Bio::SearchIO: hmmer3 cannot be found

[yzhzu]

hi, everyone, after update prokka 1.14.6, the running is wrong, the error information is following, Any help will be really appriecated. thanks very much.

[12:22:25] Deleting unwanted file: Temp/sprot.faa [12:22:25] Deleting unwanted file: Temp/sprot.blast [12:22:26] There are still 1708 unannotated CDS left (started with 4620) [12:22:26] Will use hmmer3 to search against /home/shsmu/anaconda3/bin/../db/hmm/HAMAP.hmm with 8 CPUs [12:22:26] Running: cat Temp/HAMAP.hmm.faa | parallel --gnu --plain -j 8 --block 25968 --recstart '>' --pipe hmmscan --noali --notextw --acc -E 1e-06 --cpu 1 /home/shsmu/anaconda3/bin/../db/hmm/HAMAP.hmm /dev/stdin > Temp/HAMAP.hmm.hmmer3 2> /dev/null Bio::SearchIO: hmmer3 cannot be found Exception ------------- EXCEPTION: Bio::Root::Exception ------------- MSG: 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/shsmu/anaconda3/bin/../perl5 /home/shsmu/perl5/lib/perl5/5.30.0/x86_64-linux-gnu-thread-multi /home/shsmu/perl5/lib/perl5/5.30.0 /home/shsmu/perl5/lib/perl5/x86_64-linux-gnu-thread-multi /home/shsmu/perl5/lib/perl5 /etc/perl /usr/local/lib/x86_64-linux-gnu/perl/5.30.0 /usr/local/share/perl/5.30.0 /usr/lib/x86_64-linux-gnu/perl5/5.30 /usr/share/perl5 /usr/lib/x86_64-linux-gnu/perl/5.30 /usr/share/perl/5.30 /usr/local/lib/site_perl /usr/lib/x86_64-linux-gnu/perl-base) at /usr/share/perl5/Bio/Root/Root.pm line 520.

STACK: Error::throw STACK: Bio::Root::Root::throw /usr/share/perl5/Bio/Root/Root.pm:449 STACK: Bio::Root::Root::_load_module /usr/share/perl5/Bio/Root/Root.pm:522 STACK: Bio::SearchIO::_load_format_module /usr/share/perl5/Bio/SearchIO.pm:620 STACK: Bio::SearchIO::new /usr/share/perl5/Bio/SearchIO.pm:217 STACK: /home/shsmu/anaconda3/bin/prokka:1029

For more information about the SearchIO system please see the SearchIO docs. This includes ways of checking for formats at compile time, not run time Can't call method "next_result" on an undefined value at /home/shsmu/anaconda3/bin/prokka line 1030.

[ireneortega]

Same happened to me when ussing --rnammer. Does anyone how to solve it?

[arif-tanmoy]

Did you try installing the Bio::SearchIO::hmmer3 ?? You can do it easily by using sudo cpan Bio::SearchIO::hmmer3

[ireneortega]

Thanks @arif-tanmoy. It worked after using sudo cpan Bio::SearchIO::hmmer3. However I have a problem running tbl2asn now. I will try to figure out how to solve it.

[kullrich]

Hi, I am running prokka in a conda environment. Does anyone knows how I could direclty install Bio::SearchIO::hmmer3 from within the yml file?

name: prokka
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - prokka=1.14.6

Thank you in anticipation

error message like before:

  ------------- EXCEPTION -------------
  MSG: Failed to load module Bio::SearchIO::hmmer3. Can't locate Bio/SearchIO/hmmer3.pm in @INC

[matinnuhamunada]

Hi, I am running prokka in a conda environment. Does anyone knows how I could direclty install Bio::SearchIO::hmmer3 from within the yml file?

name: prokka
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - prokka=1.14.6

Thank you in anticipation

error message like before:

  ------------- EXCEPTION -------------
  MSG: Failed to load module Bio::SearchIO::hmmer3. Can't locate Bio/SearchIO/hmmer3.pm in @INC

Hi, I think the latest BioPerl causes the issue. Sticking to BioPerl 1.7.2 seems to resolve the issue.

name: prokka
channels:
  - conda-forge
  - bioconda
  - defaults
dependencies:
  - prokka=1.14.6
  - perl-bioperl=1.7.2

[0xaf1f]

I just posted in https://github.com/tseemann/prokka/issues/614#issuecomment-1074803518 that there shouldn't be a need to pin to old versions anymore since Bio::SearchIO::hmmer3 is now in bioconda.