Notebook

Running in Docker container on Ostrich¶

Started Docker container with the following command:¶

docker run -p 8888:8888 -v /Users/sam/data/:/data -v /Users/sam/owl_home/:/owl_home -v /Users/sam/owl_web/:/owl_web -v /Users/sam/gitrepos:/gitrepos -it f99537d7e06a

The command allows access to Jupyter Notebook over port 8888 and makes my Jupyter Notebook GitHub repo and my data files on Owl/home and Owl/web accessible to the Docker container.

Once the container was started, started Jupyter Notebook with the following command inside the Docker container:

jupyter notebook

This is configured in the Docker container to launch a Jupyter Notebook without a browser on port 8888.

The Docker container is running on an image created from this Dockerfile (Git commit 443bc42)

In [1]:

%%bash
date

Wed Mar  1 20:13:26 UTC 2017

Check computer specs¶

In [2]:

%%bash
hostname

0f2bca9c664b

In [3]:

%%bash
lscpu

Architecture:          x86_64
CPU op-mode(s):        32-bit, 64-bit
Byte Order:            Little Endian
CPU(s):                8
On-line CPU(s) list:   0-7
Thread(s) per core:    1
Core(s) per socket:    8
Socket(s):             1
Vendor ID:             GenuineIntel
CPU family:            6
Model:                 26
Model name:            Intel(R) Xeon(R) CPU           E5520  @ 2.27GHz
Stepping:              5
CPU MHz:               2260.998
BogoMIPS:              4521.99
Hypervisor vendor:     KVM
Virtualization type:   full
L1d cache:             32K
L1i cache:             32K
L2 cache:              256K
L3 cache:              8192K

Copy non-demultiplexed BGI FASTQ files to local computer (Ostrich) and verfiy checksums¶

In [4]:

