 26 08:25 NR013_AD013_S2_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6504 Jan 26 08:25 NR013_AD013_S2_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6395 Jan 26 11:46 NR013_AD013_S2_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 23696944504 Jan 26 18:50 NR013_AD013_S2_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 25437014741 Jan 26 18:50 NR013_AD013_S2_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6509 Jan 26 18:50 NR013_AD013_S2_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6674 Jan 27 01:21 NR014_AD014_S5_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 45117073184 Jan 27 14:53 NR014_AD014_S5_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 48017176928 Jan 27 14:53 NR014_AD014_S5_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6894 Jan 27 14:53 NR014_AD014_S5_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6608 Jan 27 22:11 NR014_AD014_S5_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 51252846392 Jan 28 13:18 NR014_AD014_S5_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 54405899981 Jan 28 13:18 NR014_AD014_S5_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6866 Jan 28 13:18 NR014_AD014_S5_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6314 Jan 28 15:32 NR015_AD015_S6_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 15496411838 Jan 28 20:19 NR015_AD015_S6_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 16932572896 Jan 28 20:19 NR015_AD015_S6_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6503 Jan 28 20:19 NR015_AD015_S6_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6353 Jan 28 22:43 NR015_AD015_S6_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 16904415137 Jan 29 03:47 NR015_AD015_S6_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 18311321441 Jan 29 03:47 NR015_AD015_S6_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6505 Jan 29 03:48 NR015_AD015_S6_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4449 Jan 29 03:48 NR019_S7_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam     3676920 Jan 29 03:48 NR019_S7_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam     3697878 Jan 29 03:48 NR019_S7_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4656 Jan 29 03:48 NR019_S7_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4343 Jan 29 03:48 NR019_S7_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam     1930743 Jan 29 03:48 NR019_S7_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam     1921192 Jan 29 03:48 NR019_S7_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4566 Jan 29 03:48 NR019_S7_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4831 Jan 29 03:50 NR021_S8_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam   293401963 Jan 29 03:55 NR021_S8_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam   308744383 Jan 29 03:55 NR021_S8_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4992 Jan 29 03:55 NR021_S8_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4876 Jan 29 03:57 NR021_S8_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam   241735249 Jan 29 04:01 NR021_S8_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam   252776822 Jan 29 04:01 NR021_S8_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4990 Jan 29 04:02 NR021_S8_L002_R2_001.fastq.gz_trimming_report.txt

In [25]:

%%bash
ls -ltr /home/sam/gitrepos/LabDocs/jupyter_nbs/sam

total 49704
-rw-rw-r-- 1 sam sam    28693 Mar  7  2017 20160203_Olurida_Zymo_Data_Handling.ipynb
-rw-rw-r-- 1 sam sam    24004 Mar  7  2017 20160126_Pgenerosa_BGI_data_handling.ipynb
-rw-rw-r-- 1 sam sam    24090 Mar  7  2017 20160126_Olurida_BGI_data_handling.ipynb
-rw-rw-r-- 1 sam sam    13392 Mar  7  2017 20160114_wasted_space_synologies.ipynb
-rw-rw-r-- 1 sam sam    19015 Mar  7  2017 20150521_Cgigas_larvae_OA_Trimmomatic_FASTQC.ipynb
-rw-rw-r-- 1 sam sam     9497 Mar  7  2017 20150506_Cgigas_larvae_OA_trimmomatic_FASTQC.ipynb
-rw-rw-r-- 1 sam sam    23188 Mar  7  2017 20150501_Cgigas_larvae_OA_BLASTn_nt.ipynb
-rw-rw-r-- 1 sam sam    14730 Mar  7  2017 20150429_Gigas_larvae_OA_BLASTn.ipynb
-rw-rw-r-- 1 sam sam    74171 Mar  7  2017 20150414_C_virginica_LSU_Oil_Spill_Trimmomatic_FASTQC.ipynb
-rw-rw-r-- 1 sam sam    62599 Mar  7  2017 20150414_C_gigas_Larvae_OA_Trimmomatic_FASTQC.ipynb
-rw-rw-r-- 1 sam sam     5147 Mar  7  2017 20150408_Install_Bismark_bisulfite_mapper.ipynb
-rw-rw-r-- 1 sam sam     8239 Mar  7  2017 20150317_LSU_OilSpill_EpinextAdaptor1_ID.ipynb
-rw-rw-r-- 1 sam sam    14225 Mar  7  2017 20150316_LSU_OilSpill_Adapter_ID.ipynb
-rw-rw-r-- 1 sam sam    30320 Mar  7  2017 20150313_LSU_Oil_Spill_IndexID_Comparisons.ipynb
-rw-rw-r-- 1 sam sam 31709669 Mar  7  2017 20160308_find_rename_2bRAD_undetermined_fastqs.ipynb
-rw-rw-r-- 1 sam sam   167492 Mar  7  2017 20160406_STACKS_install.ipynb
-rw-rw-r-- 1 sam sam  1402108 Mar  7  2017 20160406_Oly_GBS_STACKS.ipynb
-rw-rw-r-- 1 sam sam    20652 Mar  7  2017 20160314_Olurida_GBS_data_management.ipynb
-rw-rw-r-- 1 sam sam     7461 Mar  7  2017 20160516_Oly_Small_Insert_Library_Genome_Read_Counts.ipynb
-rw-rw-r-- 1 sam sam    12166 Mar  7  2017 20160502_Oly_GBS_barcode_repair.ipynb
-rw-rw-r-- 1 sam sam    32920 Mar  7  2017 20160428_Oly_GBS_STACKS.ipynb
-rw-rw-r-- 1 sam sam     9705 Mar  7  2017 20160427_speed_comparison.ipynb
-rw-rw-r-- 1 sam sam     5380 Mar  7  2017 20160427_Oly_GBS_data_management.ipynb
-rw-rw-r-- 1 sam sam   138177 Mar  7  2017 20160418_pyrad_oly_PE-GBS.ipynb
-rw-rw-r-- 1 sam sam   116180 Mar  7  2017 20160418_Oly_GBS_PE-Pyrad_populations.ipynb
-rw-rw-r-- 1 sam sam    16182 Mar  7  2017 20160411_Concatenate_Oly_MBDseq.ipynb
-rw-rw-r-- 1 sam sam    17959 Mar  7  2017 20160525_pyrad_oly_gbs_bgi.ipynb
-rw-rw-r-- 1 sam sam  2949276 Mar  7  2017 20160523_Oly_GBS_Stacks.ipynb
-rw-rw-r-- 1 sam sam   334644 Mar  7  2017 20160715_ec2_oly_gbs_pyrad.ipynb
-rw-rw-r-- 1 sam sam    96903 Mar  7  2017 20160714_EC2_Oly_GBS_stacks_analysis.ipynb
-rw-rw-r-- 1 sam sam   431314 Mar  7  2017 20160609_pyrad_oly_gbs_bgi.ipynb
-rw-rw-r-- 1 sam sam    24394 Mar  7  2017 20170104_docker_oly_BGI_genome_corruption_solved.ipynb
-rw-rw-r-- 1 sam sam    37578 Mar  7  2017 20161230_docker_geoduck_RRBS_md5_checks.ipynb
-rw-rw-r-- 1 sam sam    22311 Mar  7  2017 20161229_docker_genewiz_geoduck_RRBS_data.ipynb
-rw-rw-r-- 1 sam sam    18693 Mar  7  2017 20161214_docker_notebook_trimming.ipynb
-rw-rw-r-- 1 sam sam    82776 Mar  7  2017 20161214_docker_BGI_data_integrity_check.ipynb
-rw-rw-r-- 1 sam sam     6509 Mar  7  2017 20161206_docker_BGI_genome_downloads.ipynb
-rw-rw-r-- 1 sam sam   395673 Mar  7  2017 20161129_docker_R_magics_failure.ipynb
-rw-rw-r-- 1 sam sam    24079 Mar  7  2017 20161117_docker_oly_vcf_analysis.ipynb
-rw-rw-r-- 1 sam sam    22623 Mar  7  2017 20161117_docker_oly_genome_fastq_corruption.ipynb
-rw-rw-r-- 1 sam sam     7544 Mar  7  2017 20161025_Pgenerosa_Small_Library_Genome_Read_Counts.ipynb
-rw-rw-r-- 1 sam sam   693032 Mar  7  2017 20160816_oly_gbs_fst_calcs.ipynb
-rwxrwxr-x 1 sam sam    17069 Mar  7  2017 PhageNGS.ipynb
-rwxrwxr-x 1 sam sam   114364 Mar  7  2017 PhageNGS_ID.ipynb
-rw-rw-r-- 1 sam sam    98935 Mar  7  2017 PE-GBS_empirical.ipynb
-rwxrwxr-x 1 sam sam    21432 Mar  7  2017 InstallingBLAST.ipynb
-rw-rw-r-- 1 sam sam   345694 Mar  7  2017 20170306_docker_fastqc_demultiplexed_bgi_oly_gbs.ipynb
-rw-rw-r-- 1 sam sam   118825 Mar  7  2017 20170227_docker_jay_ngs_data_retrieval.ipynb
-rw-rw-r-- 1 sam sam    30324 Jan 25 08:15 20170320_docker_Oly_BGI_GBS_demultiplexing_reproducibility.ipynb
-rw-rw-r-- 1 sam sam    94306 Jan 25 08:15 20170314_docker_Oly_BGI_GBS_demultiplexing_reproducibility.ipynb
-rw-rw-r-- 1 sam sam    50140 Jan 25 08:15 20170301_docker_fastqc_nondemultiplexed_bgi_oly_gbs.ipynb
-rw-rw-r-- 1 sam sam    45963 Jan 25 08:15 20170918_docker_pacbio_oly_miniasm0.2.ipynb
-rw-rw-r-- 1 sam sam    44545 Jan 25 08:15 20170907_docker_pacbio_oly_minimap2.ipynb
-rw-rw-r-- 1 sam sam    79744 Jan 25 08:15 20170622_oly_pacbio_data_management.ipynb
-rw-rw-r-- 1 sam sam  1332923 Jan 25 08:15 20170918_docker_pacbio_oly_racon0.5.0.ipynb
-rw-rw-r-- 1 sam sam  1345133 Jan 25 08:15 20171003_docker_oly_assembly_comparisons.ipynb
-rw-rw-r-- 1 sam sam  3211263 Jan 25 08:15 20171004_docker_oly_redundans.ipynb
-rw-rw-r-- 1 sam sam   297913 Jan 25 08:15 20171018_docker_oly_canu.ipynb
-rw-rw-r-- 1 sam sam  1596545 Jan 25 08:15 20171005_docker_oly_redundans.ipynb
-rw-rw-r-- 1 sam sam      240 Jan 25 08:15 README.md
-rw-rw-r-- 1 sam sam    31429 Jan 25 08:15 20180103_emu_pbjelly.ipynb
-rw-rw-r-- 1 sam sam    20436 Jan 25 08:15 20171130_emu_pbjelly.ipynb
-rw-rw-r-- 1 sam sam    26697 Jan 25 08:15 20171114_swoose_oly_assembly_comparisons_quast.ipynb
-rw-rw-r-- 1 sam sam    28575 Jan 25 08:15 20171114_emu_pbjelly_BGI_scaffold.ipynb
-rw-rw-r-- 1 sam sam    34367 Jan 25 08:15 20171113_emu_pbjelly_22mer_plat.ipynb
-rw-rw-r-- 1 sam sam    16623 Jan 25 08:15 20171023_restore_scaphapoda_data.ipynb
-rw-rw-r-- 1 sam sam    34879 Jan 25 08:15 20171023_docker_oly_redundans.ipynb
-rw-rw-r-- 1 sam sam   983417 Jan 25 08:15 20171023_docker_oly_pacbio_canu_comparisons.ipynb
-rw-rw-r-- 1 sam sam    14756 Jan 25 08:55 20180116_swoose_oly_assembly_comparisons_quast.ipynb
-rw-rw-r-- 1 sam sam     1069 Jan 25 08:58 template_linux.ipynb
-rw-rw-r-- 1 sam sam  1151178 Jan 29 07:25 multiqc_report.html
drwxrwxr-x 2 sam sam     4096 Jan 29 07:25 multiqc_data
-rw-rw-r-- 1 sam sam   390808 Jan 29 07:27 20180125_roadrunner_bwa_geoduck_novaseq.ipynb

In [26]:

%%bash
mv /home/sam/gitrepos/LabDocs/jupyter_nbs/sam/multiqc* /home/sam/data/geoduck_illumina/trimmed/

In [27]:

%%bash
ls -ltr /home/sam/data/geoduck_illumina/trimmed/multiqc*

-rw-rw-r-- 1 sam sam 1151178 Jan 29 07:25 /home/sam/data/geoduck_illumina/trimmed/multiqc_report.html

/home/sam/data/geoduck_illumina/trimmed/multiqc_data:
total 1472
-rw-rw-r-- 1 sam sam    3231 Jan 29 07:25 multiqc_cutadapt.txt
-rw-rw-r-- 1 sam sam    4966 Jan 29 07:25 multiqc_sources.txt
-rw-rw-r-- 1 sam sam    1552 Jan 29 07:25 multiqc_general_stats.txt
-rw-rw-r-- 1 sam sam 1469611 Jan 29 07:25 multiqc_data.json
-rw-rw-r-- 1 sam sam   16427 Jan 29 07:25 multiqc.log

In [28]:

%%bash
mv /home/sam/data/geoduck_illumina/trimmed/multiqc_report.html /home/sam/data/geoduck_illumina/trimmed/multiqc_data/
mv /home/sam/data/geoduck_illumina/trimmed/multiqc_data/ /home/sam/data/geoduck_illumina/trimmed/20180129_multiqc_trim01
ls -ltr /home/sam/data/geoduck_illumina/trimmed/

total 398753368
-rw-rw-r-- 1 sam sam        6262 Jan 25 14:07 AD002_S9_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 10588237401 Jan 25 17:19 AD002_S9_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 11222294155 Jan 25 17:19 AD002_S9_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6479 Jan 25 17:19 AD002_S9_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6256 Jan 25 19:11 AD002_S9_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 13062478451 Jan 25 23:04 AD002_S9_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 13843776887 Jan 25 23:04 AD002_S9_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6480 Jan 25 23:04 AD002_S9_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        3027 Jan 25 23:04 NR005_S4_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam     3141496 Jan 25 23:04 NR005_S4_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam     3245747 Jan 25 23:04 NR005_S4_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        2992 Jan 25 23:04 NR005_S4_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        2970 Jan 25 23:04 NR005_S4_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam     2574088 Jan 25 23:04 NR005_S4_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam     2660195 Jan 25 23:04 NR005_S4_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        2925 Jan 25 23:04 NR005_S4_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4473 Jan 25 23:06 NR006_S3_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam   244698326 Jan 25 23:10 NR006_S3_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam   253711980 Jan 25 23:10 NR006_S3_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4663 Jan 25 23:10 NR006_S3_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4491 Jan 25 23:12 NR006_S3_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam   201301350 Jan 25 23:15 NR006_S3_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam   209991311 Jan 25 23:15 NR006_S3_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4673 Jan 25 23:15 NR006_S3_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4759 Jan 25 23:15 NR012_S1_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam    19050757 Jan 25 23:16 NR012_S1_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam    20357336 Jan 25 23:16 NR012_S1_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4961 Jan 25 23:16 NR012_S1_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4761 Jan 25 23:16 NR012_S1_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam    21014972 Jan 25 23:17 NR012_S1_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam    22380350 Jan 25 23:17 NR012_S1_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4965 Jan 25 23:17 NR012_S1_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6300 Jan 26 02:10 NR013_AD013_S2_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 20147543284 Jan 26 08:25 NR013_AD013_S2_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 21774947842 Jan 26 08:25 NR013_AD013_S2_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6504 Jan 26 08:25 NR013_AD013_S2_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6395 Jan 26 11:46 NR013_AD013_S2_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 23696944504 Jan 26 18:50 NR013_AD013_S2_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 25437014741 Jan 26 18:50 NR013_AD013_S2_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6509 Jan 26 18:50 NR013_AD013_S2_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6674 Jan 27 01:21 NR014_AD014_S5_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 45117073184 Jan 27 14:53 NR014_AD014_S5_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 48017176928 Jan 27 14:53 NR014_AD014_S5_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6894 Jan 27 14:53 NR014_AD014_S5_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6608 Jan 27 22:11 NR014_AD014_S5_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 51252846392 Jan 28 13:18 NR014_AD014_S5_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 54405899981 Jan 28 13:18 NR014_AD014_S5_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6866 Jan 28 13:18 NR014_AD014_S5_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6314 Jan 28 15:32 NR015_AD015_S6_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 15496411838 Jan 28 20:19 NR015_AD015_S6_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 16932572896 Jan 28 20:19 NR015_AD015_S6_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6503 Jan 28 20:19 NR015_AD015_S6_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        6353 Jan 28 22:43 NR015_AD015_S6_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam 16904415137 Jan 29 03:47 NR015_AD015_S6_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam 18311321441 Jan 29 03:47 NR015_AD015_S6_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        6505 Jan 29 03:48 NR015_AD015_S6_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4449 Jan 29 03:48 NR019_S7_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam     3676920 Jan 29 03:48 NR019_S7_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam     3697878 Jan 29 03:48 NR019_S7_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4656 Jan 29 03:48 NR019_S7_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4343 Jan 29 03:48 NR019_S7_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam     1930743 Jan 29 03:48 NR019_S7_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam     1921192 Jan 29 03:48 NR019_S7_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4566 Jan 29 03:48 NR019_S7_L002_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4831 Jan 29 03:50 NR021_S8_L001_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam   293401963 Jan 29 03:55 NR021_S8_L001_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam   308744383 Jan 29 03:55 NR021_S8_L001_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4992 Jan 29 03:55 NR021_S8_L001_R2_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam        4876 Jan 29 03:57 NR021_S8_L002_R1_001.fastq.gz_trimming_report.txt
-rw-rw-r-- 1 sam sam   241735249 Jan 29 04:01 NR021_S8_L002_R1_001_val_1.fq.gz
-rw-rw-r-- 1 sam sam   252776822 Jan 29 04:01 NR021_S8_L002_R2_001_val_2.fq.gz
-rw-rw-r-- 1 sam sam        4990 Jan 29 04:02 NR021_S8_L002_R2_001.fastq.gz_trimming_report.txt
drwxrwxr-x 2 sam sam        4096 Jan 29 07:39 20180129_multiqc_trim01

In [29]:

%%bash
time /home/shared/anaconda3/bin/multiqc --ignore '.txt' /home/sam/data/geoduck_illumina/trimmed/
cat ~/.default-subject.mail | msmtp "$EMAIL"

Searching 78 files..

[INFO   ]         multiqc : This is MultiQC v1.5.dev0
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '/home/sam/data/geoduck_illumina/trimmed/'
[INFO   ]        cutadapt : Found 36 reports
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : multiqc_report.html
[INFO   ]         multiqc : Data        : multiqc_data
[INFO   ]         multiqc : MultiQC complete

real	0m4.994s
user	0m4.332s
sys	0m0.204s

In [30]:

%%bash
cd /home/sam/data/geoduck_illumina/trimmed/
pwd
rm multiqc_report.html
rm -rf multiqc_data/
time /home/shared/anaconda3/bin/multiqc --ignore '*.txt' /home/sam/data/geoduck_illumina/trimmed/
cat ~/.default-subject.mail | msmtp "$EMAIL"

/home/sam/data/geoduck_illumina/trimmed
Searching 78 files..

rm: cannot remove 'multiqc_report.html': No such file or directory
[INFO   ]         multiqc : This is MultiQC v1.5.dev0
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '/home/sam/data/geoduck_illumina/trimmed/'
[WARNING]         multiqc : No analysis results found. Cleaning up..
[INFO   ]         multiqc : MultiQC complete

real	0m4.253s
user	0m3.184s
sys	0m0.136s

In [31]:

%%bash
time fastqc *.fq.gz
cat ~/.default-subject.mail | msmtp "$EMAIL"

Skipping '*.fq.gz' which didn't exist, or couldn't be read

real	0m1.469s
user	0m0.364s
sys	0m0.084s

In [32]:

%%bash
time find -name '*.fq.gz' | xargs fastqc
cat ~/.default-subject.mail | msmtp "$EMAIL"

Exception in thread "main" java.awt.HeadlessException: 
No X11 DISPLAY variable was set, but this program performed an operation which requires it.
	at java.awt.GraphicsEnvironment.checkHeadless(GraphicsEnvironment.java:204)
	at java.awt.Window.<init>(Window.java:536)
	at java.awt.Frame.<init>(Frame.java:420)
	at java.awt.Frame.<init>(Frame.java:385)
	at javax.swing.JFrame.<init>(JFrame.java:189)
	at uk.ac.babraham.FastQC.FastQCApplication.<init>(FastQCApplication.java:63)
	at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:332)

real	0m0.368s
user	0m0.392s
sys	0m0.060s

In [33]:

%%bash
for file in /home/sam/data/geoduck_illumina/trimmed/*.gz
do
filename=${file##*/}
printf "%s\n" "$filename \\"
done

AD002_S9_L001_R1_001_val_1.fq.gz \
AD002_S9_L001_R2_001_val_2.fq.gz \
AD002_S9_L002_R1_001_val_1.fq.gz \
AD002_S9_L002_R2_001_val_2.fq.gz \
NR005_S4_L001_R1_001_val_1.fq.gz \
NR005_S4_L001_R2_001_val_2.fq.gz \
NR005_S4_L002_R1_001_val_1.fq.gz \
NR005_S4_L002_R2_001_val_2.fq.gz \
NR006_S3_L001_R1_001_val_1.fq.gz \
NR006_S3_L001_R2_001_val_2.fq.gz \
NR006_S3_L002_R1_001_val_1.fq.gz \
NR006_S3_L002_R2_001_val_2.fq.gz \
NR012_S1_L001_R1_001_val_1.fq.gz \
NR012_S1_L001_R2_001_val_2.fq.gz \
NR012_S1_L002_R1_001_val_1.fq.gz \
NR012_S1_L002_R2_001_val_2.fq.gz \
NR013_AD013_S2_L001_R1_001_val_1.fq.gz \
NR013_AD013_S2_L001_R2_001_val_2.fq.gz \
NR013_AD013_S2_L002_R1_001_val_1.fq.gz \
NR013_AD013_S2_L002_R2_001_val_2.fq.gz \
NR014_AD014_S5_L001_R1_001_val_1.fq.gz \
NR014_AD014_S5_L001_R2_001_val_2.fq.gz \
NR014_AD014_S5_L002_R1_001_val_1.fq.gz \
NR014_AD014_S5_L002_R2_001_val_2.fq.gz \
NR015_AD015_S6_L001_R1_001_val_1.fq.gz \
NR015_AD015_S6_L001_R2_001_val_2.fq.gz \
NR015_AD015_S6_L002_R1_001_val_1.fq.gz \
NR015_AD015_S6_L002_R2_001_val_2.fq.gz \
NR019_S7_L001_R1_001_val_1.fq.gz \
NR019_S7_L001_R2_001_val_2.fq.gz \
NR019_S7_L002_R1_001_val_1.fq.gz \
NR019_S7_L002_R2_001_val_2.fq.gz \
NR021_S8_L001_R1_001_val_1.fq.gz \
NR021_S8_L001_R2_001_val_2.fq.gz \
NR021_S8_L002_R1_001_val_1.fq.gz \
NR021_S8_L002_R2_001_val_2.fq.gz \

In [34]:

%%bash
time fastqc \
AD002_S9_L001_R1_001_val_1.fq.gz \
AD002_S9_L001_R2_001_val_2.fq.gz \
AD002_S9_L002_R1_001_val_1.fq.gz \
AD002_S9_L002_R2_001_val_2.fq.gz \
NR005_S4_L001_R1_001_val_1.fq.gz \
NR005_S4_L001_R2_001_val_2.fq.gz \
NR005_S4_L002_R1_001_val_1.fq.gz \
NR005_S4_L002_R2_001_val_2.fq.gz \
NR006_S3_L001_R1_001_val_1.fq.gz \
NR006_S3_L001_R2_001_val_2.fq.gz \
NR006_S3_L002_R1_001_val_1.fq.gz \
NR006_S3_L002_R2_001_val_2.fq.gz \
NR012_S1_L001_R1_001_val_1.fq.gz \
NR012_S1_L001_R2_001_val_2.fq.gz \
NR012_S1_L002_R1_001_val_1.fq.gz \
NR012_S1_L002_R2_001_val_2.fq.gz \
NR013_AD013_S2_L001_R1_001_val_1.fq.gz \
NR013_AD013_S2_L001_R2_001_val_2.fq.gz \
NR013_AD013_S2_L002_R1_001_val_1.fq.gz \
NR013_AD013_S2_L002_R2_001_val_2.fq.gz \
NR014_AD014_S5_L001_R1_001_val_1.fq.gz \
NR014_AD014_S5_L001_R2_001_val_2.fq.gz \
NR014_AD014_S5_L002_R1_001_val_1.fq.gz \
NR014_AD014_S5_L002_R2_001_val_2.fq.gz \
NR015_AD015_S6_L001_R1_001_val_1.fq.gz \
NR015_AD015_S6_L001_R2_001_val_2.fq.gz \
NR015_AD015_S6_L002_R1_001_val_1.fq.gz \
NR015_AD015_S6_L002_R2_001_val_2.fq.gz \
NR019_S7_L001_R1_001_val_1.fq.gz \
NR019_S7_L001_R2_001_val_2.fq.gz \
NR019_S7_L002_R1_001_val_1.fq.gz \
NR019_S7_L002_R2_001_val_2.fq.gz \
NR021_S8_L001_R1_001_val_1.fq.gz \
NR021_S8_L001_R2_001_val_2.fq.gz \
NR021_S8_L002_R1_001_val_1.fq.gz \
NR021_S8_L002_R2_001_val_2.fq.gz
cat ~/.default-subject.mail | msmtp "$EMAIL"

Skipping 'AD002_S9_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'AD002_S9_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'AD002_S9_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'AD002_S9_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR005_S4_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR005_S4_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR005_S4_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR005_S4_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR006_S3_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR006_S3_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR006_S3_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR006_S3_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR012_S1_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR012_S1_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR012_S1_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR012_S1_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR013_AD013_S2_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR013_AD013_S2_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR013_AD013_S2_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR013_AD013_S2_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR014_AD014_S5_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR014_AD014_S5_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR014_AD014_S5_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR014_AD014_S5_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR015_AD015_S6_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR015_AD015_S6_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR015_AD015_S6_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR015_AD015_S6_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR019_S7_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR019_S7_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR019_S7_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR019_S7_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR021_S8_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR021_S8_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR021_S8_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR021_S8_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read

real	0m0.237s
user	0m0.364s
sys	0m0.036s

In [35]:

%%bash
time \
for fq in *.gz
do
gunzip -c "$fq" | fastqc stdin
done
cat ~/.default-subject.mail | msmtp "$EMAIL"

Analysis complete for stdin

gzip: *.gz: No such file or directory
java.io.FileNotFoundException: /etc/fastqc/Configuration/adapter_list.txt (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at uk.ac.babraham.FastQC.Modules.AdapterContent.<init>(AdapterContent.java:75)
	at uk.ac.babraham.FastQC.Modules.ModuleFactory.getStandardModuleList(ModuleFactory.java:37)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:134)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:102)
	at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
Started analysis of stdin
java.io.FileNotFoundException: /etc/fastqc/Configuration/limits.txt (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at uk.ac.babraham.FastQC.Modules.ModuleConfig.readParams(ModuleConfig.java:87)
	at uk.ac.babraham.FastQC.Modules.ModuleConfig.<clinit>(ModuleConfig.java:35)
	at uk.ac.babraham.FastQC.Modules.PerBaseQualityScores.ignoreInReport(PerBaseQualityScores.java:62)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:331)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:155)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
	at java.lang.Thread.run(Thread.java:748)
Failed to process file stdin
java.lang.IllegalArgumentException: No key called gc_sequence:ignore in the config data
	at uk.ac.babraham.FastQC.Modules.ModuleConfig.getParam(ModuleConfig.java:148)
	at uk.ac.babraham.FastQC.Modules.PerSequenceGCContent.ignoreInReport(PerSequenceGCContent.java:57)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.startDocument(HTMLReportArchive.java:331)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:84)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:155)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
	at java.lang.Thread.run(Thread.java:748)

real	0m1.430s
user	0m0.620s
sys	0m0.064s

In [36]:

%%bash
find . -name "*.fq.gz"  -exec gunzip -c  '{}' ';' | fastqc  /dev/stdin
cat ~/.default-subject.mail | msmtp "$EMAIL"

Analysis complete for stdin

java.io.FileNotFoundException: /etc/fastqc/Configuration/adapter_list.txt (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at uk.ac.babraham.FastQC.Modules.AdapterContent.<init>(AdapterContent.java:75)
	at uk.ac.babraham.FastQC.Modules.ModuleFactory.getStandardModuleList(ModuleFactory.java:37)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.processFile(OfflineRunner.java:134)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.<init>(OfflineRunner.java:102)
	at uk.ac.babraham.FastQC.FastQCApplication.main(FastQCApplication.java:316)
Started analysis of stdin
Failed to process file stdin
java.io.FileNotFoundException: /dev/stdin_fastqc.zip (Permission denied)
	at java.io.FileOutputStream.open0(Native Method)
	at java.io.FileOutputStream.open(FileOutputStream.java:270)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:213)
	at java.io.FileOutputStream.<init>(FileOutputStream.java:162)
	at uk.ac.babraham.FastQC.Report.HTMLReportArchive.<init>(HTMLReportArchive.java:80)
	at uk.ac.babraham.FastQC.Analysis.OfflineRunner.analysisComplete(OfflineRunner.java:155)
	at uk.ac.babraham.FastQC.Analysis.AnalysisRunner.run(AnalysisRunner.java:110)
	at java.lang.Thread.run(Thread.java:748)

Performed fresh install of FastQC - needed sudo so ran outside of notebook.¶

In [37]:

%%bash
time fastqc \
AD002_S9_L001_R1_001_val_1.fq.gz \
AD002_S9_L001_R2_001_val_2.fq.gz \
AD002_S9_L002_R1_001_val_1.fq.gz \
AD002_S9_L002_R2_001_val_2.fq.gz \
NR005_S4_L001_R1_001_val_1.fq.gz \
NR005_S4_L001_R2_001_val_2.fq.gz \
NR005_S4_L002_R1_001_val_1.fq.gz \
NR005_S4_L002_R2_001_val_2.fq.gz \
NR006_S3_L001_R1_001_val_1.fq.gz \
NR006_S3_L001_R2_001_val_2.fq.gz \
NR006_S3_L002_R1_001_val_1.fq.gz \
NR006_S3_L002_R2_001_val_2.fq.gz \
NR012_S1_L001_R1_001_val_1.fq.gz \
NR012_S1_L001_R2_001_val_2.fq.gz \
NR012_S1_L002_R1_001_val_1.fq.gz \
NR012_S1_L002_R2_001_val_2.fq.gz \
NR013_AD013_S2_L001_R1_001_val_1.fq.gz \
NR013_AD013_S2_L001_R2_001_val_2.fq.gz \
NR013_AD013_S2_L002_R1_001_val_1.fq.gz \
NR013_AD013_S2_L002_R2_001_val_2.fq.gz \
NR014_AD014_S5_L001_R1_001_val_1.fq.gz \
NR014_AD014_S5_L001_R2_001_val_2.fq.gz \
NR014_AD014_S5_L002_R1_001_val_1.fq.gz \
NR014_AD014_S5_L002_R2_001_val_2.fq.gz \
NR015_AD015_S6_L001_R1_001_val_1.fq.gz \
NR015_AD015_S6_L001_R2_001_val_2.fq.gz \
NR015_AD015_S6_L002_R1_001_val_1.fq.gz \
NR015_AD015_S6_L002_R2_001_val_2.fq.gz \
NR019_S7_L001_R1_001_val_1.fq.gz \
NR019_S7_L001_R2_001_val_2.fq.gz \
NR019_S7_L002_R1_001_val_1.fq.gz \
NR019_S7_L002_R2_001_val_2.fq.gz \
NR021_S8_L001_R1_001_val_1.fq.gz \
NR021_S8_L001_R2_001_val_2.fq.gz \
NR021_S8_L002_R1_001_val_1.fq.gz \
NR021_S8_L002_R2_001_val_2.fq.gz
cat ~/.default-subject.mail | msmtp "$EMAIL"

Skipping 'AD002_S9_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'AD002_S9_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'AD002_S9_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'AD002_S9_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR005_S4_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR005_S4_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR005_S4_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR005_S4_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR006_S3_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR006_S3_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR006_S3_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR006_S3_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR012_S1_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR012_S1_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR012_S1_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR012_S1_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR013_AD013_S2_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR013_AD013_S2_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR013_AD013_S2_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR013_AD013_S2_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR014_AD014_S5_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR014_AD014_S5_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR014_AD014_S5_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR014_AD014_S5_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR015_AD015_S6_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR015_AD015_S6_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR015_AD015_S6_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR015_AD015_S6_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR019_S7_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR019_S7_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR019_S7_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR019_S7_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR021_S8_L001_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR021_S8_L001_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR021_S8_L002_R1_001_val_1.fq.gz' which didn't exist, or couldn't be read
Skipping 'NR021_S8_L002_R2_001_val_2.fq.gz' which didn't exist, or couldn't be read

real	0m0.275s
user	0m0.328s
sys	0m0.052s

In [38]:

%%bash
which fastqc

/usr/local/bin/fastqc

In [39]:

%%bash
time \
for fq in *.gz
do
fastqc "$fq"
done
cat ~/.default-subject.mail | msmtp "$EMAIL"

Skipping '*.gz' which didn't exist, or couldn't be read

real	0m0.234s
user	0m0.320s
sys	0m0.080s

In [40]:

%%bash
pwd

/home/sam/gitrepos/LabDocs/jupyter_nbs/sam

In [41]:

%%bash
for file in /home/sam/data/geoduck_illumina/trimmed/*.gz
do
printf "%s\n" "$file \\"
done

/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R2_001_val_2.fq.gz \

In [42]:

%%bash
time fastqc --threads 12 \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R2_001_val_2.fq.gz
cat ~/.default-subject.mail | msmtp "$EMAIL"

Analysis complete for NR005_S4_L001_R1_001_val_1.fq.gz
Analysis complete for NR005_S4_L001_R2_001_val_2.fq.gz
Analysis complete for NR005_S4_L002_R1_001_val_1.fq.gz
Analysis complete for NR005_S4_L002_R2_001_val_2.fq.gz
Analysis complete for NR012_S1_L001_R1_001_val_1.fq.gz
Analysis complete for NR012_S1_L001_R2_001_val_2.fq.gz
Analysis complete for NR012_S1_L002_R1_001_val_1.fq.gz
Analysis complete for NR012_S1_L002_R2_001_val_2.fq.gz
Analysis complete for NR006_S3_L002_R1_001_val_1.fq.gz
Analysis complete for NR006_S3_L002_R2_001_val_2.fq.gz
Analysis complete for NR006_S3_L001_R1_001_val_1.fq.gz
Analysis complete for NR006_S3_L001_R2_001_val_2.fq.gz
Analysis complete for AD002_S9_L001_R1_001_val_1.fq.gz
Analysis complete for AD002_S9_L001_R2_001_val_2.fq.gz
Analysis complete for AD002_S9_L002_R1_001_val_1.fq.gz
Analysis complete for AD002_S9_L002_R2_001_val_2.fq.gz
Analysis complete for NR013_AD013_S2_L002_R1_001_val_1.fq.gz
Analysis complete for NR019_S7_L001_R1_001_val_1.fq.gz
Analysis complete for NR019_S7_L001_R2_001_val_2.fq.gz
Analysis complete for NR019_S7_L002_R1_001_val_1.fq.gz
Analysis complete for NR019_S7_L002_R2_001_val_2.fq.gz
Analysis complete for NR021_S8_L001_R1_001_val_1.fq.gz
Analysis complete for NR015_AD015_S6_L001_R1_001_val_1.fq.gz
Analysis complete for NR021_S8_L001_R2_001_val_2.fq.gz
Analysis complete for NR021_S8_L002_R1_001_val_1.fq.gz
Analysis complete for NR021_S8_L002_R2_001_val_2.fq.gz
Analysis complete for NR013_AD013_S2_L002_R2_001_val_2.fq.gz
Analysis complete for NR015_AD015_S6_L001_R2_001_val_2.fq.gz
Analysis complete for NR015_AD015_S6_L002_R1_001_val_1.fq.gz
Analysis complete for NR013_AD013_S2_L001_R1_001_val_1.fq.gz
Analysis complete for NR013_AD013_S2_L001_R2_001_val_2.fq.gz
Analysis complete for NR015_AD015_S6_L002_R2_001_val_2.fq.gz
Analysis complete for NR014_AD014_S5_L001_R1_001_val_1.fq.gz
Analysis complete for NR014_AD014_S5_L001_R2_001_val_2.fq.gz
Analysis complete for NR014_AD014_S5_L002_R1_001_val_1.fq.gz
Analysis complete for NR014_AD014_S5_L002_R2_001_val_2.fq.gz

