hisat2 run error

Question

[XBria]

Hi,

Hisat2 has got a problem when aligning the reads to reference genome (Only chromosome X). Can anyone please help me to fix it ? notably,I downloaded hisat2 and copied all the executable files into the bin. Home/XBria/bin.

hisat2 -p 8 -dta -X '/home/XBria/bin/indexes/chrX_tran' -1 '/home/XBria/Full_data/ERR188044/ERR188044_1.fastq' -2 '/home/XBria/Full_data/ERR188044/ERR188044_2.fastq' -S ERR.sam

Error: Encountered internal HISAT exception (#1)

and

(ERR): hisat2-align exited with value 1

Thanks

[Medhat]

Try to post also the command you used to run hisat.
There is a similar error like that referring to naming issue in reference here HISAT error: Encountered internal HISAT2 exception (#1)
I suggest you may just need to re-index your reference