%%bash
echo "TODAY'S DATE:"
date
echo "------------"
echo ""
#Display operating system info
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:
Sun Apr 19 13:42:23 PDT 2020
------------
Distributor ID: Ubuntu
Description: Ubuntu 16.04.6 LTS
Release: 16.04
Codename: xenial
------------
HOSTNAME:
swoose
------------
Computer Specs:
Architecture: x86_64
CPU op-mode(s): 32-bit, 64-bit
Byte Order: Little Endian
CPU(s): 24
On-line CPU(s) list: 0-23
Thread(s) per core: 2
Core(s) per socket: 6
Socket(s): 2
NUMA node(s): 1
Vendor ID: GenuineIntel
CPU family: 6
Model: 44
Model name: Intel(R) Xeon(R) CPU X5670 @ 2.93GHz
Stepping: 2
CPU MHz: 2925.931
BogoMIPS: 5851.96
Virtualization: VT-x
L1d cache: 32K
L1i cache: 32K
L2 cache: 256K
L3 cache: 12288K
NUMA node0 CPU(s): 0-23
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 pdpe1gb rdtscp lm constant_tsc arch_perfmon pebs bts rep_good nopl xtopology nonstop_tsc aperfmperf pni pclmulqdq dtes64 monitor ds_cpl vmx smx est tm2 ssse3 cx16 xtpr pdcm pcid dca sse4_1 sse4_2 popcnt aes lahf_lm epb ssbd ibrs ibpb stibp kaiser tpr_shadow vnmi flexpriority ept vpid dtherm ida arat flush_l1d
------------
Memory Specs
total used free shared buff/cache available
Mem: 70G 2.1G 2.3G 37M 66G 67G
Swap: 4.7G 1.7G 2.9G
No LSB modules are available.
# Set data directories
%env crab_data=/home/sam/data/C_bairdi/RNAseq
%env hemat_data=/home/sam/data/Hematodinium/RNAseq
%env wd=/home/sam/analyses
%env line=------------------------------------------------------------------------
# Programs
%env seqtk=/home/sam/programs/seqtk-1.3/seqtk
env: crab_data=/home/sam/data/C_bairdi/RNAseq env: hemat_data=/home/sam/data/Hematodinium/RNAseq env: wd=/home/sam/analyses env: line=------------------------------------------------------------------------ env: seqtk=/home/sam/programs/seqtk-1.3/seqtk
FastAs: https://gannet.fish.washington.edu/Atumefaciens/20200419_cbai_MEGAN_read_extractions/
Trimmed-FastQs: https://gannet.fish.washington.edu/Atumefaciens/20200414_cbai_RNAseq_fastp_trimming/
Use FastA IDs from MEGAN6 taxonomic read extraction FastAs to pull out appropriate reads from each phylum (Arthropoda and Alveolata). This is performed because MEGAN6 strips paired read ID after the first space. As such, the resulting read extractions using MEGAN end up with a FastA file containing two reads with identicial headers. Not sure if this will cause any downstream issues (i.e. with Trinity) where paired end data is used, so playing it safe and using the truncated IDs to pull FastQs with complete sequence headers for use in subsequent data wrangling.
%%bash
# Capture start "time"
# Uses builtin bash variable called ${SECONDS}
start=${SECONDS}
# Set timestamp
timestamp=20200419
# Create associative arrays
# NOTE: These will require Bash >4.0
## Infection status
declare -A inf_status_array
## Sampling day
declare -A sample_day_array
## Sample temperature array
declare -A sample_temp_array
# Create sample list
{
echo "380820_D9_uninfected_ambient"
echo "380821_D9_infected_ambient"
echo "380822_D12_uninfected_cold"
echo "380823_D12_infected_cold"
echo "380824_D12_uninfected_warm"
echo "380825_D12_infected_warm"
} >> crab-sample-list.txt
# Populate arrays
# Uses underscore as internal field separator (IFS)
# Reads each field in as a variable name (e.g. sampl)
while IFS="_" read -r sample day infection temp
do
inf_status_array[$sample]=$infection
sample_day_array[$sample]=$day
sample_temp_array[$sample]=$temp
done < crab-sample-list.txt
# Remove the sample list file
rm crab-sample-list.txt
# Check the arrays
echo "Printing array values:"
echo ""
for key in "${!inf_status_array[@]}"
do
printf "[%s]=%s,%s,%s\n" \
"$key" \
"${inf_status_array[$key]}" \
"${sample_day_array[$key]}" \
"${sample_temp_array[$key]}"
done
echo ""
echo "${line}"
echo ""
for directory in ${crab_data} ${hemat_data}
do
# Get species name
species=$(echo "${directory}" | awk -F"/" '{print $5}')
# Make new directory and change to that directory ("$_" means use previous command's argument)
mkdir --parents "${wd}"/"${timestamp}"_"${species}"_megan_reads \
&& cd "$_" || exit
# Set seqtk list filename
seqtk_list=${timestamp}.${species}.seqtk.read_id.list
# Set output FastQ filenames
prefix=${timestamp}.${species}
R1_suffix=megan_R1.fq
R2_suffix=megan_R2.fq
######################################################
# Create FastA IDs list to use for sequence extraction
######################################################
for fasta in "${directory}"/*.fasta
do
echo "${fasta}" >> fasta-list.txt
done
for fasta in "${directory}"/*.fasta
do
grep ">" "${fasta}" | awk 'sub(/^>/, "")'
done | sort -u >> "${seqtk_list}"
echo ""
echo "Finished with FastA ID extraction."
echo ""
echo "Moving on to read extractions..."
echo ""
echo ""
######################################################
# Extract corresponding R1 and R2 reads using seqtk FastA ID list
######################################################
for fastq in "${directory}"/*R1*.gz
do
# Strip path from filename
fastq_nopath=${fastq##*/}
# Get sample ID from FastQ filename
sample=$(echo "${fastq_nopath}" | awk -F "_" '{print $1}')
# Ignore sample 304428 - it's a general pool of various sample types
if [ "${sample}" != "304428" ]
then
# Pull infection status, sample day and temp from associative arrays
inf_status=${inf_status_array[$sample]}
sample_day=${sample_day_array[$sample]}
temp=${sample_temp_array[$sample]}
# Set output filename
## Does not set temp value in filename when the temp value is empty in array
if [[ ${sample_temp_array[$sample]} ]]; then
R1_out="${prefix}.${sample}.${sample_day}.${inf_status}.${temp}.${R1_suffix}"
else
R1_out="${prefix}.${sample}.${sample_day}.${inf_status}.${R1_suffix}"
fi
echo "Extracting R1 reads from ${fastq}."
echo ""
echo "Writing R1 reads to ${R1_out}"
echo ""
echo ""
# Use seqtk to pull out desired FastQ reads
${seqtk} subseq "${fastq}" "${seqtk_list}" >> "${R1_out}"
fi
done
echo ""
echo "Done with R1 read extractions"
echo ""
echo "${line}"
echo ""
for fastq in "${directory}"/*R2*.gz
do
# Strip path from filename
fastq_nopath=${fastq##*/}
# Get sample ID from FastQ filename
sample=$(echo "${fastq_nopath}" | awk -F "_" '{print $1}')
# Ignore sample 304428 - it's a general pool of various sample types
if [ "${sample}" != "304428" ]
then
# Pull infection status and sample day from associative array
inf_status=${inf_status_array[$sample]}
sample_day=${sample_day_array[$sample]}
temp=${sample_temp_array[$sample]}
# Set output filename
## Does not set temp value in filename when the temp value is empty in array
if [[ ${sample_temp_array[$sample]} ]]; then
R2_out="${prefix}.${sample}.${sample_day}.${inf_status}.${temp}.${R2_suffix}"
else
R2_out="${prefix}.${sample}.${sample_day}.${inf_status}.${R2_suffix}"
fi
echo "Extracting R2 reads from ${fastq}."
