The pipeline crashed Error

[vinitamehlawat]

Hi Authors

I tried the V1 of this pipeline but got the following error.

[d1/4aa5ff] NOTE: Process execute_jobs (334) terminated with an error exit status (127) -- Execution is retried (2)
[b5/4f2f5d] NOTE: Process execute_jobs (332) terminated with an error exit status (127) -- Execution is retried (2)
[9c/4a16b7] NOTE: Process execute_jobs (625) terminated with an error exit status (127) -- Execution is retried (3)
[c7/851fa8] NOTE: Process execute_jobs (678) terminated with an error exit status (127) -- Execution is retried (2)
[ea/b72980] NOTE: Process execute_jobs (719) terminated with an error exit status (127) -- Execution is retried (2)
Error executing process > 'execute_jobs (67)'

Caused by:
Process execute_jobs (67) terminated with an error exit status (127)

Command executed:

/scrfs/storage/vlamba/home/make_lastz_chains-1.0.0/test_out2/TEMP_run.fillChain/runRepeatFiller.sh /scrfs/storage/vlamba/home/make_lastz_chains-1.0.0/test_out2/TEMP_run.fillChain/jobs/infillChain_158

Command exit status:
127

Command output:
..calling RepeatFiller:

Command error:
/scrfs/storage/vlamba/home/make_lastz_chains-1.0.0/test_out2/TEMP_run.fillChain/runRepeatFiller.sh: line 12: --workdir: command not found

Work dir:
/scrfs/storage/vlamba/home/make_lastz_chains-1.0.0/test_out2/TEMP_run.fillChain/fillChain_targetquery/work/21/08e1e7d44488e6d8c672adaff8864f

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named .command.sh

/home/vlamba/python3.14/lib/python3.9/site-packages/py_nf/py_nf.py:404: UserWarning: Nextflow pipeline fillChain_targetquery failed! Execute function returns 1.
warnings.warn(msg)
Uncaught exception from user code:
Command failed:
/scrfs/storage/vlamba/home/make_lastz_chains-1.0.0/test_out2/TEMP_run.fillChain/doFillChain.sh
HgAutomate::run('/scrfs/storage/vlamba/home/make_lastz_chains-1.0.0/test_out2/...') called at /scrfs/storage/vlamba/home/make_lastz_chains-1.0.0/doLastzChains/HgRemoteScript.pm line 117
HgRemoteScript::execute('HgRemoteScript=HASH(0xc3cb78)') called at /scrfs/storage/vlamba/home/make_lastz_chains-1.0.0/doLastzChains/doLastzChain.pl line 735
main::doFillChains() called at /scrfs/storage/vlamba/home/make_lastz_chains-1.0.0/doLastzChains/HgStepManager.pm line 169
HgStepManager::execute('HgStepManager=HASH(0xc39a18)') called at /scrfs/storage/vlamba/home/make_lastz_chains-1.0.0/doLastzChains/doLastzChain.pl line 877
Error!!! Output file /scrfs/storage/vlamba/home/make_lastz_chains-1.0.0/test_out2/target.query.allfilled.chain.gz not found!
The pipeline crashed. Please contact developers by creating an issue at:
https://github.com/hillerlab/make_lastz_chains