HISAT error: Encountered internal HISAT2 exception (#1)
1
1
Entering edit mode
3.9 years ago
pixie@bioinfo ★ 1.4k

Hello, I am using HISAT2 for aligning transcripts to the reference genome (rice).

I have build the index and the files are as follows:

irgsp_apr.dna.6.ht2
irgsp_apr.dna.5.ht2
irgsp_apr.dna.2.ht2
irgsp_apr.dna.1.ht2
irgsp_apr.dna.8.ht2
irgsp_apr.dna.7.ht2
irgsp_apr.dna.4.ht2
irgsp_apr.dna.3.ht2
irgsp_apr.dna.fa


I am running the following commands: ./hisat2 -x "/home/user/Desktop/hisat_index/irgsp_apr.dna" -p 4 --min-intronlen 10 --max-intronlen 10000 "/home/user/Desktop/cutadapt_DRR006571.fastq"

However, I am getting the following error: Encountered internal HISAT2 exception (#1) (ERR): hisat2-align exited with value 1

Kindly help

RNA-Seq • 14k views
1
Entering edit mode

Is that a typo or does have index file 6 have a different name?

Furthermore, you don't need the quotes in your command. Try without, that might solve it already.

0
Entering edit mode

Thanks, I'll try out. Yea, it was a typo, corrected it

0
Entering edit mode

Hi, there are many indexed file. Have you written all one by one in command line?

0
Entering edit mode

Try to simplify your command to be as simple as possible and see if the error is reproduced:

./hisat2 -p 4 -x /home/user/Desktop/hisat_index/irgsp_apr.dna /home/user/Desktop/cutadapt_DRR006571.fastq


If that still doesn't work then you'll need to reindex the genome.

0
Entering edit mode

hi every one i had faced with this error : (ERR): hisat2-align exited with value 1 after typing ../hisat2 and iam working on linux16.04 and i downloaded hisat2-2.1.0 why i faced with this error kindly help

0
Entering edit mode

Please use ADD COMMENT or ADD REPLY to answer to previous reactions, as such this thread remains logically structured and easy to follow. I have now moved your reaction but as you can see it's not optimal. Adding an answer should only be used for providing a solution to the question asked.

In addition, please provide more information, for example including the full command that you used, how you obtained the indexes,...

0
Entering edit mode

I got this error because the hisat2 indexing job was killed for exceeding memory limitation. Without checking the indexing log, I started running hisat2 alignment and that gave me this error.

0
Entering edit mode

Hi, did you solve it?

0
Entering edit mode
4 weeks ago

In most cases, the index was made improperly, e.g. using hisat2-build with a gzipped input fasta