Hisat2 alignment error

Question

[blooming.daisy333]

Hi all,

Im using Hisat2 to align RNAseq data and encountering following error:

(ERR): hisat2-align died with signal 8 (FPE) (core dumped)

using following command

./hisat2 --mp 0,0 --np 0 --pen-noncansplice 10000000 --min-intronlen 20 --max-intronlen 10000 --novel-splicesite-outfile /data/memona/hisat2-2.1.0/result/ --rna-strandness RF --dta -p64 --summary-file -x /data/memona/hisat2-2.1.0/hisat_index -1 /data/memona/Trimmomatic-0.36/SRR9591_E_1P.fq -2 /data/memona/Trimmomatic-0.36/SRR9591_E_2P.fq -S /data/memona/hisat2-2.1.0/result/hisat_align.sam

can anyone kindly suggest possible cause and solution to the problem.

Thanks

Answer 1

[lakhujanivijay]

Looks like these issues have been already taken care in the recent version. Check your HISAT version using

hisat2 --version

Update if necessary

[blooming.daisy333]

im using hisat2-2.1.0 version.

i have resolved the above problem after correcting one filter but now problem is that im unable to get information about splice junctions with this command. its producing only alignment and nothing else. any kind help???

thank you

[lakhujanivijay]

Could you try changing this

--novel-splicesite-outfile /data/memona/hisat2-2.1.0/result/

to

--novel-splicesite-outfile /data/memona/hisat2-2.1.0/result/novel.sites.txt

[blooming.daisy333]

thanks for the guidance. yes it has produced the output but is giving only 3 fields given below:;

chr1    329728  329839  -
chr1    330066  330757  -
chr1    581256  581357  +

while not mentioning the canonical/non canonical status and junction nucleotide info.

further is it important to build the index with --ss and --exon options to determine the splice sites...????