ls /owl_web/nightingales/O_lurida/20160223_gbs/

160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
1HL_10A_1.fq.gz*
1HL_10A_2.fq.gz*
1HL_11A_1.fq.gz*
1HL_11A_2.fq.gz*
1HL_12A_1.fq.gz*
1HL_12A_2.fq.gz*
1HL_13A_1.fq.gz*
1HL_13A_2.fq.gz*
1HL_14A_1.fq.gz*
1HL_14A_2.fq.gz*
1HL_15A_1.fq.gz*
1HL_15A_2.fq.gz*
1HL_16A_1.fq.gz*
1HL_16A_2.fq.gz*
1HL_17A_1.fq.gz*
1HL_17A_2.fq.gz*
1HL_19A_1.fq.gz*
1HL_19A_2.fq.gz*
1HL_1A_1.fq.gz*
1HL_1A_2.fq.gz*
1HL_20A_1.fq.gz*
1HL_20A_2.fq.gz*
1HL_21A_1.fq.gz*
1HL_21A_2.fq.gz*
1HL_22A_1.fq.gz*
1HL_22A_2.fq.gz*
1HL_23A_1.fq.gz*
1HL_23A_2.fq.gz*
1HL_24A_1.fq.gz*
1HL_24A_2.fq.gz*
1HL_25A_1.fq.gz*
1HL_25A_2.fq.gz*
1HL_26A_1.fq.gz*
1HL_26A_2.fq.gz*
1HL_27A_1.fq.gz*
1HL_27A_2.fq.gz*
1HL_28A_1.fq.gz*
1HL_28A_2.fq.gz*
1HL_29A_1.fq.gz*
1HL_29A_2.fq.gz*
1HL_2A_1.fq.gz*
1HL_2A_2.fq.gz*
1HL_31A_1.fq.gz*
1HL_31A_2.fq.gz*
1HL_33A_1.fq.gz*
1HL_33A_2.fq.gz*
1HL_34A_1.fq.gz*
1HL_34A_2.fq.gz*
1HL_35A_1.fq.gz*
1HL_35A_2.fq.gz*
1HL_3A_1.fq.gz*
1HL_3A_2.fq.gz*
1HL_4A_1.fq.gz*
1HL_4A_2.fq.gz*
1HL_5A_1.fq.gz*
1HL_5A_2.fq.gz*
1HL_6A_1.fq.gz*
1HL_6A_2.fq.gz*
1HL_7A_1.fq.gz*
1HL_7A_2.fq.gz*
1HL_8A_1.fq.gz*
1HL_8A_2.fq.gz*
1HL_9A_1.fq.gz*
1HL_9A_2.fq.gz*
1NF_10A_1.fq.gz*
1NF_10A_2.fq.gz*
1NF_11A_1.fq.gz*
1NF_11A_2.fq.gz*
1NF_12A_1.fq.gz*
1NF_12A_2.fq.gz*
1NF_13A_1.fq.gz*
1NF_13A_2.fq.gz*
1NF_14A_1.fq.gz*
1NF_14A_2.fq.gz*
1NF_15A_1.fq.gz*
1NF_15A_2.fq.gz*
1NF_16A_1.fq.gz*
1NF_16A_2.fq.gz*
1NF_17A_1.fq.gz*
1NF_17A_2.fq.gz*
1NF_18A_1.fq.gz*
1NF_18A_2.fq.gz*
1NF_19A_1.fq.gz*
1NF_19A_2.fq.gz*
1NF_1A_1.fq.gz*
1NF_1A_2.fq.gz*
1NF_20A_1.fq.gz*
1NF_20A_2.fq.gz*
1NF_21A_1.fq.gz*
1NF_21A_2.fq.gz*
1NF_22A_1.fq.gz*
1NF_22A_2.fq.gz*
1NF_23A_1.fq.gz*
1NF_23A_2.fq.gz*
1NF_24A_1.fq.gz*
1NF_24A_2.fq.gz*
1NF_25A_1.fq.gz*
1NF_25A_2.fq.gz*
1NF_26A_1.fq.gz*
1NF_26A_2.fq.gz*
1NF_27A_1.fq.gz*
1NF_27A_2.fq.gz*
1NF_28A_1.fq.gz*
1NF_28A_2.fq.gz*
1NF_29A_1.fq.gz*
1NF_29A_2.fq.gz*
1NF_2A_1.fq.gz*
1NF_2A_2.fq.gz*
1NF_30A_1.fq.gz*
1NF_30A_2.fq.gz*
1NF_31A_1.fq.gz*
1NF_31A_2.fq.gz*
1NF_32A_1.fq.gz*
1NF_32A_2.fq.gz*
1NF_33A_1.fq.gz*
1NF_33A_2.fq.gz*
1NF_4A_1.fq.gz*
1NF_4A_2.fq.gz*
1NF_5A_1.fq.gz*
1NF_5A_2.fq.gz*
1NF_6A_1.fq.gz*
1NF_6A_2.fq.gz*
1NF_7A_1.fq.gz*
1NF_7A_2.fq.gz*
1NF_8A_1.fq.gz*
1NF_8A_2.fq.gz*
1NF_9A_1.fq.gz*
1NF_9A_2.fq.gz*
1SN_10A_1.fq.gz*
1SN_10A_2.fq.gz*
1SN_11A_1.fq.gz*
1SN_11A_2.fq.gz*
1SN_12A_1.fq.gz*
1SN_12A_2.fq.gz*
1SN_13A_1.fq.gz*
1SN_13A_2.fq.gz*
1SN_14A_1.fq.gz*
1SN_14A_2.fq.gz*
1SN_15A_1.fq.gz*
1SN_15A_2.fq.gz*
1SN_16A_1.fq.gz*
1SN_16A_2.fq.gz*
1SN_17A_1.fq.gz*
1SN_17A_2.fq.gz*
1SN_18A_1.fq.gz*
1SN_18A_2.fq.gz*
1SN_19A_1.fq.gz*
1SN_19A_2.fq.gz*
1SN_1A_1.fq.gz*
1SN_1A_2.fq.gz*
1SN_20A_1.fq.gz*
1SN_20A_2.fq.gz*
1SN_21A_1.fq.gz*
1SN_21A_2.fq.gz*
1SN_22A_1.fq.gz*
1SN_22A_2.fq.gz*
1SN_23A_1.fq.gz*
1SN_23A_2.fq.gz*
1SN_24A_1.fq.gz*
1SN_24A_2.fq.gz*
1SN_25A_1.fq.gz*
1SN_25A_2.fq.gz*
1SN_26A_1.fq.gz*
1SN_26A_2.fq.gz*
1SN_27A_1.fq.gz*
1SN_27A_2.fq.gz*
1SN_28A_1.fq.gz*
1SN_28A_2.fq.gz*
1SN_29A_1.fq.gz*
1SN_29A_2.fq.gz*
1SN_2A_1.fq.gz*
1SN_2A_2.fq.gz*
1SN_30A_1.fq.gz*
1SN_30A_2.fq.gz*
1SN_31A_1.fq.gz*
1SN_31A_2.fq.gz*
1SN_32A_1.fq.gz*
1SN_32A_2.fq.gz*
1SN_3A_1.fq.gz*
1SN_3A_2.fq.gz*
1SN_4A_1.fq.gz*
1SN_4A_2.fq.gz*
1SN_5A_1.fq.gz*
1SN_5A_2.fq.gz*
1SN_6A_1.fq.gz*
1SN_6A_2.fq.gz*
1SN_7A_1.fq.gz*
1SN_7A_2.fq.gz*
1SN_8A_1.fq.gz*
1SN_8A_2.fq.gz*
1SN_9A_1.fq.gz*
1SN_9A_2.fq.gz*
UnKnow_1.fq.gz*
UnKnow_2.fq.gz*
bgi_project_summary.tar.gz*
checksums.md5
index.lst
md5.check*
md5.txt*
md51.txt
readme.md
split.sh

