I've had a long running tophat2 end with an error after 9 nine days:
Is there anyway to restart it at the point of failure on a machine with more memory rather than waiting another 9 nine days...?
...
[2012-06-07 12:57:34] Joining segment hits
[2012-06-07 17:58:10] Reporting output tracks
[FAILED]
Error: [Errno 12] Cannot allocate memory
Found 280164 junctions from happy spliced reads
[FAILED]
Error: [Errno 2] No such file or directory: './tophat_out/tmp/accepted_hits7_sorted.bam'
Found 280164 junctions from happy spliced reads
[2012-06-07 12:57:34] Joining segment hits
[2012-06-07 17:58:10] Reporting output tracks
[FAILED]
Error: [Errno 12] Cannot allocate memory
Found 280164 junctions from happy spliced reads
[FAILED]
Error: [Errno 2] No such file or directory: './tophat_out/tmp/accepted_hits7_sorted.bam'
Found 280164 junctions from happy spliced reads
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