Started analysis of AD002_S9_L001_R1_001_val_1.fq.gz
Started analysis of AD002_S9_L001_R2_001_val_2.fq.gz
Started analysis of AD002_S9_L002_R1_001_val_1.fq.gz
Started analysis of AD002_S9_L002_R2_001_val_2.fq.gz
Started analysis of NR005_S4_L001_R1_001_val_1.fq.gz
Approx 5% complete for NR005_S4_L001_R1_001_val_1.fq.gz
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Approx 75% complete for NR005_S4_L001_R1_001_val_1.fq.gz
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Started analysis of NR005_S4_L002_R2_001_val_2.fq.gz
Approx 70% complete for NR005_S4_L001_R2_001_val_2.fq.gz
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Approx 95% complete for NR005_S4_L001_R2_001_val_2.fq.gz
Approx 25% complete for NR005_S4_L002_R2_001_val_2.fq.gz
Started analysis of NR006_S3_L001_R1_001_val_1.fq.gz
Approx 30% complete for NR005_S4_L002_R2_001_val_2.fq.gz
Approx 60% complete for NR005_S4_L002_R1_001_val_1.fq.gz
Approx 65% complete for NR005_S4_L002_R1_001_val_1.fq.gz
Approx 35% complete for NR005_S4_L002_R2_001_val_2.fq.gz
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Started analysis of NR006_S3_L001_R2_001_val_2.fq.gz
Approx 90% complete for NR005_S4_L002_R1_001_val_1.fq.gz
Approx 60% complete for NR005_S4_L002_R2_001_val_2.fq.gz
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Approx 80% complete for NR005_S4_L002_R2_001_val_2.fq.gz
Approx 85% complete for NR005_S4_L002_R2_001_val_2.fq.gz
Approx 90% complete for NR005_S4_L002_R2_001_val_2.fq.gz
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Started analysis of NR006_S3_L002_R2_001_val_2.fq.gz
Approx 5% complete for NR006_S3_L001_R1_001_val_1.fq.gz
Approx 5% complete for NR006_S3_L002_R1_001_val_1.fq.gz
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Started analysis of NR012_S1_L001_R1_001_val_1.fq.gz
Approx 5% complete for NR012_S1_L001_R1_001_val_1.fq.gz
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Approx 15% complete for NR006_S3_L002_R1_001_val_1.fq.gz
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Started analysis of NR013_AD013_S2_L001_R1_001_val_1.fq.gz
Started analysis of NR013_AD013_S2_L001_R2_001_val_2.fq.gz
Approx 25% complete for NR006_S3_L001_R1_001_val_1.fq.gz
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Started analysis of NR015_AD015_S6_L001_R1_001_val_1.fq.gz
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Started analysis of NR015_AD015_S6_L002_R1_001_val_1.fq.gz
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Approx 90% complete for NR014_AD014_S5_L001_R1_001_val_1.fq.gz
Approx 75% complete for NR014_AD014_S5_L002_R2_001_val_2.fq.gz
Approx 80% complete for NR014_AD014_S5_L002_R1_001_val_1.fq.gz
Approx 90% complete for NR014_AD014_S5_L001_R2_001_val_2.fq.gz
Approx 95% complete for NR014_AD014_S5_L001_R1_001_val_1.fq.gz
Approx 80% complete for NR014_AD014_S5_L002_R2_001_val_2.fq.gz
Approx 85% complete for NR014_AD014_S5_L002_R1_001_val_1.fq.gz
Approx 95% complete for NR014_AD014_S5_L001_R2_001_val_2.fq.gz
Approx 85% complete for NR014_AD014_S5_L002_R2_001_val_2.fq.gz
Approx 90% complete for NR014_AD014_S5_L002_R1_001_val_1.fq.gz
Approx 90% complete for NR014_AD014_S5_L002_R2_001_val_2.fq.gz
Approx 95% complete for NR014_AD014_S5_L002_R1_001_val_1.fq.gz
Approx 95% complete for NR014_AD014_S5_L002_R2_001_val_2.fq.gz

real	282m31.564s
user	1338m9.276s
sys	25m38.300s

In [43]:

%%bash
mkdir /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_fastqc_01
for fastqc in /home/sam/data/geoduck_illumina/trimmed/*fastqc*
do
mv "$fastqc" /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_fastqc_01
done
ls -ltr /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_fastqc_01

total 28324
-rw-rw-r-- 1 sam sam 456483 Jan 29 08:25 NR005_S4_L002_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 480861 Jan 29 08:25 NR005_S4_L001_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 479225 Jan 29 08:25 NR005_S4_L001_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 446955 Jan 29 08:25 NR005_S4_L002_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 267316 Jan 29 08:25 NR005_S4_L002_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 268028 Jan 29 08:25 NR005_S4_L002_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 268463 Jan 29 08:25 NR005_S4_L001_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 271980 Jan 29 08:25 NR005_S4_L001_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 569702 Jan 29 08:25 NR012_S1_L001_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 250779 Jan 29 08:25 NR012_S1_L001_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 573531 Jan 29 08:25 NR012_S1_L001_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 248627 Jan 29 08:25 NR012_S1_L001_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 578221 Jan 29 08:25 NR012_S1_L002_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 249959 Jan 29 08:25 NR012_S1_L002_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 574996 Jan 29 08:25 NR012_S1_L002_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 245972 Jan 29 08:25 NR012_S1_L002_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 612551 Jan 29 08:26 NR006_S3_L002_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 259588 Jan 29 08:26 NR006_S3_L002_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 609942 Jan 29 08:26 NR006_S3_L002_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 254479 Jan 29 08:26 NR006_S3_L002_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 610803 Jan 29 08:26 NR006_S3_L001_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 259540 Jan 29 08:26 NR006_S3_L001_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 603447 Jan 29 08:26 NR006_S3_L001_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 254689 Jan 29 08:26 NR006_S3_L001_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 562157 Jan 29 09:42 AD002_S9_L001_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 232835 Jan 29 09:42 AD002_S9_L001_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 560796 Jan 29 09:47 AD002_S9_L001_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 234363 Jan 29 09:47 AD002_S9_L001_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 564514 Jan 29 10:06 AD002_S9_L002_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 229772 Jan 29 10:06 AD002_S9_L002_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 566594 Jan 29 10:18 AD002_S9_L002_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 231792 Jan 29 10:18 AD002_S9_L002_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 570162 Jan 29 11:24 NR013_AD013_S2_L002_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 233346 Jan 29 11:24 NR013_AD013_S2_L002_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 489645 Jan 29 11:24 NR019_S7_L001_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 259758 Jan 29 11:24 NR019_S7_L001_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 488701 Jan 29 11:24 NR019_S7_L001_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 258169 Jan 29 11:24 NR019_S7_L001_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 460967 Jan 29 11:24 NR019_S7_L002_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 263389 Jan 29 11:24 NR019_S7_L002_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 462735 Jan 29 11:24 NR019_S7_L002_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 264526 Jan 29 11:24 NR019_S7_L002_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 603205 Jan 29 11:26 NR021_S8_L001_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 254836 Jan 29 11:26 NR021_S8_L001_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 560445 Jan 29 11:28 NR015_AD015_S6_L001_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 231789 Jan 29 11:28 NR015_AD015_S6_L001_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 602815 Jan 29 11:28 NR021_S8_L001_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 256338 Jan 29 11:28 NR021_S8_L001_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 604313 Jan 29 11:30 NR021_S8_L002_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 253109 Jan 29 11:30 NR021_S8_L002_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 597673 Jan 29 11:30 NR021_S8_L002_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 249060 Jan 29 11:30 NR021_S8_L002_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 570723 Jan 29 11:34 NR013_AD013_S2_L002_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 233618 Jan 29 11:34 NR013_AD013_S2_L002_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 564535 Jan 29 11:36 NR015_AD015_S6_L001_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 234613 Jan 29 11:36 NR015_AD015_S6_L001_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 563160 Jan 29 11:49 NR015_AD015_S6_L002_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 227702 Jan 29 11:49 NR015_AD015_S6_L002_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 563756 Jan 29 11:50 NR013_AD013_S2_L001_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 233509 Jan 29 11:50 NR013_AD013_S2_L001_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 567421 Jan 29 11:53 NR013_AD013_S2_L001_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 236469 Jan 29 11:53 NR013_AD013_S2_L001_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 568125 Jan 29 11:58 NR015_AD015_S6_L002_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 232282 Jan 29 11:58 NR015_AD015_S6_L002_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 562916 Jan 29 12:38 NR014_AD014_S5_L001_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 232937 Jan 29 12:38 NR014_AD014_S5_L001_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 565340 Jan 29 12:45 NR014_AD014_S5_L001_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 234534 Jan 29 12:45 NR014_AD014_S5_L001_R2_001_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 569756 Jan 29 13:00 NR014_AD014_S5_L002_R1_001_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 230261 Jan 29 13:00 NR014_AD014_S5_L002_R1_001_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 569447 Jan 29 13:07 NR014_AD014_S5_L002_R2_001_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 233175 Jan 29 13:07 NR014_AD014_S5_L002_R2_001_val_2_fastqc.html

mv: cannot move '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_fastqc_01' to a subdirectory of itself, '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_fastqc_01/20180129_trimmed_fastqc_01'

In [44]:

%%bash
cd /home/sam/data/geoduck_illumina/trimmed/
/home/shared/anaconda3/bin/multiqc /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_fastqc_01/

Searching 72 files..

[INFO   ]         multiqc : This is MultiQC v1.5.dev0
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_fastqc_01/'
[INFO   ]          fastqc : Found 36 reports
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : multiqc_report.html
[INFO   ]         multiqc : Data        : multiqc_data
[INFO   ]         multiqc : MultiQC complete

In [45]:

%%bash
mkdir /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_multiqc_fastqc_01
mv /home/sam/data/geoduck_illumina/trimmed/multiqc* /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_multiqc_fastqc_01
ls -ltr /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_multiqc_fastqc_01

total 1460
-rw-rw-r-- 1 sam sam 1490524 Jan 29 13:42 multiqc_report.html
drwxrwxr-x 2 sam sam    4096 Jan 29 13:42 multiqc_data

In [46]:

%%bash
mkdir /home/sam/data/geoduck_illumina/trimmed/trimmed_again
time /home/shared/trimgalore/trim_galore \
--paired \
--output_dir /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R2_001_val_2.fq.gz
cat ~/.default-subject.mail | msmtp "$EMAIL"

1.9.1

No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001_val_1.fq.gz <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
Illumina	6622	AGATCGGAAGAGC	1000000	0.66
smallRNA	4	TGGAATTCTCGG	1000000	0.00
Nextera	0	CTGTCTCTTATA	1000000	0.00
Using Illumina adapter for trimming (count: 6622). Second best hit was smallRNA (count: 4)

Failed to write to file 'AD002_S9_L001_R1_001_val_1.fq.gz_trimming_report.txt': No such file or directory

real	0m4.498s
user	0m4.668s
sys	0m0.216s

In [47]:

%%bash
mkdir /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again
time /home/shared/trimgalore/trim_galore \
--paired \
--output_dir /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R1_001_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R2_001_val_2.fq.gz
cat ~/.default-subject.mail | msmtp "$EMAIL"

1.9.1

No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default)

Path to Cutadapt set as: 'cutadapt' (default)
Cutadapt seems to be working fine (tested command 'cutadapt --version')


AUTO-DETECTING ADAPTER TYPE
===========================
Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001_val_1.fq.gz <<)

Found perfect matches for the following adapter sequences:
Adapter type	Count	Sequence	Sequences analysed	Percentage
Illumina	6622	AGATCGGAAGAGC	1000000	0.66
smallRNA	4	TGGAATTCTCGG	1000000	0.00
Nextera	0	CTGTCTCTTATA	1000000	0.00
Using Illumina adapter for trimming (count: 6622). Second best hit was smallRNA (count: 4)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to AD002_S9_L001_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001_val_1.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 4009.23 s (24 us/read; 2.49 M reads/minute).

=== Summary ===

Total reads processed:             166,519,549
Reads with adapters:                62,950,909 (37.8%)
Reads written (passing filters):   166,519,549 (100.0%)

Total basepairs processed: 20,263,772,384 bp
Quality-trimmed:              10,658,407 bp (0.1%)
Total written (filtered):  20,075,819,474 bp (99.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 62950909 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 32.6%
  C: 22.7%
  G: 14.4%
  T: 30.1%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	45191016	41629887.2	0	45191016
2	11892878	10407471.8	0	11892878
3	3014795	2601868.0	0	3014795
4	1184885	650467.0	0	1184885
5	136203	162616.7	0	136203
6	26162	40654.2	0	26162
7	15017	10163.5	0	15017
8	16951	2540.9	0	16951
9	13393	635.2	0	11409 1984
10	20526	158.8	1	12168 8358
11	18484	39.7	1	12657 5827
12	30871	9.9	1	23904 6967
13	1883	2.5	1	977 906
14	28295	2.5	1	22411 5884
15	1728	2.5	1	845 883
16	31609	2.5	1	24109 7500
17	2352	2.5	1	1197 1155
18	22811	2.5	1	17377 5434
19	44221	2.5	1	36321 7900
20	476	2.5	1	204 272
21	735	2.5	1	260 475
22	1509	2.5	1	663 846
23	19790	2.5	1	14697 5093
24	38449	2.5	1	30670 7779
25	2192	2.5	1	1125 1067
26	16807	2.5	1	12495 4312
27	13827	2.5	1	11153 2674
28	810	2.5	1	317 493
29	16333	2.5	1	12128 4205
30	20883	2.5	1	16077 4806
31	24181	2.5	1	19042 5139
32	3089	2.5	1	1832 1257
33	29110	2.5	1	22048 7062
34	14162	2.5	1	11204 2958
35	817	2.5	1	349 468
36	16927	2.5	1	12775 4152
37	19935	2.5	1	15059 4876
38	12063	2.5	1	8977 3086
39	18055	2.5	1	13767 4288
40	16204	2.5	1	12318 3886
41	19447	2.5	1	14427 5020
42	35132	2.5	1	27593 7539
43	6650	2.5	1	5421 1229
44	9775	2.5	1	6973 2802
45	796	2.5	1	368 428
46	19159	2.5	1	14642 4517
47	14576	2.5	1	11098 3478
48	13926	2.5	1	10450 3476
49	19134	2.5	1	13988 5146
50	29774	2.5	1	23411 6363
51	10816	2.5	1	8626 2190
52	2049	2.5	1	1278 771
53	28745	2.5	1	22950 5795
54	35400	2.5	1	28635 6765
55	3293	2.5	1	2440 853
56	8907	2.5	1	6800 2107
57	29998	2.5	1	24644 5354
58	1367	2.5	1	744 623
59	3980	2.5	1	2473 1507
60	25914	2.5	1	21592 4322
61	732	2.5	1	362 370
62	2084	2.5	1	1131 953
63	7543	2.5	1	5611 1932
64	19408	2.5	1	15793 3615
65	16686	2.5	1	13541 3145
66	16846	2.5	1	13865 2981
67	9203	2.5	1	7168 2035
68	7795	2.5	1	5744 2051
69	5135	2.5	1	3682 1453
70	5891	2.5	1	4597 1294
71	8634	2.5	1	6924 1710
72	9794	2.5	1	7862 1932
73	10352	2.5	1	8360 1992
74	10759	2.5	1	8560 2199
75	11037	2.5	1	8815 2222
76	11355	2.5	1	9027 2328
77	11168	2.5	1	8869 2299
78	11167	2.5	1	8809 2358
79	11221	2.5	1	8924 2297
80	11098	2.5	1	8767 2331
81	10888	2.5	1	8548 2340
82	10994	2.5	1	8677 2317
83	10736	2.5	1	8441 2295
84	10842	2.5	1	8489 2353
85	10728	2.5	1	8418 2310
86	10495	2.5	1	8215 2280
87	10484	2.5	1	8225 2259
88	10007	2.5	1	7802 2205
89	10091	2.5	1	7857 2234
90	9940	2.5	1	7828 2112
91	9628	2.5	1	7583 2045
92	9575	2.5	1	7475 2100
93	9431	2.5	1	7431 2000
94	9329	2.5	1	7319 2010
95	8980	2.5	1	6971 2009
96	8950	2.5	1	7007 1943
97	8734	2.5	1	6774 1960
98	8538	2.5	1	6692 1846
99	8250	2.5	1	6355 1895
100	8216	2.5	1	6456 1760
101	7764	2.5	1	6063 1701
102	7618	2.5	1	5928 1690
103	7234	2.5	1	5651 1583
104	6971	2.5	1	5450 1521
105	6699	2.5	1	5123 1576
106	6627	2.5	1	5073 1554
107	6023	2.5	1	4625 1398
108	5843	2.5	1	4473 1370
109	5608	2.5	1	4271 1337
110	5329	2.5	1	4030 1299
111	5128	2.5	1	3929 1199
112	4870	2.5	1	3694 1176
113	4622	2.5	1	3450 1172
114	4528	2.5	1	3397 1131
115	4255	2.5	1	3226 1029
116	4100	2.5	1	3085 1015
117	3886	2.5	1	2902 984
118	3780	2.5	1	2870 910
119	3676	2.5	1	2785 891
120	3372	2.5	1	2520 852
121	3199	2.5	1	2440 759
122	2979	2.5	1	2269 710
123	2811	2.5	1	2107 704
124	2615	2.5	1	1971 644
125	2537	2.5	1	1908 629
126	2335	2.5	1	1795 540
127	2138	2.5	1	1639 499
128	2019	2.5	1	1567 452
129	1900	2.5	1	1514 386
130	1584	2.5	1	1268 316
131	1574	2.5	1	1292 282
132	1236	2.5	1	1037 199
133	1139	2.5	1	979 160
134	950	2.5	1	804 146
135	914	2.5	1	788 126
136	764	2.5	1	646 118
137	685	2.5	1	601 84
138	556	2.5	1	487 69
139	495	2.5	1	442 53
140	421	2.5	1	358 63
141	343	2.5	1	295 48
142	266	2.5	1	225 41
143	305	2.5	1	243 62
144	238	2.5	1	195 43
145	269	2.5	1	214 55
146	219	2.5	1	174 45
147	245	2.5	1	185 60
148	203	2.5	1	128 75
149	310	2.5	1	192 118
150	1172	2.5	1	461 711
151	114539	2.5	1	42001 72538


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R1_001_val_1.fq.gz
=============================================
166519549 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to AD002_S9_L001_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R2_001_val_2.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 4136.23 s (25 us/read; 2.42 M reads/minute).

=== Summary ===

Total reads processed:             166,519,549
Reads with adapters:                64,336,761 (38.6%)
Reads written (passing filters):   166,519,549 (100.0%)

Total basepairs processed: 20,806,009,128 bp
Quality-trimmed:              12,672,889 bp (0.1%)
Total written (filtered):  20,606,066,844 bp (99.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 64336761 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 33.0%
  C: 22.5%
  G: 14.6%
  T: 29.8%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	46320342	41629887.2	0	46320342
2	11729062	10407471.8	0	11729062
3	3131394	2601868.0	0	3131394
4	1193082	650467.0	0	1193082
5	125066	162616.7	0	125066
6	31913	40654.2	0	31913
7	21845	10163.5	0	21845
8	22466	2540.9	0	22466
9	16214	635.2	0	14145 2069
10	28137	158.8	1	17439 10698
11	22555	39.7	1	15567 6988
12	42264	9.9	1	32388 9876
13	661	2.5	1	252 409
14	28072	2.5	1	20831 7241
15	31160	2.5	1	24417 6743
16	383	2.5	1	115 268
17	24954	2.5	1	18991 5963
18	13631	2.5	1	10359 3272
19	28189	2.5	1	21318 6871
20	18450	2.5	1	13935 4515
21	15196	2.5	1	11701 3495
22	19651	2.5	1	14996 4655
23	21752	2.5	1	16404 5348
24	40107	2.5	1	29978 10129
25	18750	2.5	1	14580 4170
26	18519	2.5	1	14350 4169
27	14830	2.5	1	10978 3852
28	29641	2.5	1	23843 5798
29	9716	2.5	1	6627 3089
30	29481	2.5	1	23634 5847
31	13670	2.5	1	9881 3789
32	51895	2.5	1	43576 8319
33	24414	2.5	1	18797 5617
34	8902	2.5	1	6076 2826
35	29279	2.5	1	23981 5298
36	10624	2.5	1	7727 2897
37	15397	2.5	1	11525 3872
38	8278	2.5	1	6292 1986
39	11562	2.5	1	8638 2924
40	5567	2.5	1	4069 1498
41	17152	2.5	1	13742 3410
42	23546	2.5	1	19042 4504
43	12652	2.5	1	9789 2863
44	19653	2.5	1	15410 4243
45	36962	2.5	1	30323 6639
46	18823	2.5	1	14422 4401
47	11178	2.5	1	8633 2545
48	36958	2.5	1	30588 6370
49	14327	2.5	1	11252 3075
50	5729	2.5	1	3947 1782
51	29652	2.5	1	24002 5650
52	44916	2.5	1	38911 6005
53	15569	2.5	1	12618 2951
54	20470	2.5	1	16407 4063
55	12026	2.5	1	9700 2326
56	6551	2.5	1	4773 1778
57	11696	2.5	1	9080 2616
58	13830	2.5	1	10710 3120
59	7683	2.5	1	5618 2065
60	5817	2.5	1	3898 1919
61	4974	2.5	1	3438 1536
62	5588	2.5	1	3870 1718
63	6329	2.5	1	4654 1675
64	9893	2.5	1	7791 2102
65	13175	2.5	1	10559 2616
66	14511	2.5	1	11692 2819
67	15084	2.5	1	12069 3015
68	15405	2.5	1	12128 3277
69	15754	2.5	1	12484 3270
70	15554	2.5	1	12293 3261
71	15695	2.5	1	12342 3353
72	15542	2.5	1	12261 3281
73	15911	2.5	1	12488 3423
74	15564	2.5	1	12295 3269
75	15370	2.5	1	12091 3279
76	15235	2.5	1	12023 3212
77	15186	2.5	1	11947 3239
78	14886	2.5	1	11638 3248
79	14938	2.5	1	11741 3197
80	14749	2.5	1	11564 3185
81	14257	2.5	1	11136 3121
82	14380	2.5	1	11319 3061
83	14226	2.5	1	11240 2986
84	14050	2.5	1	11075 2975
85	14041	2.5	1	11082 2959
86	13664	2.5	1	10701 2963
87	13612	2.5	1	10731 2881
88	13323	2.5	1	10438 2885
89	13177	2.5	1	10433 2744
90	12972	2.5	1	10190 2782
91	12706	2.5	1	9910 2796
92	12299	2.5	1	9703 2596
93	12161	2.5	1	9545 2616
94	11979	2.5	1	9442 2537
95	11751	2.5	1	9172 2579
96	11612	2.5	1	9161 2451
97	11434	2.5	1	9052 2382
98	10985	2.5	1	8714 2271
99	10710	2.5	1	8346 2364
100	10595	2.5	1	8333 2262
101	10225	2.5	1	8010 2215
102	9958	2.5	1	7869 2089
103	9684	2.5	1	7551 2133
104	9139	2.5	1	7086 2053
105	8751	2.5	1	6828 1923
106	8325	2.5	1	6414 1911
107	7751	2.5	1	5910 1841
108	7293	2.5	1	5567 1726
109	6982	2.5	1	5289 1693
110	6537	2.5	1	4931 1606
111	6361	2.5	1	4812 1549
112	6064	2.5	1	4553 1511
113	5782	2.5	1	4332 1450
114	5544	2.5	1	4201 1343
115	5196	2.5	1	3928 1268
116	5079	2.5	1	3833 1246
117	4888	2.5	1	3754 1134
118	4690	2.5	1	3571 1119
119	4561	2.5	1	3506 1055
120	4166	2.5	1	3208 958
121	3912	2.5	1	2949 963
122	3756	2.5	1	2849 907
123	3499	2.5	1	2677 822
124	3279	2.5	1	2478 801
125	3078	2.5	1	2378 700
126	2873	2.5	1	2201 672
127	2645	2.5	1	2035 610
128	2353	2.5	1	1889 464
129	2192	2.5	1	1820 372
130	1761	2.5	1	1460 301
131	1690	2.5	1	1438 252
132	1293	2.5	1	1114 179
133	1195	2.5	1	1033 162
134	981	2.5	1	873 108
135	940	2.5	1	841 99
136	772	2.5	1	667 105
137	701	2.5	1	627 74
138	560	2.5	1	501 59
139	486	2.5	1	422 64
140	410	2.5	1	356 54
141	340	2.5	1	284 56
142	259	2.5	1	203 56
143	273	2.5	1	211 62
144	226	2.5	1	161 65
145	247	2.5	1	183 64
146	185	2.5	1	128 57
147	178	2.5	1	123 55
148	127	2.5	1	68 59
149	178	2.5	1	114 64
150	712	2.5	1	592 120
151	43146	2.5	1	42014 1132


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L001_R2_001_val_2.fq.gz
=============================================
166519549 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files AD002_S9_L001_R1_001_val_1_trimmed.fq.gz and AD002_S9_L001_R2_001_val_2_trimmed.fq.gz
file_1: AD002_S9_L001_R1_001_val_1_trimmed.fq.gz, file_2: AD002_S9_L001_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: AD002_S9_L001_R1_001_val_1_trimmed.fq.gz and AD002_S9_L001_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to AD002_S9_L001_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 166519549

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 577240 (0.35%)

Deleting both intermediate output files AD002_S9_L001_R1_001_val_1_trimmed.fq.gz and AD002_S9_L001_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to AD002_S9_L002_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R1_001_val_1.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 5175.37 s (24 us/read; 2.46 M reads/minute).

=== Summary ===

Total reads processed:             212,571,014
Reads with adapters:                82,462,079 (38.8%)
Reads written (passing filters):   212,571,014 (100.0%)

Total basepairs processed: 26,380,336,744 bp
Quality-trimmed:              11,282,411 bp (0.0%)
Total written (filtered):  26,072,320,126 bp (98.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 82462079 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 32.8%
  C: 22.7%
  G: 14.3%
  T: 30.1%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	59039996	53142753.5	0	59039996
2	14966438	13285688.4	0	14966438
3	3831679	3321422.1	0	3831679
4	1480847	830355.5	0	1480847
5	163128	207588.9	0	163128
6	38541	51897.2	0	38541
7	22951	12974.3	0	22951
8	27327	3243.6	0	27327
9	22259	810.9	0	19747 2512
10	31473	202.7	1	19843 11630
11	30840	50.7	1	21362 9478
12	50070	12.7	1	39221 10849
13	2844	3.2	1	1464 1380
14	47563	3.2	1	37749 9814
15	2742	3.2	1	1398 1344
16	55622	3.2	1	42339 13283
17	4406	3.2	1	2343 2063
18	38657	3.2	1	30067 8590
19	76638	3.2	1	63646 12992
20	785	3.2	1	335 450
21	1199	3.2	1	405 794
22	2135	3.2	1	907 1228
23	33554	3.2	1	25117 8437
24	69371	3.2	1	55342 14029
25	3521	3.2	1	1864 1657
26	30185	3.2	1	22674 7511
27	23530	3.2	1	19348 4182
28	1332	3.2	1	573 759
29	30080	3.2	1	22282 7798
30	36733	3.2	1	28722 8011
31	43072	3.2	1	34257 8815
32	5026	3.2	1	2892 2134
33	54705	3.2	1	41452 13253
34	25607	3.2	1	20697 4910
35	1315	3.2	1	598 717
36	29363	3.2	1	22625 6738
37	37853	3.2	1	28899 8954
38	22367	3.2	1	16611 5756
39	31698	3.2	1	24957 6741
40	28603	3.2	1	22260 6343
41	36993	3.2	1	27714 9279
42	67000	3.2	1	53293 13707
43	12117	3.2	1	10136 1981
44	17331	3.2	1	12768 4563
45	1153	3.2	1	533 620
46	32065	3.2	1	25213 6852
47	25756	3.2	1	20118 5638
48	28466	3.2	1	21563 6903
49	37422	3.2	1	27270 10152
50	55745	3.2	1	44380 11365
51	21907	3.2	1	17848 4059
52	3678	3.2	1	2299 1379
53	50349	3.2	1	40043 10306
54	73367	3.2	1	59796 13571
55	6120	3.2	1	4526 1594
56	18476	3.2	1	14265 4211
57	66431	3.2	1	54830 11601
58	2492	3.2	1	1488 1004
59	7423	3.2	1	4507 2916
60	51321	3.2	1	43286 8035
61	1057	3.2	1	524 533
62	2916	3.2	1	1514 1402
63	16873	3.2	1	12893 3980
64	34310	3.2	1	28027 6283
65	36670	3.2	1	29768 6902
66	38998	3.2	1	32040 6958
67	27680	3.2	1	21977 5703
68	30139	3.2	1	23969 6170
69	9433	3.2	1	6500 2933
70	10154	3.2	1	7699 2455
71	16385	3.2	1	13467 2918
72	19640	3.2	1	16226 3414
73	21512	3.2	1	17701 3811
74	22493	3.2	1	18430 4063
75	22985	3.2	1	18770 4215
76	23564	3.2	1	19042 4522
77	23835	3.2	1	19293 4542
78	23686	3.2	1	19111 4575
79	23946	3.2	1	19361 4585
80	23986	3.2	1	19298 4688
81	23804	3.2	1	19288 4516
82	23811	3.2	1	19206 4605
83	23556	3.2	1	18944 4612
84	23072	3.2	1	18538 4534
85	23578	3.2	1	18987 4591
86	23342	3.2	1	18729 4613
87	23024	3.2	1	18465 4559
88	22665	3.2	1	18278 4387
89	22267	3.2	1	17848 4419
90	22426	3.2	1	18024 4402
91	22119	3.2	1	17670 4449
92	21903	3.2	1	17527 4376
93	21581	3.2	1	17328 4253
94	20982	3.2	1	16814 4168
95	20719	3.2	1	16547 4172
96	20401	3.2	1	16240 4161
97	20127	3.2	1	16014 4113
98	19866	3.2	1	15899 3967
99	19812	3.2	1	15778 4034
100	19194	3.2	1	15304 3890
101	18736	3.2	1	14893 3843
102	18130	3.2	1	14414 3716
103	17646	3.2	1	14103 3543
104	17379	3.2	1	13812 3567
105	16898	3.2	1	13401 3497
106	16141	3.2	1	12757 3384
107	15731	3.2	1	12435 3296
108	15140	3.2	1	11901 3239
109	14543	3.2	1	11434 3109
110	14054	3.2	1	10931 3123
111	13746	3.2	1	10800 2946
112	13320	3.2	1	10353 2967
113	12601	3.2	1	9841 2760
114	12035	3.2	1	9427 2608
115	11563	3.2	1	9102 2461
116	11244	3.2	1	8830 2414
117	10939	3.2	1	8547 2392
118	10488	3.2	1	8214 2274
119	9944	3.2	1	7746 2198
120	9315	3.2	1	7136 2179
121	9004	3.2	1	7044 1960
122	8319	3.2	1	6468 1851
123	7911	3.2	1	6134 1777
124	7343	3.2	1	5701 1642
125	6984	3.2	1	5463 1521
126	6625	3.2	1	5163 1462
127	6127	3.2	1	4776 1351
128	5503	3.2	1	4353 1150
129	5386	3.2	1	4334 1052
130	4455	3.2	1	3636 819
131	4178	3.2	1	3487 691
132	3362	3.2	1	2811 551
133	3044	3.2	1	2598 446
134	2477	3.2	1	2143 334
135	2320	3.2	1	2028 292
136	1849	3.2	1	1616 233
137	1640	3.2	1	1429 211
138	1271	3.2	1	1112 159
139	1045	3.2	1	941 104
140	761	3.2	1	666 95
141	600	3.2	1	528 72
142	478	3.2	1	401 77
143	396	3.2	1	338 58
144	395	3.2	1	338 57
145	377	3.2	1	304 73
146	314	3.2	1	248 66
147	287	3.2	1	225 62
148	291	3.2	1	201 90
149	349	3.2	1	241 108
150	1019	3.2	1	426 593
151	158198	3.2	1	58633 99565


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R1_001_val_1.fq.gz
=============================================
212571014 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to AD002_S9_L002_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R2_001_val_2.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 5230.58 s (25 us/read; 2.44 M reads/minute).

=== Summary ===

Total reads processed:             212,571,014
Reads with adapters:                84,686,365 (39.8%)
Reads written (passing filters):   212,571,014 (100.0%)

Total basepairs processed: 27,177,135,971 bp
Quality-trimmed:              13,245,075 bp (0.0%)
Total written (filtered):  26,838,125,885 bp (98.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 84686365 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 33.1%
  C: 22.4%
  G: 14.6%
  T: 29.9%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	60674168	53142753.5	0	60674168
2	14784594	13285688.4	0	14784594
3	3967718	3321422.1	0	3967718
4	1480924	830355.5	0	1480924
5	146347	207588.9	0	146347
6	48580	51897.2	0	48580
7	33791	12974.3	0	33791
8	36656	3243.6	0	36656
9	26598	810.9	0	23963 2635
10	44418	202.7	1	29185 15233
11	38922	50.7	1	26762 12160
12	69792	12.7	1	53960 15832
13	1195	3.2	1	438 757
14	47339	3.2	1	35576 11763
15	52770	3.2	1	41608 11162
16	634	3.2	1	201 433
17	42726	3.2	1	33263 9463
18	22684	3.2	1	17428 5256
19	47567	3.2	1	36469 11098
20	31403	3.2	1	24000 7403
21	28364	3.2	1	21698 6666
22	34047	3.2	1	26354 7693
23	36561	3.2	1	28207 8354
24	65463	3.2	1	49951 15512
25	34947	3.2	1	27542 7405
26	34962	3.2	1	27304 7658
27	29006	3.2	1	21592 7414
28	53205	3.2	1	43379 9826
29	20582	3.2	1	14366 6216
30	53904	3.2	1	43886 10018
31	25572	3.2	1	18856 6716
32	104215	3.2	1	89702 14513
33	48556	3.2	1	38303 10253
34	20322	3.2	1	14286 6036
35	57948	3.2	1	48742 9206
36	17162	3.2	1	12263 4899
37	31403	3.2	1	23930 7473
38	10608	3.2	1	7550 3058
39	18784	3.2	1	13894 4890
40	6633	3.2	1	4568 2065
41	32112	3.2	1	26002 6110
42	45616	3.2	1	37841 7775
43	21704	3.2	1	16865 4839
44	37574	3.2	1	30256 7318
45	87545	3.2	1	75914 11631
46	36246	3.2	1	28464 7782
47	16572	3.2	1	12732 3840
48	80742	3.2	1	69143 11599
49	21381	3.2	1	16623 4758
50	8037	3.2	1	5550 2487
51	63171	3.2	1	53351 9820
52	96340	3.2	1	86234 10106
53	23443	3.2	1	19108 4335
54	36014	3.2	1	29600 6414
55	15334	3.2	1	12053 3281
56	10515	3.2	1	7531 2984
57	18137	3.2	1	14127 4010
58	22631	3.2	1	17766 4865
59	11751	3.2	1	8432 3319
60	10054	3.2	1	6973 3081
61	9870	3.2	1	6812 3058
62	9763	3.2	1	6789 2974
63	10788	3.2	1	7883 2905
64	17688	3.2	1	14248 3440
65	25196	3.2	1	20885 4311
66	29017	3.2	1	24067 4950
67	30511	3.2	1	25231 5280
68	31480	3.2	1	25807 5673
69	32138	3.2	1	26359 5779
70	32297	3.2	1	26434 5863
71	32854	3.2	1	26895 5959
72	32640	3.2	1	26633 6007
73	32787	3.2	1	26654 6133
74	32692	3.2	1	26640 6052
75	32484	3.2	1	26426 6058
76	32184	3.2	1	26187 5997
77	32358	3.2	1	26268 6090
78	31723	3.2	1	25744 5979
79	31696	3.2	1	25821 5875
80	31836	3.2	1	25842 5994
81	31424	3.2	1	25584 5840
82	31042	3.2	1	25270 5772
83	30875	3.2	1	25140 5735
84	30591	3.2	1	24859 5732
85	30931	3.2	1	25246 5685
86	30493	3.2	1	24853 5640
87	30152	3.2	1	24619 5533
88	29712	3.2	1	24263 5449
89	29210	3.2	1	23885 5325
90	28789	3.2	1	23402 5387
91	28484	3.2	1	23115 5369
92	28346	3.2	1	23073 5273
93	27777	3.2	1	22496 5281
94	27264	3.2	1	22205 5059
95	27108	3.2	1	22001 5107
96	26638	3.2	1	21556 5082
97	26212	3.2	1	21295 4917
98	25833	3.2	1	21100 4733
99	25454	3.2	1	20687 4767
100	24923	3.2	1	20366 4557
101	24287	3.2	1	19828 4459
102	23797	3.2	1	19329 4468
103	23126	3.2	1	18853 4273
104	22695	3.2	1	18494 4201
105	22093	3.2	1	17881 4212
106	21097	3.2	1	17034 4063
107	20219	3.2	1	16232 3987
108	19562	3.2	1	15645 3917
109	18798	3.2	1	14996 3802
110	18084	3.2	1	14372 3712
111	17805	3.2	1	14243 3562
112	17170	3.2	1	13696 3474
113	16335	3.2	1	13209 3126
114	15585	3.2	1	12555 3030
115	15021	3.2	1	12002 3019
116	14681	3.2	1	11658 3023
117	14216	3.2	1	11363 2853
118	13499	3.2	1	10813 2686
119	13000	3.2	1	10405 2595
120	12029	3.2	1	9603 2426
121	11664	3.2	1	9343 2321
122	10909	3.2	1	8712 2197
123	10511	3.2	1	8406 2105
124	9754	3.2	1	7760 1994
125	9173	3.2	1	7375 1798
126	8573	3.2	1	6946 1627
127	7964	3.2	1	6426 1538
128	6884	3.2	1	5641 1243
129	6554	3.2	1	5541 1013
130	5155	3.2	1	4404 751
131	4812	3.2	1	4172 640
132	3624	3.2	1	3207 417
133	3284	3.2	1	2958 326
134	2667	3.2	1	2388 279
135	2436	3.2	1	2207 229
136	1933	3.2	1	1774 159
137	1689	3.2	1	1566 123
138	1293	3.2	1	1168 125
139	1070	3.2	1	960 110
140	763	3.2	1	676 87
141	591	3.2	1	514 77
142	474	3.2	1	374 100
143	386	3.2	1	316 70
144	374	3.2	1	285 89
145	336	3.2	1	247 89
146	280	3.2	1	196 84
147	260	3.2	1	184 76
148	209	3.2	1	132 77
149	233	3.2	1	143 90
150	460	3.2	1	349 111
151	59702	3.2	1	58455 1247


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/AD002_S9_L002_R2_001_val_2.fq.gz
=============================================
212571014 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files AD002_S9_L002_R1_001_val_1_trimmed.fq.gz and AD002_S9_L002_R2_001_val_2_trimmed.fq.gz
file_1: AD002_S9_L002_R1_001_val_1_trimmed.fq.gz, file_2: AD002_S9_L002_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: AD002_S9_L002_R1_001_val_1_trimmed.fq.gz and AD002_S9_L002_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to AD002_S9_L002_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 212571014

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 679425 (0.32%)

Deleting both intermediate output files AD002_S9_L002_R1_001_val_1_trimmed.fq.gz and AD002_S9_L002_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR005_S4_L001_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R1_001_val_1.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.14 s (27 us/read; 2.19 M reads/minute).

