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make bwa-mem output reproducible upon changing number of threads #9

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pmenzel opened this issue Mar 4, 2022 · 1 comment
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make bwa-mem output reproducible upon changing number of threads #9

pmenzel opened this issue Mar 4, 2022 · 1 comment
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@pmenzel
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pmenzel commented Mar 4, 2022

According to lh3/bwa#121, the bwa-mem output is not stable upon changing the number of threads.

Maybe it would be good to set -K 10000000 as suggested by lh3 to make the results reproducible here:
https://github.com/jodyphelan/TBProfiler/blob/57d54be5069aa2c34c463d4576a55240dab17f9f/pathogenprofiler/fastq.py#L61

Not sure if it also affects bwa-mem2.
@jodyphelan
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Hi @pmenzel,

Thanks for letting me know, I'll put this in.

@jodyphelan jodyphelan transferred this issue from jodyphelan/TBProfiler Apr 29, 2022
jodyphelan added a commit that referenced this issue Apr 29, 2022
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/issues/9
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@jodyphelan jodyphelan added this to Done in Issues May 10, 2022
@jodyphelan jodyphelan moved this from Done to In progress in Issues May 10, 2022
Issues automation moved this from In progress to Done May 10, 2022
jodyphelan added a commit that referenced this issue May 10, 2022
@jodyphelan
Copy permissions fix (#9)
22db55d
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@pmenzel @jodyphelan