This thread is the designated place to ask questions about running the **biowardrobe_chipseq_se** workflow.

Created by James Eddy jaeddy
That was quick, thank you indeed. It worked like charm with **`rabix 1.0.0`**, and the modified tools files above. Appreciated @bogdang .
Hi @Azza Thank you for testing the workflow with rabix. Rabix 1.0.3. is a bit buggy, and we are preparing a 1.0.4. release with the fixes. In the meantime could you please retry running the workflow with rabix 1.0.0 version? Sorry about the inconvenience, hopefully in the next release it will all be stable.
Hi! Thank you for the suggestions. I'm still having problems though: ## with `rabix`: Despite following the instructions of @bogdang in https://www.synapse.org/#!Synapse:syn10208944, and replacing the mentioned tools, I'm getting the error: `[ERROR] Unsupported feature: $schemas`, and subsequent jobs are all failing. I'm using `Rabix 1.03` for this purpose, and my machine has 50G of disk space. ## with `toil`: Like @vipin , the workflow freezes at the `samtools-rmdup` stage and permenantly fails. I'm using `toil-cwl-runner 3.12.0`
I had the same issue as @vipin . Will try the same solution he used and re-run.
Hi Vipin, Did you follow instructions from this report? https://www.synapse.org/#!Synapse:syn10208944 Most importantly, step 3, to replace bamtools-stats tool and samtools-sort-index tool? Best, Bogdan
Hi Michael, Here is the error message when I was running with `rabix` version Rabix 1.0.0. ```shell [nexcbu@wfexecutor biowardrobe_chipseq_se]$ ~/tools/rabix-cli-1.0.0/rabix --tmpdir-prefix ~/tmp/ --tmp-outdir-prefix ~/tmp/ ./biowardrobe_chipseq_se.cwl biowardrobe_chipseq_se.json [2017-10-05 11:35:17.934] [ERROR] Unsupported feature: $schemas. [2017-10-05 11:35:19.673] [INFO] Job root.fastx_quality_stats has started [2017-10-05 11:35:19.674] [INFO] Job root.bowtie_aligner has started [2017-10-05 11:35:43.299] [INFO] Pulling docker image biowardrobe2/bowtie:v1.2.0 [2017-10-05 11:35:43.299] [INFO] Pulling docker image biowardrobe2/fastx_toolkit:v0.0.14 [2017-10-05 11:35:50.024] [INFO] Running command line: fastx_quality_stats -i /home/nexcbu/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/inputs/SRR1198790.fastq -o SRR1198790.fastq.fastxstat [2017-10-05 11:35:50.327] [INFO] Running command line: bowtie --best -3 0 -5 0 -m 1 -q -S --strata -p 8 -v 3 /home/nexcbu/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/references/dm3/bowtie_indices/dm3 /home/nexcbu/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/inputs/SRR1198790.fastq SRR1198790.sam 2> SRR1198790.sam.log ^[[B^[[B[2017-10-05 11:38:05.688] [INFO] Job root.fastx_quality_stats has completed [2017-10-05 11:39:29.324] [INFO] Job root.bowtie_aligner has completed [2017-10-05 11:39:30.404] [INFO] Job root.samtools_sort_index has started [2017-10-05 11:39:34.650] [INFO] Pulling docker image biowardrobe2/samtools:v1.4 [2017-10-05 11:39:37.607] [INFO] Running command line: bash -c '#!/bin/bash if [ "$0" = True ] then echo "Run: samtools sort " ${@:1} samtools sort "${@:1}" else echo "Skip samtools sort " ${@:1} fi ' True -o SRR1198790.sorted.bam -O bam -@ 8 SRR1198790.sam ; bash -c '#!/bin/bash if [ "$0" = True ] then echo "Run: samtools index " ${@:1} samtools index "${@:1}" else echo "Skip samtools index " ${@:1} fi ' True -@ 8 SRR1198790.sorted.bam SRR1198790.sorted.bam.bai [2017-10-05 11:40:37.075] [INFO] Job root.samtools_sort_index has completed [2017-10-05 11:40:37.403] [INFO] Job root.samtools_rmdup has started [2017-10-05 11:40:38.291] [INFO] Pulling docker image biowardrobe2/samtools:v1.4 [2017-10-05 11:40:41.025] [INFO] Running command line: bash -c '#!