search

bxlab / metaWRAP

MetaWRAP - a flexible pipeline for genome-resolved metagenomic data analysis
MIT License
394 stars 191 forks source link

prokka-1.13 needs to be prokka-1.13.1 to be compatible with tbl2asn #295

Open bph6212ln opened 4 years ago

bph6212ln commented 4 years ago

The version of prokka that is specified in the meta.yml file produces output with the string "dbxref" which is incompatible with tbl2asn and will cause it to error non-zero with the message:

[00:59:54] Could not run command: tbl2asn -V b -a r10k -l paired-ends -M n -N 1 -y 'Annotated using prokka 1.13 from https://github.com/tseemann/prokka' -Z FUNCT_ANNOT\/prokka_out\/bin\.10\.strict\/bin\.10\.strict\.err -i FUNCT_ANNOT\/prokka_out\/bin\.10\.strict\/bin\.10\.strict\.fsa 2> /dev/null

************************************************************************************************************************
*****                        Something went wrong with annotating bin.10.strict. Exiting...                        *****
************************************************************************************************************************

By removing the redirect on stderr and running the command directly the error is reported:

[tbl2asn] ERROR: Unknown qualifier 'dbxref', relative line 16745
[tbl2asn] ERROR: Unknown qualifier 'dbxref', relative line 16759

This was fixed in 1.13.1
https://github.com/tseemann/prokka/issues/328

The version of prokka is explicitly stated in the meta.yml file to be 1.13. It should be bumped to 1.13.1.

Also, if it makes any difference, I wish the stderr redirects weren't being used. It makes tracking down errors unnecessarily complicated. You might consider dumping stderr to a log file for the particular step or program if it can't be mixed in stdout.

ursky commented 4 years ago

Thanks for the clear report. I'll remove the hard dependency to allow for updating prokka, and make the change the error at that stage to a warning just in case (i have had Prokka fail recently while still producing the right files). The changes will go live with v1.3.1 later this week.

bph6212ln commented 4 years ago

Sorry, the comment about stderr redirects was misdirected to you but should have been directed elsewhere. I got mixed up when tracking down dependency problems in dependent packages.