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Showing content from https://github.com/samtools/samtools/issues/2185 below:

Make the "[bam_sort_core] merging from 0 files and 16 in-memory blocks..." message disappear · Issue #2185 · samtools/samtools · GitHub

Are you using the latest version of samtools and HTSlib? If not, please specify.

samtools 1.21

Please describe your environment.

OS: Linux 5.15.0-126-generic
machine architecture: x86_64
compiler: gcc (Ubuntu 9.4.0-1ubuntu1~20.04.2) 9.4.0

Please specify the steps taken to generate the issue, the command you are running and the relevant output.

Not sure it's a bug or I'm missing something, but I'm trying to run samtools sort quietly (without any messages unless there's an error). However, when I run

samtools sort -@16 --verbosity 0 remap.bam > sorted.bam

I'm getting the regular "bam_sort_core" message ([bam_sort_core] merging from 0 files and 16 in-memory blocks...). I've tried changing verbosity (not sure what are the default and non-default levels?), but nothing seems to work.

I think older samtools versions behaved differently, but I might be hallucinating.

Could you please help me get rid of this message? Thank you!

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