Invalid genome ID: binny_XXXX_CXX_PXX_Actinobacteria[class] - Githubissues

Ecogenomics / GTDBTk

GTDB-Tk: a toolkit for assigning objective taxonomic classifications to bacterial and archaeal genomes.

https://ecogenomics.github.io/GTDBTk/

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Invalid genome ID: binny_XXXX_CXX_PXX_Actinobacteria[class] #440

Closed B-1991-ing closed 2 years ago

B-1991-ing commented 2 years ago

Dear GTDB-Tk support team,

I got the error - "ERROR: The following characters are invalid: [ ) = ] ( ; ,", due to my MAG name "binny_I01R01.000347_C91_P96_Actinobacteria[class].fasta" includes square brackets "[]". Could you give some suggestion to solve it?

Log file classify_wf_species_omstrup_sillebotten_sediment_norefinem.log

Thank you very much.

Best,

Bing

aaronmussig commented 2 years ago

Hello, if you rename the MAG to not include any of those characters then it will work, e.g.

mv binny_I01R01.000347_C91_P96_Actinobacteria[class].fasta binny_I01R01.000347_C91_P96_Actinobacteria__class__.fasta

B-1991-ing commented 2 years ago

Thank you for the suggestion, I will rename the MAGs.