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xinehc / args_oap

ARGs-OAP: Online Analysis Pipeline for Antibiotic Resistance Genes Detection from Metagenomic Data Using an Integrated Structured ARG Database
MIT License
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Confusing “-t” parameter in stage two #45

Open Wang0293 opened 10 months ago

Wang0293 commented 10 months ago

“-t” parameter lose efficacy in stage two sometimes , for example: I used "-t 8" parameter in stage two, and info shows that:

INFO: BLAST settings: 21401791 bps, 232757 reads, 8 threads, mt_mode 0.

And only 1 threads used. Obviously, the mt_mode is setted incorrectly. Do you know the possible cause?

xinehc commented 10 months ago

Hi,

this is because blast requires at least 2500000 bp per thread to enable mt_mode 1.

    mt_mode = '1' if nbps / self.thread >= 2500000 else '0'

In your case the number of bp is small, so blast should not take a long time to finish even with mt_mode 0.

Wang0293 commented 10 months ago

Very thanks for your patience to my stupid😣 question.