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ENCODE-DCC / atac-seq-pipeline

ENCODE ATAC-seq pipeline
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ERROR when Validating WDL/inputs/imports with Womtool #395

Open wangxiangxiu opened 2 years ago

wangxiangxiu commented 2 years ago

Describe the bug

caper.cromwell.WomtoolValidationFailed: RC=1

OS/Platform

Caper configuration file

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

backend=local

# Local directory for localized files and Cromwell's intermediate files.
# If not defined then Caper will make .caper_tmp/ on CWD or `local-out-dir`.
# /tmp is not recommended since Caper store localized data files here.
local-loc-dir=/home/data/t0302015/Shear_stress_data/ATAC_seq/git_pipeline/caper_tmp

cromwell=/home/data/t0302015/.caper/cromwell_jar/cromwell-82.jar
womtool=/home/data/t0302015/.caper/womtool_jar/womtool-82.jar

Input JSON file

Paste contents of your input JSON file.

{
        "atac.pipeline_type" : "atac",
        "atac.genome_tsv" : "https://storage.googleapis.com/encode-pipeline-genome-data/genome_tsv/v4/hg38.tsv",
        "atac.fastqs_rep1_R1" : ["/home/data/t0302015/Shear_stress_data/ATAC_seq/SRR8734980_1.fastq.gz"],
        "atac.fastqs_rep1_R2" : ["/home/data/t0302015/Shear_stress_data/ATAC_seq/SRR8734980_2.fastq.gz"],
        "atac.fastqs_rep2_R1" : ["/home/data/t0302015/Shear_stress_data/ATAC_seq/SRR8734981_1.fastq.gz"],
        "atac.fastqs_rep2_R2" : ["/home/data/t0302015/Shear_stress_data/ATAC_seq/SRR8734981_2.fastq.gz"],
        "atac.paired_end" : true,
        "atac.auto_detect_adapter" : true,
        "atac.enable_xcor" : true,
        "atac.title" : "AdNULL samples",
        "atac.description" : "ATAC-seq on HUVECs"
}

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) with caper list and run caper debug [WORKFLOW_ID].

Paste troubleshooting result.

when run 'caper run /home/data/t0302015/bin/atac-seq-pipeline/atac.wdl --dry-run'
the same issue as present
imk1 commented 2 years ago

I am having the same problem, and I am running this on a slurm cluster.

imk1 commented 2 years ago

@wangxiangxiu I think that I solved the problem. Here is what I did:

  1. Uninstalled caper
  2. Deleted my .caper directory
  3. Uninstalled jdk
  4. Installed openjdk version 11.0.13
  5. Reinstalled caper
wangxiangxiu commented 2 years ago

@imk1 Thanks for your suggestions~ I solved it by installing Java SE 11. Thx~