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padlocbio / padloc

Locate antiviral defence systems in prokaryotic genomes
MIT License
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Sample bug report #6

Closed leightonpayne closed 3 years ago

leightonpayne commented 3 years ago

Issue description:

Try to explain your problem...

Reproducible example:

Let us know what command(s) you ran (please attach your input files to help us recreate the issue)...

padloc --fna test/GCF_004358345.1.fna

Debug output:

Re-run PADLOC using the --debug flag to give a more detailed output...

$ padloc --faa test/GCF_004358345.1.fna --debug
(15:19:20) DEBUG  >>  $FAA_FILE:
(15:19:20) DEBUG  >>  $FNA_FILE: /Users/leightonpayne/padloc/test/GCF_004358345.1.fna
(15:19:20) DEBUG  >>  $GFF_FILE:
(15:19:20) DEBUG  >>  $HMM_DATABASE: /Users/leightonpayne/padloc/data/hmm/padlocdb.hmm
(15:19:20) DEBUG  >>  $YAML_DIR: /Users/leightonpayne/padloc/data/sys/
(15:19:20) DEBUG  >>  $HMM_META: /Users/leightonpayne/padloc/data/hmm_meta.txt
(15:19:20) DEBUG  >>  $SYS_META: /Users/leightonpayne/padloc/data/sys_meta.txt
(15:19:20) DEBUG  >>  $OUT_DIR: .
(15:19:20) DEBUG  >>  $CPU: 1
(15:19:20) DEBUG  >>  Required R packages are installed
(15:19:20) >> Predicting protein-coding genes with prodigal
(15:19:20) DEBUG  >>  prodigal -i /Users/leightonpayne/padloc/test/GCF_004358345.1.fna -f gff -o ./GCF_004358345.1_prodigal.gff -a ./GCF_004358345.1_prodigal.faa -q
(15:19:31) DEBUG  >>  Finished @ Thu  8 Apr 2021 15:19:31 NZST ... SUCCESSFUL
(15:19:31) >> Scanning GCF_004358345.1 for defence system proteins
(15:19:31) DEBUG  >>  hmmsearch --cpu 1 --acc --noali --domtblout ./GCF_004358345.1.domtblout /Users/leightonpayne/padloc/data/hmm/padlocdb.hmm ./GCF_004358345.1_prodigal.faa
(15:20:24) DEBUG  >>  Finished @ Thu  8 Apr 2021 15:20:24 NZST ... SUCCESSFUL
(15:20:24) >> Searching GCF_004358345.1 for defence systems
(15:20:24) DEBUG  >>  Rscript /Users/leightonpayne/padloc/bin/padloc.R -d ./GCF_004358345.1.domtblout -f ./GCF_004358345.1_prodigal.gff -h /Users/leightonpayne/padloc/data/hmm_meta.txt -s /Users/leightonpayne/padloc/data/sys_meta.txt -y /Users/leightonpayne/padloc/data/sys/ -o . -b 1 -q 0 -p 1
(15:20:27) DEBUG >> Start time: 2021-04-08 15:20:27
(15:20:27) DEBUG >> Reading hmm_meta.txt
(15:20:27) DEBUG >> Reading sys_meta.txt
(15:20:27) DEBUG >> Reading GCF_004358345.1.domtblout
(15:20:28) DEBUG >> Reading GCF_004358345.1_prodigal.gff
(15:20:30) DEBUG >> Merging domain, alias, and feature tables
(15:20:30) DEBUG >> Searching for defence systems
(15:20:37) >> Writing output to './GCF_004358345.1_padloc.csv'
(15:20:37) DEBUG >> End time: 2021-04-08 15:20:37
(15:20:37) DEBUG >> Run time: 10.3654699325562

Attached files:

Please compress your files before attaching (e.g. gzip GCF_004358345.1.fna)...