queue option on Sherlock

[timydaley]

Hi, I'm having issues running the pipeline on a partition in Sherlock, rather than the main queue. The commands are below. TITLE=MEF+Ascl1_13d_B1_rep1;SPECIES=mm10; FASTQ1_1=/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1_1.fastq.gz FASTQ1_2=/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1_2.fastq.gz WORK=/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/$TITLE; mkdir -p $WORK; cd $WORK bds_scr $TITLE /scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/atac.bds -species $SPECIES -nth 4 -fastq1_1 $FASTQ1_1 -fastq1_2 $FASTQ1_2 -system slurm -q_for_slurm_account -q whwong -auto_detect_adapter --account whwong -align

This results in the error sbatch: error: Unable to open file whwong

changing the command to bds_scr $TITLE /scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/atac.bds -species $SPECIES -nth 4 -fastq1_1 $FASTQ1_1 -fastq1_2 $FASTQ1_2 -system slurm -q_for_slurm_account whwong -auto_detect_adapter -align results in everything being submitted to the normal queue.

Thank you for your time and help.

[leepc12]

Update your BDS https://github.com/kundajelab/atac_dnase_pipelines#bigdatascript

On Fri, Jun 1, 2018 at 10:23 AM, Timothy Daley notifications@github.com wrote:

Hi, I'm having issues running the pipeline on a partition in Sherlock, rather than the main queue. The commands are below. TITLE=MEF+Ascl1_13d_B1_rep1;SPECIES=mm10; FASTQ1_1=/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/ WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1_1.fastq.gz FASTQ1_2=/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/ WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1_2.fastq.gz WORK=/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ ATACseq/$TITLE; mkdir -p $WORK; cd $WORK bds_scr $TITLE /scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/atac.bds -species $SPECIES -nth 4 -fastq1_1 $FASTQ1_1 -fastq1_2 $FASTQ1_2 -system slurm -q_for_slurm_account -q whwong -auto_detect_adapter --account whwong -align

This results in the error sbatch: error: Unable to open file whwong

changing the command to bds_scr $TITLE /scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/atac.bds -species $SPECIES -nth 4 -fastq1_1 $FASTQ1_1 -fastq1_2 $FASTQ1_2 -system slurm -q_for_slurm_account whwong -auto_detect_adapter -align results in everything being submitted to the normal queue.

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[timydaley]

I had followed these directions the first time, but I still updated and it's still submitting jobs through the normal queue.

[timydaley]

bds --version Picked up _JAVA_OPTIONS: -Xms256M -Xmx728M -XX:ParallelGCThreads=1 Error: Unknown command line option --version Bds 0.99999e (build 2016-08-26 06:34), by Pablo Cingolani

[leepc12]

Please post output of the following.

cat ~/.bds/clusterGeneric/run.pl

[timydaley]

$ cat ~/.bds/clusterGeneric/run.pl

!/usr/bin/perl

use POSIX;

die "Error: Missing arguments.\nUsage: run.pl timeout cpus mem queue saveStdout saveStderr cmd arg1 ... argN\n" if $#ARGV < 6 ;

$timeout = shift @ARGV; $cpus = shift @ARGV; $mem = shift @ARGV; $queue = shift @ARGV; $saveStdout = shift @ARGV; $saveStderr = shift @ARGV; $cmd = join(' ', @ARGV);

$qsub = "sbatch --export=ALL "; $qsub .= "-n 1 --ntasks-per-node=1 --cpus-per-task=$cpus " if( $cpus > 0 ); if( $mem > 0 ) { $mem = ceil($mem/1000000); # MB if ( $cpu > 0 ) { $mem = $mem*$cpu } $qsub .= "--mem $mem "; } if( $timeout > 0 ) { $timeout = ceil($timeout/60); # minute $qsub .= "-t $timeout "; } if ( $queue ne "" ) { $qsub .= " $queue " }

$pid = open QSUB, " | $qsub"; die "Cannot run command '$qsub'\n" if ! kill(0, $pid); # Check that process exists print QSUB "#!/bin/sh \n"; # SLURM sbatch needs this shebang... print QSUB "$cmd\n"; # Send cluster's task via qsub's STDIN close QSUB;

exit(0);

Thank you again for your help.

[leepc12]

Remove --account whwong and try again.

