Open wangxiangxiu opened 2 years ago
I am having the same problem, and I am running this on a slurm cluster.
@wangxiangxiu I think that I solved the problem. Here is what I did:
@imk1 Thanks for your suggestions~ I solved it by installing Java SE 11. Thx~
Describe the bug
caper.cromwell.WomtoolValidationFailed: RC=1
OS/Platform
Caper configuration file
Paste contents of
~/.caper/default.conf
.Input JSON file
Paste contents of your input JSON file.
caper run /home/data/t0302015/bin/atac-seq-pipeline/atac.wdl -i sampled.json --singularity caper run /home/data/t0302015/bin/atac-seq-pipeline/atac.wdl -i sampled.json --conda
2022-08-17 13:33:09,147|caper.caper_workflow_opts|INFO| Singularity image found in WDL metadata. wdl=/home/data/t0302015/bin/atac-seq-pipeline/atac.wdl, s=https://encode-pipeline-singularity-image.s3.us-west-2.amazonaws.com/atac-seq-pipeline_v2.2.0.sif 2022-08-17 13:33:09,160|caper.cromwell|INFO| Validating WDL/inputs/imports with Womtool... 2022-08-17 13:33:09,173|caper.nb_subproc_thread|ERROR| Subprocess failed. returncode=1 Traceback (most recent call last): File "/home/data/t0302015/miniconda3/bin/caper", line 13, in
main()
File "/home/data/t0302015/miniconda3/lib/python3.9/site-packages/caper/cli.py", line 713, in main
return runner(parsed_args, nonblocking_server=nonblocking_server)
File "/home/data/t0302015/miniconda3/lib/python3.9/site-packages/caper/cli.py", line 255, in runner
subcmd_run(c, args)
File "/home/data/t0302015/miniconda3/lib/python3.9/site-packages/caper/cli.py", line 386, in subcmd_run
thread = caper_runner.run(
File "/home/data/t0302015/miniconda3/lib/python3.9/site-packages/caper/caper_runner.py", line 462, in run
self._cromwell.validate(wdl=wdl, inputs=inputs, imports=imports)
File "/home/data/t0302015/miniconda3/lib/python3.9/site-packages/caper/cromwell.py", line 160, in validate
raise WomtoolValidationFailed(
caper.cromwell.WomtoolValidationFailed: RC=1
STDERR=Error: Invalid or corrupt jarfile /home/data/t0302015/.caper/womtool_jar/womtool-82.jar
" I retry run 'caper init local' or re-download womtool-82.jar, the same issue always present "
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) withcaper list
and runcaper debug [WORKFLOW_ID]
.Paste troubleshooting result.