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hillerlab / make_lastz_chains

Portable solution to generate genome alignment chains using lastz
MIT License
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NOTE: Process `execute_jobs (64)` terminated with an error exit status (2) -- Execution is retried (1) #18

Closed gunjanpandey closed 11 months ago

gunjanpandey commented 1 year ago

Could you please help with?

N E X T F L O W  ~  version 21.10.1
Launching `XXXXX/TEMP_run.lastz/lastz_chickenNB/script.nf` [maniac_yonath] - revision: 20fae9dc0e
[-        ] process > execute_jobs -

executor >  local (17)
[37/e70339] process > execute_jobs (4) [  0%] 0 of 190

executor >  local (49)
[b9/89be59] process > execute_jobs (19) [  0%] 0 of 225

executor >  local (50)
[2a/0acf5d] process > execute_jobs (46) [  0%] 1 of 226, failed: 1, retries: 1
[2a/0acf5d] NOTE: Process `execute_jobs (46)` terminated with an error exit status (2) -- Execution is retried (1)

executor >  local (51)
[3c/cbb0c0] process > execute_jobs (51) [  0%] 2 of 227, failed: 2, retries: 2
[d2/aff088] NOTE: Process `execute_jobs (64)` terminated with an error exit status (2) -- Execution is retried (1)
BoBo2021jenny commented 1 year ago

Hi The error is ： N E X T F L O W ~ version 22.10.0 Launching /data/zhangbo/software/make_lastz_chains/Tele2Ppup/TEMP_run.lastz/lastz_PpupTele/script.nf [soggy_wescoff] DSL1 - revision: ad8af5e7ff /tmp/nxf-11857650355126268811 /software/miniconda3/envs/NF/lib/python3.8/site-packages/py_nf/py_nf.py:404: UserWarning: Nextflow pipeline lastz_PpupTele failed! Execute function returns 1. warnings.warn(msg) Could you please help me solve the problem ?

kirilenkobm commented 1 year ago

Hi @BoBo2021jenny

To solve the DSL issue please downgrade nextflow below 22.12.0. I did not have enough capacity to solve the issue in this pipeline, but it it is planned.

kirilenkobm commented 11 months ago

Hi all. Today or tomorrow I will release and updated pipeline version where the nextflow problems are sorted out. If you still experience any troubles pls create a new issue.