/bin/bash if [ "$0" = True ] then samtools rmdup "${@:1}" else echo "Skip samtools rmdup " ${@:1} fi ' False -s /home/nexcbu/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/biowardrobe_chipseq_se-2017-10-05-113515.780/root/samtools_rmdup/SRR1198790.sorted.bam SRR1198790.sorted.bam > SRR1198790.sorted.bam.rmdup 2>&1 [2017-10-05 11:40:50.278] [INFO] Job root.samtools_rmdup has completed [2017-10-05 11:40:50.406] [INFO] Job root.get_stat has started [2017-10-05 11:40:50.406] [INFO] Job root.samtools_sort_index_after_rmdup has started [2017-10-05 11:40:50.415] [INFO] Pulling docker image biowardrobe2/scidap:v0.0.2 [2017-10-05 11:40:51.310] [INFO] Pulling docker image biowardrobe2/samtools:v1.4 [2017-10-05 11:40:56.331] [INFO] Running command line: python -c '#!/usr/bin/env python import sys, re TOTAL, ALIGNED, SUPRESSED, USED = 100, 80, 0, 0 with open(sys.argv[1], '\''r'\'') as bowtie_log: for line in bowtie_log: if '\''processed:'\'' in line: TOTAL = int(line.split('\''processed:'\'')[1]) if '\''alignment:'\'' in line: ALIGNED = int(line.split('\''alignment:'\'')[1].split()[0]) if '\''due to -m:'\'' in line: SUPRESSED = int(line.split('\''due to -m:'\'')[1].split()[0]) USED = ALIGNED with open(sys.argv[2], '\''r'\'') as rmdup_log: for line in rmdup_log: if '\''/'\'' in line and '\''Skip'\'' not in line: splt = line.split('\''/'\'') USED = int((splt[1].split('\''='\''))[0].strip()) - int((splt[0].split('\'']'\''))[1].strip()) print TOTAL, ALIGNED, SUPRESSED, USED ' /home/nexcbu/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/biowardrobe_chipseq_se-2017-10-05-113515.780/root/bowtie_aligner/SRR1198790.sam.log /home/nexcbu/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/biowardrobe_chipseq_se-2017-10-05-113515.780/root/samtools_rmdup/SRR1198790.sorted.bam.rmdup > SRR1198790.sam.stat [2017-10-05 11:40:56.556] [INFO] Running command line: bash -c '#!/bin/bash if [ "$0" = True ] then echo "Run: samtools sort " ${@:1} samtools sort "${@:1}" else echo "Skip samtools sort " ${@:1} fi ' False -o SRR1198790.sorted.bam -O bam -@ 8 SRR1198790.sorted.bam ; bash -c '#!/bin/bash if [ "$0" = True ] then echo "Run: samtools index " ${@:1} samtools index "${@:1}" else echo "Skip samtools index " ${@:1} fi ' False -@ 8 SRR1198790.sorted.bam SRR1198790.sorted.bam.bai [2017-10-05 11:41:04.991] [INFO] Job root.get_stat has completed [2017-10-05 11:41:09.582] [INFO] Job root.samtools_sort_index_after_rmdup has completed [2017-10-05 11:41:10.416] [INFO] Job root.bamtools_stats has started [2017-10-05 11:41:10.416] [INFO] Job root.macs2_callpeak has started [2017-10-05 11:41:10.426] [INFO] Pulling docker image biowardrobe2/bamtools:v2.4.1 [2017-10-05 11:41:10.458] [INFO] Pulling docker image biowardrobe2/macs2:v2.1.1 [2017-10-05 11:41:16.137] [INFO] Running command line: bamtools stats -in -in -in /home/nexcbu/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/biowardrobe_chipseq_se-2017-10-05-113515.780/root/samtools_sort_index_after_rmdup/SRR1198790.sorted.bam > stats.log [2017-10-05 11:41:16.358] [INFO] Running command line: bash -c '#!