HISAT error: Encountered internal HISAT2 exception (#1)

Question

[pixie@bioinfo]

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

[WouterDeCoster]

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.

[pixie@bioinfo]

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

[HaroonPakistan]

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

[Devon Ryan]

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.

[tzahra6875]

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

[WouterDeCoster]

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,...

[Rks]

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.

[HaroonPakistan]

Hi, did you solve it?

Answer 1

[Federico Giorgi]

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