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 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
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: Processexecute_jobs (332)terminated with an error exit status (127) -- Execution is retried (2) [9c/4a16b7] NOTE: Processexecute_jobs (625)terminated with an error exit status (127) -- Execution is retried (3) [c7/851fa8] NOTE: Processexecute_jobs (678)terminated with an error exit status (127) -- Execution is retried (2) [ea/b72980] NOTE: Processexecute_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