/bin/bash if [ "$0" = True ] then echo "Run: macs2 callpeak " ${@:1} ls | grep -v ${@: -1}.log | xargs rm macs2 callpeak "${@:1}" else echo "Skip macs2 callpeak " ${@:1} fi ' True -t /home/nexcbu/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/biowardrobe_chipseq_se-2017-10-05-113515.780/root/samtools_sort_index_after_rmdup/SRR1198790.sorted.bam -f BAM -g 1.2e8 --keep-dup auto --buffer-size 10000 --bw 150 -m 4 40 -q 0.05 --nolambda --call-summits --verbose 3 -n SRR1198790.sorted 2> SRR1198790.sorted.log [2017-10-05 11:41:17.573] [ERROR] Job e1d8eba5-2edb-4aa6-b836-c164f249a6a4 failed with exit code 1. [2017-10-05 11:41:17.573] [INFO] Job e1d8eba5-2edb-4aa6-b836-c164f249a6a4 failed with exit code 1. [2017-10-05 11:41:17.664] [WARN] Job root.bamtools_stats, rootId: 0f9836a1-0830-48c2-bd1a-d27921bb1d00 failed: Job e1d8eba5-2edb-4aa6-b836-c164f249a6a4 failed with exit code 1. [2017-10-05 11:41:17.673] [WARN] Root job 0f9836a1-0830-48c2-bd1a-d27921bb1d00 failed. [2017-10-05 11:41:17.678] [INFO] Failed to execute a Job ```
Hi Michael, The error from toil is: ``` [STDOUT] ~/tools/venv/bin/cwltoil --workDir /home/nexcbu/tmp/ ../../synapse_utils/dockstore-tool-synapse-get.cwl ../../config_files/biowardrobe_chipseq_se_get.cwl.json ~/tools/venv/bin/cwltoil --workDir /home/nexcbu/tmp/ biowardrobe_chipseq_se.cwl biowardrobe_chipseq_se.json led job 'file:///home/nexcbu/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/tools/samtools-rmdup.cwl' bash -c H/A/jobce6_cU ---TOIL WORKER OUTPUT LOG--- INFO:toil:Running Toil version 3.11.0-ca24899f31a2d7f8b3f766a1c99c982ccf1044eb. WARNING:rdflib.term:http://schema.org/docs/!DOCTYPE html does not look like a valid URI, trying to serialize this will break. INFO:toil.fileStore:Starting job ('file:///home/nexcbu/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/tools/samtools-rmdup.cwl' bash -c H/A/jobce6_cU) with ID (f4407ef710be44a0b2847364fc08c19224632e7a). ['docker', 'pull', 'biowardrobe2/samtools:v1.4'] INFO:cwltool:['docker', 'pull', 'biowardrobe2/samtools:v1.4'] Trying to pull repository registry.access.redhat.com/biowardrobe2/samtools ... Trying to pull repository docker.io/biowardrobe2/samtools ... v1.4: Pulling from docker.io/biowardrobe2/samtools Digest: sha256:e4dad5f38c1b782d3f1608410c07e8dc47fb7b92bc427175a160dfa0813c48d8 [job samtools-rmdup.cwl] /home/nexcbu/tmp/out_tmpdir4VcbVf$ docker \ run \ -i \ --volume=/home/nexcbu/tmp/out_tmpdir4VcbVf:/var/spool/cwl:rw \ --volume=/home/nexcbu/tmp/toil-e757c11c-c96c-4f7a-b121-4c5cf38c0930-e272bc7e-1aa2-4a9c-9a20-23d5d0e31e3a/tmpJXCXeo/06920985-47ae-44ad-84ba-e5e488e49df3/tZNLZlyEC5C61:/tmp:rw \ --volume=/home/nexcbu/tmp/toil-e757c11c-c96c-4f7a-b121-4c5cf38c0930-e272bc7e-1aa2-4a9c-9a20-23d5d0e31e3a/tmpJXCXeo/06920985-47ae-44ad-84ba-e5e488e49df3/tmpnH13ck.tmp:/var/spool/cwl/tmpjX8uDE.sorted.bam.bai:ro \ --volume=/home/nexcbu/tmp/toil-e757c11c-c96c-4f7a-b121-4c5cf38c0930-e272bc7e-1aa2-4a9c-9a20-23d5d0e31e3a/tmpJXCXeo/06920985-47ae-44ad-84ba-e5e488e49df3/tmpIZAXjc.tmp:/var/spool/cwl/tmpjX8uDE.sorted.bam:ro \ --workdir=/var/spool/cwl \ --read-only=true \ --user=1000:1000 \ --rm \ --env=TMPDIR=/tmp \ --env=HOME=/var/spool/cwl \ --env=PATH=/usr/local/bin/:/usr/bin:/bin \ biowardrobe2/samtools:v1.4 \ /bin/sh \ -c \ 'bash' '-c' '#!