Question: HISAT error: Encountered internal HISAT2 exception (#1)
1
gravatar for pixie@bioinfo
3.2 years ago by
pixie@bioinfo1.4k
Université Paris, Saclay
pixie@bioinfo1.4k wrote:

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 • 11k views
ADD COMMENTlink modified 8 weeks ago by Rks20 • written 3.2 years ago by pixie@bioinfo1.4k
1

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.

ADD REPLYlink written 3.2 years ago by WouterDeCoster44k

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

ADD REPLYlink written 3.2 years ago by pixie@bioinfo1.4k

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.

ADD REPLYlink written 3.2 years ago by Devon Ryan96k

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

ADD REPLYlink written 2.2 years ago by tzahra68750

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,...

ADD REPLYlink written 2.2 years ago by WouterDeCoster44k

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.

ADD REPLYlink written 8 weeks ago by Rks20
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