Prokka error

[sekhwal]

It shows following error but it seems I have 'hmmer' in my system.

error: Failed to load module Bio::SearchIO::hmmer3. Can't locate Bio/SearchIO/hmmer3.pm in @INC (you may need to install the Bio::SearchIO::hmmer3 module) (@INC contains: /home/anaconda3/envs/my-env/lib/perl5/5.32/site_perl /home/anaconda3/envs/my-env/lib/perl5/site_perl /home/anaconda3/envs/my-env/lib/perl5/5.32/vendor_perl /home/anaconda3/envs/my-env/lib/perl5/vendor_perl /home/anaconda3/envs/my-env/lib/perl5/5.32/core_perl /home/anaconda3/envs/my-env/lib/perl5/core_perl .) at /home/anaconda3/envs/my-env/lib/perl5/site_perl/Bio/Root/Root.pm line 520.

STACK Bio::Root::Root::_load_module /home/anaconda3/envs/my-env/lib/perl5/site_perl/Bio/Root/Root.pm:522 STACK (eval) /home/anaconda3/envs/my-env/lib/perl5/site_perl/Bio/SearchIO.pm:620 STACK Bio::SearchIO::_load_format_module /home/anaconda3/envs/my-env/lib/perl5/site_perl/Bio/SearchIO.pm:619 STACK Bio::SearchIO::new /home/anaconda3/envs/my-env/lib/perl5/site_perl/Bio/SearchIO.pm:217 STACK toplevel /home/anaconda3/envs/my-env/bin/prokka:1113

[joneson]

I have the same issue. I have just reinstalled prokka and have also insured that hmmer is installed, but get the same error. sudo cpanm Bio::SearchIO::hmmer Bio::SearchIO::hmmer is up to date. (1.7.3)

[sekhwal]

The Bio::SearchIO::hmmer3 module was removed in v1.7.3 of BioPerl. you need BioPerl 1.7.2 and then hmmer3.

[joneson]

Current version of BioPerl is 1.7.8. Are you saying go back and install BioPerl 1.7.2?

[sekhwal]

Yup! it worked for me. I installed using the following command.

conda install -c conda-forge -c bioconda perl-bioperl=1.7.2

[joneson]

Thanks, after doing that and then updating tbl2blasn I am able to run prokka. is it possible that the original hmmer problem is related to this - in the prokka README.md?

• Why does prokka fail when it gets to hmmscan?
  Unfortunately HMMER keeps changing its database format, and they aren't upward compatible. If you upgraded HMMER (from 3.0 to 3.1 say) then you need to "re-press" the files. This can be done as follows:

cd /path/to/prokka/db/hmm
mkdir new
for D in *.hmm ; do hmmconvert $D > new/$D ; done
cd new
for D in *.hmm ; do hmmpress $D ; done
mv * ..
rmdir new

[sekhwal]

How did you update tbl2blasn. I could not find tbl2blasn in my conda env. I also did not find ..prokka/db/hmm in conda env.

[joneson]

To update tbl2blasn I followed instructions in prokka FAQ and README.mb:

Why does Prokka keeps on crashing when it gets to the "tbl2asn" stage? It seems that the tbl2asn program from NCBI "expires" after 6-12 months, and refuses to run. Unfortunately you need to install a newer version which you can download from here.

I have tbl2blasn in my usr/local/bin I can see prokka/db/hmm when I run prokka --listdb listed as * HMMs: HAMAP

[0xaf1f]

Current version of BioPerl is 1.7.8. Are you saying go back and install BioPerl 1.7.2?

@joneson this shouldn't be necessary anymore. See https://github.com/tseemann/prokka/issues/614#issuecomment-1074803518

[sekhwal]

When I install prokka using the following command, it does not work. So I have to install conda install -c conda-forge -c bioconda perl-bioperl=1.7.2

conda install -c conda-forge -c bioconda -c defaults prokka

[0xaf1f]

For me, even with regular conda (I usually use the mamba resolver), it's getting the right packages. Maybe you need to refresh your package index with conda clean -i. :man_shrugging:

In the worst case, you would just need to manually conda install perl-bio-searchio-hmmer afterwards, but that shouldn't be necessary.

[zagrosman]

To update tbl2blasn I followed instructions in prokka FAQ and README.mb:

Why does Prokka keeps on crashing when it gets to the "tbl2asn" stage? It seems that the tbl2asn program from NCBI "expires" after 6-12 months, and refuses to run. Unfortunately you need to install a newer version which you can download from here.

I have tbl2blasn in my usr/local/bin I can see prokka/db/hmm when I run prokka --listdb listed as * HMMs: HAMAP

Simply, using this instruction you can fix the problem