/bin/bash if [ "$0" = True ] then samtools rmdup "${@:1}" else echo "Skip samtools rmdup " ${@:1} fi ' 'False' '-s' '/var/spool/cwl/tmpjX8uDE.sorted.bam' 'tmpwadNA3.tmp' > tmpwadNA3.tmp.rmdup 2>&1 INFO:cwltool:[job samtools-rmdup.cwl] /home/nexcbu/tmp/out_tmpdir4VcbVf$ docker \ run \ -i \ --volume=/home/nexcbu/tmp/out_tmpdir4VcbVf:/var/spool/cwl:rw \ --volume=/home/nexcbu/tmp/toil-e757c11c-c96c-4f7a-b121-4c5cf38c0930-e272bc7e-1aa2-4a9c-9a20-23d5d0e31e3a/tmpJXCXeo/06920985-47ae-44ad-84ba-e5e488e49df3/tZNLZlyEC5C61:/tmp:rw \ --volume=/home/nexcbu/tmp/toil-e757c11c-c96c-4f7a-b121-4c5cf38c0930-e272bc7e-1aa2-4a9c-9a20-23d5d0e31e3a/tmpJXCXeo/06920985-47ae-44ad-84ba-e5e488e49df3/tmpnH13ck.tmp:/var/spool/cwl/tmpjX8uDE.sorted.bam.bai:ro \ --volume=/home/nexcbu/tmp/toil-e757c11c-c96c-4f7a-b121-4c5cf38c0930-e272bc7e-1aa2-4a9c-9a20-23d5d0e31e3a/tmpJXCXeo/06920985-47ae-44ad-84ba-e5e488e49df3/tmpIZAXjc.tmp:/var/spool/cwl/tmpjX8uDE.sorted.bam:ro \ --workdir=/var/spool/cwl \ --read-only=true \ --user=1000:1000 \ --rm \ --env=TMPDIR=/tmp \ --env=HOME=/var/spool/cwl \ --env=PATH=/usr/local/bin/:/usr/bin:/bin \ biowardrobe2/samtools:v1.4 \ /bin/sh \ -c \ 'bash' '-c' '#!/bin/bash if [ "$0" = True ] then samtools rmdup "${@:1}" else echo "Skip samtools rmdup " ${@:1} fi ' 'False' '-s' '/var/spool/cwl/tmpjX8uDE.sorted.bam' 'tmpwadNA3.tmp' > tmpwadNA3.tmp.rmdup 2>&1 [job samtools-rmdup.cwl] Job error: tools/samtools-rmdup.cwl:99:3: Error collecting output for parameter 'rmdup_output': :1:1: Did not find output file with glob pattern: '[u'tmpwadNA3.tmp']' ERROR:cwltool:[job samtools-rmdup.cwl] Job error: tools/samtools-rmdup.cwl:99:3: Error collecting output for parameter 'rmdup_output': :1:1: Did not find output file with glob pattern: '[u'tmpwadNA3.tmp']' [job samtools-rmdup.cwl] completed permanentFail WARNING:cwltool:[job samtools-rmdup.cwl] completed permanentFail Traceback (most recent call last): File "/home/nexcbu/tools/venv/lib/python2.7/site-packages/toil/worker.py", line 313, in main job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore) File "/home/nexcbu/tools/venv/lib/python2.7/site-packages/toil/job.py", line 1299, in _runner returnValues = self._run(jobGraph, fileStore) File "/home/nexcbu/tools/venv/lib/python2.7/site-packages/toil/job.py", line 1244, in _run return self.run(fileStore) File "/home/nexcbu/tools/venv/lib/python2.7/site-packages/toil/cwl/cwltoil.py", line 451, in run raise cwltool.errors.WorkflowException(status) WorkflowException: permanentFail ERROR:toil.worker:Exiting the worker because of a failed job on host wfexecutor.nexus.ethz.ch WARNING:toil.jobGraph:Due to failure we are reducing the remaining retry count of job 'file:///home/nexcbu/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/tools/samtools-rmdup.cwl' bash -c H/A/jobce6_cU with ID H/A/jobce6_cU to 0 <========= ```
Hi Michael, I looked at the documentation from Bogdan and unfortunately I am not able to find the github issue links from this readme file (https://www.synapse.org/#!Synapse:syn10208944). Both links are broken and could you pass me the issue number or a place I can see the changes. https://www.synapse.org/#!Error:7b226d657373616765223a22446964206e6f742066696e642061206d6174636820666f7220616c6961733a2055524c5f504c414345484f4c444552222c226c6162656c223a22536f727279227d https://www.synapse.org/#!Error:7b226d657373616765223a22446964206e6f742066696e642061206d6174636820666f7220616c6961733a2055524c5f504c414345484f4c444552222c226c6162656c223a22536f727279227d Regards, Vipin
Hi Vipin To run it with Rabix you can follow Bogdan's instructions https://www.synapse.org/#!Synapse:syn10208944. He already figured out which changes should be made to satisfy Rabix's requirements. As for the Toil, send me STDERR and we'll try to find the solution Michael
Hi Micheal, May be it is too much, but I just want to check with you. Did you try your workflow with `Toil` platform? I tried and I got a permanent Fail message when I ran the workflow. If you are interested to the see the STDERR I am happy to share with you. Regards, Vipin
