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tseemann / barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor
GNU General Public License v3.0
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Barrnap (nhmmer) takes an eternity to run #64

Closed erzakiev closed 1 year ago

erzakiev commented 1 year ago

Barrnap (nhmmer) takes an eternity to run. It's been stuck at that last line since at least 3h. I am running it from within the riboCleaner pipeline.

rule _barrnap:
    input: inputs/references/Mus_musculus.GRCm39.dna.toplevel.fa
    output: results/01_rDNA_identification/barrnap_rdna.gff3
    jobid: 5
    reason: Missing output files: results/01_rDNA_identification/barrnap_rdna.gff3
    threads: 10

        barrnap --kingdom euk --threads 10 inputs/references/Mus_musculus.GRCm39.dna.toplevel.fa > results/01_rDNA_identification/barrnap_rdna.gff3

[barrnap] This is barrnap 0.9
[barrnap] Written by Torsten Seemann
[barrnap] Obtained from https://github.com/tseemann/barrnap
[barrnap] Detected operating system: linux
[barrnap] Adding /opt/barrnap-0.9/bin/../binaries/linux to end of PATH
[barrnap] Checking for dependencies:
[barrnap] Found nhmmer - /opt/barrnap-0.9/bin/../binaries/linux/nhmmer
[barrnap] Found bedtools - /opt/bin/bedtools
[barrnap] Will use 10 threads
[barrnap] Setting evalue cutoff to 1e-06
[barrnap] Will tag genes < 0.8 of expected length.
[barrnap] Will reject genes < 0.25 of expected length.
[barrnap] Using database: /opt/barrnap-0.9/bin/../db/euk.hmm
[barrnap] Scanning inputs/references/Mus_musculus.GRCm39.dna.toplevel.fa for euk rRNA genes... please wait
[barrnap] Command: nhmmer --cpu 10 -E 1e-06 --w_length 3878 -o /dev/null --tblout /dev/stdout '/opt/barrnap-0.9/bin/../db/euk.hmm' 'inputs/references/Mus_musculus.GRCm39.dna.toplevel.fa'
erzakiev commented 1 year ago

sorry, that is more of a riboCleaner's problem than Barrnap's, as it is quickly done when running the barrnap directly without any pipelines