We're trying to align a set of stranded, paired-end reads to the rat genome with Tophat. Tophat runs through the early stages just fine, but then halts during segment search -- no errors, no warnings, nothing. This is an example of our output:
We've got a big machine for this (512GB memory, ~7TB free disk space, 24 processors) so I cannot believe it's a system issue.
I'm going to try several avenues: I'll run as root in case file permissions are an issue, I'll try running it on a tiny subset of the data to see if it's related to the reads. Otherwise I'm a bit stumped.
I should mention we're using Python 2.7.3 and running under Bio-Linux (Ubuntu 12.04).
Any ideas greatly appreciated!
Code:
[2014-05-07 13:22:44] Preparing reads left reads: min. length=101, max. length=101, 27329923 kept reads (10347 discarded) right reads: min. length=101, max. length=101, 27195050 kept reads (145220 discarded) [2014-05-07 13:35:52] Mapping left_kept_reads to genome Rn5 with Bowtie2 [2014-05-07 14:34:36] Mapping left_kept_reads_seg1 to genome Rn5 with Bowtie2 (1/3) [2014-05-07 15:06:40] Mapping left_kept_reads_seg2 to genome Rn5 with Bowtie2 (2/3) [2014-05-07 15:43:09] Mapping left_kept_reads_seg3 to genome Rn5 with Bowtie2 (3/3) [2014-05-07 16:34:38] Mapping right_kept_reads to genome Rn5 with Bowtie2 [2014-05-07 17:36:40] Mapping right_kept_reads_seg1 to genome Rn5 with Bowtie2 (1/3) [2014-05-07 18:11:10] Mapping right_kept_reads_seg2 to genome Rn5 with Bowtie2 (2/3)
I'm going to try several avenues: I'll run as root in case file permissions are an issue, I'll try running it on a tiny subset of the data to see if it's related to the reads. Otherwise I'm a bit stumped.
I should mention we're using Python 2.7.3 and running under Bio-Linux (Ubuntu 12.04).
Any ideas greatly appreciated!
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