=== Summary ===

Total reads processed:                  41,460
Reads with adapters:                    26,139 (63.0%)
Reads written (passing filters):        41,460 (100.0%)

Total basepairs processed:     6,228,334 bp
Quality-trimmed:                   1,175 bp (0.0%)
Total written (filtered):      5,826,371 bp (93.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 26139 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 27.4%
  C: 30.9%
  G: 21.2%
  T: 19.5%
  none/other: 1.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11126	10365.0	0	11126
2	2116	2591.2	0	2116
3	918	647.8	0	918
4	706	162.0	0	706
5	5	40.5	0	5
6	298	10.1	0	298
7	258	2.5	0	258
8	279	0.6	0	279
9	264	0.2	0	263 1
10	306	0.0	1	288 18
11	303	0.0	1	269 34
12	492	0.0	1	461 31
13	14	0.0	1	8 6
14	526	0.0	1	491 35
15	9	0.0	1	6 3
16	551	0.0	1	504 47
17	18	0.0	1	12 6
18	333	0.0	1	306 27
19	837	0.0	1	788 49
20	1	0.0	1	1
21	1	0.0	1	0 1
22	3	0.0	1	1 2
23	299	0.0	1	271 28
24	625	0.0	1	580 45
25	11	0.0	1	7 4
26	249	0.0	1	227 22
27	208	0.0	1	197 11
28	6	0.0	1	3 3
29	254	0.0	1	235 19
30	264	0.0	1	245 19
31	292	0.0	1	276 16
32	13	0.0	1	8 5
33	370	0.0	1	345 25
34	6	0.0	1	3 3
35	297	0.0	1	273 24
36	4	0.0	1	2 2
37	166	0.0	1	151 15
38	196	0.0	1	182 14
39	159	0.0	1	153 6
40	131	0.0	1	125 6
41	191	0.0	1	179 12
42	360	0.0	1	333 27
43	61	0.0	1	55 6
44	62	0.0	1	58 4
45	1	0.0	1	0 1
46	170	0.0	1	160 10
47	103	0.0	1	96 7
48	109	0.0	1	99 10
49	123	0.0	1	111 12
50	176	0.0	1	165 11
51	81	0.0	1	77 4
52	5	0.0	1	4 1
53	163	0.0	1	153 10
54	207	0.0	1	194 13
55	18	0.0	1	15 3
56	37	0.0	1	31 6
57	168	0.0	1	161 7
58	3	0.0	1	2 1
59	9	0.0	1	7 2
60	104	0.0	1	102 2
61	1	0.0	1	1
62	5	0.0	1	4 1
63	19	0.0	1	16 3
64	70	0.0	1	68 2
65	49	0.0	1	46 3
66	68	0.0	1	66 2
67	37	0.0	1	35 2
68	29	0.0	1	26 3
69	13	0.0	1	12 1
70	19	0.0	1	18 1
71	20	0.0	1	20
72	20	0.0	1	19 1
73	25	0.0	1	24 1
74	22	0.0	1	21 1
75	17	0.0	1	17
76	17	0.0	1	16 1
77	18	0.0	1	17 1
78	20	0.0	1	19 1
79	20	0.0	1	19 1
80	14	0.0	1	13 1
81	15	0.0	1	14 1
82	15	0.0	1	15
83	12	0.0	1	11 1
84	7	0.0	1	7
85	10	0.0	1	10
86	8	0.0	1	7 1
87	8	0.0	1	8
88	11	0.0	1	10 1
89	14	0.0	1	13 1
90	6	0.0	1	5 1
91	6	0.0	1	5 1
92	5	0.0	1	5
93	1	0.0	1	1
94	5	0.0	1	4 1
95	3	0.0	1	3
96	3	0.0	1	3
97	9	0.0	1	9
98	5	0.0	1	5
99	4	0.0	1	4
100	3	0.0	1	3
101	7	0.0	1	6 1
102	7	0.0	1	7
104	2	0.0	1	2
105	3	0.0	1	3
106	2	0.0	1	2
107	1	0.0	1	1
109	2	0.0	1	2
110	4	0.0	1	3 1
111	1	0.0	1	1
113	2	0.0	1	2
114	2	0.0	1	2
117	1	0.0	1	1
119	1	0.0	1	1
120	2	0.0	1	2
121	1	0.0	1	1
123	2	0.0	1	2
124	2	0.0	1	2
125	1	0.0	1	1
126	2	0.0	1	2
127	2	0.0	1	2
128	3	0.0	1	3
129	6	0.0	1	5 1
130	5	0.0	1	5
131	3	0.0	1	3
132	3	0.0	1	3
133	4	0.0	1	3 1
134	9	0.0	1	9
135	7	0.0	1	6 1
136	8	0.0	1	8
137	5	0.0	1	5
138	6	0.0	1	5 1
139	2	0.0	1	2
140	3	0.0	1	3
141	4	0.0	1	3 1
142	9	0.0	1	9
143	3	0.0	1	3
145	1	0.0	1	1
146	6	0.0	1	6
147	1	0.0	1	1
148	11	0.0	1	11
149	3	0.0	1	3
150	1	0.0	1	1
151	271	0.0	1	5 266


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R1_001_val_1.fq.gz
=============================================
41460 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR005_S4_L001_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R2_001_val_2.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.12 s (27 us/read; 2.22 M reads/minute).

=== Summary ===

Total reads processed:                  41,460
Reads with adapters:                    26,148 (63.1%)
Reads written (passing filters):        41,460 (100.0%)

Total basepairs processed:     6,219,292 bp
Quality-trimmed:                   1,420 bp (0.0%)
Total written (filtered):      5,865,672 bp (94.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 26148 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 29.5%
  C: 27.8%
  G: 22.1%
  T: 20.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	11262	10365.0	0	11262
2	2324	2591.2	0	2324
3	1069	647.8	0	1069
4	756	162.0	0	756
5	3	40.5	0	3
6	271	10.1	0	271
7	266	2.5	0	266
8	308	0.6	0	308
9	236	0.2	0	235 1
10	314	0.0	1	290 24
11	297	0.0	1	265 32
12	507	0.0	1	474 33
13	3	0.0	1	1 2
14	297	0.0	1	267 30
15	464	0.0	1	435 29
17	309	0.0	1	284 25
18	198	0.0	1	185 13
19	298	0.0	1	275 23
20	242	0.0	1	221 21
21	207	0.0	1	183 24
22	191	0.0	1	177 14
23	267	0.0	1	250 17
24	396	0.0	1	366 30
25	220	0.0	1	200 20
26	175	0.0	1	162 13
27	159	0.0	1	149 10
28	361	0.0	1	334 27
29	83	0.0	1	74 9
30	303	0.0	1	284 19
31	112	0.0	1	102 10
32	492	0.0	1	464 28
33	176	0.0	1	162 14
34	66	0.0	1	56 10
35	265	0.0	1	252 13
36	74	0.0	1	71 3
37	121	0.0	1	114 7
38	83	0.0	1	82 1
39	95	0.0	1	92 3
40	33	0.0	1	30 3
41	123	0.0	1	118 5
42	192	0.0	1	181 11
43	80	0.0	1	73 7
44	123	0.0	1	119 4
45	226	0.0	1	217 9
46	125	0.0	1	118 7
47	75	0.0	1	71 4
48	217	0.0	1	203 14
49	70	0.0	1	68 2
50	21	0.0	1	20 1
51	147	0.0	1	138 9
52	218	0.0	1	204 14
53	86	0.0	1	82 4
54	90	0.0	1	83 7
55	52	0.0	1	50 2
56	20	0.0	1	18 2
57	53	0.0	1	52 1
58	58	0.0	1	58
59	28	0.0	1	21 7
60	16	0.0	1	15 1
61	11	0.0	1	10 1
62	18	0.0	1	15 3
63	21	0.0	1	21
64	27	0.0	1	27
65	30	0.0	1	28 2
66	43	0.0	1	42 1
67	52	0.0	1	51 1
68	45	0.0	1	43 2
69	38	0.0	1	35 3
70	43	0.0	1	42 1
71	24	0.0	1	23 1
72	21	0.0	1	20 1
73	25	0.0	1	23 2
74	23	0.0	1	23
75	17	0.0	1	17
76	17	0.0	1	17
77	19	0.0	1	18 1
78	19	0.0	1	19
79	16	0.0	1	15 1
80	16	0.0	1	15 1
81	16	0.0	1	15 1
82	13	0.0	1	13
83	12	0.0	1	12
84	8	0.0	1	8
85	10	0.0	1	10
86	6	0.0	1	5 1
87	7	0.0	1	7
88	10	0.0	1	10
89	14	0.0	1	14
90	6	0.0	1	6
91	5	0.0	1	5
92	7	0.0	1	7
93	2	0.0	1	2
94	5	0.0	1	5
95	3	0.0	1	3
96	3	0.0	1	3
97	9	0.0	1	9
98	5	0.0	1	5
99	4	0.0	1	4
100	3	0.0	1	3
101	7	0.0	1	7
102	7	0.0	1	7
104	2	0.0	1	2
105	3	0.0	1	3
106	2	0.0	1	2
107	1	0.0	1	1
109	2	0.0	1	2
110	4	0.0	1	3 1
111	1	0.0	1	1
113	2	0.0	1	2
114	2	0.0	1	2
118	1	0.0	1	1
119	1	0.0	1	1
120	2	0.0	1	2
121	1	0.0	1	1
123	2	0.0	1	2
124	2	0.0	1	1 1
126	2	0.0	1	2
127	2	0.0	1	2
128	4	0.0	1	4
129	6	0.0	1	6
130	4	0.0	1	4
131	3	0.0	1	3
132	2	0.0	1	2
133	3	0.0	1	2 1
134	10	0.0	1	10
135	7	0.0	1	6 1
136	8	0.0	1	8
137	5	0.0	1	5
138	6	0.0	1	6
139	2	0.0	1	2
140	3	0.0	1	3
141	3	0.0	1	0 3
142	9	0.0	1	7 2
143	3	0.0	1	2 1
145	1	0.0	1	0 1
146	6	0.0	1	2 4
147	1	0.0	1	0 1
148	11	0.0	1	7 4
149	2	0.0	1	1 1
150	2	0.0	1	0 2
151	5	0.0	1	2 3


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L001_R2_001_val_2.fq.gz
=============================================
41460 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR005_S4_L001_R1_001_val_1_trimmed.fq.gz and NR005_S4_L001_R2_001_val_2_trimmed.fq.gz
file_1: NR005_S4_L001_R1_001_val_1_trimmed.fq.gz, file_2: NR005_S4_L001_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR005_S4_L001_R1_001_val_1_trimmed.fq.gz and NR005_S4_L001_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR005_S4_L001_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 41460

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 361 (0.87%)

Deleting both intermediate output files NR005_S4_L001_R1_001_val_1_trimmed.fq.gz and NR005_S4_L001_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR005_S4_L002_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001_val_1.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.99 s (27 us/read; 2.20 M reads/minute).

=== Summary ===

Total reads processed:                  36,456
Reads with adapters:                    23,392 (64.2%)
Reads written (passing filters):        36,456 (100.0%)

Total basepairs processed:     5,477,053 bp
Quality-trimmed:                     660 bp (0.0%)
Total written (filtered):      5,060,825 bp (92.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23392 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 26.8%
  C: 31.3%
  G: 21.4%
  T: 18.8%
  none/other: 1.6%

Overview of removed sequences
length	count	expect	max.err	error counts
1	9374	9114.0	0	9374
2	1817	2278.5	0	1817
3	794	569.6	0	794
4	622	142.4	0	622
5	2	35.6	0	2
6	253	8.9	0	253
7	249	2.2	0	249
8	292	0.6	0	292
9	244	0.1	0	243 1
10	228	0.0	1	218 10
11	253	0.0	1	234 19
12	483	0.0	1	457 26
13	7	0.0	1	3 4
14	426	0.0	1	402 24
15	8	0.0	1	2 6
16	499	0.0	1	464 35
17	9	0.0	1	6 3
18	269	0.0	1	252 17
19	848	0.0	1	812 36
20	6	0.0	1	3 3
22	2	0.0	1	2
23	231	0.0	1	221 10
24	600	0.0	1	570 30
25	7	0.0	1	4 3
26	203	0.0	1	191 12
27	194	0.0	1	191 3
28	5	0.0	1	4 1
29	219	0.0	1	212 7
30	216	0.0	1	206 10
31	289	0.0	1	283 6
32	5	0.0	1	3 2
33	325	0.0	1	302 23
34	9	0.0	1	5 4
35	313	0.0	1	303 10
36	3	0.0	1	3
37	169	0.0	1	156 13
38	177	0.0	1	168 9
39	145	0.0	1	138 7
40	125	0.0	1	119 6
41	177	0.0	1	164 13
42	362	0.0	1	338 24
43	60	0.0	1	56 4
44	58	0.0	1	58
45	1	0.0	1	1
46	118	0.0	1	115 3
47	109	0.0	1	101 8
48	116	0.0	1	114 2
49	103	0.0	1	92 11
50	178	0.0	1	170 8
51	101	0.0	1	100 1
52	7	0.0	1	3 4
53	140	0.0	1	128 12
54	218	0.0	1	208 10
55	10	0.0	1	9 1
56	32	0.0	1	27 5
57	225	0.0	1	217 8
58	2	0.0	1	2
59	3	0.0	1	2 1
60	113	0.0	1	110 3
61	2	0.0	1	2
63	51	0.0	1	50 1
64	49	0.0	1	47 2
65	50	0.0	1	46 4
66	64	0.0	1	61 3
67	44	0.0	1	43 1
68	50	0.0	1	49 1
69	8	0.0	1	8
70	11	0.0	1	9 2
71	28	0.0	1	28
72	27	0.0	1	26 1
73	26	0.0	1	24 2
74	17	0.0	1	16 1
75	23	0.0	1	21 2
76	20	0.0	1	19 1
77	19	0.0	1	19
78	26	0.0	1	26
79	18	0.0	1	16 2
80	20	0.0	1	18 2
81	17	0.0	1	17
82	14	0.0	1	13 1
83	9	0.0	1	9
84	14	0.0	1	13 1
85	13	0.0	1	12 1
86	18	0.0	1	17 1
87	13	0.0	1	13
88	11	0.0	1	10 1
89	10	0.0	1	9 1
90	15	0.0	1	15
91	5	0.0	1	5
92	10	0.0	1	10
93	9	0.0	1	9
94	3	0.0	1	2 1
95	7	0.0	1	7
96	5	0.0	1	5
97	5	0.0	1	5
98	3	0.0	1	3
99	6	0.0	1	6
100	8	0.0	1	8
101	1	0.0	1	1
102	6	0.0	1	5 1
103	1	0.0	1	1
104	4	0.0	1	3 1
105	3	0.0	1	3
106	1	0.0	1	1
107	2	0.0	1	2
108	2	0.0	1	2
109	3	0.0	1	2 1
110	1	0.0	1	1
112	2	0.0	1	2
113	1	0.0	1	1
114	2	0.0	1	2
115	2	0.0	1	2
116	2	0.0	1	2
117	4	0.0	1	3 1
118	2	0.0	1	2
120	3	0.0	1	3
121	4	0.0	1	4
122	4	0.0	1	2 2
123	1	0.0	1	1
124	2	0.0	1	2
125	3	0.0	1	2 1
126	4	0.0	1	3 1
127	4	0.0	1	3 1
128	5	0.0	1	5
129	8	0.0	1	7 1
130	5	0.0	1	4 1
131	6	0.0	1	6
132	5	0.0	1	5
133	7	0.0	1	7
134	19	0.0	1	19
135	10	0.0	1	10
136	3	0.0	1	3
137	6	0.0	1	6
138	8	0.0	1	8
139	10	0.0	1	8 2
140	5	0.0	1	5
141	4	0.0	1	4
142	9	0.0	1	8 1
143	5	0.0	1	5
144	1	0.0	1	1
145	3	0.0	1	3
146	9	0.0	1	9
147	3	0.0	1	3
148	8	0.0	1	8
149	4	0.0	1	4
150	3	0.0	1	1 2
151	381	0.0	1	3 378


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R1_001_val_1.fq.gz
=============================================
36456 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR005_S4_L002_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R2_001_val_2.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.98 s (27 us/read; 2.23 M reads/minute).

=== Summary ===

Total reads processed:                  36,456
Reads with adapters:                    23,277 (63.8%)
Reads written (passing filters):        36,456 (100.0%)

Total basepairs processed:     5,468,053 bp
Quality-trimmed:                     843 bp (0.0%)
Total written (filtered):      5,116,805 bp (93.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23277 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 29.1%
  C: 28.0%
  G: 22.5%
  T: 20.4%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	9539	9114.0	0	9539
2	1891	2278.5	0	1891
3	931	569.6	0	931
4	660	142.4	0	660
5	9	35.6	0	9
6	246	8.9	0	246
7	265	2.2	0	265
8	305	0.6	0	305
9	225	0.1	0	225
10	229	0.0	1	218 11
11	238	0.0	1	226 12
12	498	0.0	1	473 25
13	2	0.0	1	1 1
14	260	0.0	1	249 11
15	402	0.0	1	380 22
16	3	0.0	1	1 2
17	268	0.0	1	261 7
18	165	0.0	1	158 7
19	294	0.0	1	284 10
20	234	0.0	1	227 7
21	181	0.0	1	175 6
22	212	0.0	1	206 6
23	223	0.0	1	218 5
24	286	0.0	1	278 8
25	204	0.0	1	197 7
26	212	0.0	1	200 12
27	130	0.0	1	121 9
28	329	0.0	1	322 7
29	74	0.0	1	72 2
30	260	0.0	1	253 7
31	91	0.0	1	87 4
32	597	0.0	1	589 8
33	169	0.0	1	159 10
34	46	0.0	1	44 2
35	290	0.0	1	284 6
36	63	0.0	1	59 4
37	125	0.0	1	123 2
38	46	0.0	1	45 1
39	56	0.0	1	56
40	18	0.0	1	17 1
41	130	0.0	1	129 1
42	209	0.0	1	202 7
43	84	0.0	1	78 6
44	100	0.0	1	97 3
45	265	0.0	1	260 5
46	96	0.0	1	91 5
47	61	0.0	1	57 4
48	253	0.0	1	250 3
49	62	0.0	1	61 1
50	14	0.0	1	12 2
51	156	0.0	1	148 8
52	307	0.0	1	302 5
53	95	0.0	1	91 4
54	93	0.0	1	89 4
55	32	0.0	1	32
56	19	0.0	1	19
57	34	0.0	1	32 2
58	41	0.0	1	37 4
59	24	0.0	1	24
60	13	0.0	1	12 1
61	9	0.0	1	8 1
62	11	0.0	1	10 1
63	16	0.0	1	15 1
64	30	0.0	1	30
65	38	0.0	1	33 5
66	31	0.0	1	31
67	45	0.0	1	45
68	39	0.0	1	38 1
69	24	0.0	1	24
70	30	0.0	1	30
71	41	0.0	1	39 2
72	33	0.0	1	33
73	27	0.0	1	26 1
74	16	0.0	1	16
75	22	0.0	1	21 1
76	20	0.0	1	20
77	19	0.0	1	19
78	24	0.0	1	24
79	19	0.0	1	18 1
80	17	0.0	1	17
81	18	0.0	1	18
82	13	0.0	1	13
83	10	0.0	1	9 1
84	12	0.0	1	12
85	13	0.0	1	13
86	17	0.0	1	17
87	14	0.0	1	14
88	12	0.0	1	10 2
89	11	0.0	1	11
90	13	0.0	1	13
91	6	0.0	1	6
92	9	0.0	1	9
93	9	0.0	1	9
94	2	0.0	1	2
95	7	0.0	1	6 1
96	4	0.0	1	4
97	5	0.0	1	5
98	4	0.0	1	4
99	5	0.0	1	5
100	7	0.0	1	7
101	2	0.0	1	2
102	6	0.0	1	6
103	1	0.0	1	1
104	5	0.0	1	4 1
105	3	0.0	1	3
106	1	0.0	1	1
107	2	0.0	1	2
108	2	0.0	1	2
109	3	0.0	1	3
110	1	0.0	1	1
112	2	0.0	1	2
113	1	0.0	1	1
114	2	0.0	1	2
115	2	0.0	1	1 1
116	2	0.0	1	2
117	3	0.0	1	2 1
118	2	0.0	1	2
120	3	0.0	1	2 1
121	3	0.0	1	3
122	4	0.0	1	4
123	2	0.0	1	2
124	2	0.0	1	2
125	3	0.0	1	3
126	4	0.0	1	4
127	4	0.0	1	4
128	5	0.0	1	4 1
129	8	0.0	1	8
130	5	0.0	1	5
131	6	0.0	1	6
132	5	0.0	1	4 1
133	7	0.0	1	7
134	19	0.0	1	19
135	10	0.0	1	9 1
136	3	0.0	1	3
137	6	0.0	1	5 1
138	8	0.0	1	7 1
139	9	0.0	1	9
140	5	0.0	1	2 3
141	4	0.0	1	4
142	9	0.0	1	8 1
143	5	0.0	1	3 2
144	1	0.0	1	1
145	3	0.0	1	2 1
146	8	0.0	1	2 6
147	3	0.0	1	2 1
148	8	0.0	1	5 3
149	4	0.0	1	4
150	1	0.0	1	0 1
151	4	0.0	1	3 1


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR005_S4_L002_R2_001_val_2.fq.gz
=============================================
36456 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR005_S4_L002_R1_001_val_1_trimmed.fq.gz and NR005_S4_L002_R2_001_val_2_trimmed.fq.gz
file_1: NR005_S4_L002_R1_001_val_1_trimmed.fq.gz, file_2: NR005_S4_L002_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR005_S4_L002_R1_001_val_1_trimmed.fq.gz and NR005_S4_L002_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR005_S4_L002_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 36456

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 506 (1.39%)

Deleting both intermediate output files NR005_S4_L002_R1_001_val_1_trimmed.fq.gz and NR005_S4_L002_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR006_S3_L001_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R1_001_val_1.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 89.69 s (26 us/read; 2.28 M reads/minute).

=== Summary ===

Total reads processed:               3,414,678
Reads with adapters:                 2,142,823 (62.8%)
Reads written (passing filters):     3,414,678 (100.0%)

Total basepairs processed:   513,251,944 bp
Quality-trimmed:                  91,200 bp (0.0%)
Total written (filtered):    475,253,670 bp (92.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2142823 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 30.9%
  C: 25.9%
  G: 18.7%
  T: 20.0%
  none/other: 4.5%

Overview of removed sequences
length	count	expect	max.err	error counts
1	937450	853669.5	0	937450
2	176594	213417.4	0	176594
3	79181	53354.3	0	79181
4	61172	13338.6	0	61172
5	575	3334.6	0	575
6	23757	833.7	0	23757
7	20513	208.4	0	20513
8	24548	52.1	0	24548
9	21333	13.0	0	21171 162
10	22763	3.3	1	20813 1950
11	24508	0.8	1	21879 2629
12	45457	0.2	1	41600 3857
13	1018	0.1	1	561 457
14	44363	0.1	1	40404 3959
15	823	0.1	1	411 412
16	45163	0.1	1	40778 4385
17	1267	0.1	1	786 481
18	28010	0.1	1	25271 2739
19	69106	0.1	1	63733 5373
20	477	0.1	1	296 181
21	152	0.1	1	112 40
22	379	0.1	1	225 154
23	20800	0.1	1	18900 1900
24	50883	0.1	1	46328 4555
25	1164	0.1	1	785 379
26	17657	0.1	1	16052 1605
27	16136	0.1	1	14812 1324
28	390	0.1	1	248 142
29	16537	0.1	1	14907 1630
30	18828	0.1	1	17036 1792
31	25091	0.1	1	23130 1961
32	818	0.1	1	543 275
33	26222	0.1	1	23915 2307
34	1845	0.1	1	1442 403
35	22648	0.1	1	20769 1879
36	11708	0.1	1	10747 961
37	296	0.1	1	188 108
38	10935	0.1	1	9946 989
39	11259	0.1	1	10184 1075
40	9228	0.1	1	8389 839
41	11460	0.1	1	10202 1258
42	22714	0.1	1	20755 1959
43	4407	0.1	1	3986 421
44	4019	0.1	1	3591 428
45	179	0.1	1	119 60
46	7619	0.1	1	6925 694
47	6412	0.1	1	5845 567
48	6077	0.1	1	5463 614
49	6620	0.1	1	5890 730
50	10543	0.1	1	9613 930
51	4405	0.1	1	4030 375
52	259	0.1	1	177 82
53	7095	0.1	1	6434 661
54	10793	0.1	1	9775 1018
55	462	0.1	1	388 74
56	1856	0.1	1	1649 207
57	8200	0.1	1	7510 690
58	148	0.1	1	102 46
59	300	0.1	1	224 76
60	5469	0.1	1	5029 440
61	83	0.1	1	52 31
62	89	0.1	1	64 25
63	1331	0.1	1	1206 125
64	2777	0.1	1	2523 254
65	2619	0.1	1	2410 209
66	2941	0.1	1	2671 270
67	1194	0.1	1	1080 114
68	866	0.1	1	770 96
69	572	0.1	1	506 66
70	746	0.1	1	685 61
71	1065	0.1	1	979 86
72	1080	0.1	1	978 102
73	979	0.1	1	881 98
74	963	0.1	1	897 66
75	847	0.1	1	771 76
76	894	0.1	1	815 79
77	809	0.1	1	743 66
78	755	0.1	1	681 74
79	707	0.1	1	625 82
80	697	0.1	1	620 77
81	662	0.1	1	588 74
82	553	0.1	1	498 55
83	540	0.1	1	479 61
84	554	0.1	1	510 44
85	470	0.1	1	420 50
86	455	0.1	1	416 39
87	372	0.1	1	340 32
88	399	0.1	1	361 38
89	381	0.1	1	348 33
90	360	0.1	1	322 38
91	305	0.1	1	264 41
92	313	0.1	1	259 54
93	292	0.1	1	253 39
94	244	0.1	1	205 39
95	396	0.1	1	371 25
96	233	0.1	1	193 40
97	290	0.1	1	202 88
98	513	0.1	1	412 101
99	343	0.1	1	246 97
100	379	0.1	1	196 183
101	272	0.1	1	215 57
102	338	0.1	1	165 173
103	161	0.1	1	127 34
104	159	0.1	1	140 19
105	131	0.1	1	115 16
106	119	0.1	1	103 16
107	314	0.1	1	286 28
108	113	0.1	1	98 15
109	105	0.1	1	97 8
110	107	0.1	1	97 10
111	108	0.1	1	93 15
112	99	0.1	1	88 11
113	102	0.1	1	93 9
114	77	0.1	1	69 8
115	124	0.1	1	115 9
116	109	0.1	1	97 12
117	108	0.1	1	101 7
118	94	0.1	1	87 7
119	107	0.1	1	89 18
120	94	0.1	1	84 10
121	90	0.1	1	82 8
122	99	0.1	1	89 10
123	96	0.1	1	91 5
124	91	0.1	1	79 12
125	119	0.1	1	112 7
126	106	0.1	1	99 7
127	117	0.1	1	111 6
128	121	0.1	1	115 6
129	78	0.1	1	74 4
130	142	0.1	1	128 14
131	124	0.1	1	116 8
132	102	0.1	1	98 4
133	87	0.1	1	83 4
134	132	0.1	1	123 9
135	103	0.1	1	100 3
136	107	0.1	1	100 7
137	103	0.1	1	94 9
138	87	0.1	1	83 4
139	92	0.1	1	86 6
140	51	0.1	1	46 5
141	59	0.1	1	57 2
142	81	0.1	1	74 7
143	33	0.1	1	29 4
144	36	0.1	1	24 12
145	15	0.1	1	12 3
146	24	0.1	1	21 3
147	31	0.1	1	23 8
148	78	0.1	1	51 27
149	54	0.1	1	18 36
150	414	0.1	1	14 400
151	96951	0.1	1	29 96922


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R1_001_val_1.fq.gz
=============================================
3414678 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR006_S3_L001_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R2_001_val_2.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 90.38 s (26 us/read; 2.27 M reads/minute).

=== Summary ===

Total reads processed:               3,414,678
Reads with adapters:                 2,052,960 (60.1%)
Reads written (passing filters):     3,414,678 (100.0%)

Total basepairs processed:   511,788,024 bp
Quality-trimmed:                 118,164 bp (0.0%)
Total written (filtered):    489,484,820 bp (95.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2052960 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 33.3%
  C: 24.6%
  G: 20.0%
  T: 22.0%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	957570	853669.5	0	957570
2	185662	213417.4	0	185662
3	88214	53354.3	0	88214
4	62857	13338.6	0	62857
5	648	3334.6	0	648
6	22936	833.7	0	22936
7	21575	208.4	0	21575
8	26642	52.1	0	26642
9	18194	13.0	0	18044 150
10	23184	3.3	1	21583 1601
11	22594	0.8	1	20464 2130
12	44904	0.2	1	41486 3418
13	394	0.1	1	140 254
14	26379	0.1	1	23897 2482
15	37633	0.1	1	34681 2952
16	156	0.1	1	67 89
17	24969	0.1	1	23055 1914
18	15222	0.1	1	13957 1265
19	25320	0.1	1	23370 1950
20	18350	0.1	1	16863 1487
21	15725	0.1	1	14432 1293
22	17997	0.1	1	16711 1286
23	18683	0.1	1	17160 1523
24	31064	0.1	1	28646 2418
25	16194	0.1	1	15046 1148
26	15991	0.1	1	14743 1248
27	9854	0.1	1	8749 1105
28	25467	0.1	1	24052 1415
29	5203	0.1	1	4539 664
30	22296	0.1	1	21075 1221
31	7804	0.1	1	7015 789
32	37956	0.1	1	36145 1811
33	13298	0.1	1	12180 1118
34	4051	0.1	1	3571 480
35	18620	0.1	1	17659 961
36	5530	0.1	1	5038 492
37	7956	0.1	1	7339 617
38	4368	0.1	1	4085 283
39	5419	0.1	1	5047 372
40	2384	0.1	1	2228 156
41	8956	0.1	1	8433 523
42	11614	0.1	1	11004 610
43	5102	0.1	1	4746 356
44	7806	0.1	1	7359 447
45	12470	0.1	1	11850 620
46	5755	0.1	1	5352 403
47	4015	0.1	1	3771 244
48	10930	0.1	1	10468 462
49	4516	0.1	1	4246 270
50	1545	0.1	1	1442 103
51	7427	0.1	1	7059 368
52	11021	0.1	1	10573 448
53	4130	0.1	1	3937 193
54	4451	0.1	1	4236 215
55	2750	0.1	1	2622 128
56	1357	0.1	1	1273 84
57	2213	0.1	1	2091 122
58	2275	0.1	1	2152 123
59	1161	0.1	1	1103 58
60	739	0.1	1	682 57
61	628	0.1	1	577 51
62	684	0.1	1	638 46
63	847	0.1	1	799 48
64	1373	0.1	1	1321 52
65	1579	0.1	1	1493 86
66	1616	0.1	1	1543 73
67	1569	0.1	1	1490 79
68	1449	0.1	1	1378 71
69	1380	0.1	1	1323 57
70	1355	0.1	1	1285 70
71	1219	0.1	1	1169 50
72	1120	0.1	1	1065 55
73	989	0.1	1	950 39
74	939	0.1	1	898 41
75	833	0.1	1	798 35
76	880	0.1	1	836 44
77	792	0.1	1	760 32
78	719	0.1	1	680 39
79	660	0.1	1	631 29
80	658	0.1	1	626 32
81	635	0.1	1	608 27
82	550	0.1	1	524 26
83	496	0.1	1	467 29
84	532	0.1	1	505 27
85	454	0.1	1	432 22
86	439	0.1	1	419 20
87	375	0.1	1	359 16
88	384	0.1	1	363 21
89	367	0.1	1	356 11
90	357	0.1	1	347 10
91	323	0.1	1	308 15
92	278	0.1	1	267 11
93	275	0.1	1	263 12
94	227	0.1	1	214 13
95	234	0.1	1	224 10
96	199	0.1	1	183 16
97	214	0.1	1	194 20
98	342	0.1	1	285 57
99	253	0.1	1	223 30
100	225	0.1	1	211 14
101	211	0.1	1	182 29
102	180	0.1	1	168 12
103	137	0.1	1	126 11
104	155	0.1	1	143 12
105	124	0.1	1	122 2
106	113	0.1	1	104 9
107	296	0.1	1	288 8
108	113	0.1	1	107 6
109	111	0.1	1	107 4
110	108	0.1	1	102 6
111	110	0.1	1	104 6
112	105	0.1	1	101 4
113	106	0.1	1	97 9
114	81	0.1	1	76 5
115	114	0.1	1	109 5
116	105	0.1	1	94 11
117	96	0.1	1	87 9
118	97	0.1	1	88 9
119	92	0.1	1	87 5
120	93	0.1	1	89 4
121	83	0.1	1	77 6
122	91	0.1	1	88 3
123	99	0.1	1	91 8
124	107	0.1	1	92 15
125	112	0.1	1	104 8
126	95	0.1	1	89 6
127	115	0.1	1	104 11
128	105	0.1	1	101 4
129	79	0.1	1	76 3
130	138	0.1	1	127 11
131	122	0.1	1	113 9
132	107	0.1	1	97 10
133	87	0.1	1	80 7
134	123	0.1	1	109 14
135	102	0.1	1	93 9
136	106	0.1	1	92 14
137	93	0.1	1	78 15
138	89	0.1	1	76 13
139	92	0.1	1	77 15
140	45	0.1	1	35 10
141	57	0.1	1	43 14
142	78	0.1	1	61 17
143	29	0.1	1	15 14
144	27	0.1	1	13 14
145	13	0.1	1	7 6
146	19	0.1	1	9 10
147	21	0.1	1	9 12
148	50	0.1	1	29 21
149	16	0.1	1	8 8
150	19	0.1	1	10 9
151	150	0.1	1	26 124


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L001_R2_001_val_2.fq.gz
=============================================
3414678 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR006_S3_L001_R1_001_val_1_trimmed.fq.gz and NR006_S3_L001_R2_001_val_2_trimmed.fq.gz
file_1: NR006_S3_L001_R1_001_val_1_trimmed.fq.gz, file_2: NR006_S3_L001_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR006_S3_L001_R1_001_val_1_trimmed.fq.gz and NR006_S3_L001_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR006_S3_L001_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 3414678

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 99013 (2.90%)

Deleting both intermediate output files NR006_S3_L001_R1_001_val_1_trimmed.fq.gz and NR006_S3_L001_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR006_S3_L002_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R1_001_val_1.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 79.63 s (26 us/read; 2.28 M reads/minute).

=== Summary ===

Total reads processed:               3,031,025
Reads with adapters:                 1,929,386 (63.7%)
Reads written (passing filters):     3,031,025 (100.0%)

Total basepairs processed:   455,473,203 bp
Quality-trimmed:                  59,204 bp (0.0%)
Total written (filtered):    412,084,346 bp (90.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1929386 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 29.7%
  C: 25.2%
  G: 18.5%
  T: 19.2%
  none/other: 7.3%

Overview of removed sequences
length	count	expect	max.err	error counts
1	788408	757756.2	0	788408
2	151285	189439.1	0	151285
3	67064	47359.8	0	67064
4	53544	11839.9	0	53544
5	487	2960.0	0	487
6	20856	740.0	0	20856
7	19031	185.0	0	19031
8	21515	46.2	0	21515
9	19602	11.6	0	19467 135
10	20380	2.9	1	19099 1281
11	21123	0.7	1	19494 1629
12	40181	0.2	1	37607 2574
13	635	0.0	1	259 376
14	39626	0.0	1	36980 2646
15	546	0.0	1	216 330
16	40328	0.0	1	37445 2883
17	781	0.0	1	428 353
18	24020	0.0	1	22173 1847
19	64281	0.0	1	60433 3848
20	390	0.0	1	219 171
21	136	0.0	1	107 29
22	298	0.0	1	212 86
23	18040	0.0	1	16632 1408
24	47127	0.0	1	43895 3232
25	820	0.0	1	521 299
26	15602	0.0	1	14517 1085
27	14558	0.0	1	13600 958
28	317	0.0	1	213 104
29	14674	0.0	1	13589 1085
30	16895	0.0	1	15657 1238
31	23644	0.0	1	22177 1467
32	688	0.0	1	446 242
33	23967	0.0	1	22293 1674
34	1270	0.0	1	965 305
35	21680	0.0	1	20211 1469
36	10887	0.0	1	10143 744
37	243	0.0	1	157 86
38	9846	0.0	1	9114 732
39	10438	0.0	1	9648 790
40	8976	0.0	1	8310 666
41	10247	0.0	1	9296 951
42	22213	0.0	1	20655 1558
43	4212	0.0	1	3853 359
44	3399	0.0	1	3115 284
45	122	0.0	1	89 33
46	6912	0.0	1	6349 563
47	6086	0.0	1	5620 466
48	6045	0.0	1	5510 535
49	6310	0.0	1	5804 506
50	10220	0.0	1	9462 758
51	4524	0.0	1	4143 381
52	191	0.0	1	121 70
53	5734	0.0	1	5264 470
54	11519	0.0	1	10583 936
55	261	0.0	1	210 51
56	1303	0.0	1	1144 159
57	9194	0.0	1	8511 683
58	118	0.0	1	84 34
59	170	0.0	1	104 66
60	5353	0.0	1	4961 392
61	68	0.0	1	39 29
62	55	0.0	1	36 19
63	1544	0.0	1	1403 141
64	2235	0.0	1	2041 194
65	2238	0.0	1	2057 181
66	2678	0.0	1	2481 197
67	1852	0.0	1	1687 165
68	2019	0.0	1	1822 197
69	391	0.0	1	347 44
70	605	0.0	1	551 54
71	1093	0.0	1	1007 86
72	1059	0.0	1	980 79
73	1081	0.0	1	983 98
74	1093	0.0	1	991 102
75	962	0.0	1	884 78
76	906	0.0	1	823 83
77	876	0.0	1	798 78
78	823	0.0	1	723 100
79	822	0.0	1	745 77
80	790	0.0	1	713 77
81	698	0.0	1	629 69
82	635	0.0	1	575 60
83	596	0.0	1	528 68
84	583	0.0	1	530 53
85	491	0.0	1	442 49
86	475	0.0	1	424 51
87	442	0.0	1	395 47
88	480	0.0	1	412 68
89	416	0.0	1	373 43
90	372	0.0	1	332 40
91	335	0.0	1	297 38
92	347	0.0	1	300 47
93	309	0.0	1	274 35
94	312	0.0	1	265 47
95	472	0.0	1	443 29
96	279	0.0	1	253 26
97	332	0.0	1	233 99
98	520	0.0	1	407 113
99	445	0.0	1	326 119
100	435	0.0	1	249 186
101	350	0.0	1	280 70
102	357	0.0	1	182 175
103	219	0.0	1	171 48
104	248	0.0	1	222 26
105	153	0.0	1	129 24
106	144	0.0	1	127 17
107	348	0.0	1	326 22
108	186	0.0	1	156 30
109	175	0.0	1	157 18
110	163	0.0	1	148 15
111	147	0.0	1	126 21
112	146	0.0	1	137 9
113	124	0.0	1	115 9
114	124	0.0	1	112 12
115	165	0.0	1	152 13
116	161	0.0	1	142 19
117	138	0.0	1	128 10
118	144	0.0	1	132 12
119	139	0.0	1	127 12
120	132	0.0	1	114 18
121	122	0.0	1	108 14
122	147	0.0	1	137 10
123	169	0.0	1	152 17
124	133	0.0	1	126 7
125	170	0.0	1	158 12
126	123	0.0	1	109 14
127	176	0.0	1	169 7
128	143	0.0	1	135 8
129	173	0.0	1	168 5
130	186	0.0	1	169 17
131	142	0.0	1	134 8
132	129	0.0	1	123 6
133	152	0.0	1	145 7
134	164	0.0	1	158 6
135	129	0.0	1	117 12
136	152	0.0	1	140 12
137	133	0.0	1	126 7
138	125	0.0	1	119 6
139	129	0.0	1	124 5
140	75	0.0	1	66 9
141	90	0.0	1	81 9
142	137	0.0	1	125 12
143	60	0.0	1	56 4
144	50	0.0	1	42 8
145	25	0.0	1	23 2
146	51	0.0	1	45 6
147	51	0.0	1	37 14
148	107	0.0	1	79 28
149	79	0.0	1	36 43
150	395	0.0	1	14 381
151	141220	0.0	1	56 141164


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R1_001_val_1.fq.gz
=============================================
3031025 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR006_S3_L002_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R2_001_val_2.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 80.21 s (26 us/read; 2.27 M reads/minute).

