Minor issue on a source modifier

[cesimsek]

Thank you for providing a tool for GenBank submissions, the whole process can be quite confusing. I realized I cannot assign the 'country' as a source modifier and it is shown as 'USA' by default in the .sqn file. Should this be manually circumvented?

My command looks like this just in case: python run_cenote-taker2.py -am True --contigs vp1_ORF_only.fas --run_title vp1_genbank --template_file cs_template.sbt --prune_prophage False --mem 32 --cpu 28 --enforce_start_codon False --isolation_source feces --collection_date 2008 --bioproject PRJNAXXXX --host Homo sapiens --assembler metaSPADES --known_strains blast_knowns --blastn_db db/nt.fasta

[mtisza1]

Ceren,

Thanks for making the issue. There was indeed a bug in my code that specifies "USA" as the country. In reality, that information will be provided by the user in their template file ("cs_template.sbt" in your case), so I removed the "country=USA" part of the code. If you update your scripts, it should be fixed. If you are updating from v2.1.2, just do:

cd Cenote-Taker2
git pull

If you are updating from an earlier version, do:

conda activate cenote-taker2_env
conda install -c bioconda biopython bedtools
cd Cenote-Taker2
git pull

Please let me know if this helps.

Best,

Mike

[cesimsek]

Problem is fixed now, thanks!