search

tseemann / barrnap

:microscope: :leo: Bacterial ribosomal RNA predictor
GNU General Public License v3.0
210 stars 41 forks source link

Cannot specify a file on cmdline? #52

Open wwood opened 3 years ago

wwood commented 3 years ago

Hi Torsten,

Small thing - from the doco

Usage:
  barrnap [options] chr.fa

But

barrnap-0.9) $ barrnap a.fna
[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 /home/ben/e/barrnap-0.9/lib/barrnap/bin/../binaries/linux to end of PATH
[barrnap] Checking for dependencies:
[barrnap] Found nhmmer - /home/ben/e/barrnap-0.9/bin/nhmmer
[barrnap] Found bedtools - /home/ben/e/barrnap-0.9/bin/bedtools
[barrnap] Will use 1 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: /home/ben/e/barrnap-0.9/lib/barrnap/bin/../db/bac.hmm
[barrnap] ERROR: No input file on command line or stdin

Easy to workaround - just specify via stdin e.g. barrnap < a.fna, but figured I'd report. ben