Can you remove outdated flags for metabat2?

jtamames / SqueezeMeta

A complete pipeline for metagenomic analysis

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Can you remove outdated flags for metabat2? #722

Closed mkbwang closed 10 months ago

mkbwang commented 10 months ago

Hi, I notice that your metabat2 command still has "saveTNF" and "saveDistance" flags. However the latest version of metabat2 has dropped these two flags (see the README). Can you update your perl scripts accordingly? Thank you! FYI, I had to recompile metabat2 and jgi_summarize_bam_contig_depths because of binary mismatch mentioned in previous issues.

fpusan commented 10 months ago

Noted. We will shortly release v1.6.3, which will (hopefully) not need users to recompile anything. Why do you say "saveTNF" and "saveDistance" have been deprecated? They seem to be present in the README you linked

mkbwang commented 10 months ago

Thanks for your reply! I mean "saveTNF" and "saveDistance" have been ditched in metabat2. They are only available in metabat1.

fpusan commented 9 months ago

Done in 7d862f9.