Hi all, I have started human RNA-seq data analysis recently. After the mapping of draft genome against the GRCh38 & GTF by using TopHat and STAR, I tired to quantify them. For quantification I have using HTSeq-count, after the HTSeq-count command was executed am getting this error. Can anyone help me to rectify this.
Command : htseq-count -s no -i gene_id -m intersection-nonempty /home/Documents/RNA/TopHat/TopHat_out/accepted_hits.bam /home/Documents/RNA/Reference/Hsapiens_GRCh38.gtf > /home/Documents/RNA/TopHat/TopHat_out/HTseq/RNA.count
100000 GFF lines processed.
200000 GFF lines processed.
300000 GFF lines processed.
400000 GFF lines processed.
500000 GFF lines processed.
600000 GFF lines processed.
700000 GFF lines processed.
800000 GFF lines processed.
900000 GFF lines processed.
1000000 GFF lines processed.
1100000 GFF lines processed.
1200000 GFF lines processed.
1300000 GFF lines processed.
1400000 GFF lines processed.
1500000 GFF lines processed.
1600000 GFF lines processed.
1700000 GFF lines processed.
1800000 GFF lines processed.
1900000 GFF lines processed.
Error occured when processing GFF file (line 1941614 of file /home/Documents/RNA/Reference/Hsapiens_GRCh38.gtf): [Errno 5] Input/output error [Exception type: IOError, raised in __init__.py:54]
Did you check what's at that line? Can you post it here?