=== Summary ===

Total reads processed:               3,031,025
Reads with adapters:                 1,797,618 (59.3%)
Reads written (passing filters):     3,031,025 (100.0%)

Total basepairs processed:   454,130,095 bp
Quality-trimmed:                  81,905 bp (0.0%)
Total written (filtered):    432,938,122 bp (95.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1797618 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 32.9%
  C: 25.0%
  G: 20.4%
  T: 21.7%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	803750	757756.2	0	803750
2	159777	189439.1	0	159777
3	74983	47359.8	0	74983
4	55464	11839.9	0	55464
5	534	2960.0	0	534
6	20415	740.0	0	20415
7	19928	185.0	0	19928
8	23459	46.2	0	23459
9	17406	11.6	0	17255 151
10	20562	2.9	1	19800 762
11	19822	0.7	1	18851 971
12	39785	0.2	1	38357 1428
13	251	0.0	1	63 188
14	22463	0.0	1	21347 1116
15	35189	0.0	1	33798 1391
16	162	0.0	1	69 93
17	22058	0.0	1	21192 866
18	14401	0.0	1	13797 604
19	21417	0.0	1	20543 874
20	16595	0.0	1	15928 667
21	15273	0.0	1	14570 703
22	16562	0.0	1	15897 665
23	16572	0.0	1	15858 714
24	23886	0.0	1	22883 1003
25	15834	0.0	1	15311 523
26	15356	0.0	1	14732 624
27	9520	0.0	1	8970 550
28	23049	0.0	1	22321 728
29	4963	0.0	1	4603 360
30	21010	0.0	1	20327 683
31	6944	0.0	1	6487 457
32	40614	0.0	1	39579 1035
33	11790	0.0	1	11296 494
34	3553	0.0	1	3261 292
35	19784	0.0	1	19297 487
36	3727	0.0	1	3499 228
37	7832	0.0	1	7453 379
38	2360	0.0	1	2247 113
39	4177	0.0	1	4003 174
40	1155	0.0	1	1084 71
41	8529	0.0	1	8285 244
42	11564	0.0	1	11239 325
43	4405	0.0	1	4220 185
44	7519	0.0	1	7261 258
45	14908	0.0	1	14491 417
46	5316	0.0	1	5076 240
47	3010	0.0	1	2866 144
48	12584	0.0	1	12240 344
49	3165	0.0	1	3063 102
50	895	0.0	1	841 54
51	7922	0.0	1	7682 240
52	13903	0.0	1	13616 287
53	3428	0.0	1	3297 131
54	4044	0.0	1	3901 143
55	1734	0.0	1	1680 54
56	889	0.0	1	818 71
57	1690	0.0	1	1620 70
58	1719	0.0	1	1649 70
59	761	0.0	1	721 40
60	547	0.0	1	521 26
61	484	0.0	1	454 30
62	497	0.0	1	468 29
63	572	0.0	1	547 25
64	1256	0.0	1	1215 41
65	1584	0.0	1	1533 51
66	1636	0.0	1	1586 50
67	1562	0.0	1	1515 47
68	1413	0.0	1	1368 45
69	1431	0.0	1	1386 45
70	1373	0.0	1	1324 49
71	1279	0.0	1	1241 38
72	1137	0.0	1	1092 45
73	1089	0.0	1	1040 49
74	1049	0.0	1	1008 41
75	952	0.0	1	930 22
76	884	0.0	1	844 40
77	850	0.0	1	825 25
78	785	0.0	1	757 28
79	789	0.0	1	761 28
80	759	0.0	1	730 29
81	660	0.0	1	633 27
82	621	0.0	1	595 26
83	561	0.0	1	528 33
84	581	0.0	1	551 30
85	472	0.0	1	452 20
86	464	0.0	1	446 18
87	455	0.0	1	439 16
88	459	0.0	1	439 20
89	409	0.0	1	390 19
90	391	0.0	1	367 24
91	381	0.0	1	362 19
92	325	0.0	1	308 17
93	325	0.0	1	309 16
94	299	0.0	1	289 10
95	301	0.0	1	289 12
96	283	0.0	1	261 22
97	265	0.0	1	249 16
98	369	0.0	1	308 61
99	341	0.0	1	305 36
100	291	0.0	1	278 13
101	288	0.0	1	257 31
102	207	0.0	1	199 8
103	196	0.0	1	185 11
104	233	0.0	1	216 17
105	164	0.0	1	154 10
106	146	0.0	1	136 10
107	328	0.0	1	316 12
108	188	0.0	1	176 12
109	171	0.0	1	162 9
110	162	0.0	1	153 9
111	151	0.0	1	143 8
112	147	0.0	1	138 9
113	141	0.0	1	132 9
114	129	0.0	1	120 9
115	154	0.0	1	147 7
116	156	0.0	1	154 2
117	138	0.0	1	130 8
118	144	0.0	1	134 10
119	137	0.0	1	130 7
120	126	0.0	1	121 5
121	120	0.0	1	115 5
122	148	0.0	1	138 10
123	164	0.0	1	153 11
124	154	0.0	1	139 15
125	162	0.0	1	158 4
126	113	0.0	1	106 7
127	176	0.0	1	166 10
128	141	0.0	1	134 7
129	174	0.0	1	169 5
130	175	0.0	1	158 17
131	139	0.0	1	132 7
132	127	0.0	1	122 5
133	150	0.0	1	142 8
134	159	0.0	1	148 11
135	120	0.0	1	114 6
136	146	0.0	1	131 15
137	127	0.0	1	116 11
138	123	0.0	1	101 22
139	125	0.0	1	112 13
140	69	0.0	1	59 10
141	86	0.0	1	73 13
142	125	0.0	1	108 17
143	56	0.0	1	42 14
144	43	0.0	1	29 14
145	25	0.0	1	13 12
146	39	0.0	1	30 9
147	31	0.0	1	14 17
148	81	0.0	1	38 43
149	37	0.0	1	21 16
150	18	0.0	1	7 11
151	211	0.0	1	46 165


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR006_S3_L002_R2_001_val_2.fq.gz
=============================================
3031025 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR006_S3_L002_R1_001_val_1_trimmed.fq.gz and NR006_S3_L002_R2_001_val_2_trimmed.fq.gz
file_1: NR006_S3_L002_R1_001_val_1_trimmed.fq.gz, file_2: NR006_S3_L002_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR006_S3_L002_R1_001_val_1_trimmed.fq.gz and NR006_S3_L002_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR006_S3_L002_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 3031025

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 143798 (4.74%)

Deleting both intermediate output files NR006_S3_L002_R1_001_val_1_trimmed.fq.gz and NR006_S3_L002_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR012_S1_L001_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R1_001_val_1.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 7.24 s (26 us/read; 2.33 M reads/minute).

=== Summary ===

Total reads processed:                 281,472
Reads with adapters:                   121,688 (43.2%)
Reads written (passing filters):       281,472 (100.0%)

Total basepairs processed:    35,695,401 bp
Quality-trimmed:                  15,812 bp (0.0%)
Total written (filtered):     34,569,512 bp (96.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 121688 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 31.3%
  C: 23.7%
  G: 15.8%
  T: 26.8%
  none/other: 2.5%

Overview of removed sequences
length	count	expect	max.err	error counts
1	75815	70368.0	0	75815
2	19000	17592.0	0	19000
3	5354	4398.0	0	5354
4	2554	1099.5	0	2554
5	243	274.9	0	243
6	426	68.7	0	426
7	331	17.2	0	331
8	402	4.3	0	402
9	348	1.1	0	346 2
10	401	0.3	1	365 36
11	394	0.1	1	352 42
12	746	0.0	1	695 51
13	21	0.0	1	11 10
14	750	0.0	1	686 64
15	14	0.0	1	8 6
16	792	0.0	1	723 69
17	29	0.0	1	20 9
18	456	0.0	1	419 37
19	1132	0.0	1	1070 62
20	9	0.0	1	5 4
21	3	0.0	1	1 2
22	9	0.0	1	6 3
23	386	0.0	1	351 35
24	901	0.0	1	828 73
25	15	0.0	1	10 5
26	308	0.0	1	288 20
27	287	0.0	1	258 29
28	7	0.0	1	5 2
29	301	0.0	1	264 37
30	340	0.0	1	310 30
31	454	0.0	1	425 29
32	19	0.0	1	16 3
33	507	0.0	1	457 50
34	456	0.0	1	431 25
35	18	0.0	1	16 2
36	60	0.0	1	51 9
37	216	0.0	1	198 18
38	218	0.0	1	197 21
39	255	0.0	1	242 13
40	185	0.0	1	168 17
41	200	0.0	1	172 28
42	414	0.0	1	387 27
43	106	0.0	1	94 12
44	98	0.0	1	87 11
45	96	0.0	1	78 18
46	237	0.0	1	220 17
47	156	0.0	1	143 13
48	113	0.0	1	103 10
49	342	0.0	1	323 19
50	243	0.0	1	220 23
51	78	0.0	1	74 4
52	71	0.0	1	66 5
53	244	0.0	1	229 15
54	161	0.0	1	153 8
55	30	0.0	1	26 4
56	46	0.0	1	41 5
57	182	0.0	1	167 15
58	9	0.0	1	8 1
59	34	0.0	1	24 10
60	87	0.0	1	84 3
61	3	0.0	1	3
62	16	0.0	1	10 6
63	56	0.0	1	48 8
64	85	0.0	1	79 6
65	52	0.0	1	40 12
66	55	0.0	1	54 1
67	35	0.0	1	32 3
68	20	0.0	1	18 2
69	16	0.0	1	8 8
70	40	0.0	1	32 8
71	30	0.0	1	27 3
72	32	0.0	1	30 2
73	24	0.0	1	20 4
74	27	0.0	1	27
75	38	0.0	1	34 4
76	39	0.0	1	34 5
77	41	0.0	1	39 2
78	39	0.0	1	35 4
79	36	0.0	1	34 2
80	30	0.0	1	27 3
81	32	0.0	1	30 2
82	25	0.0	1	24 1
83	29	0.0	1	24 5
84	30	0.0	1	26 4
85	27	0.0	1	27
86	22	0.0	1	19 3
87	23	0.0	1	18 5
88	19	0.0	1	14 5
89	33	0.0	1	31 2
90	27	0.0	1	24 3
91	22	0.0	1	18 4
92	19	0.0	1	16 3
93	20	0.0	1	16 4
94	26	0.0	1	25 1
95	18	0.0	1	16 2
96	13	0.0	1	11 2
97	14	0.0	1	14
98	16	0.0	1	13 3
99	23	0.0	1	17 6
100	9	0.0	1	9
101	14	0.0	1	13 1
102	22	0.0	1	19 3
103	25	0.0	1	22 3
104	17	0.0	1	16 1
105	12	0.0	1	12
106	12	0.0	1	11 1
107	8	0.0	1	7 1
108	7	0.0	1	6 1
109	11	0.0	1	9 2
110	6	0.0	1	3 3
111	16	0.0	1	14 2
112	10	0.0	1	9 1
113	9	0.0	1	8 1
114	6	0.0	1	5 1
115	10	0.0	1	9 1
116	8	0.0	1	8
117	4	0.0	1	3 1
118	4	0.0	1	3 1
119	7	0.0	1	7
120	6	0.0	1	5 1
121	11	0.0	1	8 3
122	3	0.0	1	3
123	7	0.0	1	5 2
124	8	0.0	1	6 2
125	7	0.0	1	7
126	11	0.0	1	9 2
127	6	0.0	1	5 1
128	8	0.0	1	6 2
129	4	0.0	1	4
130	9	0.0	1	9
131	8	0.0	1	8
132	11	0.0	1	11
133	6	0.0	1	6
134	6	0.0	1	6
135	7	0.0	1	7
136	5	0.0	1	5
137	10	0.0	1	10
138	5	0.0	1	5
139	7	0.0	1	7
140	2	0.0	1	2
141	5	0.0	1	5
142	4	0.0	1	4
143	3	0.0	1	3
144	4	0.0	1	3 1
145	5	0.0	1	4 1
146	3	0.0	1	3
147	4	0.0	1	3 1
148	9	0.0	1	8 1
149	3	0.0	1	0 3
150	18	0.0	1	0 18
151	3005	0.0	1	83 2922


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R1_001_val_1.fq.gz
=============================================
281472 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR012_S1_L001_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R2_001_val_2.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 7.21 s (26 us/read; 2.34 M reads/minute).

=== Summary ===

Total reads processed:                 281,472
Reads with adapters:                   120,782 (42.9%)
Reads written (passing filters):       281,472 (100.0%)

Total basepairs processed:    36,447,504 bp
Quality-trimmed:                  19,787 bp (0.1%)
Total written (filtered):     35,723,779 bp (98.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 120782 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 32.5%
  C: 23.1%
  G: 16.7%
  T: 27.7%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	76746	70368.0	0	76746
2	19123	17592.0	0	19123
3	5743	4398.0	0	5743
4	2596	1099.5	0	2596
5	190	274.9	0	190
6	434	68.7	0	434
7	361	17.2	0	361
8	438	4.3	0	438
9	303	1.1	0	300 3
10	412	0.3	1	367 45
11	385	0.1	1	338 47
12	762	0.0	1	686 76
13	9	0.0	1	4 5
14	484	0.0	1	437 47
15	692	0.0	1	623 69
16	2	0.0	1	1 1
17	452	0.0	1	404 48
18	257	0.0	1	228 29
19	453	0.0	1	405 48
20	332	0.0	1	290 42
21	244	0.0	1	219 25
22	305	0.0	1	278 27
23	372	0.0	1	340 32
24	581	0.0	1	538 43
25	340	0.0	1	304 36
26	316	0.0	1	282 34
27	168	0.0	1	149 19
28	453	0.0	1	408 45
29	108	0.0	1	88 20
30	457	0.0	1	428 29
31	177	0.0	1	150 27
32	759	0.0	1	693 66
33	298	0.0	1	274 24
34	81	0.0	1	70 11
35	413	0.0	1	381 32
36	145	0.0	1	130 15
37	181	0.0	1	163 18
38	105	0.0	1	96 9
39	113	0.0	1	105 8
40	51	0.0	1	44 7
41	173	0.0	1	163 10
42	263	0.0	1	248 15
43	116	0.0	1	100 16
44	154	0.0	1	144 10
45	330	0.0	1	308 22
46	171	0.0	1	156 15
47	112	0.0	1	103 9
48	305	0.0	1	276 29
49	134	0.0	1	123 11
50	41	0.0	1	36 5
51	210	0.0	1	199 11
52	314	0.0	1	297 17
53	117	0.0	1	103 14
54	134	0.0	1	123 11
55	94	0.0	1	86 8
56	42	0.0	1	39 3
57	73	0.0	1	64 9
58	70	0.0	1	65 5
59	42	0.0	1	41 1
60	31	0.0	1	29 2
61	24	0.0	1	19 5
62	27	0.0	1	20 7
63	27	0.0	1	25 2
64	48	0.0	1	44 4
65	55	0.0	1	53 2
66	76	0.0	1	74 2
67	59	0.0	1	59
68	50	0.0	1	48 2
69	54	0.0	1	51 3
70	60	0.0	1	53 7
71	46	0.0	1	44 2
72	48	0.0	1	45 3
73	46	0.0	1	43 3
74	51	0.0	1	47 4
75	48	0.0	1	44 4
76	51	0.0	1	46 5
77	46	0.0	1	42 4
78	42	0.0	1	37 5
79	39	0.0	1	34 5
80	38	0.0	1	32 6
81	41	0.0	1	35 6
82	44	0.0	1	40 4
83	40	0.0	1	33 7
84	33	0.0	1	27 6
85	30	0.0	1	26 4
86	30	0.0	1	25 5
87	32	0.0	1	29 3
88	25	0.0	1	23 2
89	32	0.0	1	28 4
90	33	0.0	1	28 5
91	25	0.0	1	20 5
92	19	0.0	1	17 2
93	22	0.0	1	20 2
94	25	0.0	1	24 1
95	27	0.0	1	23 4
96	23	0.0	1	19 4
97	18	0.0	1	17 1
98	22	0.0	1	18 4
99	26	0.0	1	22 4
100	13	0.0	1	12 1
101	22	0.0	1	16 6
102	19	0.0	1	17 2
103	26	0.0	1	23 3
104	16	0.0	1	15 1
105	15	0.0	1	13 2
106	16	0.0	1	15 1
107	10	0.0	1	7 3
108	11	0.0	1	9 2
109	15	0.0	1	11 4
110	7	0.0	1	7
111	16	0.0	1	15 1
112	11	0.0	1	10 1
113	9	0.0	1	8 1
114	7	0.0	1	7
115	10	0.0	1	9 1
116	11	0.0	1	9 2
117	10	0.0	1	5 5
118	4	0.0	1	1 3
119	9	0.0	1	7 2
120	9	0.0	1	8 1
121	9	0.0	1	8 1
122	3	0.0	1	3
123	6	0.0	1	5 1
124	8	0.0	1	6 2
125	4	0.0	1	4
126	14	0.0	1	11 3
127	6	0.0	1	6
128	8	0.0	1	8
129	4	0.0	1	3 1
130	9	0.0	1	9
131	8	0.0	1	8
132	11	0.0	1	8 3
133	6	0.0	1	6
134	6	0.0	1	6
135	8	0.0	1	7 1
136	5	0.0	1	5
137	9	0.0	1	9
138	5	0.0	1	5
139	7	0.0	1	7
140	2	0.0	1	2
141	4	0.0	1	2 2
142	4	0.0	1	3 1
143	3	0.0	1	3
144	3	0.0	1	2 1
145	5	0.0	1	0 5
146	4	0.0	1	3 1
147	2	0.0	1	0 2
148	9	0.0	1	3 6
151	95	0.0	1	83 12


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L001_R2_001_val_2.fq.gz
=============================================
281472 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR012_S1_L001_R1_001_val_1_trimmed.fq.gz and NR012_S1_L001_R2_001_val_2_trimmed.fq.gz
file_1: NR012_S1_L001_R1_001_val_1_trimmed.fq.gz, file_2: NR012_S1_L001_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR012_S1_L001_R1_001_val_1_trimmed.fq.gz and NR012_S1_L001_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR012_S1_L001_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 281472

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3813 (1.35%)

Deleting both intermediate output files NR012_S1_L001_R1_001_val_1_trimmed.fq.gz and NR012_S1_L001_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR012_S1_L002_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R1_001_val_1.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 8.48 s (26 us/read; 2.31 M reads/minute).

=== Summary ===

Total reads processed:                 326,252
Reads with adapters:                   140,395 (43.0%)
Reads written (passing filters):       326,252 (100.0%)

Total basepairs processed:    41,596,018 bp
Quality-trimmed:                  15,103 bp (0.0%)
Total written (filtered):     40,182,403 bp (96.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 140395 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 30.8%
  C: 23.3%
  G: 15.5%
  T: 27.4%
  none/other: 3.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	89057	81563.0	0	89057
2	21691	20390.8	0	21691
3	6146	5097.7	0	6146
4	2757	1274.4	0	2757
5	208	318.6	0	208
6	391	79.7	0	391
7	349	19.9	0	349
8	371	5.0	0	371
9	332	1.2	0	327 5
10	366	0.3	1	334 32
11	354	0.1	1	331 23
12	685	0.0	1	644 41
13	17	0.0	1	12 5
14	670	0.0	1	629 41
15	12	0.0	1	6 6
16	719	0.0	1	672 47
17	24	0.0	1	18 6
18	430	0.0	1	401 29
19	1193	0.0	1	1140 53
20	4	0.0	1	3 1
21	3	0.0	1	0 3
22	10	0.0	1	6 4
23	335	0.0	1	305 30
24	840	0.0	1	795 45
25	23	0.0	1	18 5
26	324	0.0	1	298 26
27	263	0.0	1	244 19
28	1	0.0	1	0 1
29	279	0.0	1	257 22
30	328	0.0	1	297 31
31	474	0.0	1	448 26
32	15	0.0	1	9 6
33	498	0.0	1	460 38
34	453	0.0	1	429 24
35	34	0.0	1	30 4
36	70	0.0	1	62 8
37	206	0.0	1	190 16
38	233	0.0	1	226 7
39	231	0.0	1	216 15
40	180	0.0	1	165 15
41	237	0.0	1	218 19
42	398	0.0	1	371 27
43	102	0.0	1	89 13
44	87	0.0	1	70 17
45	113	0.0	1	95 18
46	178	0.0	1	161 17
47	171	0.0	1	156 15
48	141	0.0	1	120 21
49	406	0.0	1	380 26
50	244	0.0	1	236 8
51	89	0.0	1	83 6
52	91	0.0	1	80 11
53	260	0.0	1	237 23
54	197	0.0	1	192 5
55	40	0.0	1	27 13
56	88	0.0	1	75 13
57	191	0.0	1	185 6
58	6	0.0	1	4 2
59	54	0.0	1	45 9
60	82	0.0	1	75 7
61	7	0.0	1	6 1
62	19	0.0	1	13 6
63	63	0.0	1	56 7
64	91	0.0	1	81 10
65	71	0.0	1	63 8
66	71	0.0	1	61 10
67	75	0.0	1	63 12
68	49	0.0	1	43 6
69	17	0.0	1	15 2
70	35	0.0	1	33 2
71	46	0.0	1	44 2
72	41	0.0	1	40 1
73	44	0.0	1	39 5
74	40	0.0	1	32 8
75	57	0.0	1	51 6
76	53	0.0	1	49 4
77	54	0.0	1	49 5
78	44	0.0	1	41 3
79	37	0.0	1	35 2
80	57	0.0	1	49 8
81	47	0.0	1	38 9
82	52	0.0	1	49 3
83	36	0.0	1	29 7
84	46	0.0	1	34 12
85	56	0.0	1	48 8
86	47	0.0	1	40 7
87	32	0.0	1	28 4
88	49	0.0	1	41 8
89	44	0.0	1	35 9
90	41	0.0	1	33 8
91	38	0.0	1	33 5
92	41	0.0	1	35 6
93	42	0.0	1	36 6
94	32	0.0	1	27 5
95	28	0.0	1	23 5
96	29	0.0	1	28 1
97	41	0.0	1	35 6
98	35	0.0	1	26 9
99	23	0.0	1	21 2
100	25	0.0	1	22 3
101	33	0.0	1	29 4
102	19	0.0	1	18 1
103	26	0.0	1	21 5
104	17	0.0	1	14 3
105	30	0.0	1	25 5
106	26	0.0	1	20 6
107	18	0.0	1	18
108	20	0.0	1	14 6
109	17	0.0	1	16 1
110	14	0.0	1	11 3
111	15	0.0	1	14 1
112	20	0.0	1	16 4
113	17	0.0	1	12 5
114	17	0.0	1	9 8
115	21	0.0	1	18 3
116	16	0.0	1	11 5
117	14	0.0	1	11 3
118	13	0.0	1	11 2
119	24	0.0	1	21 3
120	12	0.0	1	9 3
121	10	0.0	1	6 4
122	17	0.0	1	12 5
123	11	0.0	1	9 2
124	6	0.0	1	3 3
125	12	0.0	1	9 3
126	14	0.0	1	12 2
127	14	0.0	1	11 3
128	6	0.0	1	6
129	9	0.0	1	7 2
130	13	0.0	1	11 2
131	14	0.0	1	13 1
132	7	0.0	1	7
133	9	0.0	1	9
134	14	0.0	1	13 1
135	7	0.0	1	6 1
136	5	0.0	1	5
137	10	0.0	1	10
138	6	0.0	1	6
139	8	0.0	1	8
140	5	0.0	1	5
141	3	0.0	1	3
142	5	0.0	1	4 1
143	4	0.0	1	4
144	2	0.0	1	2
145	3	0.0	1	2 1
146	4	0.0	1	4
147	4	0.0	1	2 2
148	9	0.0	1	8 1
149	3	0.0	1	1 2
150	23	0.0	1	4 19
151	4243	0.0	1	117 4126


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R1_001_val_1.fq.gz
=============================================
326252 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR012_S1_L002_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R2_001_val_2.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 8.52 s (26 us/read; 2.30 M reads/minute).

=== Summary ===

Total reads processed:                 326,252
Reads with adapters:                   139,337 (42.7%)
Reads written (passing filters):       326,252 (100.0%)

Total basepairs processed:    42,562,422 bp
Quality-trimmed:                  18,976 bp (0.0%)
Total written (filtered):     41,698,391 bp (98.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 139337 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 32.2%
  C: 23.0%
  G: 16.3%
  T: 28.4%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	90369	81563.0	0	90369
2	21799	20390.8	0	21799
3	6520	5097.7	0	6520
4	2800	1274.4	0	2800
5	171	318.6	0	171
6	409	79.7	0	409
7	410	19.9	0	410
8	426	5.0	0	426
9	296	1.2	0	293 3
10	393	0.3	1	365 28
11	373	0.1	1	327 46
12	713	0.0	1	666 47
13	1	0.0	1	1
14	417	0.0	1	385 32
15	651	0.0	1	606 45
16	4	0.0	1	2 2
17	417	0.0	1	387 30
18	271	0.0	1	253 18
19	440	0.0	1	414 26
20	340	0.0	1	332 8
21	291	0.0	1	273 18
22	366	0.0	1	341 25
23	319	0.0	1	299 20
24	493	0.0	1	459 34
25	339	0.0	1	303 36
26	319	0.0	1	302 17
27	190	0.0	1	175 15
28	444	0.0	1	430 14
29	123	0.0	1	107 16
30	446	0.0	1	422 24
31	180	0.0	1	156 24
32	875	0.0	1	837 38
33	307	0.0	1	287 20
34	94	0.0	1	85 9
35	482	0.0	1	454 28
36	93	0.0	1	84 9
37	215	0.0	1	203 12
38	67	0.0	1	64 3
39	102	0.0	1	93 9
40	35	0.0	1	31 4
41	180	0.0	1	171 9
42	278	0.0	1	265 13
43	122	0.0	1	114 8
44	173	0.0	1	158 15
45	360	0.0	1	338 22
46	177	0.0	1	165 12
47	85	0.0	1	77 8
48	420	0.0	1	397 23
49	99	0.0	1	95 4
50	38	0.0	1	28 10
51	242	0.0	1	218 24
52	450	0.0	1	439 11
53	126	0.0	1	119 7
54	140	0.0	1	129 11
55	65	0.0	1	62 3
56	46	0.0	1	38 8
57	71	0.0	1	65 6
58	90	0.0	1	86 4
59	36	0.0	1	31 5
60	23	0.0	1	21 2
61	20	0.0	1	16 4
62	24	0.0	1	21 3
63	30	0.0	1	25 5
64	37	0.0	1	34 3
65	67	0.0	1	60 7
66	79	0.0	1	71 8
67	89	0.0	1	83 6
68	91	0.0	1	82 9
69	72	0.0	1	69 3
70	79	0.0	1	68 11
71	72	0.0	1	57 15
72	73	0.0	1	68 5
73	72	0.0	1	63 9
74	61	0.0	1	54 7
75	81	0.0	1	75 6
76	71	0.0	1	62 9
77	68	0.0	1	62 6
78	65	0.0	1	59 6
79	56	0.0	1	49 7
80	66	0.0	1	59 7
81	57	0.0	1	51 6
82	60	0.0	1	53 7
83	48	0.0	1	41 7
84	47	0.0	1	41 6
85	61	0.0	1	52 9
86	47	0.0	1	40 7
87	41	0.0	1	36 5
88	60	0.0	1	56 4
89	49	0.0	1	43 6
90	54	0.0	1	52 2
91	51	0.0	1	49 2
92	50	0.0	1	43 7
93	52	0.0	1	47 5
94	49	0.0	1	37 12
95	38	0.0	1	34 4
96	36	0.0	1	33 3
97	53	0.0	1	48 5
98	40	0.0	1	32 8
99	34	0.0	1	28 6
100	33	0.0	1	26 7
101	34	0.0	1	29 5
102	33	0.0	1	28 5
103	26	0.0	1	22 4
104	27	0.0	1	20 7
105	25	0.0	1	23 2
106	31	0.0	1	26 5
107	23	0.0	1	21 2
108	17	0.0	1	15 2
109	25	0.0	1	23 2
110	20	0.0	1	15 5
111	19	0.0	1	14 5
112	30	0.0	1	24 6
113	19	0.0	1	18 1
114	27	0.0	1	18 9
115	26	0.0	1	23 3
116	20	0.0	1	17 3
117	20	0.0	1	17 3
118	28	0.0	1	18 10
119	27	0.0	1	24 3
120	15	0.0	1	12 3
121	15	0.0	1	12 3
122	19	0.0	1	12 7
123	20	0.0	1	14 6
124	6	0.0	1	4 2
125	16	0.0	1	14 2
126	13	0.0	1	12 1
127	17	0.0	1	15 2
128	8	0.0	1	6 2
129	8	0.0	1	8
130	15	0.0	1	14 1
131	14	0.0	1	14
132	8	0.0	1	7 1
133	9	0.0	1	9
134	15	0.0	1	12 3
135	8	0.0	1	7 1
136	5	0.0	1	5
137	10	0.0	1	9 1
138	7	0.0	1	7
139	8	0.0	1	8
140	5	0.0	1	5
141	3	0.0	1	2 1
142	4	0.0	1	3 1
143	4	0.0	1	2 2
144	2	0.0	1	2
145	2	0.0	1	1 1
146	4	0.0	1	2 2
147	2	0.0	1	2
148	8	0.0	1	5 3
150	4	0.0	1	3 1
151	132	0.0	1	122 10


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR012_S1_L002_R2_001_val_2.fq.gz
=============================================
326252 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR012_S1_L002_R1_001_val_1_trimmed.fq.gz and NR012_S1_L002_R2_001_val_2_trimmed.fq.gz
file_1: NR012_S1_L002_R1_001_val_1_trimmed.fq.gz, file_2: NR012_S1_L002_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR012_S1_L002_R1_001_val_1_trimmed.fq.gz and NR012_S1_L002_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR012_S1_L002_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 326252

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 5128 (1.57%)

Deleting both intermediate output files NR012_S1_L002_R1_001_val_1_trimmed.fq.gz and NR012_S1_L002_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR013_AD013_S2_L001_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001_val_1.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 7650.23 s (25 us/read; 2.43 M reads/minute).

=== Summary ===

Total reads processed:             309,877,704
Reads with adapters:               125,600,847 (40.5%)
Reads written (passing filters):   309,877,704 (100.0%)

Total basepairs processed: 39,009,495,129 bp
Quality-trimmed:              24,971,797 bp (0.1%)
Total written (filtered):  38,552,981,389 bp (98.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 125600847 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 32.1%
  C: 23.7%
  G: 14.5%
  T: 29.6%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	89424517	77469426.0	0	89424517
2	22164935	19367356.5	0	22164935
3	6130509	4841839.1	0	6130509
4	2218083	1210459.8	0	2218083
5	219378	302614.9	0	219378
6	99427	75653.7	0	99427
7	69831	18913.4	0	69831
8	81144	4728.4	0	81144
9	69327	1182.1	0	65673 3654
10	86254	295.5	1	64771 21483
11	86689	73.9	1	66818 19871
12	152618	18.5	1	127131 25487
13	8000	4.6	1	4400 3600
14	142876	4.6	1	121534 21342
15	6164	4.6	1	3175 2989
16	157524	4.6	1	129484 28040
17	9368	4.6	1	5281 4087
18	110322	4.6	1	89737 20585
19	227175	4.6	1	198294 28881
20	2286	4.6	1	1173 1113
21	2562	4.6	1	970 1592
22	5827	4.6	1	2657 3170
23	88216	4.6	1	71209 17007
24	186505	4.6	1	158602 27903
25	8216	4.6	1	4608 3608
26	76802	4.6	1	61671 15131
27	65197	4.6	1	55637 9560
28	2895	4.6	1	1382 1513
29	67938	4.6	1	55476 12462
30	88509	4.6	1	73248 15261
31	107470	4.6	1	90166 17304
32	9768	4.6	1	5863 3905
33	124009	4.6	1	102313 21696
34	3169	4.6	1	1701 1468
35	65831	4.6	1	52431 13400
36	86774	4.6	1	70190 16584
37	100365	4.6	1	83307 17058
38	4565	4.6	1	2666 1899
39	79416	4.6	1	62736 16680
40	117161	4.6	1	92493 24668
41	6185	4.6	1	3649 2536
42	79241	4.6	1	60043 19198
43	98328	4.6	1	73247 25081
44	150109	4.6	1	119150 30959
45	31815	4.6	1	25768 6047
46	43480	4.6	1	31378 12102
47	4867	4.6	1	2963 1904
48	117730	4.6	1	95666 22064
49	64655	4.6	1	50519 14136
50	49998	4.6	1	37908 12090
51	80945	4.6	1	64124 16821
52	100481	4.6	1	82422 18059
53	35864	4.6	1	29124 6740
54	8281	4.6	1	5909 2372
55	114512	4.6	1	100445 14067
56	88023	4.6	1	74060 13963
57	9008	4.6	1	6800 2208
58	16584	4.6	1	11832 4752
59	79509	4.6	1	68186 11323
60	5679	4.6	1	3243 2436
61	13090	4.6	1	8529 4561
62	64280	4.6	1	54366 9914
63	3785	4.6	1	2002 1783
64	9323	4.6	1	5891 3432
65	22289	4.6	1	17071 5218
66	58348	4.6	1	49571 8777
67	27565	4.6	1	21718 5847
68	37093	4.6	1	30329 6764
69	29029	4.6	1	23079 5950
70	25492	4.6	1	19547 5945
71	12307	4.6	1	8398 3909
72	16100	4.6	1	12236 3864
73	24087	4.6	1	19483 4604
74	28372	4.6	1	23063 5309
75	30767	4.6	1	24926 5841
76	32489	4.6	1	26238 6251
77	32880	4.6	1	26516 6364
78	33544	4.6	1	26942 6602
79	33279	4.6	1	26423 6856
80	33181	4.6	1	26360 6821
81	33195	4.6	1	26291 6904
82	33217	4.6	1	26339 6878
83	32639	4.6	1	25624 7015
84	32054	4.6	1	25344 6710
85	31961	4.6	1	25110 6851
86	31461	4.6	1	24659 6802
87	31056	4.6	1	24375 6681
88	30928	4.6	1	24346 6582
89	29979	4.6	1	23608 6371
90	29702	4.6	1	23396 6306
91	29509	4.6	1	23084 6425
92	28807	4.6	1	22489 6318
93	27764	4.6	1	21767 5997
94	27551	4.6	1	21509 6042
95	26674	4.6	1	20797 5877
96	26566	4.6	1	20764 5802
97	25897	4.6	1	20320 5577
98	25130	4.6	1	19615 5515
99	24662	4.6	1	19241 5421
100	23805	4.6	1	18513 5292
101	23057	4.6	1	17989 5068
102	22484	4.6	1	17512 4972
103	22162	4.6	1	17259 4903
104	21057	4.6	1	16304 4753
105	20635	4.6	1	15939 4696
106	19695	4.6	1	15133 4562
107	18768	4.6	1	14393 4375
108	17844	4.6	1	13675 4169
109	17123	4.6	1	13124 3999
110	16499	4.6	1	12532 3967
111	15593	4.6	1	11916 3677
112	15113	4.6	1	11560 3553
113	14481	4.6	1	11021 3460
114	13889	4.6	1	10658 3231
115	13496	4.6	1	10426 3070
116	12857	4.6	1	9829 3028
117	12269	4.6	1	9412 2857
118	11754	4.6	1	8975 2779
119	11278	4.6	1	8643 2635
120	10276	4.6	1	7870 2406
121	10062	4.6	1	7696 2366
122	8939	4.6	1	6836 2103
123	8804	4.6	1	6816 1988
124	7987	4.6	1	6117 1870
125	7642	4.6	1	5918 1724
126	7156	4.6	1	5526 1630
127	6575	4.6	1	5123 1452
128	5937	4.6	1	4721 1216
129	6086	4.6	1	5006 1080
130	4836	4.6	1	3909 927
131	4800	4.6	1	4045 755
132	3687	4.6	1	3116 571
133	3273	4.6	1	2805 468
134	2904	4.6	1	2528 376
135	2541	4.6	1	2231 310
136	2071	4.6	1	1822 249
137	1835	4.6	1	1635 200
138	1525	4.6	1	1343 182
139	1248	4.6	1	1099 149
140	1075	4.6	1	952 123
141	817	4.6	1	727 90
142	833	4.6	1	735 98
143	705	4.6	1	627 78
144	566	4.6	1	506 60
145	527	4.6	1	448 79
146	584	4.6	1	496 88
147	490	4.6	1	431 59
148	592	4.6	1	486 106
149	548	4.6	1	429 119
150	899	4.6	1	543 356
151	72200	4.6	1	36351 35849


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R1_001_val_1.fq.gz
=============================================
309877704 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR013_AD013_S2_L001_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001_val_2.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 7839.82 s (25 us/read; 2.37 M reads/minute).

