Undefined subroutine &main::translate called

[salrodpal]

Hi, I have installed PIRATE using CONDA: conda config --add channels defaults conda config --add channels bioconda conda config --add channels conda-forge conda install pirate

I am trying to check it: PIRATE --check

However it always threw out an error saying:

• ERROR: extract_feature_sequences.pl failed
• ERROR: PIRATE did not run correctly:
• ERROR: PIRATE was not able to extract sequences from GFFS
• ERROR: PIRATE was not able to construct pangenome
• ERROR: PIRATE was not able to classify paralogs
• ERROR: PIRATE could not make summary files

And when I view gff_parser_log file:

• WARNING: /home/saludrp/anaconda3/envs/pirate_env/test/HO_5096_0412_test.gff - contig HO_5096_0412 contains non-ATCGN characters - replacing with Ns Undefined subroutine &main::translate called at /home/saludrp/anaconda3/envs/pirate_env/scripts/extract_feature_sequences.pl line 214, line 2. Undefined subroutine &main::translate called at /home/saludrp/anaconda3/envs/pirate_env/scripts/extract_feature_sequences.pl line 214, line 2. Undefined subroutine &main::translate called at /home/saludrp/anaconda3/envs/pirate_env/scripts/extract_feature_sequences.pl line 214, line 2. Undefined subroutine &main::translate called at /home/saludrp/anaconda3/envs/pirate_env/scripts/extract_feature_sequences.pl line 214, line 2.

I don´t know where the problem is, and how I can solve it. Thanks a lot!

[SionBayliss]

This seems to be an issue with a recently updated dependency, namely bioperl.

I will get that corrected on the conda recipe, but in the mean time you can downgrade bioperl using:

conda install perl-bioperl==1.7.2

I have tested this and it should fix your issue.

I will leave this open until I have fixed the conda recipe. I am unavailable for ~1 week but should have it fixed on my return in mid-March.

All the best, Sion

[salrodpal]

I have fixed with your recommendation. Thank you!!