I'm working on Cloudman doing RNASeq transcriptome analysis. I've made BAM file using TopHat2 and RefSeq mm10 gtf file for Junctions.
I'm now trying to run them through HTSeq-Count to obtain reads per gene but after a few successful run [with disappointing results] I'm now getting failed runs with the following error:
Fatal error: Unknown error occured 100000 GFF lines processed. 200000 GFF lines processed. 300000 GFF lines processed.
16400000 SAM alignment records processed. 16497350 SAM alignments processed. [bam_header_read] EOF marker is absent. The input is probably truncated. [sam_header_read2] 66 sequences loaded. [sam_read1] reference '' is recognized as '*'. Parse error at line 1: invalid CIGAR character
It may be that my previous successful runs were with BAM files with which I used an Ensembl gtf file, so the nomenclature may be different? Any thoughts?