=== Summary ===

Total reads processed:             309,877,704
Reads with adapters:               125,884,928 (40.6%)
Reads written (passing filters):   309,877,704 (100.0%)

Total basepairs processed: 39,922,240,804 bp
Quality-trimmed:              30,422,029 bp (0.1%)
Total written (filtered):  39,426,232,820 bp (98.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 125884928 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 32.1%
  C: 23.1%
  G: 15.3%
  T: 29.6%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	88845909	77469426.0	0	88845909
2	22125586	19367356.5	0	22125586
3	6391789	4841839.1	0	6391789
4	2247257	1210459.8	0	2247257
5	199820	302614.9	0	199820
6	110118	75653.7	0	110118
7	87861	18913.4	0	87861
8	95299	4728.4	0	95299
9	63978	1182.1	0	59832 4146
10	105395	295.5	1	75720 29675
11	89578	73.9	1	66659 22919
12	173465	18.5	1	138196 35269
13	2389	4.6	1	887 1502
14	113395	4.6	1	87505 25890
15	135634	4.6	1	111210 24424
16	1253	4.6	1	397 856
17	104209	4.6	1	83034 21175
18	56976	4.6	1	45269 11707
19	114574	4.6	1	90053 24521
20	75891	4.6	1	60021 15870
21	61297	4.6	1	49070 12227
22	78310	4.6	1	62289 16021
23	85866	4.6	1	66959 18907
24	167954	4.6	1	130753 37201
25	73002	4.6	1	58910 14092
26	70090	4.6	1	56535 13555
27	47016	4.6	1	35691 11325
28	117783	4.6	1	97694 20089
29	33129	4.6	1	23153 9976
30	112586	4.6	1	92542 20044
31	48002	4.6	1	35771 12231
32	193298	4.6	1	165534 27764
33	87671	4.6	1	68658 19013
34	32056	4.6	1	22676 9380
35	109513	4.6	1	91086 18427
36	39661	4.6	1	30104 9557
37	57789	4.6	1	44412 13377
38	30027	4.6	1	23398 6629
39	42527	4.6	1	32645 9882
40	18198	4.6	1	13575 4623
41	61586	4.6	1	49843 11743
42	83440	4.6	1	68575 14865
43	42319	4.6	1	32603 9716
44	66878	4.6	1	52939 13939
45	115546	4.6	1	95285 20261
46	62010	4.6	1	47751 14259
47	39415	4.6	1	31070 8345
48	114841	4.6	1	94405 20436
49	50075	4.6	1	39582 10493
50	22207	4.6	1	15934 6273
51	93791	4.6	1	76265 17526
52	129976	4.6	1	111177 18799
53	52101	4.6	1	42431 9670
54	70208	4.6	1	57057 13151
55	41534	4.6	1	33481 8053
56	22914	4.6	1	17128 5786
57	38141	4.6	1	29953 8188
58	44206	4.6	1	34293 9913
59	25694	4.6	1	18853 6841
60	18689	4.6	1	13090 5599
61	16750	4.6	1	11632 5118
62	17922	4.6	1	12604 5318
63	19917	4.6	1	14689 5228
64	30669	4.6	1	23972 6697
65	39466	4.6	1	31318 8148
66	43956	4.6	1	34720 9236
67	45097	4.6	1	35359 9738
68	45768	4.6	1	35779 9989
69	45954	4.6	1	35668 10286
70	46047	4.6	1	35770 10277
71	45745	4.6	1	35257 10488
72	45607	4.6	1	35117 10490
73	45024	4.6	1	34813 10211
74	44498	4.6	1	34307 10191
75	44017	4.6	1	34003 10014
76	43540	4.6	1	33431 10109
77	43090	4.6	1	33125 9965
78	42637	4.6	1	32752 9885
79	41853	4.6	1	32164 9689
80	41286	4.6	1	31721 9565
81	40929	4.6	1	31441 9488
82	40505	4.6	1	31156 9349
83	39595	4.6	1	30373 9222
84	39003	4.6	1	29871 9132
85	38856	4.6	1	29840 9016
86	38308	4.6	1	29168 9140
87	37828	4.6	1	28974 8854
88	37411	4.6	1	28579 8832
89	36119	4.6	1	27688 8431
90	35621	4.6	1	27246 8375
91	35130	4.6	1	26933 8197
92	34667	4.6	1	26480 8187
93	33625	4.6	1	25771 7854
94	33191	4.6	1	25409 7782
95	32138	4.6	1	24554 7584
96	32105	4.6	1	24550 7555
97	31392	4.6	1	24148 7244
98	30486	4.6	1	23462 7024
99	29633	4.6	1	22786 6847
100	28698	4.6	1	22036 6662
101	28001	4.6	1	21491 6510
102	27082	4.6	1	20760 6322
103	26784	4.6	1	20505 6279
104	25275	4.6	1	19359 5916
105	24641	4.6	1	18707 5934
106	23433	4.6	1	17836 5597
107	22242	4.6	1	16750 5492
108	21167	4.6	1	15837 5330
109	20140	4.6	1	15032 5108
110	19354	4.6	1	14351 5003
111	18430	4.6	1	13727 4703
112	17600	4.6	1	13157 4443
113	16947	4.6	1	12800 4147
114	16325	4.6	1	12306 4019
115	15895	4.6	1	11983 3912
116	15307	4.6	1	11534 3773
117	14514	4.6	1	10941 3573
118	13913	4.6	1	10507 3406
119	13245	4.6	1	10078 3167
120	12231	4.6	1	9245 2986
121	11796	4.6	1	8977 2819
122	10638	4.6	1	8118 2520
123	10402	4.6	1	7982 2420
124	9446	4.6	1	7197 2249
125	9015	4.6	1	6866 2149
126	8486	4.6	1	6462 2024
127	7804	4.6	1	6024 1780
128	6749	4.6	1	5384 1365
129	6747	4.6	1	5588 1159
130	5261	4.6	1	4337 924
131	5109	4.6	1	4384 725
132	3835	4.6	1	3252 583
133	3353	4.6	1	2896 457
134	2940	4.6	1	2598 342
135	2590	4.6	1	2262 328
136	2123	4.6	1	1857 266
137	1846	4.6	1	1629 217
138	1530	4.6	1	1332 198
139	1244	4.6	1	1106 138
140	1074	4.6	1	916 158
141	858	4.6	1	679 179
142	851	4.6	1	632 219
143	728	4.6	1	535 193
144	621	4.6	1	433 188
145	543	4.6	1	369 174
146	592	4.6	1	362 230
147	522	4.6	1	326 196
148	596	4.6	1	302 294
149	511	4.6	1	299 212
150	928	4.6	1	667 261
151	37859	4.6	1	36758 1101


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L001_R2_001_val_2.fq.gz
=============================================
309877704 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR013_AD013_S2_L001_R1_001_val_1_trimmed.fq.gz and NR013_AD013_S2_L001_R2_001_val_2_trimmed.fq.gz
file_1: NR013_AD013_S2_L001_R1_001_val_1_trimmed.fq.gz, file_2: NR013_AD013_S2_L001_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR013_AD013_S2_L001_R1_001_val_1_trimmed.fq.gz and NR013_AD013_S2_L001_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 309877704

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 827042 (0.27%)

Deleting both intermediate output files NR013_AD013_S2_L001_R1_001_val_1_trimmed.fq.gz and NR013_AD013_S2_L001_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR013_AD013_S2_L002_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R1_001_val_1.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
330000000 sequences processed
340000000 sequences processed
350000000 sequences processed
360000000 sequences processed
370000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 9397.15 s (25 us/read; 2.42 M reads/minute).

=== Summary ===

Total reads processed:             379,535,476
Reads with adapters:               157,413,392 (41.5%)
Reads written (passing filters):   379,535,476 (100.0%)

Total basepairs processed: 48,465,312,024 bp
Quality-trimmed:              27,720,181 bp (0.1%)
Total written (filtered):  47,689,069,992 bp (98.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 157413392 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 32.2%
  C: 23.6%
  G: 14.5%
  T: 29.6%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	110667740	94883869.0	0	110667740
2	26663149	23720967.2	0	26663149
3	7393392	5930241.8	0	7393392
4	2653451	1482560.5	0	2653451
5	254168	370640.1	0	254168
6	128511	92660.0	0	128511
7	88935	23165.0	0	88935
8	105904	5791.3	0	105904
9	92612	1447.8	0	88170 4442
10	114990	362.0	1	85274 29716
11	123270	90.5	1	91224 32046
12	208554	22.6	1	169873 38681
13	11285	5.7	1	6138 5147
14	194395	5.7	1	161652 32743
15	8680	5.7	1	4299 4381
16	223910	5.7	1	178592 45318
17	15102	5.7	1	8422 6680
18	154776	5.7	1	123797 30979
19	313056	5.7	1	268766 44290
20	3143	5.7	1	1583 1560
21	3876	5.7	1	1369 2507
22	8827	5.7	1	3921 4906
23	127107	5.7	1	99437 27670
24	274885	5.7	1	228223 46662
25	12392	5.7	1	6883 5509
26	115765	5.7	1	90881 24884
27	92682	5.7	1	78305 14377
28	4103	5.7	1	1994 2109
29	103986	5.7	1	82555 21431
30	131306	5.7	1	107052 24254
31	162960	5.7	1	133400 29560
32	14793	5.7	1	8688 6105
33	194807	5.7	1	157828 36979
34	4998	5.7	1	2683 2315
35	105963	5.7	1	82175 23788
36	137630	5.7	1	110316 27314
37	159200	5.7	1	129691 29509
38	6660	5.7	1	3982 2678
39	127764	5.7	1	98518 29246
40	199028	5.7	1	153865 45163
41	9971	5.7	1	5999 3972
42	136600	5.7	1	101299 35301
43	178520	5.7	1	129574 48946
44	262367	5.7	1	204880 57487
45	52027	5.7	1	41943 10084
46	73660	5.7	1	52825 20835
47	8441	5.7	1	5143 3298
48	174363	5.7	1	139828 34535
49	108253	5.7	1	83992 24261
50	108727	5.7	1	83186 25541
51	161423	5.7	1	124375 37048
52	175183	5.7	1	140943 34240
53	74326	5.7	1	61229 13097
54	16107	5.7	1	11671 4436
55	194176	5.7	1	167170 27006
56	185187	5.7	1	155240 29947
57	17080	5.7	1	13135 3945
58	31574	5.7	1	22573 9001
59	182957	5.7	1	156639 26318
60	10462	5.7	1	6373 4089
61	24520	5.7	1	15594 8926
62	128782	5.7	1	109288 19494
63	5151	5.7	1	2694 2457
64	13518	5.7	1	8092 5426
65	51853	5.7	1	40861 10992
66	103903	5.7	1	87611 16292
67	66440	5.7	1	53152 13288
68	88880	5.7	1	72897 15983
69	82619	5.7	1	66722 15897
70	96138	5.7	1	77885 18253
71	25150	5.7	1	16131 9019
72	27241	5.7	1	19801 7440
73	45344	5.7	1	36516 8828
74	57484	5.7	1	47405 10079
75	64067	5.7	1	52679 11388
76	68089	5.7	1	55772 12317
77	70462	5.7	1	57543 12919
78	72065	5.7	1	58687 13378
79	72745	5.7	1	58952 13793
80	72785	5.7	1	58704 14081
81	73449	5.7	1	59389 14060
82	73456	5.7	1	59165 14291
83	72939	5.7	1	58314 14625
84	72785	5.7	1	58258 14527
85	72185	5.7	1	57856 14329
86	71613	5.7	1	57074 14539
87	70864	5.7	1	56677 14187
88	71145	5.7	1	56961 14184
89	69194	5.7	1	55323 13871
90	69287	5.7	1	55262 14025
91	68129	5.7	1	54295 13834
92	67451	5.7	1	53886 13565
93	65864	5.7	1	52572 13292
94	64955	5.7	1	51832 13123
95	64272	5.7	1	51150 13122
96	63370	5.7	1	50414 12956
97	61971	5.7	1	49449 12522
98	61411	5.7	1	48937 12474
99	60080	5.7	1	47918 12162
100	59076	5.7	1	46891 12185
101	57691	5.7	1	45837 11854
102	56341	5.7	1	44779 11562
103	54946	5.7	1	43824 11122
104	53301	5.7	1	42151 11150
105	51774	5.7	1	41142 10632
106	50125	5.7	1	39682 10443
107	48776	5.7	1	38650 10126
108	47554	5.7	1	37248 10306
109	45662	5.7	1	36058 9604
110	43668	5.7	1	34299 9369
111	42524	5.7	1	33304 9220
112	41006	5.7	1	32171 8835
113	39805	5.7	1	31283 8522
114	38467	5.7	1	30150 8317
115	36917	5.7	1	28981 7936
116	35474	5.7	1	27902 7572
117	33548	5.7	1	26390 7158
118	32583	5.7	1	25558 7025
119	31091	5.7	1	24329 6762
120	29303	5.7	1	22921 6382
121	27728	5.7	1	21825 5903
122	25972	5.7	1	20442 5530
123	24465	5.7	1	19214 5251
124	22898	5.7	1	17993 4905
125	21621	5.7	1	16995 4626
126	20014	5.7	1	15694 4320
127	18987	5.7	1	15019 3968
128	16876	5.7	1	13491 3385
129	16593	5.7	1	13625 2968
130	13421	5.7	1	10974 2447
131	12382	5.7	1	10375 2007
132	9875	5.7	1	8394 1481
133	8952	5.7	1	7759 1193
134	7501	5.7	1	6524 977
135	6534	5.7	1	5675 859
136	5217	5.7	1	4621 596
137	4587	5.7	1	4093 494
138	3588	5.7	1	3198 390
139	2812	5.7	1	2534 278
140	2065	5.7	1	1837 228
141	1568	5.7	1	1398 170
142	1250	5.7	1	1114 136
143	1100	5.7	1	961 139
144	839	5.7	1	710 129
145	842	5.7	1	725 117
146	755	5.7	1	637 118
147	688	5.7	1	589 99
148	799	5.7	1	669 130
149	662	5.7	1	532 130
150	933	5.7	1	583 350
151	101421	5.7	1	50281 51140


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R1_001_val_1.fq.gz
=============================================
379535476 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR013_AD013_S2_L002_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R2_001_val_2.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
330000000 sequences processed
340000000 sequences processed
350000000 sequences processed
360000000 sequences processed
370000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 9482.79 s (25 us/read; 2.40 M reads/minute).

=== Summary ===

Total reads processed:             379,535,476
Reads with adapters:               158,202,642 (41.7%)
Reads written (passing filters):   379,535,476 (100.0%)

Total basepairs processed: 49,672,679,182 bp
Quality-trimmed:              30,573,885 bp (0.1%)
Total written (filtered):  48,791,766,215 bp (98.2%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 158202642 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 32.0%
  C: 22.9%
  G: 15.3%
  T: 29.8%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	109580322	94883869.0	0	109580322
2	26576548	23720967.2	0	26576548
3	7597769	5930241.8	0	7597769
4	2680993	1482560.5	0	2680993
5	226898	370640.1	0	226898
6	150660	92660.0	0	150660
7	122142	23165.0	0	122142
8	131733	5791.3	0	131733
9	90844	1447.8	0	86022 4822
10	150905	362.0	1	107502 43403
11	135349	90.5	1	97607 37742
12	252946	22.6	1	199121 53825
13	3530	5.7	1	1331 2199
14	168638	5.7	1	128925 39713
15	195609	5.7	1	158466 37143
16	1950	5.7	1	608 1342
17	154612	5.7	1	121576 33036
18	83683	5.7	1	65735 17948
19	170549	5.7	1	131905 38644
20	113819	5.7	1	88764 25055
21	99079	5.7	1	77374 21705
22	121474	5.7	1	94946 26528
23	131152	5.7	1	101603 29549
24	248335	5.7	1	190265 58070
25	123183	5.7	1	98568 24615
26	116509	5.7	1	93505 23004
27	85593	5.7	1	63827 21766
28	187504	5.7	1	154503 33001
29	63599	5.7	1	44467 19132
30	187277	5.7	1	152585 34692
31	82799	5.7	1	60937 21862
32	355185	5.7	1	306261 48924
33	158641	5.7	1	124646 33995
34	64822	5.7	1	45842 18980
35	195418	5.7	1	164137 31281
36	58936	5.7	1	42343 16593
37	108180	5.7	1	83522 24658
38	35568	5.7	1	25724 9844
39	64341	5.7	1	47554 16787
40	20127	5.7	1	13603 6524
41	106196	5.7	1	85625 20571
42	153301	5.7	1	126849 26452
43	68625	5.7	1	52544 16081
44	121927	5.7	1	96858 25069
45	262336	5.7	1	224010 38326
46	116328	5.7	1	90525 25803
47	58043	5.7	1	44637 13406
48	248028	5.7	1	209929 38099
49	75167	5.7	1	58530 16637
50	31491	5.7	1	21928 9563
51	198900	5.7	1	165930 32970
52	287281	5.7	1	253422 33859
53	78856	5.7	1	63865 14991
54	119169	5.7	1	97179 21990
55	55266	5.7	1	43255 12011
56	35422	5.7	1	25390 10032
57	60972	5.7	1	46938 14034
58	72809	5.7	1	56312 16497
59	38555	5.7	1	27522 11033
60	31487	5.7	1	21444 10043
61	31013	5.7	1	21204 9809
62	31200	5.7	1	21560 9640
63	34441	5.7	1	24740 9701
64	55775	5.7	1	44093 11682
65	78736	5.7	1	63960 14776
66	90620	5.7	1	73458 17162
67	95517	5.7	1	76780 18737
68	97188	5.7	1	77764 19424
69	99204	5.7	1	79345 19859
70	99963	5.7	1	79546 20417
71	100406	5.7	1	79933 20473
72	99798	5.7	1	79578 20220
73	99683	5.7	1	79316 20367
74	99331	5.7	1	78979 20352
75	98621	5.7	1	78425 20196
76	97932	5.7	1	77457 20475
77	97135	5.7	1	77151 19984
78	97028	5.7	1	77056 19972
79	96260	5.7	1	76466 19794
80	94810	5.7	1	75454 19356
81	94602	5.7	1	75244 19358
82	94004	5.7	1	74771 19233
83	92945	5.7	1	73823 19122
84	92419	5.7	1	73182 19237
85	91632	5.7	1	72790 18842
86	91035	5.7	1	72317 18718
87	90050	5.7	1	71548 18502
88	89894	5.7	1	71506 18388
89	87725	5.7	1	69845 17880
90	87185	5.7	1	69399 17786
91	84618	5.7	1	66960 17658
92	84186	5.7	1	66945 17241
93	82900	5.7	1	65834 17066
94	81370	5.7	1	64473 16897
95	80429	5.7	1	63919 16510
96	79457	5.7	1	63127 16330
97	78199	5.7	1	62179 16020
98	77342	5.7	1	61569 15773
99	75264	5.7	1	59801 15463
100	74042	5.7	1	58980 15062
101	72181	5.7	1	57310 14871
102	70827	5.7	1	56161 14666
103	69379	5.7	1	55477 13902
104	66924	5.7	1	53369 13555
105	64860	5.7	1	51608 13252
106	63171	5.7	1	50167 13004
107	60966	5.7	1	48666 12300
108	59572	5.7	1	47230 12342
109	57458	5.7	1	45484 11974
110	54410	5.7	1	43114 11296
111	53126	5.7	1	41972 11154
112	51049	5.7	1	40361 10688
113	49939	5.7	1	39585 10354
114	48143	5.7	1	38288 9855
115	46204	5.7	1	36627 9577
116	44751	5.7	1	35508 9243
117	42469	5.7	1	33654 8815
118	41251	5.7	1	32738 8513
119	39131	5.7	1	31188 7943
120	37000	5.7	1	29225 7775
121	34921	5.7	1	27767 7154
122	32786	5.7	1	26075 6711
123	30986	5.7	1	24656 6330
124	29117	5.7	1	23102 6015
125	27519	5.7	1	21859 5660
126	25495	5.7	1	20373 5122
127	23925	5.7	1	19306 4619
128	20431	5.7	1	16762 3669
129	19497	5.7	1	16497 3000
130	15325	5.7	1	13045 2280
131	13886	5.7	1	12078 1808
132	10761	5.7	1	9519 1242
133	9402	5.7	1	8413 989
134	7873	5.7	1	7096 777
135	6890	5.7	1	6211 679
136	5416	5.7	1	4918 498
137	4724	5.7	1	4317 407
138	3681	5.7	1	3347 334
139	2838	5.7	1	2579 259
140	2088	5.7	1	1837 251
141	1592	5.7	1	1358 234
142	1256	5.7	1	990 266
143	1102	5.7	1	852 250
144	825	5.7	1	603 222
145	848	5.7	1	562 286
146	752	5.7	1	465 287
147	697	5.7	1	449 248
148	750	5.7	1	456 294
149	606	5.7	1	356 250
150	664	5.7	1	440 224
151	51839	5.7	1	50778 1061


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR013_AD013_S2_L002_R2_001_val_2.fq.gz
=============================================
379535476 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR013_AD013_S2_L002_R1_001_val_1_trimmed.fq.gz and NR013_AD013_S2_L002_R2_001_val_2_trimmed.fq.gz
file_1: NR013_AD013_S2_L002_R1_001_val_1_trimmed.fq.gz, file_2: NR013_AD013_S2_L002_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR013_AD013_S2_L002_R1_001_val_1_trimmed.fq.gz and NR013_AD013_S2_L002_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 379535476

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 942696 (0.25%)

Deleting both intermediate output files NR013_AD013_S2_L002_R1_001_val_1_trimmed.fq.gz and NR013_AD013_S2_L002_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR014_AD014_S5_L001_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R1_001_val_1.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
330000000 sequences processed
340000000 sequences processed
350000000 sequences processed
360000000 sequences processed
370000000 sequences processed
380000000 sequences processed
390000000 sequences processed
400000000 sequences processed
410000000 sequences processed
420000000 sequences processed
430000000 sequences processed
440000000 sequences processed
450000000 sequences processed
460000000 sequences processed
470000000 sequences processed
480000000 sequences processed
490000000 sequences processed
500000000 sequences processed
510000000 sequences processed
520000000 sequences processed
530000000 sequences processed
540000000 sequences processed
550000000 sequences processed
560000000 sequences processed
570000000 sequences processed
580000000 sequences processed
590000000 sequences processed
600000000 sequences processed
610000000 sequences processed
620000000 sequences processed
630000000 sequences processed
640000000 sequences processed
650000000 sequences processed
660000000 sequences processed
670000000 sequences processed
680000000 sequences processed
690000000 sequences processed
700000000 sequences processed
710000000 sequences processed
720000000 sequences processed
730000000 sequences processed
740000000 sequences processed
750000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 17866.55 s (24 us/read; 2.52 M reads/minute).

=== Summary ===

Total reads processed:             750,570,443
Reads with adapters:               289,187,209 (38.5%)
Reads written (passing filters):   750,570,443 (100.0%)

Total basepairs processed: 88,547,063,621 bp
Quality-trimmed:              51,479,249 bp (0.1%)
Total written (filtered):  86,834,377,140 bp (98.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 289187209 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 31.0%
  C: 23.5%
  G: 15.1%
  T: 29.7%
  none/other: 0.7%

Overview of removed sequences
length	count	expect	max.err	error counts
1	192909668	187642610.8	0	192909668
2	54350674	46910652.7	0	54350674
3	14030638	11727663.2	0	14030638
4	5645418	2931915.8	0	5645418
5	644053	732978.9	0	644053
6	309787	183244.7	0	309787
7	237428	45811.2	0	237428
8	281248	11452.8	0	281248
9	249313	2863.2	0	241008 8305
10	279192	715.8	1	232507 46685
11	286431	178.9	1	241423 45008
12	515773	44.7	1	463019 52754
13	18367	11.2	1	11839 6528
14	508262	11.2	1	456715 51547
15	14833	11.2	1	8724 6109
16	544414	11.2	1	480512 63902
17	23775	11.2	1	14558 9217
18	359075	11.2	1	315603 43472
19	825945	11.2	1	762424 63521
20	5665	11.2	1	3478 2187
21	4990	11.2	1	2183 2807
22	10358	11.2	1	5510 4848
23	299789	11.2	1	264190 35599
24	667172	11.2	1	605345 61827
25	19949	11.2	1	12651 7298
26	256354	11.2	1	226389 29965
27	230460	11.2	1	210212 20248
28	6568	11.2	1	3872 2696
29	245569	11.2	1	216886 28683
30	317069	11.2	1	286417 30652
31	374473	11.2	1	339859 34614
32	19468	11.2	1	12962 6506
33	450331	11.2	1	403885 46446
34	7586	11.2	1	4925 2661
35	238662	11.2	1	207824 30838
36	250935	11.2	1	221628 29307
37	254545	11.2	1	225209 29336
38	414582	11.2	1	369817 44765
39	210154	11.2	1	191129 19025
40	7717	11.2	1	4738 2979
41	255519	11.2	1	224930 30589
42	220673	11.2	1	196986 23687
43	253997	11.2	1	221561 32436
44	538821	11.2	1	489058 49763
45	109189	11.2	1	100829 8360
46	120125	11.2	1	102249 17876
47	6331	11.2	1	3868 2463
48	235082	11.2	1	208233 26849
49	198823	11.2	1	177604 21219
50	193998	11.2	1	170789 23209
51	239801	11.2	1	208357 31444
52	380896	11.2	1	343749 37147
53	166334	11.2	1	152005 14329
54	16602	11.2	1	12011 4591
55	330481	11.2	1	297411 33070
56	505188	11.2	1	464589 40599
57	31464	11.2	1	26508 4956
58	89482	11.2	1	78503 10979
59	471636	11.2	1	438787 32849
60	13294	11.2	1	9635 3659
61	31799	11.2	1	22753 9046
62	348119	11.2	1	323874 24245
63	6467	11.2	1	4271 2196
64	13543	11.2	1	8483 5060
65	105779	11.2	1	94646 11133
66	228594	11.2	1	209330 19264
67	202694	11.2	1	185615 17079
68	246807	11.2	1	228830 17977
69	144456	11.2	1	130812 13644
70	116936	11.2	1	103663 13273
71	54946	11.2	1	47030 7916
72	75718	11.2	1	67992 7726
73	114178	11.2	1	105273 8905
74	127551	11.2	1	117131 10420
75	133108	11.2	1	121830 11278
76	135663	11.2	1	124030 11633
77	135833	11.2	1	123792 12041
78	135999	11.2	1	123523 12476
79	134513	11.2	1	122024 12489
80	132353	11.2	1	119792 12561
81	131502	11.2	1	119043 12459
82	129476	11.2	1	117100 12376
83	127413	11.2	1	115100 12313
84	125209	11.2	1	113013 12196
85	124152	11.2	1	112064 12088
86	122198	11.2	1	110146 12052
87	119141	11.2	1	107493 11648
88	118327	11.2	1	106680 11647
89	114684	11.2	1	103226 11458
90	112928	11.2	1	101561 11367
91	110169	11.2	1	99211 10958
92	107113	11.2	1	96201 10912
93	105103	11.2	1	94518 10585
94	103054	11.2	1	92695 10359
95	101527	11.2	1	91241 10286
96	98938	11.2	1	88802 10136
97	96670	11.2	1	87063 9607
98	93458	11.2	1	83912 9546
99	91216	11.2	1	82070 9146
100	88277	11.2	1	79256 9021
101	84267	11.2	1	75500 8767
102	81040	11.2	1	72488 8552
103	76881	11.2	1	68764 8117
104	71322	11.2	1	63577 7745
105	66845	11.2	1	59357 7488
106	61236	11.2	1	54084 7152
107	54672	11.2	1	47874 6798
108	49926	11.2	1	43230 6696
109	43801	11.2	1	37446 6355
110	40718	11.2	1	34799 5919
111	39329	11.2	1	33521 5808
112	37285	11.2	1	31675 5610
113	36474	11.2	1	31067 5407
114	34974	11.2	1	29828 5146
115	34356	11.2	1	29518 4838
116	33052	11.2	1	28418 4634
117	32570	11.2	1	28040 4530
118	31661	11.2	1	27284 4377
119	31114	11.2	1	27029 4085
120	30169	11.2	1	26088 4081
121	29542	11.2	1	25780 3762
122	27978	11.2	1	24484 3494
123	27542	11.2	1	24306 3236
124	26034	11.2	1	22997 3037
125	27797	11.2	1	24853 2944
126	24952	11.2	1	22306 2646
127	27223	11.2	1	24604 2619
128	24870	11.2	1	22619 2251
129	44965	11.2	1	42042 2923
130	23224	11.2	1	21466 1758
131	35351	11.2	1	33515 1836
132	21416	11.2	1	20253 1163
133	23072	11.2	1	22010 1062
134	19541	11.2	1	18686 855
135	22239	11.2	1	21349 890
136	18813	11.2	1	18114 699
137	20313	11.2	1	19612 701
138	17790	11.2	1	17295 495
139	17086	11.2	1	16597 489
140	15218	11.2	1	14783 435
141	14618	11.2	1	14200 418
142	12159	11.2	1	11781 378
143	13967	11.2	1	13572 395
144	11090	11.2	1	10754 336
145	11962	11.2	1	11529 433
146	9230	11.2	1	8851 379
147	8773	11.2	1	8302 471
148	7357	11.2	1	6629 728
149	8441	11.2	1	7255 1186
150	18295	11.2	1	9802 8493
151	2054622	11.2	1	682481 1372141


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R1_001_val_1.fq.gz
=============================================
750570443 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR014_AD014_S5_L001_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R2_001_val_2.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
330000000 sequences processed
340000000 sequences processed
350000000 sequences processed
360000000 sequences processed
370000000 sequences processed
380000000 sequences processed
390000000 sequences processed
400000000 sequences processed
410000000 sequences processed
420000000 sequences processed
430000000 sequences processed
440000000 sequences processed
450000000 sequences processed
460000000 sequences processed
470000000 sequences processed
480000000 sequences processed
490000000 sequences processed
500000000 sequences processed
510000000 sequences processed
520000000 sequences processed
530000000 sequences processed
540000000 sequences processed
550000000 sequences processed
560000000 sequences processed
570000000 sequences processed
580000000 sequences processed
590000000 sequences processed
600000000 sequences processed
610000000 sequences processed
620000000 sequences processed
630000000 sequences processed
640000000 sequences processed
650000000 sequences processed
660000000 sequences processed
670000000 sequences processed
680000000 sequences processed
690000000 sequences processed
700000000 sequences processed
710000000 sequences processed
720000000 sequences processed
730000000 sequences processed
740000000 sequences processed
750000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 18489.76 s (25 us/read; 2.44 M reads/minute).

=== Summary ===

Total reads processed:             750,570,443
Reads with adapters:               299,526,533 (39.9%)
Reads written (passing filters):   750,570,443 (100.0%)

Total basepairs processed: 91,326,369,816 bp
Quality-trimmed:              58,430,294 bp (0.1%)
Total written (filtered):  89,411,521,810 bp (97.9%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 299526533 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 31.5%
  C: 22.9%
  G: 15.6%
  T: 29.8%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	195508272	187642610.8	0	195508272
2	53701405	46910652.7	0	53701405
3	14830289	11727663.2	0	14830289
4	5884365	2931915.8	0	5884365
5	580478	732978.9	0	580478
6	433990	183244.7	0	433990
7	373366	45811.2	0	373366
8	443852	11452.8	0	443852
9	319608	2863.2	0	310462 9146
10	425138	715.8	1	356030 69108
11	405396	178.9	1	341837 63559
12	791929	44.7	1	699759 92170
13	7085	11.2	1	3337 3748
14	479779	11.2	1	414019 65760
15	666605	11.2	1	597374 69231
16	3296	11.2	1	1405 1891
17	447935	11.2	1	395018 52917
18	283150	11.2	1	249797 33353
19	479301	11.2	1	420748 58553
20	348868	11.2	1	308297 40571
21	318834	11.2	1	280791 38043
22	359445	11.2	1	319023 40422
23	383741	11.2	1	337154 46587
24	609570	11.2	1	532241 77329
25	355609	11.2	1	317427 38182
26	376193	11.2	1	333823 42370
27	287577	11.2	1	246800 40777
28	564034	11.2	1	513550 50484
29	164754	11.2	1	134266 30488
30	537878	11.2	1	487749 50129
31	235999	11.2	1	202289 33710
32	1053810	11.2	1	982245 71565
33	439075	11.2	1	388688 50387
34	143201	11.2	1	117029 26172
35	549014	11.2	1	503741 45273
36	171248	11.2	1	147222 24026
37	269301	11.2	1	234512 34789
38	138046	11.2	1	122921 15125
39	190077	11.2	1	166107 23970
40	72430	11.2	1	62897 9533
41	307972	11.2	1	280936 27036
42	435964	11.2	1	401434 34530
43	197707	11.2	1	175590 22117
44	332032	11.2	1	299779 32253
45	743685	11.2	1	691844 51841
46	293743	11.2	1	258266 35477
47	147612	11.2	1	131958 15654
48	642368	11.2	1	594726 47642
49	205842	11.2	1	185331 20511
50	69850	11.2	1	59300 10550
51	482885	11.2	1	444980 37905
52	819026	11.2	1	777011 42015
53	279581	11.2	1	258697 20884
54	371032	11.2	1	342874 28158
55	201835	11.2	1	186009 15826
56	93525	11.2	1	81149 12376
57	181125	11.2	1	164075 17050
58	201528	11.2	1	181670 19858
59	106205	11.2	1	92181 14024
60	72144	11.2	1	60589 11555
61	67276	11.2	1	56173 11103
62	73654	11.2	1	62651 11003
63	88612	11.2	1	77301 11311
64	160280	11.2	1	146493 13787
65	211526	11.2	1	194467 17059
66	230118	11.2	1	211041 19077
67	233193	11.2	1	213309 19884
68	232801	11.2	1	212622 20179
69	232837	11.2	1	212661 20176
70	230956	11.2	1	210679 20277
71	230712	11.2	1	210035 20677
72	227427	11.2	1	206864 20563
73	224834	11.2	1	204801 20033
74	220854	11.2	1	200966 19888
75	217348	11.2	1	197730 19618
76	213212	11.2	1	193853 19359
77	210130	11.2	1	191101 19029
78	207107	11.2	1	188351 18756
79	201762	11.2	1	183564 18198
80	198242	11.2	1	180336 17906
81	195772	11.2	1	178095 17677
82	191787	11.2	1	174331 17456
83	188512	11.2	1	171336 17176
84	186114	11.2	1	169107 17007
85	183104	11.2	1	166525 16579
86	180176	11.2	1	164018 16158
87	176875	11.2	1	161108 15767
88	173208	11.2	1	157369 15839
89	168365	11.2	1	153113 15252
90	163173	11.2	1	148130 15043
91	159873	11.2	1	145102 14771
92	154865	11.2	1	140836 14029
93	152411	11.2	1	138467 13944
94	148681	11.2	1	135244 13437
95	145839	11.2	1	132601 13238
96	141809	11.2	1	129026 12783
97	137914	11.2	1	125518 12396
98	133616	11.2	1	121504 12112
99	130159	11.2	1	118199 11960
100	125571	11.2	1	114128 11443
101	120631	11.2	1	109465 11166
102	114670	11.2	1	103928 10742
103	108518	11.2	1	98139 10379
104	98959	11.2	1	89090 9869
105	90807	11.2	1	81324 9483
106	80925	11.2	1	72014 8911
107	69986	11.2	1	61403 8583
108	61928	11.2	1	53842 8086
109	51721	11.2	1	44112 7609
110	47044	11.2	1	39803 7241
111	44643	11.2	1	37536 7107
112	42188	11.2	1	35304 6884
113	40737	11.2	1	34327 6410
114	39256	11.2	1	33071 6185
115	38548	11.2	1	32442 6106
116	37109	11.2	1	31381 5728
117	36299	11.2	1	30884 5415
118	35146	11.2	1	29963 5183
119	34570	11.2	1	29658 4912
120	33134	11.2	1	28543 4591
121	32475	11.2	1	28113 4362
122	30765	11.2	1	26673 4092
123	30432	11.2	1	26520 3912
124	28512	11.2	1	24762 3750
125	30138	11.2	1	26594 3544
126	27221	11.2	1	24034 3187
127	29101	11.2	1	26126 2975
128	26261	11.2	1	23747 2514
129	46487	11.2	1	44023 2464
130	23963	11.2	1	22173 1790
131	35973	11.2	1	34287 1686
132	21567	11.2	1	20281 1286
133	23281	11.2	1	22074 1207
134	19695	11.2	1	18575 1120
135	22376	11.2	1	21283 1093
136	18882	11.2	1	17760 1122
137	20353	11.2	1	19196 1157
138	17856	11.2	1	16607 1249
139	17077	11.2	1	15902 1175
140	15173	11.2	1	13937 1236
141	14561	11.2	1	13203 1358
142	12110	11.2	1	10652 1458
143	13944	11.2	1	12264 1680
144	11169	11.2	1	9336 1833
145	11834	11.2	1	9757 2077
146	9067	11.2	1	7040 2027
147	8590	11.2	1	6651 1939
148	6792	11.2	1	5016 1776
149	7588	11.2	1	5615 1973
150	14895	11.2	1	12078 2817
151	701267	11.2	1	683500 17767


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L001_R2_001_val_2.fq.gz
=============================================
750570443 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR014_AD014_S5_L001_R1_001_val_1_trimmed.fq.gz and NR014_AD014_S5_L001_R2_001_val_2_trimmed.fq.gz
file_1: NR014_AD014_S5_L001_R1_001_val_1_trimmed.fq.gz, file_2: NR014_AD014_S5_L001_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR014_AD014_S5_L001_R1_001_val_1_trimmed.fq.gz and NR014_AD014_S5_L001_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 750570443

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 4761104 (0.63%)

Deleting both intermediate output files NR014_AD014_S5_L001_R1_001_val_1_trimmed.fq.gz and NR014_AD014_S5_L001_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR014_AD014_S5_L002_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R1_001_val_1.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
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150000000 sequences processed
160000000 sequences processed
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180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
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250000000 sequences processed
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290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
330000000 sequences processed
340000000 sequences processed
350000000 sequences processed
360000000 sequences processed
370000000 sequences processed
380000000 sequences processed
390000000 sequences processed
400000000 sequences processed
410000000 sequences processed
420000000 sequences processed
430000000 sequences processed
440000000 sequences processed
450000000 sequences processed
460000000 sequences processed
470000000 sequences processed
480000000 sequences processed
490000000 sequences processed
500000000 sequences processed
510000000 sequences processed
520000000 sequences processed
530000000 sequences processed
540000000 sequences processed
550000000 sequences processed
560000000 sequences processed
570000000 sequences processed
580000000 sequences processed
590000000 sequences processed
600000000 sequences processed
610000000 sequences processed
620000000 sequences processed
630000000 sequences processed
640000000 sequences processed
650000000 sequences processed
660000000 sequences processed
670000000 sequences processed
680000000 sequences processed
690000000 sequences processed
700000000 sequences processed
710000000 sequences processed
720000000 sequences processed
730000000 sequences processed
740000000 sequences processed
750000000 sequences processed
760000000 sequences processed
770000000 sequences processed
780000000 sequences processed
790000000 sequences processed
800000000 sequences processed
810000000 sequences processed
820000000 sequences processed
830000000 sequences processed
840000000 sequences processed
850000000 sequences processed
860000000 sequences processed
870000000 sequences processed
880000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 21050.32 s (24 us/read; 2.51 M reads/minute).