[timydaley]

Command is now bds_scr $TITLE /scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/atac.bds -species $SPECIES -nth 4 -fastq1_1 $FASTQ1_1 -fastq1_2 $FASTQ1_2 -system slurm -q_for_slurm_account -queue whwong -auto_detect_adapter -align

same error, see below

00:00:15.007 Waiting for all tasks to finish. 00:00:15.007 Wait: Waiting for task to finish: atac.bds.20180601_122100_921_parallel_28/task.align_trim_adapter.trim_adapters_PE_rep1.line_134.id_10, state: SCHEDULED 00:00:15.009 ExecutionerClusterGeneric 'ClusterGeneric[29]': Started running 00:00:15.016 ExecutionerClusterGeneric 'ClusterGeneric[29]': Task selected 'atac.bds.20180601_122100_921_parallel_28/task.align_trim_adapter.trim_adapters_PE_rep1.line_134.id_10' on host 'localhost' sbatch: error: Unable to open file whwong Task failed: Program & line : '/scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/modules/align_trim_adapter.bds', line 134 Task Name : 'trim_adapters_PE rep1' Task ID : 'atac.bds.20180601_122100_921_parallel_28/task.align_trim_adapter.trim_adapters_PE_rep1.line_134.id_10' Task PID : 'null' Task hint : 'cutadapt -m 5 -e 0.10 -a CTGTCTCTTATA -A CTGTCTCTTATA -o /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_1.trim.fastq -p /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl113d' Task resources : 'cpus: -1 mem: 12.0 GB timeout: 82800 wall-timeout: 8640000' State : 'START_FAILED' Dependency state : 'ERROR' Retries available : '1' Input files : '[/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1_1.fastq.gz, /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1_2.fastq.gz]' Output files : '[/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_1.trim.fastq.gz, /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_2.trim.fastq.gz]' Script file : '/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/atac.bds.20180601_122100_921_parallel_28/task.align_trim_adapter.trim_adapters_PE_rep1.line_134.id_10.sh' Error message : 'sbatch: error: Unable to open file whwong ' Exit status : '1' Program :

    # SYS command. line 136

     if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi;  export PATH=/scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/.:/scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/modules:/scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

    # SYS command. line 138

     cutadapt -m 5 -e 0.10 -a CTGTCTCTTATA -A CTGTCTCTTATA -o /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_1.trim.fastq -p /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_2.trim.fastq /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1_1.fastq.gz /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1_2.fastq.gz

    # SYS command. line 140

     gzip -f /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_1.trim.fastq

    # SYS command. line 141

     gzip -f /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_2.trim.fastq

    # SYS command. line 143

     TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; sleep 30; fi

00:00:15.273 Wait: Task 'atac.bds.20180601_122100_921_parallel_28/task.align_trim_adapter.trim_adapters_PE_rep1.line_134.id_10' finished. Fatal error: /scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/atac.bds, line 767, pos 3. Task/s failed.

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. 00:00:15.454 Parallel 'atac.bds.20180601_122100_921_parallel_28' finished, exit value: 1, tasks executed: 1, tasks failed: 1, tasks failed names: trim_adapters_PE rep1. Fatal error: /scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/atac.bds, line 426, pos 2. Task/s failed. atac.bds, line 82 : main() atac.bds, line 85 : void main() { // atac pipeline starts here atac.bds, line 95 : do_align() atac.bds, line 394 : void do_align() { atac.bds, line 426 : wait

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. 00:00:15.827 Writing report file 'atac.bds.20180601_122100_921.report.html' 00:00:15.923 Program 'atac.bds.20180601_122100_921' finished, exit value: 1, tasks executed: 1, tasks failed: 1, tasks failed names: trim_adapters_PE rep1. 00:00:15.924 Finished. Exit code: 1 00:00:15.924 ExecutionerClusterGeneric 'ClusterGeneric[29]': Killed

[leepc12]

What is your pipeline version? You can check latest commit for the pipeline in the top of the log.

Can you update the pipeline and try again?

$ cd [PIPELINE_GIT_DIR]
$ git pull
$ cd ataqc
$ git pull origin master

On Fri, Jun 1, 2018 at 12:43 PM, Timothy Daley notifications@github.com wrote:

