Hi there,
I just installed the new TopHat version 2.0.7 along with the new Bowtie 2.0.6. Everything works fine and without errors, except for the fact that it seems to run on only one core. Before this update, I used TopHat 2.0.6 with Bowtie 2.0.4 and -p 8 worked absolutely perfectly. Now with the new version, I use the exact same command, including -p 8, but the runs take forever and the CPU usage shows only 100% CPU usage instead of the expected 800%. Should I downgrade to Bowtie 2.0.5 (as this is the version stated in the news post of TopHat 2.0.7) or is this a bug? Does anyone else have this problem?
Jens
Edit: The complete command I'm using is the following:
tophat -r 50 --mate-std-dev 30 -p 8 --no-coverage-search --microexon-search --library-type fr-unstranded
I just installed the new TopHat version 2.0.7 along with the new Bowtie 2.0.6. Everything works fine and without errors, except for the fact that it seems to run on only one core. Before this update, I used TopHat 2.0.6 with Bowtie 2.0.4 and -p 8 worked absolutely perfectly. Now with the new version, I use the exact same command, including -p 8, but the runs take forever and the CPU usage shows only 100% CPU usage instead of the expected 800%. Should I downgrade to Bowtie 2.0.5 (as this is the version stated in the news post of TopHat 2.0.7) or is this a bug? Does anyone else have this problem?
Jens
Edit: The complete command I'm using is the following:
tophat -r 50 --mate-std-dev 30 -p 8 --no-coverage-search --microexon-search --library-type fr-unstranded
Comment