Hi Micheal, I have one more question to you. I would like to know whether it possible to run your workflow with `rabix` runner? I tried to run as follows: ```shell ~/tools/rabix-cli-1.0.0/rabix --tmpdir-prefix ~/tmp/ --tmp-outdir-prefix ~/tmp/ biowardrobe_chipseq_se.cwl biowardrobe_chipseq_se.json ``` but returns me the error message: ```shell [2017-09-24 13:57:08.748] [ERROR] Error: file://biowardrobe_chipseq_se.cwl is not a valid app! Unknown error when parsing the app! ``` Let me know if you have any fix for this. Regards, Vipin
Thank you Micheal for the quick fix! Yes the solution worked. I opted for the option 2 and I will update this to my README. ```shell cat results.json ``` ``` { "steps": { "macs2_callpeak_forced": "true", "macs2_callpeak": "true", "samtools_sort_index_after_rmdup": "true", "bam_to_bigwig": "true", "macs_island_count": "true", "samtools_sort_index": "true", "bowtie_aligner": "true", "samtools_rmdup": "true", "fastx_quality_stats": "true", "bamtools_stats": "true" }, "overall": "true" } ``` Regards, Vipin
Hey, I have a solution! You have two options: 1. Downgrade your cwltool to **1.0.20170217172322**, which I used for testing my workflow 2. Update `biowardrobe_chipseq_se/tools/samtools-sort-index.cwl` with ``` outputs: if (inputs.sort_input.secondaryFiles && inputs.trigger == false){ return inputs.sort_input.secondaryFiles; } else { - return self.location + ext(); + return self.basename+ext(); } } ``` If you chose the second option, document these changes in a description that you will write after submission. This problem is caused by the slightly different interpretation of secondary files in a newer version of cwltool. Michael
Hi Michael, Thank you for the quick response. Here is the version of my runner `cwltool 1.0.20170828135420`. Sorry I forgot to attach the contents from log.txt file: cat log.txt ``` samtools idxstats: fail to load index for "/var/lib/cwl/stgbbce3dc3-04e6-488c-9b36-c6007541c63b/check_dir/SRR1198790.sorted.bam" LOAD control directory Found BAM file SRR1198790.sorted.bam (/var/lib/cwl/stgbbce3dc3-04e6-488c-9b36-c6007541c63b/check_dir/controls/SRR1198790.sorted.bam) Replaced /var/lib/cwl/stgbbce3dc3-04e6-488c-9b36-c6007541c63b/check_dir/controls/SRR1198790.sorted.bam --> /var/spool/cwl/9ef7430e-5410-4ee5-91ef-63c715573353.idxstats LOAD output directory Found BAM file SRR1198790.sorted.bam (/var/lib/cwl/stgbbce3dc3-04e6-488c-9b36-c6007541c63b/check_dir/SRR1198790.sorted.bam) Command 'samtools idxstats /var/lib/cwl/stgbbce3dc3-04e6-488c-9b36-c6007541c63b/check_dir/SRR1198790.sorted.bam > 1e98d72c-0eee-4f12-a1ad-473b7c163fe9.idxstats' returned non-zero exit status 1 PROCESS - SRR1198790.sorted_peaks.xls (/var/lib/cwl/stgbbce3dc3-04e6-488c-9b36-c6007541c63b/check_dir/controls/SRR1198790.sorted_peaks.xls) Ok - SRR1198790.sam.log (/var/lib/cwl/stgbbce3dc3-04e6-488c-9b36-c6007541c63b/check_dir/controls/SRR1198790.sam.log) Ok - SRR1198790.sorted.sorted.bigwig (/var/lib/cwl/stgbbce3dc3-04e6-488c-9b36-c6007541c63b/check_dir/controls/SRR1198790.sorted.sorted.bigwig) Ok - SRR1198790.fastq.fastxstat (/var/lib/cwl/stgbbce3dc3-04e6-488c-9b36-c6007541c63b/check_dir/controls/SRR1198790.fastq.fastxstat) Ok - SRR1198790.sorted.bam.bai (/var/lib/cwl/stgbbce3dc3-04e6-488c-9b36-c6007541c63b/check_dir/controls/SRR1198790.sorted.bam.bai) Fail: missing output file SRR1198790.sorted.bam.bai - SRR1198790.sam.stat (/var/lib/cwl/stgbbce3dc3-04e6-488c-9b36-c6007541c63b/check_dir/controls/SRR1198790.sam.stat) Ok - SRR1198790.sorted.bam (/var/spool/cwl/9ef7430e-5410-4ee5-91ef-63c715573353.idxstats) Fail: size comparison ``` I have used `--debug` option during the workflow run. I didn't find anything failed message in stdout. I found a warning message in the beginning as follows: ``` Resolved 'biowardrobe_chipseq_se.cwl' to 'file:///home/wfrunner/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se/biowardrobe_chipseq_se.cwl' biowardrobe_chipseq_se.cwl:1:1: unrecognized extension field `http://schema.org/name`. Did you include a $schemas section? biowardrobe_chipseq_se.cwl:1:1: unrecognized extension field `http://schema.org/downloadUrl`. Did you include a $schemas section? biowardrobe_chipseq_se.cwl:1:1: unrecognized extension field `http://schema.org/codeRepository`. Did you include a $schemas section? biowardrobe_chipseq_se.cwl:1:1: unrecognized extension field `http://schema.org/license`. Did you include a $schemas section? biowardrobe_chipseq_se.cwl:1:1: unrecognized extension field `http://schema.org/isPartOf`. Did you include a $schemas section? biowardrobe_chipseq_se.cwl:1:1: unrecognized extension field `http://schema.org/creator`. Did you include a $schemas section? biowardrobe_chipseq_se.cwl:1:1: unrecognized extension field `http://schema.org/about`. Did you include a $schemas section? No handlers could be found for logger "rdflib.term" ``` Hope this will help you, please let me know if you need any further information from my side. Cheers! Vipin
Hi Vipin Thank you for running **biowardrobe_chipseq_se** workflow and for your feedback. Could you please tell me the version of **cwltool** runner you use. **biowardrobe_chipseq_se_checker** also generates **log.txt**. This file will help me to find the reason why checker tool failed. The output of running **biowardrobe_chipseq_se** workflow with -**-debug** will be helpful too. Michael
Hello, I am using `cwltool` to run **biowardrobe_chipseq_se** workflow on RHEL 7 workstation. I have downloaded the workflow input files and ran the workflow without any error. ```shell cd ~/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se cwltool --tmpdir-prefix ~/tmp/ --cachedir ~/tmp/cache --debug --non-strict ~/synapse_utils/dockstore-tool-synapse-get.cwl ~/config_files/biowardrobe_chipseq_se_get.cwl.json cwltool --tmpdir-prefix ~/tmp/ --cachedir ~/tmp/cache --debug --non-strict biowardrobe_chipseq_se.cwl biowardrobe_chipseq_se.json ```   But when I validated the output before submitting the result, I found few `false` items in the result comparison file. ```shell cd ~/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se cwltool --tmpdir-prefix ~/tmp/ --cachedir ~/tmp/cache --debug --non-strict biowardrobe_chipseq_se_checker.cwl biowardrobe_chipseq_se_checker.json ```   Checking the results: ```shell cd ~/dream_challenge/2017/workflow_execution/workflows/biowardrobe_chipseq_se cat results.json ``` ```json { "steps": { "macs2_callpeak_forced": "true", "macs2_callpeak": "true", "samtools_sort_index_after_rmdup": "false", "bam_to_bigwig": "true", "macs_island_count": "true", "samtools_sort_index": "false", "bowtie_aligner": "false", "samtools_rmdup": "false", "fastx_quality_stats": "true", "bamtools_stats": "true" }, "overall": "false" } ``` I didn't see any particular error message on my console, it will be good if you can point me anything which I missed in trace backing the error. Thank you, Vipin

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