In [5]:

%%bash
mkdir /data/20170301_fastqc_gbs

In [6]:

cd /data/20170301_fastqc_gbs/

/data/20170301_fastqc_gbs

In [7]:

%%bash
time for file in /owl_web/nightingales/O_lurida/20160223_gbs/160123*
    do
    cp "$file" .
    done

real	31m9.816s
user	0m0.020s
sys	5m31.590s

Generate MD5 checksums & compare to original checksums¶

In [8]:

%%bash
time for file in *.gz
    do
    md5 "$file" >> temp_checksums.md5
    done

bash: line 3: md5: command not found
bash: line 3: md5: command not found

real	0m0.020s
user	0m0.010s
sys	0m0.000s

In [9]:

%%bash
cat temp_checksums.md5_checksums.md5

In [10]:

%%bash
ls -lh

total 37G
-rw-r--r-- 1 srlab staff 17G Mar  1 20:36 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
-rw-r--r-- 1 srlab staff 20G Mar  1 20:54 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
-rw-r--r-- 1 srlab staff   0 Mar  1 20:54 temp_checksums.md5

Whoops! Typos in both of the above commands. Will re-run...

In [13]:

%%bash
time for file in *.gz
    do
    md5sum "$file" >> temp_checksums.md5
    done

real	7m1.077s
user	0m3.950s
sys	4m11.280s

In [14]:

%%bash
cat temp_checksums.md5

afd18614b9f5694af1a59672821cd0db  160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
2894dd9b54c1388d3d74e8f8642aa267  160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz

In [15]:

%%bash
awk '/160123_I132/[print $0]' /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5

awk: line 1: syntax error at or near [

Bracket typo. Redo...

In [16]:

%%bash
awk '/160123_I132/{print $0}' /owl_web/nightingales/O_lurida/20160223_gbs/checksums.md5

MD5 (/Volumes/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz) = afd18614b9f5694af1a59672821cd0db
MD5 (/Volumes/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz) = 2894dd9b54c1388d3d74e8f8642aa267

Visual comparison looks good. Will proceed with FastQC

FastQC Analysis¶

In [17]:

%%bash
which fastqc

/usr/local/bioinformatics/FastQC/fastqc

In [18]:

%%bash
time fastqc --extract 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz

Analysis complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Analysis complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz

Started analysis of 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 5% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 10% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 15% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 20% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 25% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 30% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 35% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 40% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 45% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 50% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 55% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 60% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 65% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 70% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 75% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 80% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 85% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 90% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Approx 95% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
Started analysis of 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 5% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 10% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 15% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 20% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 25% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 30% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 35% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 40% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 45% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 50% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 55% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 60% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 65% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 70% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 75% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 80% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 85% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 90% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
Approx 95% complete for 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz

real	353m56.148s
user	28m26.990s
sys	215m31.450s

In [19]:

ls -lh

total 37G
-rw-r--r-- 1 srlab staff  17G Mar  1 20:36 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
drwxr-xr-x 1 srlab staff  272 Mar  2 00:35 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/
-rw-r--r-- 1 srlab staff 294K Mar  2 00:35 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc.html
-rw-r--r-- 1 srlab staff 403K Mar  2 00:35 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc.zip
-rw-r--r-- 1 srlab staff  20G Mar  1 20:54 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
drwxr-xr-x 1 srlab staff  272 Mar  2 03:12 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/
-rw-r--r-- 1 srlab staff 347K Mar  2 03:12 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc.html
-rw-r--r-- 1 srlab staff 489K Mar  2 03:12 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc.zip
-rw-r--r-- 1 srlab staff  186 Mar  1 21:10 temp_checksums.md5

