Hisat keeps running indefinetly on some FastQ files, they do work in Hisat2

[npklein]

I have some FastQ files that I can sadly not share as they are patient data. The problem with them is that when I run Hisat with default parameters, they keep running indefinitely (longest I left them on was 7 days), while all other samples finish within half an hour. These samples do finish correctly, and quickly, with Hisat2. However, I want to compare them to data from other samples ran with Hisat, so I hope to be able to align these as well. Do you know of an issue that causes Hisat to hang, that got fixed in Hisat2? If so, is there a workaround for it in Hisat?