Closed mattbawn closed 4 years ago
Hi Matt,
yes, Pantagruel expects a strain_infos_database.txt
file whenever you provide custom assemblies with option -a
, not only if you annotate them within Pantagruel pipeline. The pipeline relies on this file to tag the genomes and link basic metadata (species and strain name).
And yes indeed you can annotate the genomes directly within the pipeline, as long as you have prokka
command available in your path (best having prokka v1.14; v1.13 should work too)
Hi Florent,
I'm sorry, perhaps I wasn't clear,
"Is Pantagruel expecting the strain
info in strain_infos_database.txt
to also be in the annotation?"
I mean, is the strain tag in strain_infos_database.txt
expected to be present in the *.GFF
and '*.GBK` files?
Thanks,
Matt
OK, I get you.
Yes the script add_taxid_feature2prokkaGBK.py
was expecting that the strain tag in strain_infos_database.txt
be present in the *.GBK
file; it's not the case anymore with commit 7f68302. Please try see if it goes.
Hi again,
Thanks for doing this. I now get:
This is Pantagruel pipeline version 37ff955f16336d331307812ee5c6231b6b793600 using source code from repository '/opt/software/pantagruel'
# will run tasks: 0 1 2 3 4 5 6 7 8 9
[2019-11-28 13:17:34] Pantagruel pipeline task 0: fetch public genome data from NCBI sequence databases and annotate private genomes.
Create new task folder '/nbi/Research-Groups/IFR/Rob-Kingsley/R134_Pantagruel/database/00.input_data'
/opt/software/pantagruel/scripts/pipeline/pantagruel_pipeline_00_fetch_data.sh: line 488: syntax error: unexpected end of file
ERROR: Pantagruel pipeline task 0: failed.
Thanks
Matt
Oh that was bad of me not to test this after recent changes.... I introduced the bug in commit 0368237. This is now fixed with feaa9e0. Thank you for reporting.
Hi Florent,
Thank you for your previous fix(es).
I am getting the following:
Is Pantagruel expecting the
strain
info instrain_infos_database.txt
to also be in the annotation?If so can I use Pantagruel to annotate the assemblies? (this may be easier as it seems to be quite specific with certain file expectations)
Thanks,
Matt