Error in rule SignalPN_aggregate
Hello,
I am running a large file and I got this error:
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[Tue Apr 5 20:11:45 2022] Error in rule SignalPN_aggregate: jobid: 289 output: /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/contigs_Argal/gramn_summary.signalp5 shell: cat /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/Gram-/contigs_Argal/group_1_summary.signalp5 /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/Gram-/contigs_Argal/group_2_summary.signalp5
Then there is a whole list of files that ends with:
/data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/Gram-/contigs_Argal/group_3087_summary.signalp5 > /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/contigs_Argal/gramn_summary.signalp5 (exited with non-zero exit code) [Tue Apr 5 20:11:55 2022] Finished job 3376. 13147 of 14486 steps (91%) done [Tue Apr 5 20:12:03 2022] Finished job 2839. 13148 of 14486 steps (91%) done [Tue Apr 5 20:14:28 2022] Finished job 206. 13149 of 14486 steps (91%) done
This is the second time I have tried this and the last time I got a similar error but it was:
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[Fri Apr 1 05:13:24 2022] Error in rule SignalPP_aggregate: jobid: 1644 output: /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/contigs_Argal/gramp_summary.signalp5 shell: cat /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/Gram+/contigs_Argal/group_1_summary.signalp5... /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/Gram+/contigs_Argal/group_3087_summary.signalp5 > /data2/ekantor/Argal/PathoFact_results_Argal/PathoFact_intermediate/SignalP/contigs_Argal/gramp_summary.signalp5 (exited with non-zero exit code) [Fri Apr 1 05:13:25 2022] Finished job 7819. 13271 of 14604 steps (91%) done [Fri Apr 1 05:15:16 2022] Finished job 124. 13272 of 14604 steps (91%) done
Again, it stopped after that message and there was no progress for a few days. I force killed the program after that but I do not have the log file anymore unfortunately. I reinstalled PathoFact afterwards and ran the test successfully before trying again.
I am running conda version 4.11.0. I installed snakemake newest version 7.3.4 via mamba from the installation instructions on the snakemake docs. I used 12 cores for the most recent run and 10 cores for the one before it. Could this have something to do with the size of the file?
Thank you, Ella