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padlocbio / padloc

Locate antiviral defence systems in prokaryotic genomes
MIT License
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Error when I include a new system #10

Closed alexandergz1983 closed 2 years ago

alexandergz1983 commented 2 years ago

I am trying to include a new system, however I always get the same error.

padloc --fna GCF_902849975.1_HP-ISR-7_genomic.fna --force --data /home/alex/miniconda3/envs/padloc/padloc-db/ --debug --raw-out (18:35:28) DEBUG >> $FAA_FILE: (18:35:28) DEBUG >> $FNA_FILE: /test/GCF_902849975.1_HP-ISR-7_genomic.fna (18:35:28) DEBUG >> $GFF_FILE: (18:35:28) DEBUG >> $HMM_DATABASE: /miniconda3/envs/padloc/padloc-db//hmm/padlocdb.hmm (18:35:28) DEBUG >> $YAML_DIR: /miniconda3/envs/padloc/padloc-db//sys/ (18:35:28) DEBUG >> $HMM_META: miniconda3/envs/padloc/padloc-db//hmm_meta.txt (18:35:28) DEBUG >> $SYS_META:/miniconda3/envs/padloc/padloc-db//sys_meta.txt (18:35:28) DEBUG >> $OUT_DIR: . (18:35:28) DEBUG >> $CPU: 1 (18:35:28) >> Predicting protein-coding genes with prodigal (18:35:28) DEBUG >> prodigal -i /scratch/mauve_pro//GCF_902849975.1_HP-ISR-7_genomic.fna -f gff -o ./GCF_902849975.1_HP-ISR-7_genomic_prodigal.gff -a ./GCF_902849975.1_HP-ISR-7_genomic_prodigal.faa -q (18:35:30) DEBUG >> Finished @ mar nov 2 18:35:30 CET 2021 ... SUCCESSFUL (18:35:30) >> Scanning GCF_902849975.1_HP-ISR-7_genomic for defence system proteins (18:35:30) DEBUG >> hmmsearch --cpu 1 --acc --noali --domtblout ./GCF_902849975.1_HP-ISR-7_genomic.domtblout /home/alex/miniconda3/envs/padloc/padloc-db//hmm/padlocdb.hmm ./GCF_902849975.1_HP-ISR-7_genomic_prodigal.faa (18:35:30) DEBUG >> Finished @ mar nov 2 18:35:30 CET 2021 ... SUCCESSFUL (18:35:30) >> Searching GCF_902849975.1_HP-ISR-7_genomic for defence systems (18:35:30) DEBUG >> Rscript /miniconda3/envs/padloc/bin/bin/padloc.R -d ./GCF_902849975.1_HP-ISR-7_genomic.domtblout -f ./GCF_902849975.1_HP-ISR-7_genomic_prodigal.gff -h /miniconda3/envs/padloc/padloc-db//hmm_meta.txt -s /miniconda3/envs/padloc/padloc-db//sys_meta.txt -y /miniconda3/envs/padloc/padloc-db//sys/ -o . -b 1 -q 0 -p 1(18:35:31) DEBUG >> Start time: 2021-11-02 18:35:31 (18:35:31) DEBUG >> Reading hmm_meta.txt (18:35:31) WARNING >> hmm_meta.tsv - Missing values () in required columns - ET (e.value.threshold), HC (hmm.coverage.threshold), TC (target.coverage.threshold) - see below

hmm.acc      hmm.name hmm.description protein.name

1 PDLC02225 PglZ_bacteria phosphatase PglZ 2 PDLC02227 BrxC_bacteria ATPase BrxC system.definition.shortcut author number.seq length.hmm e.value.threshold 1 Payne LJ NA NA 1e-05 2 Payne LJ NA NA 1e-05 hmm.coverage.threshold target.coverage.threshold system literature.ref 1 NA NA BREX 10/ggqhzm 2 NA NA BREX 10/ggqhzm database.ref comments 1 2

(18:35:31) WARNING >> hmm_meta.tsv - Filling with defaults (1E-05, 0.3, 0.3) Warning message: One or more parsing issues, see problems() for details (18:35:31) DEBUG >> Reading sys_meta.txt (18:35:31) DEBUG >> Reading GCF_902849975.1_HP-ISR-7_genomic.domtblout (18:35:31) DEBUG >> Reading GCF_902849975.1_HP-ISR-7_genomic_prodigal.gff (18:35:32) DEBUG >> Merging domain, alias, and feature tables (18:35:32) DEBUG >> Searching for defence systems (18:35:32) >> Nothing found for GCF_902849975.1_HP-ISR-7_genomic (18:35:32) DEBUG >> End time: 2021-11-02 18:35:32 (18:35:32) DEBUG >> Run time: 1.25623941421509