Leader job attempts to run non-existent shell script

[sbresnahan]

Describe the bug

Running the example on the README (caper hpc submit atac.wdl -i "${INPUT_JSON}" --singularity --leader-job-name ANY_GOOD_LEADER_JOB_NAME) submits leader job to LSF, but immediately fails with "exit code 127" due to a shell script not being found:

/home/stbresnahan/.lsbatch/1724344190.9833039: line 8: **/rsrch5/home/epi/stbresnahan/o7cw6oj0.sh: No such file or directory**

------------------------------------------------------------
Sender: LSF System <[email protected]>
Subject: Job 9833039: <CAPER_ANY_GOOD_LEADER_JOB_NAME> in cluster <seadragon_cluster> Exited

Job <CAPER_ANY_GOOD_LEADER_JOB_NAME> was submitted from host <ldragon5> by user <stbresnahan> in cluster <seadragon_cluster> at Thu Aug 22 11:29:50
Job was executed on host(s) <cdragon148.cm.cluster>, in queue <long>, as user <stbresnahan> in cluster <seadragon_cluster> at Thu Aug 22 11:29:52 2024
</home/stbresnahan> was used as the home directory.
</rsrch5/home/epi/stbresnahan/scratch/atac-seq-pipeline> was used as the working directory.
Started at Thu Aug 22 11:29:52 2024
Terminated at Thu Aug 22 11:29:55 2024
Results reported at Thu Aug 22 11:29:55 2024

Your job looked like:

------------------------------------------------------------
# LSBATCH: User input
/rsrch5/home/epi/stbresnahan/o7cw6oj0.sh
------------------------------------------------------------

Exited with exit code 127.

OS/Platform

• OS/Platform: linux-gnu with LSF
• Pipeline version: v2.2.3

Caper configuration file

backend=lsf

lsf-leader-job-resource-param=-W 48:00 -M 48 -q long -o /rsrch5/home/epi/stbresnahan/scratch/ENCODE_ATAC -e /rsrch5/home/epi/stbresnahan/scratch/ENCODE_ATAC
lsf-resource-param=${"-o /rsrch5/home/epi/stbresnahan/scratch/ENCODE_ATAC"} ${"-e /rsrch5/home/epi/stbresnahan/scratch/ENCODE_ATAC"} ${"-n 10"} ${"-M 48"} ${"-W 48:00"} ${"-q long"}

# 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=/rsrch5/home/epi/stbresnahan/scratch/ENCODE_ATAC

cromwell=/rsrch5/home/epi/stbresnahan/.caper/cromwell_jar/cromwell-82.jar
womtool=/rsrch5/home/epi/stbresnahan/.caper/womtool_jar/womtool-82.jar

Input JSON file

https://storage.googleapis.com/encode-pipeline-test-samples/encode-atac-seq-pipeline/ENCSR356KRQ_subsampled.json

[ljl-suosi]

Hi sbresnahan, I’m experiencing the same problem you mentioned and was curious if you’ve found a solution. If you have, could you kindly share how you resolved it?

[sbresnahan]

Hi sbresnahan, I’m experiencing the same problem you mentioned and was curious if you’ve found a solution. If you have, could you kindly share how you resolved it?

No solution yet.