=== Summary ===

Total reads processed:             882,029,208
Reads with adapters:               346,789,678 (39.3%)
Reads written (passing filters):   882,029,208 (100.0%)

Total basepairs processed: 106,455,935,222 bp
Quality-trimmed:              52,712,555 bp (0.0%)
Total written (filtered):  104,195,667,043 bp (97.9%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 346789678 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 31.0%
  C: 23.5%
  G: 15.0%
  T: 29.7%
  none/other: 0.8%

Overview of removed sequences
length	count	expect	max.err	error counts
1	232624048	220507302.0	0	232624048
2	63171145	55126825.5	0	63171145
3	16364041	13781706.4	0	16364041
4	6416328	3445426.6	0	6416328
5	712237	861356.6	0	712237
6	338291	215339.2	0	338291
7	256798	53834.8	0	256798
8	299385	13458.7	0	299385
9	269984	3364.7	0	260119 9865
10	307146	841.2	1	253539 53607
11	315713	210.3	1	264417 51296
12	562598	52.6	1	503159 59439
13	19773	13.1	1	12157 7616
14	552117	13.1	1	496927 55190
15	16227	13.1	1	8906 7321
16	596749	13.1	1	526191 70558
17	27757	13.1	1	16526 11231
18	393755	13.1	1	344817 48938
19	910749	13.1	1	842499 68250
20	6613	13.1	1	4009 2604
21	6467	13.1	1	2594 3873
22	12592	13.1	1	6281 6311
23	329115	13.1	1	286324 42791
24	753373	13.1	1	681700 71673
25	22850	13.1	1	14018 8832
26	290173	13.1	1	254343 35830
27	256563	13.1	1	234123 22440
28	7769	13.1	1	4433 3336
29	277229	13.1	1	243555 33674
30	351843	13.1	1	315504 36339
31	436338	13.1	1	392748 43590
32	23439	13.1	1	14948 8491
33	525669	13.1	1	466840 58829
34	9392	13.1	1	5925 3467
35	281455	13.1	1	240818 40637
36	294552	13.1	1	257293 37259
37	297296	13.1	1	259132 38164
38	493224	13.1	1	434828 58396
39	243583	13.1	1	220510 23073
40	9618	13.1	1	5695 3923
41	303835	13.1	1	265494 38341
42	254452	13.1	1	224354 30098
43	308613	13.1	1	264246 44367
44	654339	13.1	1	589647 64692
45	128733	13.1	1	118218 10515
46	140916	13.1	1	118230 22686
47	7614	13.1	1	4438 3176
48	271899	13.1	1	238607 33292
49	234233	13.1	1	207020 27213
50	249540	13.1	1	216599 32941
51	294191	13.1	1	248847 45344
52	475128	13.1	1	423307 51821
53	212764	13.1	1	192266 20498
54	20848	13.1	1	14202 6646
55	373944	13.1	1	327143 46801
56	656108	13.1	1	595438 60670
57	35360	13.1	1	28048 7312
58	102150	13.1	1	84835 17315
59	650539	13.1	1	597527 53012
60	16480	13.1	1	11648 4832
61	38073	13.1	1	25058 13015
62	443604	13.1	1	406917 36687
63	7517	13.1	1	4909 2608
64	13872	13.1	1	7818 6054
65	151378	13.1	1	133918 17460
66	259795	13.1	1	232048 27747
67	261332	13.1	1	232395 28937
68	305222	13.1	1	274651 30571
69	238490	13.1	1	212414 26076
70	300674	13.1	1	271942 28732
71	60371	13.1	1	47219 13152
72	78053	13.1	1	66578 11475
73	145094	13.1	1	131164 13930
74	168443	13.1	1	152721 15722
75	178369	13.1	1	161202 17167
76	183267	13.1	1	165070 18197
77	185332	13.1	1	166059 19273
78	185669	13.1	1	166032 19637
79	184689	13.1	1	164958 19731
80	183758	13.1	1	163905 19853
81	182961	13.1	1	162933 20028
82	181147	13.1	1	161071 20076
83	179647	13.1	1	159268 20379
84	179288	13.1	1	158666 20622
85	176739	13.1	1	156220 20519
86	175156	13.1	1	154930 20226
87	172269	13.1	1	152575 19694
88	171226	13.1	1	151246 19980
89	167198	13.1	1	147679 19519
90	165543	13.1	1	145909 19634
91	162119	13.1	1	142744 19375
92	159287	13.1	1	140282 19005
93	157565	13.1	1	138859 18706
94	155466	13.1	1	136859 18607
95	151105	13.1	1	133065 18040
96	150049	13.1	1	132085 17964
97	146097	13.1	1	128574 17523
98	143252	13.1	1	125855 17397
99	139784	13.1	1	122884 16900
100	136912	13.1	1	120038 16874
101	132459	13.1	1	116012 16447
102	129407	13.1	1	113040 16367
103	123250	13.1	1	107686 15564
104	116965	13.1	1	101765 15200
105	111444	13.1	1	96645 14799
106	104382	13.1	1	89841 14541
107	95932	13.1	1	82076 13856
108	90857	13.1	1	76743 14114
109	82767	13.1	1	69467 13300
110	78135	13.1	1	65334 12801
111	75752	13.1	1	63276 12476
112	73108	13.1	1	61040 12068
113	70775	13.1	1	59264 11511
114	68614	13.1	1	57411 11203
115	67336	13.1	1	56534 10802
116	64527	13.1	1	54287 10240
117	63276	13.1	1	53412 9864
118	61181	13.1	1	51519 9662
119	59921	13.1	1	50861 9060
120	57524	13.1	1	48564 8960
121	56580	13.1	1	48099 8481
122	53484	13.1	1	45411 8073
123	51725	13.1	1	44332 7393
124	48421	13.1	1	41518 6903
125	50894	13.1	1	44326 6568
126	46143	13.1	1	39934 6209
127	48871	13.1	1	42933 5938
128	43008	13.1	1	38170 4838
129	72254	13.1	1	66995 5259
130	39005	13.1	1	35333 3672
131	55946	13.1	1	52525 3421
132	34239	13.1	1	31874 2365
133	36791	13.1	1	34839 1952
134	29888	13.1	1	28301 1587
135	32842	13.1	1	31413 1429
136	27536	13.1	1	26434 1102
137	28779	13.1	1	27737 1042
138	24740	13.1	1	23988 752
139	23461	13.1	1	22794 667
140	20629	13.1	1	20112 517
141	19394	13.1	1	18916 478
142	15752	13.1	1	15304 448
143	18237	13.1	1	17814 423
144	14377	13.1	1	13941 436
145	15679	13.1	1	15212 467
146	11999	13.1	1	11562 437
147	11281	13.1	1	10783 498
148	9039	13.1	1	8390 649
149	10320	13.1	1	9341 979
150	16689	13.1	1	10308 6381
151	2792571	13.1	1	930915 1861656


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R1_001_val_1.fq.gz
=============================================
882029208 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR014_AD014_S5_L002_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R2_001_val_2.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
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180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
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250000000 sequences processed
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290000000 sequences processed
300000000 sequences processed
310000000 sequences processed
320000000 sequences processed
330000000 sequences processed
340000000 sequences processed
350000000 sequences processed
360000000 sequences processed
370000000 sequences processed
380000000 sequences processed
390000000 sequences processed
400000000 sequences processed
410000000 sequences processed
420000000 sequences processed
430000000 sequences processed
440000000 sequences processed
450000000 sequences processed
460000000 sequences processed
470000000 sequences processed
480000000 sequences processed
490000000 sequences processed
500000000 sequences processed
510000000 sequences processed
520000000 sequences processed
530000000 sequences processed
540000000 sequences processed
550000000 sequences processed
560000000 sequences processed
570000000 sequences processed
580000000 sequences processed
590000000 sequences processed
600000000 sequences processed
610000000 sequences processed
620000000 sequences processed
630000000 sequences processed
640000000 sequences processed
650000000 sequences processed
660000000 sequences processed
670000000 sequences processed
680000000 sequences processed
690000000 sequences processed
700000000 sequences processed
710000000 sequences processed
720000000 sequences processed
730000000 sequences processed
740000000 sequences processed
750000000 sequences processed
760000000 sequences processed
770000000 sequences processed
780000000 sequences processed
790000000 sequences processed
800000000 sequences processed
810000000 sequences processed
820000000 sequences processed
830000000 sequences processed
840000000 sequences processed
850000000 sequences processed
860000000 sequences processed
870000000 sequences processed
880000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 21417.12 s (24 us/read; 2.47 M reads/minute).

=== Summary ===

Total reads processed:             882,029,208
Reads with adapters:               357,804,367 (40.6%)
Reads written (passing filters):   882,029,208 (100.0%)

Total basepairs processed: 109,686,944,991 bp
Quality-trimmed:              57,793,498 bp (0.1%)
Total written (filtered):  107,213,258,754 bp (97.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 357804367 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 31.4%
  C: 23.0%
  G: 15.5%
  T: 29.8%
  none/other: 0.3%

Overview of removed sequences
length	count	expect	max.err	error counts
1	235099366	220507302.0	0	235099366
2	62543836	55126825.5	0	62543836
3	17144245	13781706.4	0	17144245
4	6646447	3445426.6	0	6646447
5	639554	861356.6	0	639554
6	474891	215339.2	0	474891
7	405448	53834.8	0	405448
8	466848	13458.7	0	466848
9	348446	3364.7	0	337673 10773
10	461105	841.2	1	386657 74448
11	439665	210.3	1	373444 66221
12	854670	52.6	1	764149 90521
13	7135	13.1	1	2811 4324
14	514702	13.1	1	447955 66747
15	722304	13.1	1	657406 64898
16	3921	13.1	1	1665 2256
17	483893	13.1	1	430625 53268
18	311726	13.1	1	280786 30940
19	508462	13.1	1	447409 61053
20	376124	13.1	1	336875 39249
21	359883	13.1	1	322088 37795
22	398674	13.1	1	356521 42153
23	416959	13.1	1	370051 46908
24	611113	13.1	1	529458 81655
25	410127	13.1	1	370095 40032
26	415762	13.1	1	375188 40574
27	327612	13.1	1	286723 40889
28	609543	13.1	1	556927 52616
29	205545	13.1	1	171345 34200
30	596568	13.1	1	542203 54365
31	263996	13.1	1	228833 35163
32	1289400	13.1	1	1212993 76407
33	512660	13.1	1	459500 53160
34	184716	13.1	1	153208 31508
35	692795	13.1	1	644767 48028
36	158296	13.1	1	131258 27038
37	342624	13.1	1	302501 40123
38	97006	13.1	1	81760 15246
39	183704	13.1	1	157551 26153
40	45254	13.1	1	35800 9454
41	355563	13.1	1	324511 31052
42	528472	13.1	1	488465 40007
43	208242	13.1	1	182929 25313
44	390129	13.1	1	351993 38136
45	1128825	13.1	1	1066223 62602
46	345095	13.1	1	302774 42321
47	117084	13.1	1	100592 16492
48	873716	13.1	1	814718 58998
49	169284	13.1	1	146835 22449
50	52750	13.1	1	40938 11812
51	646744	13.1	1	599590 47154
52	1193783	13.1	1	1142866 50917
53	250287	13.1	1	227517 22770
54	380803	13.1	1	348438 32365
55	138543	13.1	1	122337 16206
56	90468	13.1	1	75051 15417
57	169985	13.1	1	149829 20156
58	203858	13.1	1	180530 23328
59	93592	13.1	1	77303 16289
60	78787	13.1	1	63686 15101
61	82444	13.1	1	67562 14882
62	79746	13.1	1	65366 14380
63	94126	13.1	1	79609 14517
64	179996	13.1	1	162738 17258
65	257597	13.1	1	235879 21718
66	285315	13.1	1	261166 24149
67	292126	13.1	1	266275 25851
68	295475	13.1	1	268387 27088
69	295990	13.1	1	268443 27547
70	296714	13.1	1	268419 28295
71	300117	13.1	1	271207 28910
72	295102	13.1	1	266729 28373
73	297780	13.1	1	269028 28752
74	291630	13.1	1	263445 28185
75	287606	13.1	1	259336 28270
76	282934	13.1	1	254551 28383
77	279808	13.1	1	251854 27954
78	276410	13.1	1	248663 27747
79	271068	13.1	1	243712 27356
80	266965	13.1	1	240369 26596
81	264294	13.1	1	238046 26248
82	260238	13.1	1	233644 26594
83	258826	13.1	1	232425 26401
84	255117	13.1	1	229078 26039
85	252997	13.1	1	227278 25719
86	250320	13.1	1	224751 25569
87	246703	13.1	1	221934 24769
88	243894	13.1	1	219163 24731
89	237391	13.1	1	212725 24666
90	232269	13.1	1	207825 24444
91	227208	13.1	1	203062 24146
92	222180	13.1	1	198614 23566
93	219038	13.1	1	195701 23337
94	215630	13.1	1	192779 22851
95	212171	13.1	1	189594 22577
96	208724	13.1	1	186441 22283
97	203591	13.1	1	181707 21884
98	198733	13.1	1	177288 21445
99	195082	13.1	1	174344 20738
100	190416	13.1	1	169973 20443
101	185717	13.1	1	165304 20413
102	177447	13.1	1	157905 19542
103	169476	13.1	1	150354 19122
104	158041	13.1	1	139594 18447
105	149050	13.1	1	130821 18229
106	137972	13.1	1	120204 17768
107	124510	13.1	1	107417 17093
108	115302	13.1	1	98640 16662
109	103287	13.1	1	87118 16169
110	95710	13.1	1	80359 15351
111	92391	13.1	1	77278 15113
112	88978	13.1	1	74373 14605
113	86338	13.1	1	72405 13933
114	83339	13.1	1	69681 13658
115	81009	13.1	1	68155 12854
116	78418	13.1	1	65893 12525
117	76604	13.1	1	64480 12124
118	73600	13.1	1	61978 11622
119	72003	13.1	1	60976 11027
120	68625	13.1	1	57886 10739
121	67484	13.1	1	57305 10179
122	63641	13.1	1	53989 9652
123	61549	13.1	1	52545 9004
124	57810	13.1	1	49218 8592
125	59751	13.1	1	51688 8063
126	54119	13.1	1	46626 7493
127	56196	13.1	1	49390 6806
128	48450	13.1	1	43017 5433
129	77040	13.1	1	72208 4832
130	41906	13.1	1	38198 3708
131	58208	13.1	1	55170 3038
132	35365	13.1	1	33000 2365
133	37604	13.1	1	35650 1954
134	30524	13.1	1	28823 1701
135	33388	13.1	1	31868 1520
136	27789	13.1	1	26293 1496
137	28933	13.1	1	27576 1357
138	24891	13.1	1	23429 1462
139	23476	13.1	1	22117 1359
140	20658	13.1	1	19184 1474
141	19395	13.1	1	17726 1669
142	15659	13.1	1	13873 1786
143	18154	13.1	1	16108 2046
144	14333	13.1	1	12303 2030
145	15517	13.1	1	12894 2623
146	11673	13.1	1	9220 2453
147	10903	13.1	1	8531 2372
148	8478	13.1	1	6288 2190
149	9455	13.1	1	6948 2507
150	11337	13.1	1	8415 2922
151	948058	13.1	1	929339 18719


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR014_AD014_S5_L002_R2_001_val_2.fq.gz
=============================================
882029208 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR014_AD014_S5_L002_R1_001_val_1_trimmed.fq.gz and NR014_AD014_S5_L002_R2_001_val_2_trimmed.fq.gz
file_1: NR014_AD014_S5_L002_R1_001_val_1_trimmed.fq.gz, file_2: NR014_AD014_S5_L002_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR014_AD014_S5_L002_R1_001_val_1_trimmed.fq.gz and NR014_AD014_S5_L002_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 882029208

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 5672977 (0.64%)

Deleting both intermediate output files NR014_AD014_S5_L002_R1_001_val_1_trimmed.fq.gz and NR014_AD014_S5_L002_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR015_AD015_S6_L001_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R1_001_val_1.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 5993.33 s (24 us/read; 2.52 M reads/minute).

=== Summary ===

Total reads processed:             251,960,784
Reads with adapters:                98,150,549 (39.0%)
Reads written (passing filters):   251,960,784 (100.0%)

Total basepairs processed: 30,292,882,260 bp
Quality-trimmed:              14,880,179 bp (0.0%)
Total written (filtered):  29,870,391,799 bp (98.6%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 98150549 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 31.6%
  C: 23.5%
  G: 14.7%
  T: 29.7%
  none/other: 0.4%

Overview of removed sequences
length	count	expect	max.err	error counts
1	67647589	62990196.0	0	67647589
2	18152045	15747549.0	0	18152045
3	4775986	3936887.2	0	4775986
4	1890969	984221.8	0	1890969
5	207664	246055.5	0	207664
6	98537	61513.9	0	98537
7	74846	15378.5	0	74846
8	88166	3844.6	0	88166
9	80952	961.2	0	78131 2821
10	87335	240.3	1	73607 13728
11	89943	60.1	1	76934 13009
12	160853	15.0	1	146405 14448
13	4569	3.8	1	2624 1945
14	159804	3.8	1	145131 14673
15	3985	3.8	1	2223 1762
16	170314	3.8	1	151711 18603
17	7416	3.8	1	4591 2825
18	108590	3.8	1	97058 11532
19	256789	3.8	1	238071 18718
20	1865	3.8	1	1095 770
21	1505	3.8	1	703 802
22	3383	3.8	1	1937 1446
23	95821	3.8	1	85516 10305
24	198167	3.8	1	181758 16409
25	6239	3.8	1	4186 2053
26	75965	3.8	1	68109 7856
27	68321	3.8	1	63163 5158
28	2319	3.8	1	1409 910
29	72530	3.8	1	64801 7729
30	89129	3.8	1	80867 8262
31	111877	3.8	1	103485 8392
32	5769	3.8	1	4052 1717
33	127778	3.8	1	116285 11493
34	2818	3.8	1	1949 869
35	69936	3.8	1	61722 8214
36	66317	3.8	1	59395 6922
37	71065	3.8	1	64414 6651
38	107872	3.8	1	99240 8632
39	2490	3.8	1	1707 783
40	62577	3.8	1	55534 7043
41	60445	3.8	1	53846 6599
42	72395	3.8	1	63133 9262
43	79730	3.8	1	67556 12174
44	174322	3.8	1	155148 19174
45	33434	3.8	1	29737 3697
46	48312	3.8	1	40644 7668
47	8868	3.8	1	7169 1699
48	363712	3.8	1	346160 17552
49	159049	3.8	1	148984 10065
50	28469	3.8	1	24000 4469
51	87615	3.8	1	81660 5955
52	83971	3.8	1	77843 6128
53	16110	3.8	1	13174 2936
54	5077	3.8	1	3616 1461
55	40249	3.8	1	37342 2907
56	25311	3.8	1	22425 2886
57	4914	3.8	1	3521 1393
58	9531	3.8	1	7750 1781
59	15683	3.8	1	13352 2331
60	6108	3.8	1	4537 1571
61	9553	3.8	1	7756 1797
62	30625	3.8	1	28085 2540
63	6646	3.8	1	5279 1367
64	10476	3.8	1	8893 1583
65	12129	3.8	1	10311 1818
66	32496	3.8	1	30129 2367
67	9348	3.8	1	7566 1782
68	14758	3.8	1	12818 1940
69	17456	3.8	1	15424 2032
70	20192	3.8	1	18162 2030
71	8547	3.8	1	6817 1730
72	7395	3.8	1	5884 1511
73	13127	3.8	1	11639 1488
74	20669	3.8	1	18903 1766
75	24963	3.8	1	22902 2061
76	27047	3.8	1	24893 2154
77	27841	3.8	1	25567 2274
78	28052	3.8	1	25700 2352
79	28023	3.8	1	25545 2478
80	27896	3.8	1	25399 2497
81	27733	3.8	1	25291 2442
82	27390	3.8	1	24949 2441
83	26697	3.8	1	24265 2432
84	26722	3.8	1	24290 2432
85	25927	3.8	1	23433 2494
86	25310	3.8	1	22865 2445
87	25046	3.8	1	22605 2441
88	24529	3.8	1	22179 2350
89	24483	3.8	1	22077 2406
90	23988	3.8	1	21625 2363
91	22741	3.8	1	20617 2124
92	22201	3.8	1	20056 2145
93	21627	3.8	1	19471 2156
94	20771	3.8	1	18675 2096
95	20353	3.8	1	18316 2037
96	20197	3.8	1	18120 2077
97	19416	3.8	1	17499 1917
98	18926	3.8	1	17057 1869
99	18141	3.8	1	16272 1869
100	17620	3.8	1	15816 1804
101	17151	3.8	1	15427 1724
102	16211	3.8	1	14534 1677
103	15119	3.8	1	13497 1622
104	13828	3.8	1	12253 1575
105	12712	3.8	1	11213 1499
106	11640	3.8	1	10264 1376
107	10351	3.8	1	9001 1350
108	9064	3.8	1	7742 1322
109	8038	3.8	1	6793 1245
110	7411	3.8	1	6192 1219
111	6953	3.8	1	5785 1168
112	6592	3.8	1	5468 1124
113	6501	3.8	1	5458 1043
114	6362	3.8	1	5319 1043
115	6222	3.8	1	5249 973
116	5855	3.8	1	4900 955
117	6026	3.8	1	5076 950
118	5657	3.8	1	4820 837
119	5546	3.8	1	4708 838
120	5427	3.8	1	4637 790
121	5303	3.8	1	4551 752
122	4956	3.8	1	4286 670
123	5000	3.8	1	4290 710
124	4630	3.8	1	4031 599
125	5010	3.8	1	4393 617
126	4540	3.8	1	3960 580
127	4791	3.8	1	4274 517
128	4506	3.8	1	4038 468
129	7579	3.8	1	7009 570
130	4174	3.8	1	3794 380
131	6400	3.8	1	6002 398
132	4137	3.8	1	3882 255
133	4484	3.8	1	4219 265
134	3766	3.8	1	3564 202
135	4268	3.8	1	4046 222
136	3911	3.8	1	3717 194
137	4096	3.8	1	3915 181
138	3517	3.8	1	3375 142
139	3308	3.8	1	3157 151
140	3107	3.8	1	2996 111
141	3026	3.8	1	2901 125
142	2772	3.8	1	2650 122
143	3177	3.8	1	3054 123
144	2245	3.8	1	2121 124
145	2434	3.8	1	2302 132
146	2314	3.8	1	2195 119
147	2036	3.8	1	1898 138
148	1674	3.8	1	1487 187
149	1931	3.8	1	1679 252
150	4377	3.8	1	3025 1352
151	379957	3.8	1	180456 199501


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R1_001_val_1.fq.gz
=============================================
251960784 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR015_AD015_S6_L001_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R2_001_val_2.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 6193.60 s (25 us/read; 2.44 M reads/minute).

=== Summary ===

Total reads processed:             251,960,784
Reads with adapters:               100,979,622 (40.1%)
Reads written (passing filters):   251,960,784 (100.0%)

Total basepairs processed: 31,155,879,786 bp
Quality-trimmed:              21,545,872 bp (0.1%)
Total written (filtered):  30,661,317,524 bp (98.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 100979622 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 31.8%
  C: 23.0%
  G: 15.4%
  T: 29.6%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	68313199	62990196.0	0	68313199
2	18143166	15747549.0	0	18143166
3	5124109	3936887.2	0	5124109
4	1954723	984221.8	0	1954723
5	188739	246055.5	0	188739
6	129140	61513.9	0	129140
7	108832	15378.5	0	108832
8	128886	3844.6	0	128886
9	91260	961.2	0	87928 3332
10	126203	240.3	1	104830 21373
11	115077	60.1	1	96709 18368
12	226745	15.0	1	199323 27422
13	2194	3.8	1	959 1235
14	138238	3.8	1	118664 19574
15	191130	3.8	1	169718 21412
16	995	3.8	1	353 642
17	129094	3.8	1	113633 15461
18	79704	3.8	1	69960 9744
19	138252	3.8	1	121219 17033
20	100096	3.8	1	87894 12202
21	86564	3.8	1	75650 10914
22	101219	3.8	1	89374 11845
23	107692	3.8	1	94087 13605
24	189955	3.8	1	167177 22778
25	98024	3.8	1	87166 10858
26	98295	3.8	1	86572 11723
27	64815	3.8	1	54515 10300
28	155492	3.8	1	141126 14366
29	40546	3.8	1	32691 7855
30	146697	3.8	1	132730 13967
31	60422	3.8	1	51220 9202
32	268474	3.8	1	249368 19106
33	110795	3.8	1	97259 13536
34	38204	3.8	1	31226 6978
35	143638	3.8	1	131450 12188
36	47890	3.8	1	41399 6491
37	72520	3.8	1	63288 9232
38	37867	3.8	1	33785 4082
39	50949	3.8	1	44733 6216
40	20848	3.8	1	18228 2620
41	79085	3.8	1	71910 7175
42	111036	3.8	1	101963 9073
43	50564	3.8	1	44806 5758
44	82737	3.8	1	74481 8256
45	151990	3.8	1	139894 12096
46	71723	3.8	1	63298 8425
47	48816	3.8	1	44185 4631
48	148377	3.8	1	136657 11720
49	61498	3.8	1	55998 5500
50	23050	3.8	1	20044 3006
51	119426	3.8	1	109607 9819
52	183281	3.8	1	172910 10371
53	71389	3.8	1	66191 5198
54	89936	3.8	1	82844 7092
55	52537	3.8	1	48707 3830
56	25438	3.8	1	22287 3151
57	46738	3.8	1	42457 4281
58	50540	3.8	1	45618 4922
59	28544	3.8	1	25164 3380
60	18858	3.8	1	16100 2758
61	17190	3.8	1	14584 2606
62	18991	3.8	1	16327 2664
63	22581	3.8	1	19907 2674
64	38653	3.8	1	35535 3118
65	48769	3.8	1	44750 4019
66	52547	3.8	1	48219 4328
67	52683	3.8	1	48131 4552
68	52201	3.8	1	47603 4598
69	52101	3.8	1	47443 4658
70	51853	3.8	1	47277 4576
71	51340	3.8	1	46653 4687
72	50223	3.8	1	45673 4550
73	49914	3.8	1	45383 4531
74	48369	3.8	1	43891 4478
75	47815	3.8	1	43411 4404
76	46803	3.8	1	42428 4375
77	46237	3.8	1	42021 4216
78	44826	3.8	1	40634 4192
79	43489	3.8	1	39420 4069
80	43261	3.8	1	39363 3898
81	42442	3.8	1	38480 3962
82	41492	3.8	1	37628 3864
83	40374	3.8	1	36728 3646
84	39695	3.8	1	36017 3678
85	39208	3.8	1	35580 3628
86	38171	3.8	1	34599 3572
87	38016	3.8	1	34553 3463
88	36525	3.8	1	33092 3433
89	41258	3.8	1	33003 8255
90	34752	3.8	1	31007 3745
91	33218	3.8	1	30100 3118
92	32601	3.8	1	29475 3126
93	31952	3.8	1	28947 3005
94	31006	3.8	1	28057 2949
95	30263	3.8	1	27427 2836
96	29561	3.8	1	26776 2785
97	28672	3.8	1	25981 2691
98	27549	3.8	1	24930 2619
99	26632	3.8	1	24067 2565
100	25886	3.8	1	23427 2459
101	24490	3.8	1	22115 2375
102	23311	3.8	1	21015 2296
103	21482	3.8	1	19313 2169
104	19671	3.8	1	17609 2062
105	17882	3.8	1	15906 1976
106	15683	3.8	1	13909 1774
107	13366	3.8	1	11584 1782
108	11524	3.8	1	9775 1749
109	9805	3.8	1	8171 1634
110	8591	3.8	1	7096 1495
111	8086	3.8	1	6610 1476
112	7566	3.8	1	6240 1326
113	7509	3.8	1	6118 1391
114	7162	3.8	1	5878 1284
115	7027	3.8	1	5812 1215
116	6711	3.8	1	5506 1205
117	6602	3.8	1	5438 1164
118	6295	3.8	1	5252 1043
119	6307	3.8	1	5204 1103
120	6026	3.8	1	5073 953
121	5936	3.8	1	5017 919
122	5503	3.8	1	4654 849
123	5535	3.8	1	4715 820
124	5175	3.8	1	4422 753
125	5396	3.8	1	4729 667
126	5052	3.8	1	4370 682
127	5194	3.8	1	4586 608
128	4771	3.8	1	4258 513
129	7872	3.8	1	7315 557
130	4352	3.8	1	3923 429
131	6565	3.8	1	6168 397
132	4192	3.8	1	3862 330
133	4550	3.8	1	4240 310
134	3843	3.8	1	3560 283
135	4287	3.8	1	4041 246
136	3693	3.8	1	3402 291
137	4048	3.8	1	3789 259
138	3506	3.8	1	3254 252
139	3304	3.8	1	3036 268
140	3120	3.8	1	2843 277
141	3010	3.8	1	2684 326
142	2563	3.8	1	2214 349
143	2946	3.8	1	2557 389
144	2247	3.8	1	1857 390
145	2380	3.8	1	1931 449
146	1903	3.8	1	1439 464
147	1848	3.8	1	1414 434
148	1435	3.8	1	985 450
149	1587	3.8	1	1131 456
150	3495	3.8	1	2865 630
151	169848	3.8	1	165158 4690


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L001_R2_001_val_2.fq.gz
=============================================
251960784 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR015_AD015_S6_L001_R1_001_val_1_trimmed.fq.gz and NR015_AD015_S6_L001_R2_001_val_2_trimmed.fq.gz
file_1: NR015_AD015_S6_L001_R1_001_val_1_trimmed.fq.gz, file_2: NR015_AD015_S6_L001_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR015_AD015_S6_L001_R1_001_val_1_trimmed.fq.gz and NR015_AD015_S6_L001_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 251960784

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1195829 (0.47%)

Deleting both intermediate output files NR015_AD015_S6_L001_R1_001_val_1_trimmed.fq.gz and NR015_AD015_S6_L001_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR015_AD015_S6_L002_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R1_001_val_1.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 6925.44 s (24 us/read; 2.48 M reads/minute).

=== Summary ===

Total reads processed:             286,345,514
Reads with adapters:               112,959,695 (39.4%)
Reads written (passing filters):   286,345,514 (100.0%)

Total basepairs processed: 35,038,018,789 bp
Quality-trimmed:              13,805,282 bp (0.0%)
Total written (filtered):  34,518,982,225 bp (98.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 112959695 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 31.6%
  C: 23.5%
  G: 14.7%
  T: 29.7%
  none/other: 0.5%

Overview of removed sequences
length	count	expect	max.err	error counts
1	78396135	71586378.5	0	78396135
2	20488392	17896594.6	0	20488392
3	5379582	4474148.7	0	5379582
4	2080584	1118537.2	0	2080584
5	223491	279634.3	0	223491
6	100154	69908.6	0	100154
7	75732	17477.1	0	75732
8	86633	4369.3	0	86633
9	80998	1092.3	0	77642 3356
10	88682	273.1	1	74287 14395
11	90629	68.3	1	77841 12788
12	161905	17.1	1	148361 13544
13	4301	4.3	1	2285 2016
14	160121	4.3	1	146934 13187
15	3804	4.3	1	1935 1869
16	171383	4.3	1	153699 17684
17	7255	4.3	1	4345 2910
18	107431	4.3	1	96486 10945
19	265068	4.3	1	247099 17969
20	1979	4.3	1	1118 861
21	1742	4.3	1	801 941
22	3763	4.3	1	2101 1662
23	95718	4.3	1	85159 10559
24	206250	4.3	1	190203 16047
25	6546	4.3	1	4203 2343
26	78594	4.3	1	70732 7862
27	70370	4.3	1	65520 4850
28	2519	4.3	1	1512 1007
29	75709	4.3	1	67862 7847
30	91570	4.3	1	83304 8266
31	117793	4.3	1	109087 8706
32	6339	4.3	1	4304 2035
33	137342	4.3	1	124884 12458
34	3254	4.3	1	2205 1049
35	75697	4.3	1	66263 9434
36	70974	4.3	1	63418 7556
37	76030	4.3	1	68817 7213
38	118275	4.3	1	108426 9849
39	2841	4.3	1	1941 900
40	69529	4.3	1	61210 8319
41	68776	4.3	1	60720 8056
42	82760	4.3	1	70525 12235
43	94151	4.3	1	77798 16353
44	204930	4.3	1	180380 24550
45	38013	4.3	1	33457 4556
46	54282	4.3	1	44999 9283
47	11755	4.3	1	9625 2130
48	492920	4.3	1	471229 21691
49	144283	4.3	1	132748 11535
50	29210	4.3	1	23840 5370
51	111750	4.3	1	103977 7773
52	84336	4.3	1	76899 7437
53	14904	4.3	1	11273 3631
54	6028	4.3	1	4207 1821
55	38270	4.3	1	34920 3350
56	20143	4.3	1	16575 3568
57	4741	4.3	1	3048 1693
58	9097	4.3	1	6744 2353
59	20031	4.3	1	17035 2996
60	6411	4.3	1	4486 1925
61	9287	4.3	1	6932 2355
62	31197	4.3	1	28051 3146
63	5622	4.3	1	4034 1588
64	9211	4.3	1	7161 2050
65	14746	4.3	1	12258 2488
66	33048	4.3	1	29926 3122
67	11214	4.3	1	8789 2425
68	24371	4.3	1	21564 2807
69	30605	4.3	1	27502 3103
70	44875	4.3	1	41184 3691
71	17999	4.3	1	15248 2751
72	8543	4.3	1	6252 2291
73	12632	4.3	1	10441 2191
74	22706	4.3	1	20346 2360
75	30225	4.3	1	27494 2731
76	33537	4.3	1	30537 3000
77	35713	4.3	1	32516 3197
78	36158	4.3	1	32668 3490
79	36710	4.3	1	33136 3574
80	36902	4.3	1	33217 3685
81	36541	4.3	1	32897 3644
82	36501	4.3	1	32621 3880
83	35623	4.3	1	31806 3817
84	35658	4.3	1	31851 3807
85	35471	4.3	1	31655 3816
86	34536	4.3	1	30760 3776
87	33782	4.3	1	30227 3555
88	33922	4.3	1	30047 3875
89	33565	4.3	1	29789 3776
90	33858	4.3	1	30148 3710
91	32373	4.3	1	28635 3738
92	31605	4.3	1	28042 3563
93	30634	4.3	1	27154 3480
94	30011	4.3	1	26517 3494
95	29452	4.3	1	25995 3457
96	29070	4.3	1	25623 3447
97	28471	4.3	1	25113 3358
98	27941	4.3	1	24728 3213
99	27386	4.3	1	24187 3199
100	26522	4.3	1	23386 3136
101	25249	4.3	1	22180 3069
102	24525	4.3	1	21350 3175
103	23581	4.3	1	20579 3002
104	22163	4.3	1	19173 2990
105	20739	4.3	1	17886 2853
106	19555	4.3	1	16798 2757
107	17970	4.3	1	15280 2690
108	16213	4.3	1	13719 2494
109	14971	4.3	1	12491 2480
110	14369	4.3	1	11949 2420
111	13676	4.3	1	11409 2267
112	13279	4.3	1	10889 2390
113	12986	4.3	1	10823 2163
114	12529	4.3	1	10316 2213
115	12359	4.3	1	10273 2086
116	11824	4.3	1	9721 2103
117	11521	4.3	1	9680 1841
118	11341	4.3	1	9443 1898
119	10814	4.3	1	9101 1713
120	10536	4.3	1	8822 1714
121	10223	4.3	1	8608 1615
122	9654	4.3	1	8123 1531
123	9335	4.3	1	7885 1450
124	8797	4.3	1	7489 1308
125	8983	4.3	1	7661 1322
126	8427	4.3	1	7191 1236
127	8872	4.3	1	7688 1184
128	7881	4.3	1	6883 998
129	11912	4.3	1	10868 1044
130	7024	4.3	1	6278 746
131	10003	4.3	1	9240 763
132	6500	4.3	1	5991 509
133	6890	4.3	1	6514 376
134	5695	4.3	1	5351 344
135	6358	4.3	1	6012 346
136	5449	4.3	1	5171 278
137	5778	4.3	1	5554 224
138	4758	4.3	1	4570 188
139	4546	4.3	1	4383 163
140	4169	4.3	1	3998 171
141	3895	4.3	1	3759 136
142	3337	4.3	1	3215 122
143	3888	4.3	1	3761 127
144	3019	4.3	1	2893 126
145	3195	4.3	1	3069 126
146	2750	4.3	1	2613 137
147	2411	4.3	1	2277 134
148	1979	4.3	1	1816 163
149	2200	4.3	1	2002 198
150	3790	4.3	1	2743 1047
151	507649	4.3	1	240906 266743


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R1_001_val_1.fq.gz
=============================================
286345514 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR015_AD015_S6_L002_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R2_001_val_2.fq.gz <<< 
10000000 sequences processed
20000000 sequences processed
30000000 sequences processed
40000000 sequences processed
50000000 sequences processed
60000000 sequences processed
70000000 sequences processed
80000000 sequences processed
90000000 sequences processed
100000000 sequences processed
110000000 sequences processed
120000000 sequences processed
130000000 sequences processed
140000000 sequences processed
150000000 sequences processed
160000000 sequences processed
170000000 sequences processed
180000000 sequences processed
190000000 sequences processed
200000000 sequences processed
210000000 sequences processed
220000000 sequences processed
230000000 sequences processed
240000000 sequences processed
250000000 sequences processed
260000000 sequences processed
270000000 sequences processed
280000000 sequences processed
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 7061.45 s (25 us/read; 2.43 M reads/minute).

