Error in rule R_script:
Dear PathoFact developers,
Thanks for your effort developping that very usefull tool.
I am trying to use PathoFact using already annotated contigs i.e., ORFs https://gitlab.lcsb.uni.lu/laura.denies/PathoFact/-/tree/orf
.
I prepared the necessary files of a toy dataset: 1 sample of 1 contig and 2 orfs:
and I am using the enclosed config.yaml
I run the pipeline using snakemake -s Snakefile --use-conda --reason --cores 2 --configfile test_orfs_human1_1cont/config.yaml
everything went smooth until the following error - gene_table_library.log 2022-06-16T202537.905206.snakemake.log
[Thu Jun 16 20:26:42 2022]
Error in rule R_script:
jobid: 2
output: /datadrive05/Flo/tools/PathoFact_orf/test_orfs_human1_1cont/PathoFact_results_orf/PathoFact_report/Toxin_gene_library_sample_megahit_253073_report.tsv, /datadrive05/Flo/tools/PathoFact_orf/test_orfs_human1_1cont/PathoFact_results_orf/PathoFact_report/Toxin_prediction_sample_megahit_253073_report.tsv
log: /datadrive05/Flo/tools/PathoFact_orf/test_orfs_human1_1cont/PathoFact_results_orf/logs/sample_megahit_253073/gene_table_library.log (check log file(s) for error message)
conda-env: /datadrive05/Flo/tools/PathoFact_orf/.snakemake/conda/5f694c2e
RuleException:
CalledProcessError in line 29 of /datadrive05/Flo/tools/PathoFact_orf/rules/Toxin/Combine_Toxin_SignalP.smk:
Command 'source /home/constancias/miniconda3/envs/atlas-metagenomes/bin/activate '/datadrive05/Flo/tools/PathoFact_orf/.snakemake/conda/5f694c2e'; set -euo pipefail; Rscript --vanilla /datadrive05/Flo/tools/PathoFact_orf/.snakemake/scripts/tmp_ujrww4f.ownHMM_library.R' returned non-zero exit status 1.
File "/datadrive05/Flo/tools/PathoFact_orf/rules/Toxin/Combine_Toxin_SignalP.smk", line 29, in __rule_R_script
File "/home/constancias/miniconda3/envs/atlas-metagenomes/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:
/datadrive05/Flo/tools/PathoFact_orf/test_orfs_human1_1cont/PathoFact_results_orf/PathoFact_report/Toxin_gene_library_sample_megahit_253073_report.tsv
Activating conda environment: /datadrive05/Flo/tools/PathoFact_orf/.snakemake/conda/5f694c2e
Thanks for your help.
EDIT: My test dataset works well using AMR
and VIR
workflows.
EDIT2: Might be worth to add an orf test dataset for the https://gitlab.lcsb.uni.lu/laura.denies/PathoFact/-/tree/orf
branch.