pyhmmer not found

[samlipworth]

Hello,

Installed via conda,

ERROR: Pyhmmer could not be executed! Please make sure Pyhmmer is installed and executable or skip requiring workflow steps via via '--skip-cds --skip-sorf'.

mamba install pyhmmer tells me that it is already installed.

Any ideas?

THanks, Sam

[oschwengers]

Hi, could you run Bakta in --debug mode and provide the *.log file?

[samlipworth]

ST131_HG941718.1.log

[oschwengers]

Thanks, could you please try to execute the following within the Bakta conda env?

$ python3
>>> import pyhmmer
>>> print(pyhmmer.__version__)

[samlipworth]

Python 3.10.14 | packaged by conda-forge | (main, Mar 20 2024, 12:45:18) [GCC 12.3.0] on linux
Type "help", "copyright", "credits" or "license" for more information.
>>> import pyhmmer
>>> print(pyhmmer.__version__)
0.10.13
>>> 

[oschwengers]

Interesting! This is the first time this is being reported and I cannot reproduce it. Have you tried to start from a fresh conda environment, just to make sure there are no side effects?

[samlipworth]

deleted conda env, cleared cache, created new conda env and re-installed using conda - still getting the same error.

[kenken86]

I have the same problem

[kenken86]

ERROR: Pyhmmer could not be executed! Please make sure Pyhmmer is installed and executable or skip requiring workflow steps via via '--skip-cds --skip-sorf'.

[oschwengers]

Thanks all for reporting. Unfortunately, I cannot reproduce this error on Ubuntu 20.4 using Mamba and creating a fresh env with Bakta 1.9.3:

mamba create --quiet --yes -p ./conda-env bakta=1.9.3
mamba activate ./conda-env/
bakta --db db-v5.1-light/ --skip-trna --skip-rrna --skip-ncrna --skip-ncrna-region --skip-plot --debug GCF_000008865.2.fna.gz
Bakta v1.9.3
Options and arguments:
    input: .../GCF_000008865.2.fna.gz
    db: .../db-v5.1-light, version 5.1, light
    output: .../bakta-gh-297
    tmp directory: /tmp/tmpj2ogjx7x
    prefix: GCF_000008865.2.fna
    threads: 8
    debug: True
    translation table: 11
    skip tRNA: True
    skip rRNA: True
    skip ncRNA: True
    skip ncRNA region: True
    skip plot: True

Bakta runs in DEBUG mode! Temporary data will not be destroyed at: /tmp/tmpj2ogjx7x

parse genome sequences...
...
start annotation...
...
predict & annotate CDSs...
    predicted: 5387 
    discarded spurious: 11
    revised translational exceptions: 0
    detected IPSs: 0
    found PSCCs: 4995
    lookup annotations...
    conduct expert systems...
        amrfinder: 39
        protein sequences: 792
    combine annotations and mark hypotheticals...
...
annotation summary:
    tRNAs: 0
    tmRNAs: 1
    rRNAs: 0
    ncRNAs: 0
    ncRNA regions: 0
    CRISPR arrays: 1
    CDSs: 5377
        hypotheticals: 435
        pseudogenes: 0
        signal peptides: 0
    sORFs: 19
    gaps: 0
    oriCs/oriVs: 3
    oriTs: 1
...

I'm a bit puzzled. Are you running Bakta on Linux or Mac?

[kenken86]

Linux

[oschwengers]

That's weird. I'm sorry but I can neither reproduce this error nor grasp why this could potentially happen - besides mixed-up conda environments.

[oschwengers]

@samlipworth @kenken86 I just released v1.9.4 with a potential fix for this issue. Could you please give it a try (best in a fresh Conda env)? Thanks!

[samlipworth]

Thanks so much for your persistance - I have just installed on a fresh conda env and can confirm the problem is fixed. Look forward to using Bakta in anger!

BW, Sam

[oschwengers]

OK, I tentatively assume that this issue is fixed and thus, close this issue.

Just in case these issues remain after updating Bakta to v1.9.4 in a fresh Conda env, @kenken86 , please do not hesitate to re-open this.