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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 (605)` terminated with an error exit status (1) -- Execution is retried (1) #48

Open kuangzhuoran opened 7 months ago

kuangzhuoran commented 7 months ago

Hi ! I get this error if I use 'slurm' to submit the job, but I don't get it if I run the command directly on another server.

The programme was running normally for some time before this error occurred

The version of my nextflow is "version 23.10.0.5889", I am trying to downgrade nextflow below 22.12.0, as mentioned in "https://github.com/hillerlab/make_lastz_chains/issues/18".

The following is a portion of the run log file “ executor > local (627) [77/314080] process > execute_jobs (618) [ 25%] 620 of 2414

executor > local (627) [77/314080] process > execute_jobs (618) [ 25%] 621 of 2414

executor > local (628) [33/b87af4] process > execute_jobs (620) [ 25%] 621 of 2414

executor > local (629) [a0/766938] process > execute_jobs (605) [ 25%] 622 of 2415, failed: 1, retri... [a0/766938] NOTE: Process execute_jobs (605) terminated with an error exit status (1) -- Execution is retried (1)

executor > local (630) [37/c0e27f] process > execute_jobs (622) [ 25%] 623 of 2416, failed: 2, retri... [5f/02fc3c] NOTE: Process execute_jobs (606) terminated with an error exit status (1) -- Execution is retried (1)

executor > local (631) [8f/b9b0ef] process > execute_jobs (624) [ 25%] 624 of 2416, failed: 2, retri...

executor > local (632) [67/ff4d54] process > execute_jobs (623) [ 25%] 625 of 2416, failed: 2, retri...

”

kuangzhuoran commented 7 months ago

my command is "make_chains.py Ebaileyi Efontanierii Ebaileyi.softmasked.fa Efontanierii.softmasked.fa --project_dir Ebaileyi -f --chaining_memory 70"

Sorry for the inaccuracy of my description, I put "make_chains.py Ebaileyi Efontanierii Ebaileyi.softmasked.fa Efontanierii.softmasked.fa --project_dir Ebaileyi -f --chaining_memory 70" sbatch on it.

lynnyummy commented 4 months ago

Hi ! I get this error if I use 'slurm' to submit the job, but I don't get it if I run the command directly on another server.

The programme was running normally for some time before this error occurred

The version of my nextflow is "version 23.10.0.5889", I am trying to downgrade nextflow below 22.12.0, as mentioned in "#18".

The following is a portion of the run log file “ executor > local (627) [77/314080] process > execute_jobs (618) [ 25%] 620 of 2414

executor > local (627) [77/314080] process > execute_jobs (618) [ 25%] 621 of 2414

executor > local (628) [33/b87af4] process > execute_jobs (620) [ 25%] 621 of 2414

executor > local (629) [a0/766938] process > execute_jobs (605) [ 25%] 622 of 2415, failed: 1, retri... [a0/766938] NOTE: Process execute_jobs (605) terminated with an error exit status (1) -- Execution is retried (1)

executor > local (630) [37/c0e27f] process > execute_jobs (622) [ 25%] 623 of 2416, failed: 2, retri... [5f/02fc3c] NOTE: Process execute_jobs (606) terminated with an error exit status (1) -- Execution is retried (1)

executor > local (631) [8f/b9b0ef] process > execute_jobs (624) [ 25%] 624 of 2416, failed: 2, retri...

executor > local (632) [67/ff4d54] process > execute_jobs (623) [ 25%] 625 of 2416, failed: 2, retri...

”

I have similar error, executor > local (120) [1a/cecd5e] process > execute_jobs (120) [ 7%] 116 of 1645, failed: 25, retr... [3c/3fc378] NOTE: Processexecute_jobs (114)failed -- Execution is retried (1).

Does it mean that we need to specify more process time for the analysis? I even set a month... but failed...