Hi
I know this error has been reported before for previous versions of Tophat2; well, its still happening in 2.0.10. As suggested by the tophat webpage, I've posted a report in the tuxedo-tools-users google group that has remained stubbornly unanswered and un-addressed.
Changing the number or cpus, amount of RAM or changing the --coverage-search/--no-coverage-search flags doesn't seem to make any difference.
Originally I thought it was associated with the -G <gtffile> flag, but now I am getting it for runs even without this flag.
It is an odd error because it seems to be data-dependant. The same command-line, run on two different sets of 100bp paired end data (even if one is just a trimmed version of the other), can result in one set running smoothly and the other failing.
If anyone has any insights on this I'd love to hear it. Failing that, I think its time for a move to STAR
I know this error has been reported before for previous versions of Tophat2; well, its still happening in 2.0.10. As suggested by the tophat webpage, I've posted a report in the tuxedo-tools-users google group that has remained stubbornly unanswered and un-addressed.
Changing the number or cpus, amount of RAM or changing the --coverage-search/--no-coverage-search flags doesn't seem to make any difference.
Originally I thought it was associated with the -G <gtffile> flag, but now I am getting it for runs even without this flag.
It is an odd error because it seems to be data-dependant. The same command-line, run on two different sets of 100bp paired end data (even if one is just a trimmed version of the other), can result in one set running smoothly and the other failing.
If anyone has any insights on this I'd love to hear it. Failing that, I think its time for a move to STAR
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