=== Summary ===

Total reads processed:             286,345,514
Reads with adapters:               115,866,451 (40.5%)
Reads written (passing filters):   286,345,514 (100.0%)

Total basepairs processed: 35,998,085,991 bp
Quality-trimmed:              19,015,689 bp (0.1%)
Total written (filtered):  35,401,915,461 bp (98.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 115866451 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 31.7%
  C: 23.1%
  G: 15.2%
  T: 29.8%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	79078292	71586378.5	0	79078292
2	20457949	17896594.6	0	20457949
3	5667589	4474148.7	0	5667589
4	2136345	1118537.2	0	2136345
5	203396	279634.3	0	203396
6	132501	69908.6	0	132501
7	111365	17477.1	0	111365
8	128366	4369.3	0	128366
9	94532	1092.3	0	90994 3538
10	126018	273.1	1	105952 20066
11	117446	68.3	1	100812 16634
12	229409	17.1	1	207524 21885
13	1726	4.3	1	637 1089
14	137420	4.3	1	121594 15826
15	195930	4.3	1	179871 16059
16	1019	4.3	1	406 613
17	129235	4.3	1	116497 12738
18	83174	4.3	1	75604 7570
19	134882	4.3	1	120454 14428
20	102012	4.3	1	92451 9561
21	94539	4.3	1	85162 9377
22	104963	4.3	1	94978 9985
23	109241	4.3	1	97982 11259
24	169194	4.3	1	149865 19329
25	108190	4.3	1	98765 9425
26	106700	4.3	1	97468 9232
27	72292	4.3	1	63329 8963
28	159462	4.3	1	147411 12051
29	47180	4.3	1	39638 7542
30	153244	4.3	1	140978 12266
31	63196	4.3	1	55159 8037
32	317234	4.3	1	300225 17009
33	121994	4.3	1	109974 12020
34	43615	4.3	1	36635 6980
35	170310	4.3	1	159614 10696
36	39610	4.3	1	33583 6027
37	87306	4.3	1	77969 9337
38	24050	4.3	1	20856 3194
39	45657	4.3	1	39827 5830
40	11498	4.3	1	9445 2053
41	86757	4.3	1	79909 6848
42	126694	4.3	1	117946 8748
43	49611	4.3	1	44116 5495
44	91218	4.3	1	83312 7906
45	219772	4.3	1	207168 12604
46	80363	4.3	1	71838 8525
47	41363	4.3	1	37265 4098
48	199800	4.3	1	187096 12704
49	51044	4.3	1	45831 5213
50	15676	4.3	1	13062 2614
51	148760	4.3	1	138677 10083
52	266390	4.3	1	255506 10884
53	63589	4.3	1	58598 4991
54	90051	4.3	1	83057 6994
55	36487	4.3	1	32986 3501
56	21520	4.3	1	18377 3143
57	40871	4.3	1	36643 4228
58	47319	4.3	1	42462 4857
59	22625	4.3	1	19152 3473
60	17420	4.3	1	14369 3051
61	17831	4.3	1	14783 3048
62	17975	4.3	1	15025 2950
63	21863	4.3	1	18777 3086
64	41409	4.3	1	37784 3625
65	56629	4.3	1	52276 4353
66	61832	4.3	1	56984 4848
67	62658	4.3	1	57537 5121
68	62434	4.3	1	56987 5447
69	62709	4.3	1	57086 5623
70	62901	4.3	1	57266 5635
71	63182	4.3	1	57483 5699
72	61596	4.3	1	55910 5686
73	61973	4.3	1	56417 5556
74	60575	4.3	1	54925 5650
75	59734	4.3	1	54144 5590
76	58840	4.3	1	53256 5584
77	58095	4.3	1	52527 5568
78	56618	4.3	1	51156 5462
79	55726	4.3	1	50288 5438
80	55092	4.3	1	49744 5348
81	53834	4.3	1	48554 5280
82	53585	4.3	1	48277 5308
83	52377	4.3	1	47209 5168
84	51678	4.3	1	46445 5233
85	51400	4.3	1	46389 5011
86	50090	4.3	1	45163 4927
87	49563	4.3	1	44686 4877
88	49536	4.3	1	44418 5118
89	54300	4.3	1	43261 11039
90	46966	4.3	1	41887 5079
91	45879	4.3	1	41024 4855
92	44543	4.3	1	39873 4670
93	43755	4.3	1	39186 4569
94	42755	4.3	1	38214 4541
95	42335	4.3	1	37965 4370
96	41082	4.3	1	36743 4339
97	40279	4.3	1	36050 4229
98	39428	4.3	1	35127 4301
99	38622	4.3	1	34464 4158
100	37168	4.3	1	33149 4019
101	35893	4.3	1	31952 3941
102	34270	4.3	1	30464 3806
103	33129	4.3	1	29302 3827
104	30511	4.3	1	26863 3648
105	28506	4.3	1	24942 3564
106	26155	4.3	1	22782 3373
107	23714	4.3	1	20265 3449
108	21008	4.3	1	17830 3178
109	18868	4.3	1	15779 3089
110	17607	4.3	1	14520 3087
111	16874	4.3	1	13908 2966
112	16298	4.3	1	13432 2866
113	16100	4.3	1	13251 2849
114	15299	4.3	1	12620 2679
115	15136	4.3	1	12454 2682
116	14617	4.3	1	12112 2505
117	13972	4.3	1	11656 2316
118	13701	4.3	1	11408 2293
119	13361	4.3	1	11090 2271
120	12786	4.3	1	10659 2127
121	12428	4.3	1	10405 2023
122	11591	4.3	1	9643 1948
123	11405	4.3	1	9595 1810
124	10712	4.3	1	9030 1682
125	10763	4.3	1	9166 1597
126	10062	4.3	1	8468 1594
127	10400	4.3	1	9011 1389
128	8928	4.3	1	7828 1100
129	12877	4.3	1	11900 977
130	7703	4.3	1	6939 764
131	10433	4.3	1	9779 654
132	6733	4.3	1	6237 496
133	7084	4.3	1	6711 373
134	5808	4.3	1	5437 371
135	6472	4.3	1	6149 323
136	5338	4.3	1	5038 300
137	5793	4.3	1	5496 297
138	4805	4.3	1	4489 316
139	4583	4.3	1	4269 314
140	4150	4.3	1	3832 318
141	3861	4.3	1	3532 329
142	3205	4.3	1	2860 345
143	3735	4.3	1	3317 418
144	2991	4.3	1	2562 429
145	3152	4.3	1	2627 525
146	2370	4.3	1	1827 543
147	2265	4.3	1	1773 492
148	1796	4.3	1	1247 549
149	1873	4.3	1	1345 528
150	2305	4.3	1	1737 568
151	228767	4.3	1	224062 4705


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR015_AD015_S6_L002_R2_001_val_2.fq.gz
=============================================
286345514 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR015_AD015_S6_L002_R1_001_val_1_trimmed.fq.gz and NR015_AD015_S6_L002_R2_001_val_2_trimmed.fq.gz
file_1: NR015_AD015_S6_L002_R1_001_val_1_trimmed.fq.gz, file_2: NR015_AD015_S6_L002_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR015_AD015_S6_L002_R1_001_val_1_trimmed.fq.gz and NR015_AD015_S6_L002_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 286345514

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1343740 (0.47%)

Deleting both intermediate output files NR015_AD015_S6_L002_R1_001_val_1_trimmed.fq.gz and NR015_AD015_S6_L002_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR019_S7_L001_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001_val_1.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.13 s (27 us/read; 2.19 M reads/minute).

=== Summary ===

Total reads processed:                  41,244
Reads with adapters:                    22,174 (53.8%)
Reads written (passing filters):        41,244 (100.0%)

Total basepairs processed:     5,571,801 bp
Quality-trimmed:                  10,796 bp (0.2%)
Total written (filtered):      5,496,658 bp (98.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22174 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 41.0%
  C: 22.0%
  G: 10.3%
  T: 26.5%
  none/other: 0.2%

Overview of removed sequences
length	count	expect	max.err	error counts
1	17489	10311.0	0	17489
2	2472	2577.8	0	2472
3	1088	644.4	0	1088
4	354	161.1	0	354
5	17	40.3	0	17
6	10	10.1	0	10
7	9	2.5	0	9
8	9	0.6	0	9
9	9	0.2	0	9
10	16	0.0	1	11 5
11	16	0.0	1	12 4
12	18	0.0	1	16 2
13	2	0.0	1	2
14	23	0.0	1	15 8
15	1	0.0	1	1
16	25	0.0	1	11 14
17	1	0.0	1	1
18	29	0.0	1	20 9
19	29	0.0	1	19 10
21	1	0.0	1	1
22	1	0.0	1	0 1
23	15	0.0	1	11 4
24	32	0.0	1	20 12
25	1	0.0	1	1
26	7	0.0	1	6 1
27	10	0.0	1	9 1
29	9	0.0	1	6 3
30	13	0.0	1	11 2
31	15	0.0	1	10 5
32	2	0.0	1	1 1
33	24	0.0	1	21 3
35	18	0.0	1	13 5
36	11	0.0	1	9 2
37	5	0.0	1	3 2
38	8	0.0	1	5 3
39	11	0.0	1	8 3
40	12	0.0	1	11 1
41	1	0.0	1	0 1
42	12	0.0	1	8 4
43	20	0.0	1	10 10
44	27	0.0	1	20 7
45	6	0.0	1	5 1
46	8	0.0	1	5 3
48	32	0.0	1	18 14
49	14	0.0	1	10 4
50	6	0.0	1	4 2
51	9	0.0	1	8 1
52	10	0.0	1	8 2
53	3	0.0	1	2 1
55	2	0.0	1	2
56	9	0.0	1	7 2
58	3	0.0	1	3
59	6	0.0	1	3 3
61	1	0.0	1	1
62	3	0.0	1	3
63	1	0.0	1	1
64	1	0.0	1	1
65	1	0.0	1	0 1
66	3	0.0	1	2 1
67	4	0.0	1	3 1
68	2	0.0	1	1 1
69	2	0.0	1	1 1
70	3	0.0	1	3
71	2	0.0	1	0 2
72	1	0.0	1	0 1
73	4	0.0	1	4
74	5	0.0	1	3 2
75	1	0.0	1	0 1
76	1	0.0	1	0 1
77	2	0.0	1	2
78	3	0.0	1	2 1
79	4	0.0	1	2 2
80	3	0.0	1	3
81	4	0.0	1	3 1
82	7	0.0	1	7
83	6	0.0	1	5 1
84	3	0.0	1	2 1
85	4	0.0	1	3 1
86	6	0.0	1	5 1
87	2	0.0	1	1 1
88	1	0.0	1	1
89	3	0.0	1	2 1
90	7	0.0	1	5 2
91	4	0.0	1	3 1
93	3	0.0	1	2 1
94	1	0.0	1	1
95	3	0.0	1	2 1
96	3	0.0	1	2 1
97	1	0.0	1	1
98	4	0.0	1	4
100	2	0.0	1	1 1
101	1	0.0	1	0 1
102	1	0.0	1	1
104	3	0.0	1	1 2
105	1	0.0	1	1
106	2	0.0	1	1 1
107	2	0.0	1	0 2
109	2	0.0	1	2
111	3	0.0	1	2 1
115	1	0.0	1	1
116	2	0.0	1	2
119	2	0.0	1	1 1
120	1	0.0	1	1
121	2	0.0	1	0 2
126	3	0.0	1	2 1
127	1	0.0	1	0 1
128	1	0.0	1	0 1
130	1	0.0	1	0 1
131	1	0.0	1	1
135	1	0.0	1	1
139	1	0.0	1	1
140	1	0.0	1	1
143	1	0.0	1	0 1
144	1	0.0	1	1
150	3	0.0	1	3
151	45	0.0	1	16 29


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R1_001_val_1.fq.gz
=============================================
41244 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR019_S7_L001_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R2_001_val_2.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 1.10 s (27 us/read; 2.25 M reads/minute).

=== Summary ===

Total reads processed:                  41,244
Reads with adapters:                    20,983 (50.9%)
Reads written (passing filters):        41,244 (100.0%)

Total basepairs processed:     5,533,654 bp
Quality-trimmed:                  11,962 bp (0.2%)
Total written (filtered):      5,452,710 bp (98.5%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 20983 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 38.6%
  C: 21.7%
  G: 13.3%
  T: 26.4%
  none/other: 0.1%

Overview of removed sequences
length	count	expect	max.err	error counts
1	15569	10311.0	0	15569
2	2875	2577.8	0	2875
3	1260	644.4	0	1260
4	347	161.1	0	347
5	17	40.3	0	17
6	20	10.1	0	20
7	14	2.5	0	14
8	9	0.6	0	9
9	9	0.2	0	8 1
10	22	0.0	1	15 7
11	19	0.0	1	13 6
12	26	0.0	1	15 11
14	23	0.0	1	12 11
15	25	0.0	1	16 9
17	14	0.0	1	11 3
18	17	0.0	1	14 3
19	23	0.0	1	16 7
20	14	0.0	1	10 4
21	10	0.0	1	6 4
22	19	0.0	1	13 6
23	16	0.0	1	10 6
24	28	0.0	1	20 8
25	13	0.0	1	9 4
26	10	0.0	1	8 2
27	10	0.0	1	5 5
28	15	0.0	1	13 2
29	6	0.0	1	4 2
30	22	0.0	1	18 4
31	11	0.0	1	8 3
32	18	0.0	1	13 5
33	20	0.0	1	17 3
34	10	0.0	1	6 4
35	14	0.0	1	7 7
36	10	0.0	1	8 2
37	9	0.0	1	8 1
38	6	0.0	1	2 4
39	7	0.0	1	5 2
41	11	0.0	1	10 1
42	15	0.0	1	11 4
43	7	0.0	1	5 2
44	11	0.0	1	7 4
45	18	0.0	1	14 4
46	9	0.0	1	6 3
47	7	0.0	1	4 3
48	23	0.0	1	20 3
49	8	0.0	1	5 3
50	1	0.0	1	1
51	13	0.0	1	11 2
52	8	0.0	1	7 1
53	11	0.0	1	6 5
54	10	0.0	1	8 2
55	2	0.0	1	2
56	1	0.0	1	0 1
57	5	0.0	1	3 2
58	4	0.0	1	4
59	3	0.0	1	2 1
60	4	0.0	1	3 1
62	4	0.0	1	3 1
63	4	0.0	1	4
64	5	0.0	1	4 1
65	2	0.0	1	0 2
66	9	0.0	1	4 5
67	6	0.0	1	4 2
68	6	0.0	1	5 1
69	5	0.0	1	3 2
70	6	0.0	1	5 1
71	5	0.0	1	4 1
72	6	0.0	1	3 3
73	7	0.0	1	5 2
74	8	0.0	1	6 2
75	1	0.0	1	0 1
76	5	0.0	1	4 1
77	4	0.0	1	2 2
78	7	0.0	1	7
79	5	0.0	1	4 1
80	5	0.0	1	3 2
81	7	0.0	1	5 2
82	4	0.0	1	4
83	6	0.0	1	5 1
84	3	0.0	1	2 1
85	3	0.0	1	3
86	6	0.0	1	4 2
87	4	0.0	1	3 1
88	5	0.0	1	3 2
89	9	0.0	1	4 5
90	5	0.0	1	4 1
91	4	0.0	1	3 1
92	2	0.0	1	1 1
93	2	0.0	1	1 1
94	2	0.0	1	0 2
95	3	0.0	1	1 2
96	8	0.0	1	5 3
97	2	0.0	1	2
98	7	0.0	1	6 1
99	1	0.0	1	1
100	2	0.0	1	1 1
101	2	0.0	1	1 1
102	2	0.0	1	2
103	4	0.0	1	3 1
104	1	0.0	1	1
105	1	0.0	1	1
106	3	0.0	1	2 1
107	2	0.0	1	0 2
109	3	0.0	1	3
111	1	0.0	1	1
112	1	0.0	1	1
113	1	0.0	1	0 1
115	3	0.0	1	1 2
118	1	0.0	1	0 1
119	3	0.0	1	1 2
120	1	0.0	1	1
121	1	0.0	1	0 1
122	1	0.0	1	1
124	1	0.0	1	1
126	2	0.0	1	1 1
127	3	0.0	1	2 1
128	1	0.0	1	1
130	1	0.0	1	0 1
131	3	0.0	1	2 1
135	1	0.0	1	1
137	1	0.0	1	0 1
138	1	0.0	1	0 1
139	1	0.0	1	1
140	1	0.0	1	1
150	2	0.0	1	1 1
151	21	0.0	1	11 10


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L001_R2_001_val_2.fq.gz
=============================================
41244 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR019_S7_L001_R1_001_val_1_trimmed.fq.gz and NR019_S7_L001_R2_001_val_2_trimmed.fq.gz
file_1: NR019_S7_L001_R1_001_val_1_trimmed.fq.gz, file_2: NR019_S7_L001_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR019_S7_L001_R1_001_val_1_trimmed.fq.gz and NR019_S7_L001_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR019_S7_L001_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR019_S7_L001_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 41244

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 208 (0.50%)

Deleting both intermediate output files NR019_S7_L001_R1_001_val_1_trimmed.fq.gz and NR019_S7_L001_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR019_S7_L002_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R1_001_val_1.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.61 s (27 us/read; 2.20 M reads/minute).

=== Summary ===

Total reads processed:                  22,310
Reads with adapters:                    11,594 (52.0%)
Reads written (passing filters):        22,310 (100.0%)

Total basepairs processed:     3,005,909 bp
Quality-trimmed:                   4,316 bp (0.1%)
Total written (filtered):      2,944,393 bp (98.0%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11594 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 39.7%
  C: 22.0%
  G: 11.3%
  T: 26.4%
  none/other: 0.6%

Overview of removed sequences
length	count	expect	max.err	error counts
1	8570	5577.5	0	8570
2	1444	1394.4	0	1444
3	596	348.6	0	596
4	178	87.1	0	178
5	11	21.8	0	11
6	13	5.4	0	13
7	8	1.4	0	8
8	9	0.3	0	9
9	8	0.1	0	7 1
10	23	0.0	1	18 5
11	15	0.0	1	7 8
12	24	0.0	1	18 6
13	2	0.0	1	1 1
14	19	0.0	1	16 3
16	23	0.0	1	16 7
17	1	0.0	1	1
18	22	0.0	1	19 3
19	34	0.0	1	30 4
22	1	0.0	1	1
23	14	0.0	1	10 4
24	24	0.0	1	18 6
25	2	0.0	1	1 1
26	7	0.0	1	5 2
27	10	0.0	1	8 2
29	16	0.0	1	14 2
30	12	0.0	1	10 2
31	12	0.0	1	7 5
32	3	0.0	1	0 3
33	25	0.0	1	24 1
34	1	0.0	1	1
35	20	0.0	1	12 8
36	12	0.0	1	9 3
37	14	0.0	1	9 5
38	6	0.0	1	4 2
39	3	0.0	1	2 1
40	15	0.0	1	8 7
41	2	0.0	1	1 1
42	12	0.0	1	8 4
43	13	0.0	1	11 2
44	16	0.0	1	13 3
45	3	0.0	1	3
46	6	0.0	1	4 2
47	1	0.0	1	0 1
48	19	0.0	1	16 3
49	8	0.0	1	8
50	2	0.0	1	2
51	8	0.0	1	6 2
52	11	0.0	1	9 2
53	2	0.0	1	1 1
54	3	0.0	1	3
55	13	0.0	1	11 2
56	7	0.0	1	5 2
57	3	0.0	1	2 1
58	2	0.0	1	1 1
59	11	0.0	1	9 2
61	7	0.0	1	3 4
62	6	0.0	1	5 1
63	3	0.0	1	2 1
64	1	0.0	1	1
65	4	0.0	1	1 3
66	6	0.0	1	3 3
67	2	0.0	1	2
68	3	0.0	1	2 1
69	4	0.0	1	3 1
70	6	0.0	1	4 2
71	1	0.0	1	0 1
72	1	0.0	1	1
73	5	0.0	1	4 1
74	2	0.0	1	2
75	3	0.0	1	3
76	2	0.0	1	1 1
77	4	0.0	1	3 1
78	4	0.0	1	4
79	4	0.0	1	4
80	4	0.0	1	3 1
81	8	0.0	1	8
82	1	0.0	1	1
83	4	0.0	1	4
84	1	0.0	1	1
85	4	0.0	1	4
86	5	0.0	1	4 1
87	1	0.0	1	0 1
89	4	0.0	1	4
90	4	0.0	1	4
91	4	0.0	1	4
93	2	0.0	1	1 1
94	2	0.0	1	2
95	7	0.0	1	5 2
96	2	0.0	1	1 1
97	4	0.0	1	4
98	2	0.0	1	2
99	2	0.0	1	1 1
100	1	0.0	1	0 1
101	5	0.0	1	4 1
102	3	0.0	1	2 1
103	2	0.0	1	2
107	1	0.0	1	1
108	1	0.0	1	1
109	1	0.0	1	1
110	4	0.0	1	3 1
111	2	0.0	1	1 1
112	1	0.0	1	1
116	2	0.0	1	2
117	1	0.0	1	1
118	2	0.0	1	2
119	3	0.0	1	3
120	2	0.0	1	1 1
121	2	0.0	1	2
123	1	0.0	1	1
124	1	0.0	1	1
126	1	0.0	1	1
127	2	0.0	1	1 1
129	2	0.0	1	1 1
131	4	0.0	1	3 1
132	1	0.0	1	1
133	3	0.0	1	2 1
135	3	0.0	1	3
136	1	0.0	1	0 1
137	3	0.0	1	3
138	1	0.0	1	1
139	1	0.0	1	1
143	1	0.0	1	1
146	1	0.0	1	1
149	1	0.0	1	0 1
150	2	0.0	1	2
151	64	0.0	1	36 28


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R1_001_val_1.fq.gz
=============================================
22310 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR019_S7_L002_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R2_001_val_2.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 0.61 s (27 us/read; 2.18 M reads/minute).

=== Summary ===

Total reads processed:                  22,310
Reads with adapters:                    11,102 (49.8%)
Reads written (passing filters):        22,310 (100.0%)

Total basepairs processed:     2,948,137 bp
Quality-trimmed:                   5,764 bp (0.2%)
Total written (filtered):      2,883,202 bp (97.8%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11102 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 37.2%
  C: 22.4%
  G: 13.8%
  T: 26.4%
  none/other: 0.3%

Overview of removed sequences
length	count	expect	max.err	error counts
1	7858	5577.5	0	7858
2	1557	1394.4	0	1557
3	609	348.6	0	609
4	171	87.1	0	171
5	12	21.8	0	12
6	17	5.4	0	17
7	12	1.4	0	12
8	12	0.3	0	12
9	5	0.1	0	5
10	18	0.0	1	15 3
11	10	0.0	1	9 1
12	22	0.0	1	15 7
14	17	0.0	1	13 4
15	21	0.0	1	19 2
17	26	0.0	1	19 7
18	15	0.0	1	13 2
19	21	0.0	1	16 5
20	15	0.0	1	13 2
21	11	0.0	1	9 2
22	10	0.0	1	5 5
23	18	0.0	1	14 4
24	15	0.0	1	8 7
25	13	0.0	1	11 2
26	12	0.0	1	9 3
27	10	0.0	1	6 4
28	21	0.0	1	18 3
29	12	0.0	1	8 4
30	17	0.0	1	15 2
31	8	0.0	1	6 2
32	20	0.0	1	18 2
33	13	0.0	1	9 4
34	3	0.0	1	3
35	21	0.0	1	17 4
36	13	0.0	1	10 3
37	13	0.0	1	9 4
38	2	0.0	1	2
39	8	0.0	1	3 5
40	1	0.0	1	0 1
41	6	0.0	1	5 1
42	8	0.0	1	6 2
43	4	0.0	1	4
44	9	0.0	1	7 2
45	21	0.0	1	18 3
46	9	0.0	1	6 3
47	5	0.0	1	3 2
48	18	0.0	1	15 3
49	3	0.0	1	3
50	2	0.0	1	1 1
51	10	0.0	1	10
52	25	0.0	1	20 5
53	10	0.0	1	8 2
54	7	0.0	1	5 2
55	4	0.0	1	3 1
56	4	0.0	1	4
57	5	0.0	1	2 3
58	9	0.0	1	6 3
59	1	0.0	1	1
60	4	0.0	1	3 1
61	3	0.0	1	3
62	1	0.0	1	1
63	3	0.0	1	3
64	3	0.0	1	2 1
65	3	0.0	1	2 1
66	8	0.0	1	6 2
67	3	0.0	1	3
68	7	0.0	1	7
69	11	0.0	1	7 4
70	3	0.0	1	3
71	4	0.0	1	3 1
72	5	0.0	1	3 2
73	4	0.0	1	4
74	7	0.0	1	6 1
75	2	0.0	1	2
76	3	0.0	1	3
77	4	0.0	1	2 2
78	6	0.0	1	6
79	5	0.0	1	4 1
80	6	0.0	1	4 2
81	6	0.0	1	4 2
82	3	0.0	1	3
83	6	0.0	1	4 2
84	2	0.0	1	1 1
85	6	0.0	1	6
86	5	0.0	1	2 3
87	2	0.0	1	1 1
88	1	0.0	1	0 1
89	10	0.0	1	4 6
90	5	0.0	1	4 1
91	6	0.0	1	3 3
92	2	0.0	1	1 1
93	1	0.0	1	1
94	3	0.0	1	1 2
95	9	0.0	1	7 2
96	3	0.0	1	3
97	3	0.0	1	2 1
98	3	0.0	1	3
99	5	0.0	1	5
100	4	0.0	1	1 3
101	4	0.0	1	3 1
102	2	0.0	1	2
103	2	0.0	1	2
104	1	0.0	1	0 1
107	4	0.0	1	3 1
108	3	0.0	1	3
109	1	0.0	1	1
110	5	0.0	1	4 1
111	1	0.0	1	1
116	2	0.0	1	1 1
117	2	0.0	1	2
118	3	0.0	1	2 1
119	3	0.0	1	3
120	2	0.0	1	0 2
121	5	0.0	1	5
123	2	0.0	1	2
124	1	0.0	1	1
126	3	0.0	1	3
127	2	0.0	1	1 1
129	1	0.0	1	1
131	4	0.0	1	3 1
132	2	0.0	1	2
133	2	0.0	1	2
134	1	0.0	1	0 1
135	5	0.0	1	4 1
137	4	0.0	1	4
139	1	0.0	1	1
143	1	0.0	1	0 1
144	1	0.0	1	0 1
146	1	0.0	1	1
148	1	0.0	1	0 1
151	31	0.0	1	22 9


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR019_S7_L002_R2_001_val_2.fq.gz
=============================================
22310 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR019_S7_L002_R1_001_val_1_trimmed.fq.gz and NR019_S7_L002_R2_001_val_2_trimmed.fq.gz
file_1: NR019_S7_L002_R1_001_val_1_trimmed.fq.gz, file_2: NR019_S7_L002_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR019_S7_L002_R1_001_val_1_trimmed.fq.gz and NR019_S7_L002_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR019_S7_L002_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR019_S7_L002_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 22310

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 159 (0.71%)

Deleting both intermediate output files NR019_S7_L002_R1_001_val_1_trimmed.fq.gz and NR019_S7_L002_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR021_S8_L001_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001_val_1.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 105.81 s (26 us/read; 2.27 M reads/minute).

=== Summary ===

Total reads processed:               3,996,315
Reads with adapters:                 2,414,527 (60.4%)
Reads written (passing filters):     3,996,315 (100.0%)

Total basepairs processed:   593,062,263 bp
Quality-trimmed:                 140,474 bp (0.0%)
Total written (filtered):    563,799,510 bp (95.1%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2414527 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 30.7%
  C: 27.6%
  G: 20.3%
  T: 20.3%
  none/other: 1.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1131131	999078.8	0	1131131
2	218514	249769.7	0	218514
3	92634	62442.4	0	92634
4	69282	15610.6	0	69282
5	947	3902.7	0	947
6	26669	975.7	0	26669
7	23335	243.9	0	23335
8	27529	61.0	0	27529
9	24387	15.2	0	24268 119
10	25314	3.8	1	23754 1560
11	26283	1.0	1	23938 2345
12	49032	0.2	1	45917 3115
13	1383	0.1	1	889 494
14	48217	0.1	1	44794 3423
15	1073	0.1	1	659 414
16	50306	0.1	1	46248 4058
17	1566	0.1	1	1024 542
18	30527	0.1	1	28070 2457
19	76707	0.1	1	72330 4377
20	483	0.1	1	293 190
21	170	0.1	1	116 54
22	411	0.1	1	266 145
23	23809	0.1	1	22004 1805
24	56486	0.1	1	52715 3771
25	1264	0.1	1	847 417
26	20025	0.1	1	18597 1428
27	17927	0.1	1	16880 1047
28	351	0.1	1	223 128
29	17811	0.1	1	16451 1360
30	21046	0.1	1	19611 1435
31	27126	0.1	1	25585 1541
32	916	0.1	1	652 264
33	29781	0.1	1	27735 2046
34	397	0.1	1	263 134
35	13349	0.1	1	12548 801
36	13531	0.1	1	12645 886
37	14307	0.1	1	13290 1017
38	22347	0.1	1	20934 1413
39	332	0.1	1	246 86
40	11397	0.1	1	10684 713
41	9994	0.1	1	9415 579
42	12897	0.1	1	12021 876
43	9858	0.1	1	8895 963
44	23703	0.1	1	22141 1562
45	4875	0.1	1	4557 318
46	4502	0.1	1	4081 421
47	589	0.1	1	397 192
48	31741	0.1	1	30092 1649
49	16981	0.1	1	16147 834
50	2554	0.1	1	2298 256
51	7633	0.1	1	7163 470
52	7621	0.1	1	7210 411
53	1435	0.1	1	1306 129
54	296	0.1	1	239 57
55	4039	0.1	1	3828 211
56	2670	0.1	1	2494 176
57	335	0.1	1	292 43
58	887	0.1	1	818 69
59	1073	0.1	1	980 93
60	420	0.1	1	369 51
61	755	0.1	1	685 70
62	2440	0.1	1	2318 122
63	473	0.1	1	428 45
64	769	0.1	1	725 44
65	690	0.1	1	625 65
66	2129	0.1	1	2034 95
67	407	0.1	1	365 42
68	567	0.1	1	529 38
69	620	0.1	1	561 59
70	613	0.1	1	564 49
71	236	0.1	1	214 22
72	340	0.1	1	305 35
73	568	0.1	1	529 39
74	809	0.1	1	763 46
75	909	0.1	1	847 62
76	869	0.1	1	818 51
77	850	0.1	1	806 44
78	779	0.1	1	728 51
79	785	0.1	1	753 32
80	767	0.1	1	722 45
81	665	0.1	1	622 43
82	614	0.1	1	569 45
83	595	0.1	1	557 38
84	523	0.1	1	491 32
85	468	0.1	1	441 27
86	442	0.1	1	408 34
87	418	0.1	1	376 42
88	418	0.1	1	393 25
89	362	0.1	1	339 23
90	368	0.1	1	341 27
91	365	0.1	1	321 44
92	279	0.1	1	261 18
93	253	0.1	1	238 15
94	279	0.1	1	262 17
95	199	0.1	1	180 19
96	252	0.1	1	226 26
97	220	0.1	1	204 16
98	201	0.1	1	191 10
99	180	0.1	1	163 17
100	173	0.1	1	158 15
101	153	0.1	1	143 10
102	113	0.1	1	105 8
103	147	0.1	1	131 16
104	129	0.1	1	114 15
105	101	0.1	1	95 6
106	102	0.1	1	92 10
107	98	0.1	1	85 13
108	70	0.1	1	62 8
109	95	0.1	1	86 9
110	76	0.1	1	63 13
111	84	0.1	1	77 7
112	76	0.1	1	69 7
113	89	0.1	1	82 7
114	51	0.1	1	43 8
115	79	0.1	1	67 12
116	56	0.1	1	52 4
117	50	0.1	1	45 5
118	70	0.1	1	64 6
119	55	0.1	1	49 6
120	74	0.1	1	66 8
121	52	0.1	1	41 11
122	71	0.1	1	69 2
123	47	0.1	1	42 5
124	67	0.1	1	63 4
125	73	0.1	1	71 2
126	91	0.1	1	86 5
127	66	0.1	1	62 4
128	106	0.1	1	100 6
129	102	0.1	1	100 2
130	70	0.1	1	64 6
131	90	0.1	1	84 6
132	90	0.1	1	84 6
133	85	0.1	1	83 2
134	91	0.1	1	86 5
135	99	0.1	1	91 8
136	79	0.1	1	74 5
137	108	0.1	1	102 6
138	76	0.1	1	74 2
139	97	0.1	1	93 4
140	46	0.1	1	43 3
141	50	0.1	1	49 1
142	69	0.1	1	66 3
143	52	0.1	1	49 3
144	30	0.1	1	28 2
145	32	0.1	1	27 5
146	64	0.1	1	56 8
147	41	0.1	1	34 7
148	113	0.1	1	102 11
149	47	0.1	1	32 15
150	176	0.1	1	16 160
151	24625	0.1	1	199 24426


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R1_001_val_1.fq.gz
=============================================
3996315 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR021_S8_L001_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001_val_2.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 106.50 s (27 us/read; 2.25 M reads/minute).

=== Summary ===

Total reads processed:               3,996,315
Reads with adapters:                 2,365,417 (59.2%)
Reads written (passing filters):     3,996,315 (100.0%)

Total basepairs processed:   593,688,021 bp
Quality-trimmed:                 161,140 bp (0.0%)
Total written (filtered):    568,208,959 bp (95.7%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2365417 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 30.9%
  C: 23.9%
  G: 22.7%
  T: 22.5%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	1092119	999078.8	0	1092119
2	237188	249769.7	0	237188
3	105726	62442.4	0	105726
4	70512	15610.6	0	70512
5	833	3902.7	0	833
6	25608	975.7	0	25608
7	24439	243.9	0	24439
8	30007	61.0	0	30007
9	19423	15.2	0	19324 99
10	27007	3.8	1	24438 2569
11	24193	1.0	1	21508 2685
12	49848	0.2	1	44992 4856
13	417	0.1	1	163 254
14	30409	0.1	1	26982 3427
15	41366	0.1	1	37549 3817
16	176	0.1	1	77 99
17	27857	0.1	1	25162 2695
18	16568	0.1	1	14861 1707
19	29519	0.1	1	26578 2941
20	21091	0.1	1	19067 2024
21	16792	0.1	1	14962 1830
22	20201	0.1	1	18364 1837
23	21276	0.1	1	19178 2098
24	37690	0.1	1	34176 3514
25	18430	0.1	1	16766 1664
26	17597	0.1	1	15864 1733
27	10354	0.1	1	8997 1357
28	28466	0.1	1	26325 2141
29	5853	0.1	1	4981 872
30	25322	0.1	1	23457 1865
31	8773	0.1	1	7711 1062
32	40024	0.1	1	37612 2412
33	15124	0.1	1	13686 1438
34	5040	0.1	1	4387 653
35	21707	0.1	1	20267 1440
36	7141	0.1	1	6402 739
37	9565	0.1	1	8710 855
38	5456	0.1	1	5052 404
39	7199	0.1	1	6631 568
40	2942	0.1	1	2733 209
41	9827	0.1	1	9198 629
42	12807	0.1	1	11985 822
43	5830	0.1	1	5380 450
44	8947	0.1	1	8286 661
45	14044	0.1	1	13176 868
46	7086	0.1	1	6524 562
47	4907	0.1	1	4585 322
48	12935	0.1	1	12161 774
49	5201	0.1	1	4855 346
50	2042	0.1	1	1867 175
51	8681	0.1	1	8150 531
52	11816	0.1	1	11253 563
53	4853	0.1	1	4571 282
54	5760	0.1	1	5434 326
55	3489	0.1	1	3286 203
56	1741	0.1	1	1609 132
57	2940	0.1	1	2759 181
58	3041	0.1	1	2850 191
59	1674	0.1	1	1550 124
60	1051	0.1	1	942 109
61	883	0.1	1	805 78
62	943	0.1	1	873 70
63	1034	0.1	1	960 74
64	1718	0.1	1	1633 85
65	1982	0.1	1	1863 119
66	1986	0.1	1	1876 110
67	1871	0.1	1	1749 122
68	1762	0.1	1	1657 105
69	1718	0.1	1	1620 98
70	1574	0.1	1	1476 98
71	1413	0.1	1	1317 96
72	1343	0.1	1	1269 74
73	1190	0.1	1	1122 68
74	1114	0.1	1	1048 66
75	1075	0.1	1	1009 66
76	935	0.1	1	881 54
77	910	0.1	1	852 58
78	809	0.1	1	773 36
79	788	0.1	1	753 35
80	783	0.1	1	742 41
81	682	0.1	1	644 38
82	640	0.1	1	583 57
83	582	0.1	1	557 25
84	530	0.1	1	496 34
85	475	0.1	1	450 25
86	434	0.1	1	407 27
87	422	0.1	1	396 26
88	440	0.1	1	409 31
89	363	0.1	1	343 20
90	367	0.1	1	338 29
91	370	0.1	1	350 20
92	288	0.1	1	265 23
93	266	0.1	1	246 20
94	285	0.1	1	268 17
95	198	0.1	1	180 18
96	259	0.1	1	242 17
97	224	0.1	1	206 18
98	211	0.1	1	201 10
99	195	0.1	1	180 15
100	179	0.1	1	160 19
101	176	0.1	1	157 19
102	129	0.1	1	118 11
103	144	0.1	1	128 16
104	130	0.1	1	119 11
105	99	0.1	1	92 7
106	105	0.1	1	94 11
107	98	0.1	1	92 6
108	78	0.1	1	70 8
109	101	0.1	1	92 9
110	71	0.1	1	67 4
111	92	0.1	1	89 3
112	81	0.1	1	72 9
113	95	0.1	1	91 4
114	53	0.1	1	45 8
115	80	0.1	1	69 11
116	66	0.1	1	56 10
117	54	0.1	1	46 8
118	77	0.1	1	69 8
119	60	0.1	1	53 7
120	77	0.1	1	69 8
121	55	0.1	1	46 9
122	73	0.1	1	68 5
123	54	0.1	1	49 5
124	66	0.1	1	59 7
125	73	0.1	1	69 4
126	97	0.1	1	89 8
127	62	0.1	1	60 2
128	116	0.1	1	104 12
129	102	0.1	1	90 12
130	77	0.1	1	66 11
131	97	0.1	1	83 14
132	85	0.1	1	81 4
133	93	0.1	1	83 10
134	94	0.1	1	76 18
135	95	0.1	1	81 14
136	77	0.1	1	69 8
137	107	0.1	1	99 8
138	79	0.1	1	72 7
139	95	0.1	1	79 16
140	45	0.1	1	33 12
141	49	0.1	1	34 15
142	67	0.1	1	43 24
143	52	0.1	1	38 14
144	30	0.1	1	15 15
145	27	0.1	1	16 11
146	60	0.1	1	13 47
147	42	0.1	1	21 21
148	106	0.1	1	62 44
149	32	0.1	1	21 11
150	21	0.1	1	14 7
151	252	0.1	1	185 67


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001_val_2.fq.gz
=============================================
3996315 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR021_S8_L001_R1_001_val_1_trimmed.fq.gz and NR021_S8_L001_R2_001_val_2_trimmed.fq.gz
file_1: NR021_S8_L001_R1_001_val_1_trimmed.fq.gz, file_2: NR021_S8_L001_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR021_S8_L001_R1_001_val_1_trimmed.fq.gz and NR021_S8_L001_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR021_S8_L001_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR021_S8_L001_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 3996315

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 27040 (0.68%)

Deleting both intermediate output files NR021_S8_L001_R1_001_val_1_trimmed.fq.gz and NR021_S8_L001_R2_001_val_2_trimmed.fq.gz

====================================================================================================

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R1_001_val_1.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R1_001_val_1.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR021_S8_L002_R1_001_val_1_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R1_001_val_1.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R1_001_val_1.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 91.64 s (26 us/read; 2.31 M reads/minute).

