hisat2-align died with signal 11 about hisat2 HOT 4 CLOSED

Thank you for reporting a new issue with such detailed information. I'll look into it next week after I get back from my trip.

from hisat2.

Okay, I was finally able to look into this.
(1) This issue is due to stack overflow, which happens when dealing with long reads (ESTs). I increased stack size to 4MB from previously 512KB.
(2) You can increase the mapping rate by lowering --score-min (see the manual for details).

The fix is available at GitHub, and I'll release the fixed version probably within a month.

Thanks,
Daehwan

from hisat2.

Awesome! Thank you so much!

----- Original Message -----
From: "Daehwan Kim" [email protected]
To: "infphilo/hisat2" [email protected]
Cc: "jstrohm" [email protected]
Sent: Friday, April 15, 2016 8:06:12 AM
Subject: Re: [infphilo/hisat2] hisat2-align died with signal 11 (#32)

Okay, I was finally able to look into this.
(1) This issue is due to stack overflow, which happens when dealing with long reads (ESTs). I increased stack size to 4MB from previously 512KB.
(2) You can increase the mapping rate by lowering --score-min (see the manual for details).

The fix is available at GitHub, and I'll release the fixed version probably within a month.

Thanks,
Daehwan

You are receiving this because you authored the thread.
Reply to this email directly or view it on GitHub:
https://github.com/infphilo/hisat2/issues/32#issuecomment-210497549

from hisat2.

Although i have installed the lastest version of hisat2, i still got the error message as following! It seems the hisat2 works well with some RNA-seq datasets, but failed for some other datasets.
Any clues.

Thank you.

from hisat2.