In [20]:

ls 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/

Icons/  Images/  fastqc.fo  fastqc_data.txt  fastqc_report.html  summary.txt

In [21]:

cat 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/summary.txt

PASS	Basic Statistics	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
PASS	Per base sequence quality	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
WARN	Per tile sequence quality	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
PASS	Per sequence quality scores	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
WARN	Per base sequence content	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
PASS	Per sequence GC content	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
PASS	Per base N content	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
PASS	Sequence Length Distribution	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
FAIL	Sequence Duplication Levels	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
PASS	Overrepresented sequences	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
FAIL	Adapter Content	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz
FAIL	Kmer Content	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1.fq.gz

In [22]:

ls 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/

Icons/  Images/  fastqc.fo  fastqc_data.txt  fastqc_report.html  summary.txt

In [23]:

cat 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/s

cat: 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/: Is a directory

In [24]:

cat 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/summary.txt

PASS	Basic Statistics	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
FAIL	Per base sequence quality	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
FAIL	Per tile sequence quality	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
PASS	Per sequence quality scores	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
FAIL	Per base sequence content	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
PASS	Per sequence GC content	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
WARN	Per base N content	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
PASS	Sequence Length Distribution	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
FAIL	Sequence Duplication Levels	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
WARN	Overrepresented sequences	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
FAIL	Adapter Content	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz
FAIL	Kmer Content	160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2.fq.gz

Move the FastQC Outputs to Nightingales¶

In [25]:

%%bash
mv -v 160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/ \
160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/ \
-t /owl_web/nightingales/O_lurida/20160223_gbs/

'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc.fo' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc.fo'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_data.txt' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_data.txt'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_report.html' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_report.html'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/error.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/error.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/fastqc_icon.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/fastqc_icon.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/tick.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/tick.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/warning.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/warning.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/adapter_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/adapter_content.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/duplication_levels.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/duplication_levels.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/kmer_profiles.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/kmer_profiles.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_n_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_n_content.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_quality.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_sequence_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_sequence_content.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_gc_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_gc_content.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_quality.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_tile_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_tile_quality.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/sequence_length_distribution.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/sequence_length_distribution.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/summary.txt' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/summary.txt'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc.fo'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_data.txt'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_report.html'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/error.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/fastqc_icon.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/tick.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons/warning.png'
removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Icons'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/adapter_content.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/duplication_levels.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/kmer_profiles.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_n_content.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_quality.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_base_sequence_content.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_gc_content.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_sequence_quality.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/per_tile_quality.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images/sequence_length_distribution.png'
removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/Images'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/summary.txt'
removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc.fo' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc.fo'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_data.txt' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_data.txt'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_report.html' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_report.html'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/error.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/error.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/fastqc_icon.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/fastqc_icon.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/tick.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/tick.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/warning.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/warning.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/adapter_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/adapter_content.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/duplication_levels.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/duplication_levels.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/kmer_profiles.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/kmer_profiles.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_n_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_n_content.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_quality.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_sequence_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_sequence_content.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_gc_content.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_gc_content.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_quality.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_tile_quality.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_tile_quality.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/sequence_length_distribution.png' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/sequence_length_distribution.png'
'160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/summary.txt' -> '/owl_web/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/summary.txt'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc.fo'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_data.txt'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_report.html'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/error.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/fastqc_icon.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/tick.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons/warning.png'
removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Icons'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/adapter_content.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/duplication_levels.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/kmer_profiles.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_n_content.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_quality.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_base_sequence_content.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_gc_content.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_sequence_quality.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/per_tile_quality.png'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images/sequence_length_distribution.png'
removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/Images'
removed '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/summary.txt'
removed directory: '160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/'

View FastQC Reports¶

Easier viewing can be had by visiting the two folling links:

In [27]:

%%HTML
<iframe width="100%" height="500" src="http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_1_fastqc/fastqc_report.html"></iframe>

In [28]:

%%HTML
<iframe width="100%" height="500" src="http://owl.fish.washington.edu/nightingales/O_lurida/20160223_gbs/160123_I132_FCH3YHMBBXX_L4_OYSzenG1AAD96FAAPEI-109_2_fastqc/fastqc_report.html"></iframe>

These results aren't terribly surprising since these data haven't been quality trimmed to remove adapter/barcode sequences.