Some reference entries show up as duplicates about bowtie HOT 1 OPEN

Hmm. I think I have traced the source of the problem. I ran multiple (too many) instances of bowtie using different combinations of flags to see if it was any of the flags that was causing the problem. Then I was wondering whether the memory buffer on the HPC was generating the same results in spite of me changing the files (The m7b.fa file did previously have duplicate headers). So I switched to a different computer node and ran bowtie again, but the problem was still there.

Then I tried changing the computer node and building the index again, and that apparently solved the problem.

TL;DR: I believe it was the memory buffer. The program is fine.

from bowtie.