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Gitlab will go into maintenance Friday 3rd February from 9:00 to 10:00

  • Laura Denies
  • PathoFact
  • Issues
  • #69
Closed
Open
Issue created May 05, 2021 by Owenke247@Owenke247

Config file config.yaml not found

Script: snakemake -s /proj/spteds/spted00/software/PathoFact/Snakefile --use-conda --cores 1 --configfile /proj/spteds/spted00/software/PathoFact/configfile.yaml

Error report: WorkflowError in line 3 of /proj/spteds/spted00/software/PathoFact/Snakefile: Config file config.yaml not found. File "/proj/spteds/spted00/software/PathoFact/Snakefile", line 3, in

configfile.yaml: pathofact: sample: ["M.036","R3.099"] # requires user input project: "PathoFact_res" # requires user input datadir: "/proj/spteds/spted00/Project/CDI/pathfact/contig" # requires user input workflow: "complete" #options: "complete", "AMR", "Tox", "Vir" size_fasta: 10000 #Adjustable to preference scripts: "scripts" signalp: "/proj/spteds/spted00/software/PathoFact/signalP/signalp-5.0b/bin" # requires user input deepvirfinder: "submodules/DeepVirFinder/dvf.py" tox_hmm: "databases/toxins/combined_Toxin.hmm" tox_lib: "databases/library_HMM_Toxins.csv" tox_threshold: 40 #Bitscore threshold of the toxin prediction, adjustable by user to preference vir_hmm: "databases/virulence/Virulence_factor.hmm" vir_domains: "databases/models_and_domains" plasflow_threshold: 0.7 plasflow_minlen: 1000 runtime: short: "00:10:00" medium: "01:00:00" long: "02:00:00" mem: normal_mem_per_core_gb: "4G" big_mem_cores: 4 big_mem_per_core_gb: "30G"

Your comments will be much appreciated.

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