=== Summary ===

Total reads processed:               3,532,417
Reads with adapters:                 2,146,057 (60.8%)
Reads written (passing filters):     3,532,417 (100.0%)

Total basepairs processed:   522,802,866 bp
Quality-trimmed:                 102,517 bp (0.0%)
Total written (filtered):    493,335,822 bp (94.4%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2146057 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 30.2%
  C: 27.5%
  G: 20.7%
  T: 20.0%
  none/other: 1.6%

Overview of removed sequences
length	count	expect	max.err	error counts
1	962828	883104.2	0	962828
2	190615	220776.1	0	190615
3	79318	55194.0	0	79318
4	61991	13798.5	0	61991
5	878	3449.6	0	878
6	24256	862.4	0	24256
7	21651	215.6	0	21651
8	24057	53.9	0	24057
9	22585	13.5	0	22500 85
10	22526	3.4	1	21612 914
11	23516	0.8	1	22109 1407
12	44734	0.2	1	42931 1803
13	915	0.1	1	541 374
14	43908	0.1	1	41920 1988
15	629	0.1	1	342 287
16	45177	0.1	1	42939 2238
17	992	0.1	1	649 343
18	26506	0.1	1	25049 1457
19	72561	0.1	1	69795 2766
20	462	0.1	1	263 199
21	116	0.1	1	93 23
22	353	0.1	1	232 121
23	20249	0.1	1	19187 1062
24	53005	0.1	1	50663 2342
25	791	0.1	1	527 264
26	17722	0.1	1	16903 819
27	16734	0.1	1	16040 694
28	327	0.1	1	222 105
29	16504	0.1	1	15682 822
30	18747	0.1	1	17875 872
31	26015	0.1	1	25060 955
32	648	0.1	1	440 208
33	27918	0.1	1	26622 1296
34	326	0.1	1	210 116
35	12569	0.1	1	12057 512
36	12619	0.1	1	12021 598
37	13184	0.1	1	12533 651
38	21713	0.1	1	20828 885
39	339	0.1	1	246 93
40	10499	0.1	1	10040 459
41	9561	0.1	1	9084 477
42	11337	0.1	1	10789 548
43	9078	0.1	1	8480 598
44	23113	0.1	1	22033 1080
45	4765	0.1	1	4517 248
46	3889	0.1	1	3598 291
47	597	0.1	1	398 199
48	39522	0.1	1	38097 1425
49	12892	0.1	1	12326 566
50	1792	0.1	1	1603 189
51	9666	0.1	1	9248 418
52	6354	0.1	1	6086 268
53	740	0.1	1	658 82
54	247	0.1	1	216 31
55	3374	0.1	1	3241 133
56	1493	0.1	1	1419 74
57	137	0.1	1	114 23
58	524	0.1	1	470 54
59	965	0.1	1	894 71
60	223	0.1	1	184 39
61	416	0.1	1	387 29
62	2071	0.1	1	1977 94
63	195	0.1	1	170 25
64	461	0.1	1	425 36
65	562	0.1	1	520 42
66	1783	0.1	1	1723 60
67	320	0.1	1	285 35
68	845	0.1	1	795 50
69	1033	0.1	1	974 59
70	1298	0.1	1	1227 71
71	382	0.1	1	338 44
72	162	0.1	1	143 19
73	419	0.1	1	400 19
74	737	0.1	1	699 38
75	940	0.1	1	884 56
76	991	0.1	1	942 49
77	930	0.1	1	877 53
78	909	0.1	1	857 52
79	883	0.1	1	825 58
80	831	0.1	1	784 47
81	759	0.1	1	714 45
82	727	0.1	1	679 48
83	645	0.1	1	611 34
84	585	0.1	1	548 37
85	543	0.1	1	505 38
86	507	0.1	1	465 42
87	472	0.1	1	439 33
88	457	0.1	1	432 25
89	410	0.1	1	381 29
90	403	0.1	1	371 32
91	387	0.1	1	355 32
92	362	0.1	1	333 29
93	280	0.1	1	260 20
94	317	0.1	1	296 21
95	291	0.1	1	264 27
96	284	0.1	1	256 28
97	233	0.1	1	215 18
98	248	0.1	1	232 16
99	230	0.1	1	214 16
100	227	0.1	1	206 21
101	194	0.1	1	178 16
102	185	0.1	1	168 17
103	184	0.1	1	162 22
104	182	0.1	1	166 16
105	119	0.1	1	109 10
106	126	0.1	1	115 11
107	154	0.1	1	136 18
108	142	0.1	1	123 19
109	138	0.1	1	130 8
110	132	0.1	1	112 20
111	118	0.1	1	108 10
112	85	0.1	1	74 11
113	148	0.1	1	137 11
114	91	0.1	1	85 6
115	98	0.1	1	86 12
116	101	0.1	1	93 8
117	76	0.1	1	69 7
118	91	0.1	1	86 5
119	83	0.1	1	77 6
120	99	0.1	1	92 7
121	82	0.1	1	73 9
122	87	0.1	1	82 5
123	75	0.1	1	69 6
124	79	0.1	1	71 8
125	92	0.1	1	82 10
126	158	0.1	1	138 20
127	119	0.1	1	112 7
128	165	0.1	1	151 14
129	147	0.1	1	139 8
130	130	0.1	1	124 6
131	111	0.1	1	106 5
132	152	0.1	1	144 8
133	99	0.1	1	91 8
134	149	0.1	1	140 9
135	105	0.1	1	101 4
136	125	0.1	1	121 4
137	167	0.1	1	159 8
138	107	0.1	1	105 2
139	118	0.1	1	114 4
140	89	0.1	1	84 5
141	53	0.1	1	51 2
142	108	0.1	1	103 5
143	61	0.1	1	57 4
144	46	0.1	1	44 2
145	53	0.1	1	49 4
146	99	0.1	1	91 8
147	59	0.1	1	46 13
148	177	0.1	1	169 8
149	66	0.1	1	52 14
150	129	0.1	1	16 113
151	35017	0.1	1	286 34731


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R1_001_val_1.fq.gz
=============================================
3532417 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Writing report to '/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2.fq.gz_trimming_report.txt'

SUMMARISING RUN PARAMETERS
==========================
Input filename: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R2_001_val_2.fq.gz
Trimming mode: paired-end
Trim Galore version: 0.4.4
Cutadapt version: 1.9.1
Quality Phred score cutoff: 20
Quality encoding type selected: ASCII+33
Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected)
Maximum trimming error rate: 0.1 (default)
Minimum required adapter overlap (stringency): 1 bp
Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp
Output file(s) will be GZIP compressed

Writing final adapter and quality trimmed output to NR021_S8_L002_R2_001_val_2_trimmed.fq.gz


  >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R2_001_val_2.fq.gz <<< 
This is cutadapt 1.9.1 with Python 2.7.12
Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R2_001_val_2.fq.gz
Trimming 1 adapter with at most 10.0% errors in single-end mode ...
Finished in 92.95 s (26 us/read; 2.28 M reads/minute).

=== Summary ===

Total reads processed:               3,532,417
Reads with adapters:                 2,104,235 (59.6%)
Reads written (passing filters):     3,532,417 (100.0%)

Total basepairs processed:   523,752,676 bp
Quality-trimmed:                 107,379 bp (0.0%)
Total written (filtered):    499,307,219 bp (95.3%)

=== Adapter 1 ===

Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2104235 times.

No. of allowed errors:
0-9 bp: 0; 10-13 bp: 1

Bases preceding removed adapters:
  A: 30.6%
  C: 24.2%
  G: 22.9%
  T: 22.2%
  none/other: 0.0%

Overview of removed sequences
length	count	expect	max.err	error counts
1	935006	883104.2	0	935006
2	205452	220776.1	0	205452
3	90078	55194.0	0	90078
4	63626	13798.5	0	63626
5	727	3449.6	0	727
6	23747	862.4	0	23747
7	22619	215.6	0	22619
8	26870	53.9	0	26870
9	19116	13.5	0	19027 89
10	23453	3.4	1	22285 1168
11	22380	0.8	1	21062 1318
12	45677	0.2	1	43499 2178
13	267	0.1	1	86 181
14	26102	0.1	1	24555 1547
15	39664	0.1	1	37859 1805
16	155	0.1	1	69 86
17	25075	0.1	1	23887 1188
18	16252	0.1	1	15419 833
19	25135	0.1	1	23806 1329
20	19314	0.1	1	18388 926
21	17365	0.1	1	16477 888
22	18767	0.1	1	17902 865
23	18776	0.1	1	17846 930
24	28530	0.1	1	27083 1447
25	18607	0.1	1	17836 771
26	17570	0.1	1	16733 837
27	10369	0.1	1	9719 650
28	26829	0.1	1	25809 1020
29	5986	0.1	1	5499 487
30	23753	0.1	1	22893 860
31	8001	0.1	1	7469 532
32	44562	0.1	1	43349 1213
33	13829	0.1	1	13159 670
34	4413	0.1	1	4065 348
35	23178	0.1	1	22495 683
36	4811	0.1	1	4512 299
37	9949	0.1	1	9472 477
38	3118	0.1	1	2940 178
39	5489	0.1	1	5229 260
40	1309	0.1	1	1223 86
41	9613	0.1	1	9261 352
42	13101	0.1	1	12699 402
43	4956	0.1	1	4710 246
44	8731	0.1	1	8370 361
45	16619	0.1	1	16155 464
46	6813	0.1	1	6510 303
47	3769	0.1	1	3616 153
48	15026	0.1	1	14589 437
49	3833	0.1	1	3678 155
50	1098	0.1	1	1019 79
51	9289	0.1	1	9011 278
52	15274	0.1	1	14904 370
53	4134	0.1	1	3986 148
54	5251	0.1	1	5085 166
55	2132	0.1	1	2063 69
56	1191	0.1	1	1138 53
57	2299	0.1	1	2215 84
58	2389	0.1	1	2297 92
59	1056	0.1	1	1001 55
60	693	0.1	1	647 46
61	708	0.1	1	657 51
62	635	0.1	1	588 47
63	777	0.1	1	738 39
64	1588	0.1	1	1524 64
65	1955	0.1	1	1868 87
66	2047	0.1	1	1964 83
67	1954	0.1	1	1884 70
68	1866	0.1	1	1781 85
69	1667	0.1	1	1603 64
70	1558	0.1	1	1492 66
71	1433	0.1	1	1377 56
72	1397	0.1	1	1343 54
73	1311	0.1	1	1253 58
74	1112	0.1	1	1053 59
75	1134	0.1	1	1085 49
76	1075	0.1	1	1029 46
77	961	0.1	1	919 42
78	969	0.1	1	932 37
79	908	0.1	1	843 65
80	855	0.1	1	827 28
81	788	0.1	1	751 37
82	752	0.1	1	717 35
83	664	0.1	1	638 26
84	608	0.1	1	580 28
85	572	0.1	1	531 41
86	517	0.1	1	491 26
87	500	0.1	1	472 28
88	502	0.1	1	477 25
89	425	0.1	1	408 17
90	412	0.1	1	384 28
91	406	0.1	1	376 30
92	378	0.1	1	364 14
93	311	0.1	1	288 23
94	349	0.1	1	317 32
95	314	0.1	1	289 25
96	291	0.1	1	270 21
97	264	0.1	1	244 20
98	273	0.1	1	258 15
99	249	0.1	1	231 18
100	247	0.1	1	231 16
101	235	0.1	1	217 18
102	198	0.1	1	182 16
103	191	0.1	1	180 11
104	207	0.1	1	191 16
105	136	0.1	1	123 13
106	155	0.1	1	138 17
107	158	0.1	1	139 19
108	156	0.1	1	138 18
109	149	0.1	1	134 15
110	149	0.1	1	132 17
111	131	0.1	1	121 10
112	93	0.1	1	83 10
113	159	0.1	1	147 12
114	108	0.1	1	96 12
115	101	0.1	1	86 15
116	117	0.1	1	105 12
117	88	0.1	1	80 8
118	113	0.1	1	106 7
119	91	0.1	1	81 10
120	112	0.1	1	105 7
121	89	0.1	1	78 11
122	94	0.1	1	88 6
123	90	0.1	1	78 12
124	87	0.1	1	79 8
125	95	0.1	1	83 12
126	156	0.1	1	149 7
127	127	0.1	1	116 11
128	168	0.1	1	156 12
129	151	0.1	1	127 24
130	134	0.1	1	121 13
131	117	0.1	1	99 18
132	152	0.1	1	143 9
133	115	0.1	1	98 17
134	148	0.1	1	126 22
135	102	0.1	1	93 9
136	125	0.1	1	103 22
137	166	0.1	1	149 17
138	110	0.1	1	99 11
139	119	0.1	1	100 19
140	89	0.1	1	72 17
141	49	0.1	1	42 7
142	108	0.1	1	81 27
143	58	0.1	1	46 12
144	46	0.1	1	30 16
145	49	0.1	1	28 21
146	94	0.1	1	39 55
147	49	0.1	1	34 15
148	167	0.1	1	115 52
149	50	0.1	1	29 21
150	21	0.1	1	11 10
151	338	0.1	1	261 77


RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L002_R2_001_val_2.fq.gz
=============================================
3532417 sequences processed in total
The length threshold of paired-end sequences gets evaluated later on (in the validation step)

Validate paired-end files NR021_S8_L002_R1_001_val_1_trimmed.fq.gz and NR021_S8_L002_R2_001_val_2_trimmed.fq.gz
file_1: NR021_S8_L002_R1_001_val_1_trimmed.fq.gz, file_2: NR021_S8_L002_R2_001_val_2_trimmed.fq.gz


>>>>> Now validing the length of the 2 paired-end infiles: NR021_S8_L002_R1_001_val_1_trimmed.fq.gz and NR021_S8_L002_R2_001_val_2_trimmed.fq.gz <<<<<
Writing validated paired-end read 1 reads to NR021_S8_L002_R1_001_val_1_val_1.fq.gz
Writing validated paired-end read 2 reads to NR021_S8_L002_R2_001_val_2_val_2.fq.gz

Total number of sequences analysed: 3532417

Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 37926 (1.07%)

Deleting both intermediate output files NR021_S8_L002_R1_001_val_1_trimmed.fq.gz and NR021_S8_L002_R2_001_val_2_trimmed.fq.gz

====================================================================================================


real	4901m40.787s
user	10209m3.532s
sys	213m39.764s

In [48]:

%%bash
ls /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/

AD002_S9_L001_R1_001_val_1.fq.gz_trimming_report.txt
AD002_S9_L001_R1_001_val_1_val_1.fq.gz
AD002_S9_L001_R2_001_val_2.fq.gz_trimming_report.txt
AD002_S9_L001_R2_001_val_2_val_2.fq.gz
AD002_S9_L002_R1_001_val_1.fq.gz_trimming_report.txt
AD002_S9_L002_R1_001_val_1_val_1.fq.gz
AD002_S9_L002_R2_001_val_2.fq.gz_trimming_report.txt
AD002_S9_L002_R2_001_val_2_val_2.fq.gz
NR005_S4_L001_R1_001_val_1.fq.gz_trimming_report.txt
NR005_S4_L001_R1_001_val_1_val_1.fq.gz
NR005_S4_L001_R2_001_val_2.fq.gz_trimming_report.txt
NR005_S4_L001_R2_001_val_2_val_2.fq.gz
NR005_S4_L002_R1_001_val_1.fq.gz_trimming_report.txt
NR005_S4_L002_R1_001_val_1_val_1.fq.gz
NR005_S4_L002_R2_001_val_2.fq.gz_trimming_report.txt
NR005_S4_L002_R2_001_val_2_val_2.fq.gz
NR006_S3_L001_R1_001_val_1.fq.gz_trimming_report.txt
NR006_S3_L001_R1_001_val_1_val_1.fq.gz
NR006_S3_L001_R2_001_val_2.fq.gz_trimming_report.txt
NR006_S3_L001_R2_001_val_2_val_2.fq.gz
NR006_S3_L002_R1_001_val_1.fq.gz_trimming_report.txt
NR006_S3_L002_R1_001_val_1_val_1.fq.gz
NR006_S3_L002_R2_001_val_2.fq.gz_trimming_report.txt
NR006_S3_L002_R2_001_val_2_val_2.fq.gz
NR012_S1_L001_R1_001_val_1.fq.gz_trimming_report.txt
NR012_S1_L001_R1_001_val_1_val_1.fq.gz
NR012_S1_L001_R2_001_val_2.fq.gz_trimming_report.txt
NR012_S1_L001_R2_001_val_2_val_2.fq.gz
NR012_S1_L002_R1_001_val_1.fq.gz_trimming_report.txt
NR012_S1_L002_R1_001_val_1_val_1.fq.gz
NR012_S1_L002_R2_001_val_2.fq.gz_trimming_report.txt
NR012_S1_L002_R2_001_val_2_val_2.fq.gz
NR013_AD013_S2_L001_R1_001_val_1.fq.gz_trimming_report.txt
NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
NR013_AD013_S2_L001_R2_001_val_2.fq.gz_trimming_report.txt
NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
NR013_AD013_S2_L002_R1_001_val_1.fq.gz_trimming_report.txt
NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
NR013_AD013_S2_L002_R2_001_val_2.fq.gz_trimming_report.txt
NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
NR014_AD014_S5_L001_R1_001_val_1.fq.gz_trimming_report.txt
NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
NR014_AD014_S5_L001_R2_001_val_2.fq.gz_trimming_report.txt
NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz
NR014_AD014_S5_L002_R1_001_val_1.fq.gz_trimming_report.txt
NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz
NR014_AD014_S5_L002_R2_001_val_2.fq.gz_trimming_report.txt
NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz
NR015_AD015_S6_L001_R1_001_val_1.fq.gz_trimming_report.txt
NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
NR015_AD015_S6_L001_R2_001_val_2.fq.gz_trimming_report.txt
NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
NR015_AD015_S6_L002_R1_001_val_1.fq.gz_trimming_report.txt
NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
NR015_AD015_S6_L002_R2_001_val_2.fq.gz_trimming_report.txt
NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz
NR019_S7_L001_R1_001_val_1.fq.gz_trimming_report.txt
NR019_S7_L001_R1_001_val_1_val_1.fq.gz
NR019_S7_L001_R2_001_val_2.fq.gz_trimming_report.txt
NR019_S7_L001_R2_001_val_2_val_2.fq.gz
NR019_S7_L002_R1_001_val_1.fq.gz_trimming_report.txt
NR019_S7_L002_R1_001_val_1_val_1.fq.gz
NR019_S7_L002_R2_001_val_2.fq.gz_trimming_report.txt
NR019_S7_L002_R2_001_val_2_val_2.fq.gz
NR021_S8_L001_R1_001_val_1.fq.gz_trimming_report.txt
NR021_S8_L001_R1_001_val_1_val_1.fq.gz
NR021_S8_L001_R2_001_val_2.fq.gz_trimming_report.txt
NR021_S8_L001_R2_001_val_2_val_2.fq.gz
NR021_S8_L002_R1_001_val_1.fq.gz_trimming_report.txt
NR021_S8_L002_R1_001_val_1_val_1.fq.gz
NR021_S8_L002_R2_001_val_2.fq.gz_trimming_report.txt
NR021_S8_L002_R2_001_val_2_val_2.fq.gz

In [49]:

%%bash
cd /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/
pwd

/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again

In [50]:

%%bash
for file in /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/*.gz
do
printf "%s\n" "$file \\"
done

/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fq.gz \

In [51]:

%%bash
time fastqc --threads 12 \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR019_S7_L002_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L001_R2_001_val_2_val_2.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R1_001_val_1_val_1.fq.gz \
/home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fq.gz
cat ~/.default-subject.mail | msmtp "$EMAIL"

Analysis complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Analysis complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Analysis complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Analysis complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Analysis complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Analysis complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Analysis complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Analysis complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Analysis complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Analysis complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Analysis complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Analysis complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Analysis complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Analysis complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Analysis complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Analysis complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Analysis complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Analysis complete for NR019_S7_L001_R1_001_val_1_val_1.fq.gz
Analysis complete for NR019_S7_L001_R2_001_val_2_val_2.fq.gz
Analysis complete for NR019_S7_L002_R1_001_val_1_val_1.fq.gz
Analysis complete for NR019_S7_L002_R2_001_val_2_val_2.fq.gz
Analysis complete for NR021_S8_L001_R1_001_val_1_val_1.fq.gz
Analysis complete for NR021_S8_L001_R2_001_val_2_val_2.fq.gz
Analysis complete for NR021_S8_L002_R1_001_val_1_val_1.fq.gz
Analysis complete for NR021_S8_L002_R2_001_val_2_val_2.fq.gz
Analysis complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Analysis complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Analysis complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Analysis complete for NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Analysis complete for NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
Analysis complete for NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
Analysis complete for NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz
Analysis complete for NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
Analysis complete for NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz
Analysis complete for NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz
Analysis complete for NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz

Started analysis of AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Started analysis of AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Started analysis of AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Started analysis of AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Started analysis of NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 30% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 35% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 40% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 45% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 50% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Started analysis of NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 55% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 60% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 65% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 70% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 75% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 80% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 30% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 85% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 35% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 90% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Started analysis of NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 40% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 95% complete for NR005_S4_L001_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 45% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 10% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 50% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 15% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 55% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 20% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 60% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 65% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 35% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 70% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Started analysis of NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 40% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 75% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 5% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 45% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 80% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 50% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 85% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 55% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 20% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 60% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 90% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 25% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 65% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 95% complete for NR005_S4_L001_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 70% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Started analysis of NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 75% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 35% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 80% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 40% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 85% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 45% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 50% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 90% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Approx 55% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 95% complete for NR005_S4_L002_R1_001_val_1_val_1.fq.gz
Started analysis of NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 60% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 65% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 70% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 75% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 80% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 85% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Started analysis of NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 90% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Approx 95% complete for NR005_S4_L002_R2_001_val_2_val_2.fq.gz
Started analysis of NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 5% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 5% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 10% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 10% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Started analysis of NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 5% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Started analysis of NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 10% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Started analysis of NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 20% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Started analysis of NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 5% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 15% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 20% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 10% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 25% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 35% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 35% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 40% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 40% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 45% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 30% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 45% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 50% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 50% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 35% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 55% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 30% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 55% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 40% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 60% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 35% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 60% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 45% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 65% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 40% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 65% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 50% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 70% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 70% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 45% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 55% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 75% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 75% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 50% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 60% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 80% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 80% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 55% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 65% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 85% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 85% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 60% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 70% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 90% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 90% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 65% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 95% complete for NR012_S1_L001_R1_001_val_1_val_1.fq.gz
Approx 75% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 95% complete for NR012_S1_L001_R2_001_val_2_val_2.fq.gz
Approx 70% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 80% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 85% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 75% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 90% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 80% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 25% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 95% complete for NR012_S1_L002_R1_001_val_1_val_1.fq.gz
Approx 85% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 90% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 95% complete for NR012_S1_L002_R2_001_val_2_val_2.fq.gz
Approx 25% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Started analysis of NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Started analysis of NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Started analysis of NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Started analysis of NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 35% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 35% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 40% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 40% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 35% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 35% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 45% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 45% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 40% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 40% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 50% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 50% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 45% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 45% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 55% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 55% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 50% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 60% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 50% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 60% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 55% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 65% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 65% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 55% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 70% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 70% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 60% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 60% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 75% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 75% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 65% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 65% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 80% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 80% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 70% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 70% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 85% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 85% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 75% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 90% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 75% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 90% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 80% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 95% complete for NR006_S3_L002_R2_001_val_2_val_2.fq.gz
Approx 95% complete for NR006_S3_L002_R1_001_val_1_val_1.fq.gz
Approx 80% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 85% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 85% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Started analysis of NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
Started analysis of NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz
Approx 90% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 90% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Approx 95% complete for NR006_S3_L001_R1_001_val_1_val_1.fq.gz
Approx 95% complete for NR006_S3_L001_R2_001_val_2_val_2.fq.gz
Started analysis of NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz
Started analysis of NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz
Approx 5% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 5% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 5% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 5% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 5% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 10% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 10% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 5% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 5% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 10% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 10% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 15% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 15% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 15% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 15% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 10% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 20% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 10% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 20% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 25% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz
Approx 25% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 15% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 25% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 30% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 25% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 30% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 15% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 35% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 30% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 35% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 20% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 30% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 20% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 40% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 35% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 40% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 20% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 35% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 45% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 25% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
Approx 40% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 45% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 10% complete for NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz
Approx 25% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 40% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 50% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 50% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 45% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 30% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 55% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 45% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 25% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 55% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 50% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 60% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 50% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 60% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 35% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 30% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 55% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 65% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 55% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 15% complete for NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
Approx 35% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 65% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 70% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 60% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz
Approx 40% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 70% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 60% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 35% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 75% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 65% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 40% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 75% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 35% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 65% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 80% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 45% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 70% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 80% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 85% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 40% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 70% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 45% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 75% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 85% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 90% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
Approx 40% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 50% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 75% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 80% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 90% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Approx 95% complete for AD002_S9_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz
Approx 45% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 50% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 80% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 95% complete for AD002_S9_L001_R2_001_val_2_val_2.fq.gz
Started analysis of NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Approx 85% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 55% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 45% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Started analysis of NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
Approx 85% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 90% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 50% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 55% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 60% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Approx 90% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Approx 95% complete for AD002_S9_L002_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
Approx 50% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 5% complete for NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
Approx 60% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 55% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 95% complete for AD002_S9_L002_R2_001_val_2_val_2.fq.gz
Started analysis of NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz
Approx 10% complete for NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Approx 65% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
Started analysis of NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz
Approx 55% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 5% complete for NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Approx 65% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 70% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 60% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
Approx 5% complete for NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz
Approx 20% complete for NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Approx 30% complete for NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
Approx 60% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 70% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 75% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
Approx 65% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 30% complete for NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz
Approx 25% complete for NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Approx 10% complete for NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz
Approx 15% complete for NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
Approx 75% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 80% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
Approx 65% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Approx 15% complete for NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz
Approx 20% complete for NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
Approx 70% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR014_AD014_S5_L002_R1_001_val_1_val_1.fq.gz
Approx 30% complete for NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
Approx 85% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 35% complete for NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
Approx 80% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 35% complete for NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Approx 20% complete for NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz
Approx 25% complete for NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR014_AD014_S5_L002_R2_001_val_2_val_2.fq.gz
Approx 70% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 75% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 35% complete for NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
Approx 40% complete for NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Approx 35% complete for NR014_AD014_S5_L001_R2_001_val_2_val_2.fq.gz
Approx 90% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 85% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
Approx 25% complete for NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz
Approx 45% complete for NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Approx 40% complete for NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
Approx 75% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Approx 80% complete for NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz
Approx 95% complete for NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz
Approx 35% complete for NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
Approx 90% complete for NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz
Approx 30% complete for NR015_AD015_S6_L002_R2_001_val_2_val_2.fq.gz
Approx 40% complete for NR014_AD014_S5_L001_R1_001_val_1_val_1.fq.gz
Approx 50% complete for NR015_AD015_S6_L001_R1_001_val_1_val_1.fq.gz
Approx 45% complete for NR015_AD015_S6_L001_R2_001_val_2_val_2.fq.gz
Approx 40% complete for NR015_AD015_S6_L002_R1_001_val_1_val_1.fq.gz
Approx 80% complete for NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz
Started analysis of NR019_S7_L001_R1_001_val_1_val_1.fq.gz
Approx 5% complete for NR019_S7_L001_R1_001_val_1_val_1.fq.gz
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Started analysis of NR019_S7_L001_R2_001_val_2_val_2.fq.gz
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Started analysis of NR021_S8_L001_R1_001_val_1_val_1.fq.gz
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real	302m11.414s
user	1299m46.092s
sys	25m18.036s

In [52]:

%%bash
mkdir /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02
for fastqc in /home/sam/data/geoduck_illumina/trimmed/trimmed_agai/*fastqc*
do
mv "$fastqc" /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02
done
ls -ltr /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02

total 0

mv: cannot stat '/home/sam/data/geoduck_illumina/trimmed/trimmed_again/*fastqc*': No such file or directory

In [53]:

%%bash
mkdir /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02
for fastqc in /home/sam/data/geoduck_illumina/trimmed/20180129_trimmed_again/*fastqc*
do
mv "$fastqc" /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02
done
ls -ltr /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02

total 28176
-rw-rw-r-- 1 sam sam 432759 Feb  5 06:47 NR005_S4_L002_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 428273 Feb  5 06:47 NR005_S4_L002_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 473117 Feb  5 06:47 NR005_S4_L001_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 467261 Feb  5 06:47 NR005_S4_L001_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 263344 Feb  5 06:47 NR005_S4_L002_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 264908 Feb  5 06:47 NR005_S4_L002_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 272103 Feb  5 06:47 NR005_S4_L001_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 272816 Feb  5 06:47 NR005_S4_L001_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 569441 Feb  5 06:47 NR012_S1_L001_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 249922 Feb  5 06:47 NR012_S1_L001_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 574263 Feb  5 06:47 NR012_S1_L001_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 253596 Feb  5 06:47 NR012_S1_L001_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 568629 Feb  5 06:47 NR012_S1_L002_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 245651 Feb  5 06:47 NR012_S1_L002_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 571514 Feb  5 06:47 NR012_S1_L002_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 245277 Feb  5 06:47 NR012_S1_L002_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 598763 Feb  5 06:48 NR006_S3_L002_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 248346 Feb  5 06:48 NR006_S3_L002_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 599179 Feb  5 06:48 NR006_S3_L002_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 248355 Feb  5 06:48 NR006_S3_L002_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 601016 Feb  5 06:49 NR006_S3_L001_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 252349 Feb  5 06:49 NR006_S3_L001_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 597042 Feb  5 06:49 NR006_S3_L001_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 251931 Feb  5 06:49 NR006_S3_L001_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 565380 Feb  5 07:56 AD002_S9_L001_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 234393 Feb  5 07:56 AD002_S9_L001_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 567265 Feb  5 08:00 AD002_S9_L001_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 236565 Feb  5 08:00 AD002_S9_L001_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 565041 Feb  5 08:09 AD002_S9_L002_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 230950 Feb  5 08:09 AD002_S9_L002_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 569229 Feb  5 08:13 AD002_S9_L002_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 234354 Feb  5 08:13 AD002_S9_L002_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 565214 Feb  5 08:56 NR013_AD013_S2_L001_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 234139 Feb  5 08:56 NR013_AD013_S2_L001_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 491407 Feb  5 08:56 NR019_S7_L001_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 261531 Feb  5 08:56 NR019_S7_L001_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 490020 Feb  5 08:56 NR019_S7_L001_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 263448 Feb  5 08:56 NR019_S7_L001_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 464351 Feb  5 08:56 NR019_S7_L002_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 268708 Feb  5 08:56 NR019_S7_L002_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 460821 Feb  5 08:56 NR019_S7_L002_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 267356 Feb  5 08:56 NR019_S7_L002_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 596763 Feb  5 08:58 NR021_S8_L001_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 251757 Feb  5 08:58 NR021_S8_L001_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 596186 Feb  5 09:00 NR021_S8_L001_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 253280 Feb  5 09:00 NR021_S8_L001_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 590527 Feb  5 09:02 NR021_S8_L002_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 244933 Feb  5 09:02 NR021_S8_L002_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 598134 Feb  5 09:04 NR021_S8_L002_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 250190 Feb  5 09:04 NR021_S8_L002_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 568372 Feb  5 09:05 NR013_AD013_S2_L001_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 236771 Feb  5 09:05 NR013_AD013_S2_L001_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 570468 Feb  5 09:15 NR013_AD013_S2_L002_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 234176 Feb  5 09:15 NR013_AD013_S2_L002_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 568442 Feb  5 09:20 NR013_AD013_S2_L002_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 233208 Feb  5 09:20 NR013_AD013_S2_L002_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 566327 Feb  5 09:28 NR015_AD015_S6_L001_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 234855 Feb  5 09:28 NR015_AD015_S6_L001_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 567567 Feb  5 09:32 NR015_AD015_S6_L001_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 236195 Feb  5 09:32 NR015_AD015_S6_L001_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 563250 Feb  5 09:39 NR015_AD015_S6_L002_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 229424 Feb  5 09:39 NR015_AD015_S6_L002_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 568920 Feb  5 09:43 NR015_AD015_S6_L002_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 234268 Feb  5 09:43 NR015_AD015_S6_L002_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 563439 Feb  5 10:28 NR014_AD014_S5_L001_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 232903 Feb  5 10:28 NR014_AD014_S5_L001_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 567511 Feb  5 10:33 NR014_AD014_S5_L001_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 236851 Feb  5 10:33 NR014_AD014_S5_L001_R2_001_val_2_val_2_fastqc.html
-rw-rw-r-- 1 sam sam 566778 Feb  5 11:45 NR014_AD014_S5_L002_R1_001_val_1_val_1_fastqc.zip
-rw-rw-r-- 1 sam sam 231140 Feb  5 11:45 NR014_AD014_S5_L002_R1_001_val_1_val_1_fastqc.html
-rw-rw-r-- 1 sam sam 566274 Feb  5 11:49 NR014_AD014_S5_L002_R2_001_val_2_val_2_fastqc.zip
-rw-rw-r-- 1 sam sam 232224 Feb  5 11:49 NR014_AD014_S5_L002_R2_001_val_2_val_2_fastqc.html

mkdir: cannot create directory ‘/home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02’: File exists

In [54]:

%%bash
cd /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02/
/home/shared/anaconda3/bin/multiqc /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02/

Searching 72 files..

[INFO   ]         multiqc : This is MultiQC v1.5.dev0
[INFO   ]         multiqc : Template    : default
[INFO   ]         multiqc : Searching '/home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02/'
[INFO   ]          fastqc : Found 36 reports
[INFO   ]         multiqc : Compressing plot data
[INFO   ]         multiqc : Report      : multiqc_report.html
[INFO   ]         multiqc : Data        : multiqc_data
[INFO   ]         multiqc : MultiQC complete

In [55]:

%%bash
mkdir /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_multiqc_fastqc_02
mv /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_fastqc_02/multiqc* /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_multiqc_fastqc_02
ls -ltr /home/sam/data/geoduck_illumina/trimmed/20180205_trimmed_multiqc_fastqc_02

total 1444
-rw-rw-r-- 1 sam sam 1474437 Feb  5 13:01 multiqc_report.html
drwxrwxr-x 2 sam sam    4096 Feb  5 13:01 multiqc_data

Updating this to show new file structure/locations on Owl.

In [1]:

%bash
ls /home/sam/owl/Athaliana/20180125_geoduck_novaseq/

  File "<ipython-input-1-40adfff0d201>", line 2
    ls /home/sam/owl/Athaliana/20180125_geoduck_novaseq/
                                       ^
SyntaxError: invalid token

In [2]:

ls /home/sam/owl/Athaliana/20180125_geoduck_novaseq/

20180125_trim_galore_reports/
20180129_multiqc_trim01/
20180129_trimmed_fastqc_01/
20180129_trimmed_multiqc_fastqc_01/
20180205_trim_galore_reports/
20180205_trimmed_fastqc_02/
20180205_trimmed_multiqc_fastqc_02/
20180206_kmergenie/
AD002_S9_L001_R1_001_val_1_val_1.fq.gz*
AD002_S9_L001_R2_001_val_2_val_2.fq.gz*
AD002_S9_L002_R1_001_val_1_val_1.fq.gz*
AD002_S9_L002_R2_001_val_2_val_2.fq.gz*
NR005_S4_L001_R1_001_val_1_val_1.fq.gz*
NR005_S4_L001_R2_001_val_2_val_2.fq.gz*
NR005_S4_L002_R1_001_val_1_val_1.fq.gz*
NR005_S4_L002_R2_001_val_2_val_2.fq.gz*
NR006_S3_L001_R1_001_val_1_val_1.fq.gz*
NR006_S3_L001_R2_001_val_2_val_2.fq.gz*
NR006_S3_L002_R1_001_val_1_val_1.fq.gz*
NR006_S3_L002_R2_001_val_2_val_2.fq.gz*
NR012_S1_L001_R1_001_val_1_val_1.fq.gz*
NR012_S1_L001_R2_001_val_2_val_2.fq.gz*
NR012_S1_L002_R1_001_val_1_val_1.fq.gz*
NR012_S1_L002_R2_001_val_2_val_2.fq.gz*
NR013_AD013_S2_L001_R1_001_val_1_val_1.fq.gz*
NR013_AD013_S2_L001_R2_001_val_2_val_2.fq.gz*
NR013_AD013_S2_L002_R1_001_val_1_val_1.fq.gz*
NR013_AD013_S2_L002_R2_001_val_2_val_2.fq.gz*

In [ ]: