HISAT2 alignment never finishes

[pascalg]

Hi there,
I am running hisat2 for paired end alignment using several cores (-p parameter) on an index I built myself. Seems like the program never exits and runs forever, also the SAM file seem to be complete.

Thanks,
Pascal

[infphilo]

With this minimal information, I could not tell what went wrong. I recently released a new version of HISAT2 in which the issue you had might have been fixed. If you still have the problem, please let me know with some details so that I'll be able to reproduce and fix it.