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?