Duplicate unmapped paired reads and empty unmapped single reads files -bowtie2-2.3.4.1-macos-x86_64

[mireji]

While mapping reads, the output for unmapped paired reads are duplicated while the one for unmapped paired reads is empty. I am running this on -bowtie2-2.3.4.1-macos-x86_64 Output: Control_output_paired_unmapped.1 Control_output_paired_unmapped.2 Control_output_paired.sam Control_output_unpaired_unmapped

[ch4rr0]

Apologies for the late response. Can you at all recall the command that caused this issue? We fixed this exact issue in a prior release, v2.3.1, so it puzzling that it is happening again.

    * Fixed a bug whereby combining `-—un-conc*` with `-k` or `-a`
      would cause `bowtie2` to print duplicate reads in one or both
      of the `--un-conc*` output files, causing the ends to be
      misaligned.