echo ""
echo "Writing R2 reads to ${R2_out}"
echo ""
echo ""
${seqtk} subseq "${fastq}" "${seqtk_list}" >> "${R2_out}"
fi
done
echo "${line}"
echo ""
# Print working directory and list files
pwd
ls -lh
echo ""
echo "${line}"
echo ""
done
# Caputure end "time"
end=${SECONDS}
# Calculate runtime
runtime=$((end-start))
# Print runtime, in seconds
echo ""
echo "${line}"
echo ""
echo "Total runtime was: ${runtime} seconds"
Printing array values: [380823]=infected,D12,cold [380822]=uninfected,D12,cold [380821]=infected,D9,ambient [380820]=uninfected,D9,ambient [380825]=infected,D12,warm [380824]=uninfected,D12,warm ------------------------------------------------------------------------ Finished with FastA ID extraction. Moving on to read extractions... Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380820_S1_L001_R1_001.fastp-trim.202004143431.fq.gz. Writing R1 reads to 20200419.C_bairdi.380820.D9.uninfected.ambient.megan_R1.fq Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380820_S1_L002_R1_001.fastp-trim.202004143700.fq.gz. Writing R1 reads to 20200419.C_bairdi.380820.D9.uninfected.ambient.megan_R1.fq Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380821_S2_L001_R1_001.fastp-trim.202004143925.fq.gz. Writing R1 reads to 20200419.C_bairdi.380821.D9.infected.ambient.megan_R1.fq Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380821_S2_L002_R1_001.fastp-trim.202004144145.fq.gz. Writing R1 reads to 20200419.C_bairdi.380821.D9.infected.ambient.megan_R1.fq Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380822_S3_L001_R1_001.fastp-trim.202004144409.fq.gz. Writing R1 reads to 20200419.C_bairdi.380822.D12.uninfected.cold.megan_R1.fq Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380822_S3_L002_R1_001.fastp-trim.202004144633.fq.gz. Writing R1 reads to 20200419.C_bairdi.380822.D12.uninfected.cold.megan_R1.fq Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380823_S4_L001_R1_001.fastp-trim.202004144852.fq.gz. Writing R1 reads to 20200419.C_bairdi.380823.D12.infected.cold.megan_R1.fq Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380823_S4_L002_R1_001.fastp-trim.202004145106.fq.gz. Writing R1 reads to 20200419.C_bairdi.380823.D12.infected.cold.megan_R1.fq Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380824_S5_L001_R1_001.fastp-trim.202004145320.fq.gz. Writing R1 reads to 20200419.C_bairdi.380824.D12.uninfected.warm.megan_R1.fq Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380824_S5_L002_R1_001.fastp-trim.202004145558.fq.gz. Writing R1 reads to 20200419.C_bairdi.380824.D12.uninfected.warm.megan_R1.fq Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380825_S6_L001_R1_001.fastp-trim.202004145835.fq.gz. Writing R1 reads to 20200419.C_bairdi.380825.D12.infected.warm.megan_R1.fq Extracting R1 reads from /home/sam/data/C_bairdi/RNAseq/380825_S6_L002_R1_001.fastp-trim.202004140109.fq.gz. Writing R1 reads to 20200419.C_bairdi.380825.D12.infected.warm.megan_R1.fq Done with R1 read extractions ------------------------------------------------------------------------ Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380820_S1_L001_R2_001.fastp-trim.202004143431.fq.gz. Writing R2 reads to 20200419.C_bairdi.380820.D9.uninfected.ambient.megan_R2.fq Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380820_S1_L002_R2_001.fastp-trim.202004143700.fq.gz. Writing R2 reads to 20200419.C_bairdi.380820.D9.uninfected.ambient.megan_R2.fq Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380821_S2_L001_R2_001.fastp-trim.202004143925.fq.gz. Writing R2 reads to 20200419.C_bairdi.380821.D9.infected.ambient.megan_R2.fq Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380821_S2_L002_R2_001.fastp-trim.202004144145.fq.gz. Writing R2 reads to 20200419.C_bairdi.380821.D9.infected.ambient.megan_R2.fq Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380822_S3_L001_R2_001.fastp-trim.202004144409.fq.gz. Writing R2 reads to 20200419.C_bairdi.380822.D12.uninfected.cold.megan_R2.fq Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380822_S3_L002_R2_001.fastp-trim.202004144633.fq.gz. Writing R2 reads to 20200419.C_bairdi.380822.D12.uninfected.cold.megan_R2.fq Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380823_S4_L001_R2_001.fastp-trim.202004144852.fq.gz. Writing R2 reads to 