HISAT2 SRR error

0

Entering edit mode

5.5 years ago

NAVID.BAVI • 0

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

rna-seq alignment SRA SRR HISAT2 • 1.9k views

ADD COMMENT • link updated 5.5 years ago by GenoMax 141k • written 5.5 years ago by NAVID.BAVI • 0

1

Entering edit mode

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

ADD REPLY • link 5.5 years ago by ATpoint 82k

0

Entering edit mode

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

ADD REPLY • link 5.5 years ago by NAVID.BAVI • 0

Login before adding your answer.