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ENCODE-DCC / atac-seq-pipeline

ENCODE ATAC-seq pipeline
MIT License
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conda environment #357

Open zhangpicb opened 2 years ago

zhangpicb commented 2 years ago

Describe the bug

conda environment python2

OS/Platform

Caper configuration file

Paste contents of ~/.caper/default.conf.

local-loc-dir=/picb/lilab3/pipeline/ENCODE_ATAC-seqPipline_v2.0.3/atac_pipeline_tmp

cromwell=/home/zhangpicb/.caper/cromwell_jar/cromwell-72.jar
womtool=/home/zhangpicb/.caper/womtool_jar/womtool-72.jar

Troubleshooting result

If you ran caper run without Caper server then Caper automatically runs a troubleshooter for failed workflows. Find troubleshooting result in the bottom of Caper's screen log.

If you ran caper submit with a running Caper server then first find your workflow ID (1st column) with caper list and run caper debug [WORKFLOW_ID].

Paste troubleshooting result.

2021-12-18 19:15:11,046|caper.cromwell|INFO| Workflow failed. Auto-troubleshooting...
2021-12-18 19:15:11,050|caper.nb_subproc_thread|ERROR| Cromwell failed. returncode=1
2021-12-18 19:15:11,050|caper.cli|ERROR| Check stdout in /picb/lilab3/zhangpicb/ATAC/mesp1/cromwell.out

I check this file /picb/lilab3/zhangpicb/ATAC/mesp1/cromwell.out and find conda run --name=encode-atac-seq-pipeline-python2 /bin/bash commond in this file, and I find conda run --name=encode-atac-seq-pipeline-python2 script is ok, but conda run --name=encode-atac-seq-pipeline-python2 /bin/bash script is wrong

leepc12 commented 2 years ago

Can you try this for debugging?

$ conda run --name=encode-atac-seq-pipeline-python2 /bin/bash -c "echo hello world"
zhangpicb commented 2 years ago

It works!