Command is now bds_scr $TITLE /scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/atac.bds -species $SPECIES -nth 4 -fastq1_1 $FASTQ1_1 -fastq1_2 $FASTQ1_2 -system slurm -q_for_slurm_account -queue whwong -auto_detect_adapter -align

same error, see below

00:00:15.007 Waiting for all tasks to finish. 00:00:15.007 Wait: Waiting for task to finish: atac.bds.20180601_122100_921_parallel_28/task.aligntrim adapter.trim_adapters_PE_rep1.line_134.id_10, state: SCHEDULED 00:00:15.009 ExecutionerClusterGeneric 'ClusterGeneric[29]': Started running 00:00:15.016 ExecutionerClusterGeneric 'ClusterGeneric[29]': Task selected 'atac.bds.20180601_122100_921_parallel_28/task.aligntrim adapter.trim_adapters_PE_rep1.line_134.id_10' on host 'localhost' sbatch: error: Unable to open file whwong Task failed: Program & line : '/scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/ modules/align_trim_adapter.bds', line 134 Task Name : 'trim_adapters_PE rep1' Task ID : 'atac.bds.20180601_122100_921_parallel_28/task.aligntrim adapter.trim_adapters_PE_rep1.line_134.id_10' Task PID : 'null' Task hint : 'cutadapt -m 5 -e 0.10 -a CTGTCTCTTATA -A CTGTCTCTTATA -o /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_1.trim.fastq -p /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ ATACseq/MEF+Ascl113d' Task resources : 'cpus: -1 mem: 12.0 GB timeout: 82800 wall-timeout: 8640000' State : 'START_FAILED' Dependency state : 'ERROR' Retries available : '1' Input files : '[/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/ WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1_1.fastq.gz, /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ ATACseq/MEF+Ascl1_13d_B1_rep1_2.fastq.gz]' Output files : '[/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/ WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/ out/align/rep1/MEF+Ascl1_13d_B1_rep1_1.trim.fastq.gz, /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl113d B1_rep1_2.trim.fastq.gz]' Script file : '/scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/ WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/ atac.bds.20180601_122100_921_parallel_28/task.aligntrim adapter.trim_adapters_PE_rep1.line_134.id_10.sh' Error message : 'sbatch: error: Unable to open file whwong ' Exit status : '1' Program :

SYS command. line 136

if [[ -f $(which conda) && $(conda env list | grep bds_atac | wc -l) != "0" ]]; then source activate bds_atac; sleep 5; fi; export PATH=/scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/.:/scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/modules:/scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/utils:${PATH}:/bin:/usr/bin:/usr/local/bin:${HOME}/.bds; set -o pipefail; STARTTIME=$(date +%s)

SYS command. line 138

cutadapt -m 5 -e 0.10 -a CTGTCTCTTATA -A CTGTCTCTTATA -o /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_1.trim.fastq -p /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_2.trim.fastq /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1_1.fastq.gz /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1_2.fastq.gz

SYS command. line 140

gzip -f /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_1.trim.fastq

SYS command. line 141

gzip -f /scratch/PI/whwong/tdaley/YanxiaRNAseq/Public/WapinksiAscl1Induction/ATACseq/MEF+Ascl1_13d_B1_rep1/out/align/rep1/MEF+Ascl1_13d_B1_rep1_2.trim.fastq

SYS command. line 143

TASKTIME=$[$(date +%s)-${STARTTIME}]; if [ ${TASKTIME} -lt 60 ]; then echo "Waiting for $[60-${TASKTIME}] seconds."; sleep $[60-${TASKTIME}]; sleep 30; fi

00:00:15.273 Wait: Task 'atac.bds.20180601_122100921 parallel_28/task.align_trim_adapter.trim_adapters_PE_rep1.line_134.id_10' finished. Fatal error: /scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/atac.bds, line 767, pos 3. Task/s failed.

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. 00:00:15.454 Parallel 'atac.bds.20180601_122100_921_parallel_28' finished, exit value: 1, tasks executed: 1, tasks failed: 1, tasks failed names: trim_adapters_PE rep1. Fatal error: /scratch/PI/whwong/tdaley/programs/atac_dnase_pipelines/atac.bds, line 426, pos 2. Task/s failed. atac.bds, line 82 : main() atac.bds, line 85 : void main() { // atac pipeline starts here atac.bds, line 95 : do_align() atac.bds, line 394 : void do_align() { atac.bds, line 426 : wait

Creating checkpoint file: Config or command line option disabled checkpoint file creation, nothing done. 00:00:15.827 Writing report file 'atac.bds.20180601_122100_921. report.html' 00:00:15.923 Program 'atac.bds.20180601_122100_921' finished, exit value: 1, tasks executed: 1, tasks failed: 1, tasks failed names: trim_adapters_PE rep1. 00:00:15.924 Finished. Exit code: 1 00:00:15.924 ExecutionerClusterGeneric 'ClusterGeneric[29]': Killed

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[timydaley]

Excellent. That seemed worked. I apologize for not doing this from the start. Thank you so much for your help.