CalledProcessError in line 29 of Combine_Toxin_SignalP.smk:
I run PathoFact with snakemake -s Snakefile --use-conda --rerun-incomplete --cores 28 -p
and encountered a CalledProcessError. The run is not interrupted but remains at the current step for two days now (with average CPU usage of 15). I have seen another user experiencing a similar issue (#90 (closed)) but all my FASTA files contain more than one contig. What effect has the CalledProcessError on the final outcome? Thanks!
RuleException:
CalledProcessError in line 29 of /pathofact/PathoFact/rules/Toxin/Combine_Toxin_SignalP.smk:
Command 'source /miniconda3/bin/activate '/pathofact/PathoFact/.snakemake/conda/fb1f3485'; set -euo pipefail; Rscript --vanilla /pathofact/PathoFact/.snakemake/scripts/tmp23lfmhsd.ownHMM_library.R' returned non-zero exit status 1.
File "/protect/pathofact/PathoFact/rules/Toxin/Combine_Toxin_SignalP.smk", line 29, in __rule_R_script
File "/miniconda3/envs/PathoFact/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Removing output files of failed job R_script since they might be corrupted:
/pathofact/contigs_raw_files/PathoFact_results/PathoFact_report/Toxin_gene_library_ABC.tsv
[Sun Jul 24 10:14:54 2022]
Finished job 37616.
31250 of 33263 steps (94%) done
[Sun Jul 24 10:14:58 2022]
Finished job 289.
31251 of 33263 steps (94%) done