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labgem / PPanGGOLiN

Build a partitioned pangenome graph from microbial genomes
https://ppanggolin.readthedocs.io
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gbff.gz vs gbff only #289

Closed survivor77 closed 1 day ago

survivor77 commented 5 days ago

Hello there,

Thank you for this tool. I was able to run the tool successfully with 5 genomes and annotation files. All these had the suffix .gz at the end.

However, I plan to run the tool on more that 500 strains. The files that I download from the NCBI datasets website have no .gz. I tried running the tool without the .gz suffix for the annotation files and the program gave an error that the files should have a .gz suffix.

Is there a workaround for the next analysis without .gz suffixes? Thanks and apologies if this was asked earlier.

axbazin commented 1 day ago

Hi,

Apologies for the delay. To answer you, normally the files can be given either compressed (with .gz) or not, and it should work the same way.

Adelme

survivor77 commented 1 day ago

No problem. I got the problem solved and ppanggolin worked like a charm. As you mentioned, it should work with either file format, and it did. Thank you!