I had run tophat with following options:
tophat --bowtie1 -p 6 -o CT16 -r 150 --mate-std-dev 75 --no-discordant --no-mixed --transcriptome-index Transcriptome
and I get tophat_reports running error:
[2014-05-27 15:47:24] Reporting output tracks
Error running /usr/local/bin/tophat_reports
Another sample of the same study is not giving any problem. The difference between these two filesets is that the one that worked is relatively smaller ~6GB per pair compared to ~18GB per pair for the one that didn't work. Assuming that it could have been a runtime error I ran tophat resume
(tophat -R CT16) but still it gave the same error. I have seen other people also reporting the same error but the precise reason is not mentioned anywhere. I checked if it is because of lack of space but i have ~500GB free!! There are no RAM issues either. I am using tophat v2.0.11. Is this a bug? How do I fix it?