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Old 02-10-2010, 10:26 AM   #1
jling
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Default Tophat - Error using Paired End

I tried using Tophat for paired end analysis.

[Tue Feb 9 23:26:32 2010] Mapping reads against m_musculus with Bowtie
[Tue Feb 9 23:46:06 2010] Joining segment hits
[Tue Feb 9 23:53:48 2010] Mapping reads against m_musculus with Bowtie
[Tue Feb 10 00:13:47 2010] Joining segment hits
[Tue Feb 10 00:20:47 2010] Searching for junctions via segment mapping
Warning: junction database is empty!
[Tue Feb 10 01:40:00 2010] Joining segment hits
IOError: [Errno 28] No space left on drive

Are these two separate errors? I'm going to try repartitioning so my harddrive has more space but I would have thought that ~30Gb would have been more than sufficient. Does paired-end analysis require that much more space? I've run non paired end samples successfully with Tophat on the same machine.

If anyone can help, thanks!
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