A pipeline for comprehensive analysis of HTGTS-Rep-seq.

• HTGTSrep on GitHub
• HTGTSrep on BitBucket

• Module Name: HTGTSrep (see the modules page for more information)
• This application is run on Biowulf using a staff-written wrapper script. Simply run the command htgtsrep after loading the module. Do not try to invoke the HTGTSrep.py script using python.

Allocate an interactive session and run the program.
Sample session (user input in bold):

[user@biowulf ~]$ sinteractive --cpus-per-task=4 --mem=8g --gres=lscratch:10
salloc.exe: Pending job allocation 51996182
salloc.exe: job 51996182 queued and waiting for resources
salloc.exe: job 51996182 has been allocated resources
salloc.exe: Granted job allocation 51996182
salloc.exe: Waiting for resource configuration
salloc.exe: Nodes cn0861 are ready for job
srun: error: x11: no local DISPLAY defined, skipping

[user@cn0861 ~]$ git clone https://github.com/Yyx2626/HTGTSrep.git /lscratch/$SLURM_JOB_ID
Cloning into '/lscratch/51996182'...
remote: Enumerating objects: 4, done.
remote: Counting objects: 100% (4/4), done.
remote: Compressing objects: 100% (4/4), done.
remote: Total 1203 (delta 0), reused 0 (delta 0), pack-reused 1199
Receiving objects: 100% (1203/1203), 485.90 MiB | 51.51 MiB/s, done.
Resolving deltas: 100% (324/324), done.
Checking out files: 100% (1226/1226), done.

[user@cn0861 ~]$ cd /lscratch/$SLURM_JOB_ID/HTGTSrep/test

[user@cn0861 test]$ module load HTGTSrep
[+] Loading HTGTSrep  9fe74ff  on cn0861
[+] Loading singularity  3.5.3  on cn0861

[user@cn0861 test]$ htgtsrep run -m metadata.txt -r1 r1.fq.gz -r2 r2.fq.gz -o out
Welcome to HTGTSrep pipeline!!!
INFO  @ Fri, 13 Mar 2020 16:40:31: Parameters: /opt/HTGTSrep/HTGTSrep/HTGTSrep.py run -m metadata.txt -r1 r1.fq.gz -r2 r2.fq.gz -o out
INFO  @ Fri, 13 Mar 2020 16:40:31: Parsing meta files.....
INFO  @ Fri, 13 Mar 2020 16:40:31: Preprocessing read files.....
INFO  @ Fri, 13 Mar 2020 16:40:32: fastq-multx -m 0 -x -b -d 0 -B out/barcodes.txt out/raw.r1.fq out/raw.r2.fq -o out/%_R1.fq out/%_R2.fq
Using Barcode File: out/barcodes.txt
Id      Count   File(s)
HC091_Alt231    16333   out/HC091_Alt231_R1.fq  out/HC091_Alt231_R2.fq
HC092_Alt231    13145   out/HC092_Alt231_R1.fq  out/HC092_Alt231_R2.fq
unmatched       0       out/unmatched_R1.fq     out/unmatched_R2.fq
total   29478
INFO  @ Fri, 13 Mar 2020 16:40:32: Joining reads......
[snip...]

[user@cn0861 test]$ ls out/
barcodes.txt  HC091_Alt231  HC092_Alt231  logs  metadata.txt  stat

[user@cn0861 test]$ cp -r out/ /data/$USER/

[user@cn0861 test]$ exit
exit
salloc.exe: Relinquishing job allocation 51996182
salloc.exe: Job allocation 51996182 has been revoked.

[user@biowulf ~]$ 

Create a batch input file (e.g. HTGTSrep.sh). For example:

#!/bin/bash
set -e
module load HTGTSrep
cd /data/$USER/HTGTSrep/test
htgtsrep run -m metadata.txt -r1 r1.fq.gz -r2 r2.fq.gz -o /data/$USER/out

Submit this job using the Slurm sbatch command.

sbatch [--cpus-per-task=#] [--mem=#] HTGTSrep.sh

Create a swarmfile (e.g. HTGTSrep.swarm). For example:

htgtsrep run -m metadata.txt -r1 r1A.fq.gz -r2 r2A.fq.gz -o /data/$USER/outA
htgtsrep run -m metadata.txt -r1 r1B.fq.gz -r2 r2B.fq.gz -o /data/$USER/outB
htgtsrep run -m metadata.txt -r1 r1C.fq.gz -r2 r2C.fq.gz -o /data/$USER/outC
htgtsrep run -m metadata.txt -r1 r1D.fq.gz -r2 r2D.fq.gz -o /data/$USER/outD

Submit this job using the swarm command.

swarm -f HTGTSrep.swarm [-g #] [-t #] --module HTGTSrep