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kbaseapps / kb_gtdbtk

GTDB-Tk App
MIT License
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GTDB doesn't recognize fasta assembly type input #91

Open ghost opened 7 months ago

ghost commented 7 months ago

I added two fasta files with contigs in my KBASE narrative and assigned them to FASTA assembly type, but GTDB does not recognize my input. Am I doing something wrong? Captura de tela 2024-01-12 160728

kmmarcello commented 1 month ago

This is 7 mo later, but I am also having this issue. Did you ever get it resolved?

crockettz commented 1 month ago

Hi @kmmarcello, This new version only takes "set-like" inputs - GenomeSets, AssemblySets, or BinnedContigs. That tradeoff is a design choice to streamline job submissions of 1 set rather than a bunch of individual jobs, but it comes at the expense of cases like yours where there is only 1 or 2. You'll need to create a set which contains those assemblies using the Build AssemblySet app, and then input that AssemblySet into GTDB.

kmmarcello commented 1 month ago

thank you @crockettz, this worked!