HMM db incorrect location

[Middle-Author-Bioinformatics]

Just installed via conda and getting this error, which was solved by moving the HMM db files around:

barrnap --kingdom euk --threads 24 --outseq PCIT.rrna.fa PCIT.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/ark/miniconda3/envs/barrnap_env/lib/barrnap/bin/../binaries/linux to end of PATH
[barrnap] Checking for dependencies:
[barrnap] Found nhmmer - /home/ark/miniconda3/envs/barrnap_env/bin/nhmmer
[barrnap] Found bedtools - /home/ark/miniconda3/envs/barrnap_env/bin/bedtools
[barrnap] Will use 24 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/ark/miniconda3/envs/barrnap_env/lib/barrnap/bin/../db/euk.hmm
[barrnap] Scanning PCIT.fna for euk rRNA genes... please wait
[barrnap] Command: nhmmer --dna --cpu 24 -E 1e-06 --w_length 3878 -o /dev/null --tblout /dev/stdout '/home/ark/miniconda3/envs/barrnap_env/lib/barrnap/bin/../db/euk.hmm' 'PCIT.fna'
[barrnap] ERROR: nhmmer failed to run - Error: Error reading hmm from file /home/ark/miniconda3/envs/barrnap_env/lib/barrnap/bin/../db/euk.hmm (10)

This was solved by mv ~/miniconda3/envs/barrnap_env/lib/barrnap/db/*hmm ~/miniconda3/envs/barrnap_env/lib/barrnap/bin/../db/

Thanks, Arkadiy

[Middle-Author-Bioinformatics]

Never mind, that didn't fix it. Not sure what is causing the issue.

Thanks, Arkadiy

[mzwaig]

Hi!

I'm also having this issue but only for the sorghum plant genome. I ran barrnap install with conda on the maize genome without issues.

I tried a local install of hmmer/barrnap and get the same error.

Thanks, Melissa

[tseemann]

conda upgrade -n base --all --yes
conda create -n barrnap barrnap --yes
conda activate barrnap
barrnap --version

Can you try this please?