The unknown task termination of multiple input genomes
Dear PathoFact team, Thanks for your such amazing work. My issue is that I got unknown job termination when I run PathoFact with multiple input genomes.
- Systems:Ubuntu 20.04.1 LTS
- Snakemake 5.5.4
- Python 3.6.4
command
nohup time snakemake -s Snakefile --configfile config.yaml --cores --use-conda -p &>iso.log&
config.yaml
(PathoFact) [u@h@PathoFact]$ cat config.yaml
pathofact:
sample: ["ISO_102-3","ISO_1051","ISO_108-2","ISO_10SP3-6-1","ISO_10SP3-6-3","ISO_130","ISO_138","ISO_167","ISO_174","ISO_194-2","ISO_197","ISO_20-2-1.001","ISO_20-2-1.002","ISO_32-3-3","ISO_83-1","ISO_83-3-2","ISO_95"]
project: PathoFact_results # requires user input
datadir: "/mnt/nfs/software/PathoFact/Test" # requires user input
workflow: "complete" #options: "complete", "AMR", "Tox", "Vir"
size_fasta: 10000 #Adjustable to preference
scripts: "scripts"
signalp: "/mnt/nfs/software/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: "10G"
big_mem_cores: 10
big_mem_per_core_gb: "30G"
Logs(part)
17 HMM_VIR_report
17 HMM_correct_format_2
17 HMM_correct_format_2_vir
17 HMM_correct_format_3
17 Plasmid_aggregate
34 Prodigal
17 R_script
17 SignalPN_aggregate
17 SignalPP_aggregate
17 aggregate_RGI
17 aggregate_VirFinder
17 aggregate_VirSorter
17 aggregate_deepARG
17 aggregate_signalP
1 all
17 clean_all
17 combine_AMR
17 combine_AMR_plasmid
17 combine_PathoFact
17 filter_seq
17 format_classifier
17 format_classifier_2
17 generate_ContigTranslation
34 generate_ID
17 generate_contigID
17 generate_translation
17 mapping_file
17 merge_SignalPVir
17 run_VirSorter
17 select
17 splitcontig
17 splitplasmid
34 splitting
17 splittingsignalP
664
767 of 857 steps (89%) done
[Tue May 11 10:01:52 2021]
Finished job 326.
768 of 857 steps (90%) done
[Tue May 11 10:02:28 2021]
Finished job 270.
769 of 857 steps (90%) done
[Tue May 11 10:03:00 2021]
Finished job 278.
770 of 857 steps (90%) done
[Tue May 11 10:03:22 2021]
Finished job 342.
771 of 857 steps (90%) done
[Tue May 11 10:05:56 2021]
Finished job 246.
772 of 857 steps (90%) done
[Tue May 11 10:07:47 2021]
Finished job 294.
773 of 857 steps (90%) done
It blocked on the 90% step, and I checked the output reasult no other error message. I am looking forward your reply, Thanks a lot