20200419.C_bairdi.380823.D12.infected.cold.megan_R2.fq Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380823_S4_L002_R2_001.fastp-trim.202004145106.fq.gz. Writing R2 reads to 20200419.C_bairdi.380823.D12.infected.cold.megan_R2.fq Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380824_S5_L001_R2_001.fastp-trim.202004145320.fq.gz. Writing R2 reads to 20200419.C_bairdi.380824.D12.uninfected.warm.megan_R2.fq Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380824_S5_L002_R2_001.fastp-trim.202004145558.fq.gz. Writing R2 reads to 20200419.C_bairdi.380824.D12.uninfected.warm.megan_R2.fq Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380825_S6_L001_R2_001.fastp-trim.202004145835.fq.gz. Writing R2 reads to 20200419.C_bairdi.380825.D12.infected.warm.megan_R2.fq Extracting R2 reads from /home/sam/data/C_bairdi/RNAseq/380825_S6_L002_R2_001.fastp-trim.202004140109.fq.gz. Writing R2 reads to 20200419.C_bairdi.380825.D12.infected.warm.megan_R2.fq ------------------------------------------------------------------------ /home/sam/analyses/20200419_C_bairdi_megan_reads total 4.9G -rw-rw-r-- 1 sam sam 395M Jun 15 08:31 20200419.C_bairdi.380820.D9.uninfected.ambient.megan_R1.fq -rw-rw-r-- 1 sam sam 395M Jun 15 08:37 20200419.C_bairdi.380820.D9.uninfected.ambient.megan_R2.fq -rw-rw-r-- 1 sam sam 370M Jun 15 08:32 20200419.C_bairdi.380821.D9.infected.ambient.megan_R1.fq -rw-rw-r-- 1 sam sam 370M Jun 15 08:38 20200419.C_bairdi.380821.D9.infected.ambient.megan_R2.fq -rw-rw-r-- 1 sam sam 380M Jun 15 08:33 20200419.C_bairdi.380822.D12.uninfected.cold.megan_R1.fq -rw-rw-r-- 1 sam sam 380M Jun 15 08:39 20200419.C_bairdi.380822.D12.uninfected.cold.megan_R2.fq -rw-rw-r-- 1 sam sam 345M Jun 15 08:34 20200419.C_bairdi.380823.D12.infected.cold.megan_R1.fq -rw-rw-r-- 1 sam sam 345M Jun 15 08:40 20200419.C_bairdi.380823.D12.infected.cold.megan_R2.fq -rw-rw-r-- 1 sam sam 444M Jun 15 08:35 20200419.C_bairdi.380824.D12.uninfected.warm.megan_R1.fq -rw-rw-r-- 1 sam sam 444M Jun 15 08:41 20200419.C_bairdi.380824.D12.uninfected.warm.megan_R2.fq -rw-rw-r-- 1 sam sam 408M Jun 15 08:36 20200419.C_bairdi.380825.D12.infected.warm.megan_R1.fq -rw-rw-r-- 1 sam sam 408M Jun 15 08:42 20200419.C_bairdi.380825.D12.infected.warm.megan_R2.fq -rw-rw-r-- 1 sam sam 339M Jun 15 08:30 20200419.C_bairdi.seqtk.read_id.list -rw-rw-r-- 1 sam sam 450 Jun 15 08:27 fasta-list.txt ------------------------------------------------------------------------ Finished with FastA ID extraction. Moving on to read extractions... Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380820_S1_L001_R1_001.fastp-trim.202004143431.fq.gz. Writing R1 reads to 20200419.Hematodinium.380820.D9.uninfected.ambient.megan_R1.fq Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380820_S1_L002_R1_001.fastp-trim.202004143700.fq.gz. Writing R1 reads to 20200419.Hematodinium.380820.D9.uninfected.ambient.megan_R1.fq Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380821_S2_L001_R1_001.fastp-trim.202004143925.fq.gz. Writing R1 reads to 20200419.Hematodinium.380821.D9.infected.ambient.megan_R1.fq Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380821_S2_L002_R1_001.fastp-trim.202004144145.fq.gz. Writing R1 reads to 20200419.Hematodinium.380821.D9.infected.ambient.megan_R1.fq Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380822_S3_L001_R1_001.fastp-trim.202004144409.fq.gz. Writing R1 reads to 20200419.Hematodinium.380822.D12.uninfected.cold.megan_R1.fq Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380822_S3_L002_R1_001.fastp-trim.202004144633.fq.gz. Writing R1 reads to 20200419.Hematodinium.380822.D12.uninfected.cold.megan_R1.fq Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380823_S4_L001_R1_001.fastp-trim.202004144852.fq.gz. Writing R1 reads to 20200419.Hematodinium.380823.D12.infected.cold.megan_R1.fq Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380823_S4_L002_R1_001.fastp-trim.202004145106.fq.gz. Writing R1 reads to 20200419.Hematodinium.380823.D12.infected.cold.megan_R1.fq Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380824_S5_L001_R1_001.fastp-trim.202004145320.fq.gz. Writing R1 reads to 20200419.Hematodinium.380824.D12.uninfected.warm.megan_R1.fq Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380824_S5_L002_R1_001.fastp-trim.202004145558.fq.gz. Writing R1 reads to 