Hello Everyone,

I'm using tophat 2.1.1 and bowtie2 2.2.9 versions for mapping reads to reference genome. I had run the following command for 6 samples.

tophat -p 8 -G genes.gtf -o reference genome S1_1.fq S1_2.fq

For three samples this worked and gave the accepted_hits.bam file as output. Along with this I also got align_summary.txt, deletions.bed, insertions.bed, junctions.bed, prep_reads.info, logs (folder) and output run summary file.

In the End of the Output run summary file following is mentioned:

• A summary of the alignment counts can be found in align_summary.txt
• Run complete: 05:48:48 elapsed

For one sample it gave accepted_hits.bam file and also gave "tmp" folder and in the end of the output run summary file it gave "Reporting output tracks". There is no Run complete.

For other two samples it gave deletions.bed, insertions.bed, junctions.bed, prep_reads.info, logs (folder), tmp(folder) and output run summary file. In the end of the output run summary file it gave "Reporting output tracks". There is no Run complete. And there are no accepted_hits.bam output files.

Can anyone tell why there is no accepted_hits.bam file for two of these samples. I don't understand why it is missing.

Thank you !