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Old 04-02-2019, 08:07 AM   #671
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Location: East Coast USA

Join Date: Feb 2008
Posts: 7,014

I am not sure I am understanding what seems to be happening. Is the flagstat command showing no reads aligned?

At this point in time samtools 0.1.19 is ancient and should really NOT be used for anything. Errors you are seeing also are about samtools options that only the new versions have.

You should upgrade to latest samtools which is now in v.1.9. As long as samtools is in your $PATH, BBMap is able to directly write BAM files so there is no need to create SAM files. Just specify out=yourfile.bam.
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