20200419.Hematodinium.380824.D12.uninfected.warm.megan_R1.fq Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380825_S6_L001_R1_001.fastp-trim.202004145835.fq.gz. Writing R1 reads to 20200419.Hematodinium.380825.D12.infected.warm.megan_R1.fq Extracting R1 reads from /home/sam/data/Hematodinium/RNAseq/380825_S6_L002_R1_001.fastp-trim.202004140109.fq.gz. Writing R1 reads to 20200419.Hematodinium.380825.D12.infected.warm.megan_R1.fq Done with R1 read extractions ------------------------------------------------------------------------ Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380820_S1_L001_R2_001.fastp-trim.202004143431.fq.gz. Writing R2 reads to 20200419.Hematodinium.380820.D9.uninfected.ambient.megan_R2.fq Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380820_S1_L002_R2_001.fastp-trim.202004143700.fq.gz. Writing R2 reads to 20200419.Hematodinium.380820.D9.uninfected.ambient.megan_R2.fq Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380821_S2_L001_R2_001.fastp-trim.202004143925.fq.gz. Writing R2 reads to 20200419.Hematodinium.380821.D9.infected.ambient.megan_R2.fq Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380821_S2_L002_R2_001.fastp-trim.202004144145.fq.gz. Writing R2 reads to 20200419.Hematodinium.380821.D9.infected.ambient.megan_R2.fq Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380822_S3_L001_R2_001.fastp-trim.202004144409.fq.gz. Writing R2 reads to 20200419.Hematodinium.380822.D12.uninfected.cold.megan_R2.fq Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380822_S3_L002_R2_001.fastp-trim.202004144633.fq.gz. Writing R2 reads to 20200419.Hematodinium.380822.D12.uninfected.cold.megan_R2.fq Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380823_S4_L001_R2_001.fastp-trim.202004144852.fq.gz. Writing R2 reads to 20200419.Hematodinium.380823.D12.infected.cold.megan_R2.fq Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380823_S4_L002_R2_001.fastp-trim.202004145106.fq.gz. Writing R2 reads to 20200419.Hematodinium.380823.D12.infected.cold.megan_R2.fq Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380824_S5_L001_R2_001.fastp-trim.202004145320.fq.gz. Writing R2 reads to 20200419.Hematodinium.380824.D12.uninfected.warm.megan_R2.fq Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380824_S5_L002_R2_001.fastp-trim.202004145558.fq.gz. Writing R2 reads to 20200419.Hematodinium.380824.D12.uninfected.warm.megan_R2.fq Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380825_S6_L001_R2_001.fastp-trim.202004145835.fq.gz. Writing R2 reads to 20200419.Hematodinium.380825.D12.infected.warm.megan_R2.fq Extracting R2 reads from /home/sam/data/Hematodinium/RNAseq/380825_S6_L002_R2_001.fastp-trim.202004140109.fq.gz. Writing R2 reads to 20200419.Hematodinium.380825.D12.infected.warm.megan_R2.fq ------------------------------------------------------------------------ /home/sam/analyses/20200419_Hematodinium_megan_reads total 40M -rw-rw-r-- 1 sam sam 0 Jun 15 08:42 20200419.Hematodinium.380820.D9.uninfected.ambient.megan_R1.fq -rw-rw-r-- 1 sam sam 0 Jun 15 08:45 20200419.Hematodinium.380820.D9.uninfected.ambient.megan_R2.fq -rw-rw-r-- 1 sam sam 2.5M Jun 15 08:43 20200419.Hematodinium.380821.D9.infected.ambient.megan_R1.fq -rw-rw-r-- 1 sam sam 2.5M Jun 15 08:46 20200419.Hematodinium.380821.D9.infected.ambient.megan_R2.fq -rw-rw-r-- 1 sam sam 0 Jun 15 08:43 20200419.Hematodinium.380822.D12.uninfected.cold.megan_R1.fq -rw-rw-r-- 1 sam sam 0 Jun 15 08:46 20200419.Hematodinium.380822.D12.uninfected.cold.megan_R2.fq -rw-rw-r-- 1 sam sam 4.8M Jun 15 08:44 20200419.Hematodinium.380823.D12.infected.cold.megan_R1.fq -rw-rw-r-- 1 sam sam 4.8M Jun 15 08:47 20200419.Hematodinium.380823.D12.infected.cold.megan_R2.fq -rw-rw-r-- 1 sam sam 0 Jun 15 08:44 20200419.Hematodinium.380824.D12.uninfected.warm.megan_R1.fq -rw-rw-r-- 1 sam sam 0 Jun 15 08:47 20200419.Hematodinium.380824.D12.uninfected.warm.megan_R2.fq -rw-rw-r-- 1 sam sam 12M Jun 15 08:45 20200419.Hematodinium.380825.D12.infected.warm.megan_R1.fq -rw-rw-r-- 1 sam sam 12M Jun 15 08:48 20200419.Hematodinium.380825.D12.infected.warm.megan_R2.fq -rw-rw-r-- 1 sam sam 2.7M Jun 15 08:42 20200419.Hematodinium.seqtk.read_id.list -rw-rw-r-- 1 sam sam 234 Jun 15 08:42 fasta-list.txt ------------------------------------------------------------------------ ------------------------------------------------------------------------ Total runtime was: 1281 seconds