Tophat Reporting Output Step Is Very Slow

Question

[Nicolas Rosewick]

Hi,

For on of my samples, tophat 2 is stuck into the reporting output step. In the tmp/ directory, it seems that the accepted_hits.bam is currently been constructed (but very very slowly). It's strange because on my other samples, it works well. And this sample is not different compared to the other (in size).

FYI, I use tophat 2.0.0.3 with bowtie 2 beta 6

Anyone has an idea to resolve this problem ..

Thanks,

N.

Answer 1

[Nicolas Rosewick]

Still running and accepted_hits.bam still in construction , so I guess tophat execution is fine but I've no idea why it takes so long to report output (now it's been 4 days...)

[Dan D]

how many threads are you using, and what reference genome are you mapping against? Is this genome different than ones you have used previously?

[Nicolas Rosewick]

I contact the author of tophat 2 and he resolved the problem in the last release :)

[karl.stamm]

Please tell us about it so that this thread can have some value the next time this problem arises.