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Problems with . in sample names #26

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crarlus opened this issue Dec 6, 2022 · 0 comments
Open

Problems with . in sample names #26

crarlus opened this issue Dec 6, 2022 · 0 comments

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@crarlus
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crarlus commented Dec 6, 2022

Hi,
thanks for plasmidid, a very useful tool.

I encountered a problem when sample names contain a . The program crashes and returns the following error messages:

ERROR in Script plasmidID on or near line 863; exiting with status 1
MESSAGE:

See results_plsdb_test/GCA_019841085/logs/plasmidID.log for more information.
command:
blast_to_link.sh -i  results_plsdb_test/GCA_019841085/E_marmotae/GCA_019841085.1/data/GCA_019841085.1".plasmids.blast" -I -l 20 -b 90

My command was

 plasmidID -T 20 -c GCA_019841085.1.fasta -d plasmids.fna -s GCA_019841085.1 -g 'E_coli' -o results_test/GCA_019841085.1

When I remove the . in the sample argument GCA_019841085.1 -> GCA_019841085 the program runs smoothly.

Still, I think it would be important to be able to name samples such as this is the offocial NCBI Refseq/Genbank naming convention (accession.version).

Thanks,
Carlus

P.S.:

$ plasmidID --version
1.6.4

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