Question: HISAT2 SRR error
gravatar for NAVID.BAVI
2.1 years ago by
NAVID.BAVI0 wrote:

Hi all,

I'm trying to run hisat2 for aligning an available DRG rna seq using the following command:

/data/local/hisat2-2.1.0/hisat2 -p 4 -q --dta  --known-splicesite-infile $ANNOT/splicesites.txt --dta-cufflinks -x $HST2IDX --sra-acc SRR1330498 -S $WORKDIR/SRR1330498.sam

However I get the following error:

Warning: Could not access "SRR1330498" for reading; skipping...
Error: No input SRA accessions were valid
(ERR): hisat2-align exited with value 1

I couldn't find anything related to it by googling this error. I get the same error if I try other DRG accession numbers such as SRR3734493 or SRR3734494 (all from a recent publication), and I checked the SRA number in the NCBI and it was correctly related to the human DRG cells that I am interested in. The hisat2 command however works fin for a previous SRR that I worked with, e.g SRR5853082.

Does anyone have any advice?

Cheers, Navid

hisat2 rna-seq alignment sra srr • 855 views
ADD COMMENTlink modified 2.1 years ago by genomax92k • written 2.1 years ago by NAVID.BAVI0

This is a restriced file, requiring access to dbGaP accession phs000424.

ADD REPLYlink written 2.1 years ago by ATpoint42k

Thanks, yes that's why, though a bit surprised by such restrictions.

ADD REPLYlink written 2.1 years ago by NAVID.BAVI0
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