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Old 09-04-2012, 06:30 AM   #1
arrchi
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Location: ma

Join Date: Mar 2011
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Default tophat warning and files in /tmp are not cleared

Hi there,

I ran tophat on human 50-bp PE reads generated by HiSeq 2000, it seems it finished because all files should be generated by tophat were generated (such as bam and bed files), but the files in /tmp folder are not cleared, and there is a warning: "couldn't remove all temporary files in ../tmp/".

I wonder what the files in /tmp are still exist? Does it indicate is a big problem? Or is it a new feature of tophat (version 2.0.4)?

I did not use "keep-tmp" option.

Has anybody had the same warning before?

Thanks.
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Old 09-04-2012, 10:51 AM   #2
arrchi
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Posts: 46
Default update

I re-installed tophat (v 2.0.4) and the problem is fixed
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