ownHMM_library.R script fails with empty input files
rule R_script
from the Combine_Toxin_SignalP.smk
throws an error (below) if the input file is empty:
RuleException:
CalledProcessError in line 29 of /mnt/irisgpfs/users/sbusi/apps/PathoFact/rules/Toxin/Combine_Toxin_SignalP.smk:
Command 'source /scratch/users/sbusi/tools/miniconda3/bin/activate '/mnt/irisgpfs/users/sbusi/apps/PathoFact/.snakemake/conda/c6514c6c'; set -euo pipefail; Rscript --vanilla /mnt/irisgpfs/users/sbusi/apps/PathoFact/.snakemake/scripts/tmpxk7hk0_a.ownHMM_library.R' returned non-zero exit status 1.
File "/mnt/irisgpfs/users/sbusi/apps/PathoFact/rules/Toxin/Combine_Toxin_SignalP.smk", line 29, in __rule_R_script
File "/scratch/users/sbusi/tools/miniconda3/envs/PathoFact/lib/python3.6/concurrent/futures/thread.py", line 56, in run
Failed file example:
==> /work/projects/amrwd/results/PathoFact/PathoFact_space_output/PathoFact_intermediate/TOXIN/HMM_toxin/IG4SW-M_F1_L4_NORM_GC.Input_HMM_R.csv <==
Query_sequence HMM_Name Significance_Evalue Score
#Toxin
Working file example:
==> /work/projects/amrwd/results/PathoFact/PathoFact_space_output/PathoFact_intermediate/TOXIN/HMM_toxin/IIF1SW-M_F2_L1_NORM_FLT.Input_HMM_R.csv <==
Query_sequence HMM_Name Significance_Evalue Score
#Toxin
0000010215 K01114_780_95_420 3.8e-78 262.5
0000013630 K01186_172 5.1e-103 344.2
0000012319 K01186_172 1.7e-08 33.1
0000019322 K01197_243 0.29 8.8
0000018125 K03699_483 2.8e-112 374.6
0000018124 K03699_483 2.3e-71 239.7
0000010016 K03699_483 1.8e-63 213.7
0000011228 K03699_483 1.5e-62 210.6