Prokka running error #33356
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I've submitted a PR to address this issue: #33411 |
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Not sure about the issue. |
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The |
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I think I have already installed Bioperl v1.7.8. Please see my command below: |
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Yep, you need BioPerl 1.7.2 |
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Could you please let me know how to install BioPerl 1.7.2. I was trying to follow the instruction using the page. However, it does not help me. |
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I could not find Bioperl 1.7.2 at Metacpan. |
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Thank you very much for your help. It works now. In addition, I was wondering if you could help me to solve following message it occurs when I install a package using conda: Solving environment: failed with initial frozen solve. Retrying with flexible solve. |
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Awesome! And, those "solving envrionment" messages can be ignored. Going to close this for now, cheers! |
This module was split out of the main bioperl distribution in version 1.7.3 (https://metacpan.org/dist/BioPerl/changes), but is still needed by Prokka (bioconda#33356).
This module was split out of the main bioperl distribution in version 1.7.3 (https://metacpan.org/dist/BioPerl/changes), but is still needed by Prokka (bioconda#33356).
Merge PR #33805, commits were: * Update meta.yaml * perl-bioperl: make test-command a string I meant to use the program 'true', but yaml interpreted it as a bool without the quotes. * Avoid the solver giving broken dependencies. * Merge remote-tracking branch 'upstream/master' into perl-bio-searchio-hmmer * perl-bioperl{,-core}: clean up pre-existing lint * prokka: remove pinning of perl and bioperl versions Now that Bio::SearchIO::hmmer is packaged, we can use it as part of the latest bioperl distribution and there's no longer a need for this pinning. This reverts the workaround a32603c in favor of resolving the underlying problem. * Add perl-bio-searchio-hmmer This module was split out of the main bioperl distribution in version 1.7.3 (https://metacpan.org/dist/BioPerl/changes), but is still needed by Prokka (#33356). * perl-bioperl-core: add run-time depends on perl-db_file This is needed for Bio::Index objects and classes that descend from it for the creation of index files.
Hi,
I am trying to install prokka using conda. However, it shows an error when I run it. I tried in different ways to install prokka but it still shows the error while running and does not produce output files.
I using the command for installation:
conda install -c conda-forge -c bioconda -c defaults prokka
error:::
------------- 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/anaconda3/envs/genome-anno/lib/perl5/5.32/site_perl /home/anaconda3/envs/genome-anno/lib/perl5/site_perl /home/anaconda3/envs/genome-anno/lib/perl5/5.32/vendor_perl /home/anaconda3/envs/genome-anno/lib/perl5/vendor_perl /home/anaconda3/envs/genome-anno/lib/perl5/5.32/core_perl /home/anaconda3/envs/genome-anno/lib/perl5/core_perl .) at /home/anaconda3/envs/genome-anno/lib/perl5/site_perl/Bio/Root/Root.pm line 520.
STACK Bio::Root::Root::_load_module /home/anaconda3/envs/genome-anno/lib/perl5/site_perl/Bio/Root/Root.pm:522 STACK (eval) /home/anaconda3/envs/genome-anno/lib/perl5/site_perl/Bio/SearchIO.pm:620 STACK Bio::SearchIO::_load_format_module /home/anaconda3/envs/genome-anno/lib/perl5/site_perl/Bio/SearchIO.pm:619 STACK Bio::SearchIO::new /home/anaconda3/envs/genome-anno/lib/perl5/site_perl/Bio/SearchIO.pm:217
STACK toplevel /home/anaconda3/envs/genome-anno/bin/prokka:1113
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/anaconda3/envs/genome-anno/bin/prokka line 1114.
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