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jiarong / VirSorter2

customizable pipeline to identify viral sequences from (meta)genomic data
GNU General Public License v2.0
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Stuck on step 3 #153

Open dnolin13 opened 1 year ago

dnolin13 commented 1 year ago

Hello, I have been running VS2 and my code has been running the classify step for over 2 days now, and for ~24 hrs it has been stuck at the step running the script "add-extra-to-lt2gene-fasta-header.py". Just wondering if this is normal, my contig file is 7.2 GB. Thanks so much, any help is much appreciated!

command from "top" python /home/delaney/miniconda3/envs/vs2/lib/python3.9/site-packages/virsorter/./scripts/add-extra-to-lt2gene-fasta-header.py iter-0/viral-lt2gene-w-hallmark.fa.tmp iter-0/dsDNAphage/all.pdg.gff,iter-0/ssDNA/all.pdg.gff iter-0/dsDNAphage/all.pdg.hmm.tax,iter-0/ssDNA/all.pdg.hmm.tax dsDNAphage,ssDNA

jiarong commented 1 year ago

Hi, it's not normal to see the add-extra-to-lt2gene-fasta-header.py to run so long. You can check there are any hardware issues, eg. hitting disk space or file number limits?

dnolin13 commented 1 year ago

There shouldn't be! It's running on our remote server but usage is consistently below ~60% and there is enough storage for the files