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Old 05-22-2009, 08:52 AM   #1
Location: ca

Join Date: Feb 2008
Posts: 39
Default TopHat error: disk full

Hi All
I am analyzing one PE lane with read files 's_3_1_sequence.txt and 's_3_2_sequence.txt;
here are the first lines the read files:


M1-80330:reads jdhahbi$

the command-line I used:
tophat -r 200 /mydir/bowtie- s_3_1_sequence.txt s_3_2_sequence.txt

the output with the error is below; I checked the disk space and there are more than 100 GB available:

[Thu May 21 16:53:57 2009] Beginning TopHat run (v1.0.7)
[Thu May 21 16:53:57 2009] Preparing output location ./tophat_out/
[Thu May 21 16:53:57 2009] Checking for Bowtie index files
[Thu May 21 16:53:57 2009] Checking for reference FASTA file
[Thu May 21 16:53:57 2009] Checking for Bowtie
Bowtie version:
[Thu May 21 16:53:58 2009] Checking reads
seed length: 34bp
format: fastq
quality scale: phred
Splitting reads into 1 segments
[Thu May 21 17:00:49 2009] Mapping reads against h_sapiens_asm with Bowtie
Splitting reads into 1 segments
[Thu May 21 18:03:09 2009] Mapping reads against h_sapiens_asm with Bowtie
[Thu May 21 18:51:52 2009] Searching for junctions via coverage islands
[Thu May 21 18:59:12 2009] Searching for junctions via mate-pair closures
[Fri May 22 05:40:00 2009] Retrieving sequences for splices
[Fri May 22 05:48:53 2009] Indexing splices
Index is corrupt: File size for ./tophat_out/tmp/segment_juncs.1.ebwt should have been 3799224901 but is actually -495742395.
Please check if there is a problem with the disk or if disk is full.
Error: Splice sequence indexing failed

Any suggestions are appreciated,

joseph is offline   Reply With Quote
Old 05-22-2009, 09:56 AM   #2
Cole Trapnell
Senior Member
Location: Boston, MA

Join Date: Nov 2008
Posts: 212

Hi Joseph,

This is most likely the same bug as a few other users have reported, where with short, paired reads, it's possible for the splice index to become unreasonably large and that may be tripping Bowtie's index integrity checks. I have fixed this in my source tree, and the new version should be released next week. I am just tying up a few loose ends with the latest build.

Sorry for the inconvenience. If you'd like to test out a snapshot of the code to see if it resolves the problem for you, please email me directly.
Cole Trapnell is offline   Reply With Quote
Old 12-01-2010, 05:17 PM   #3
Junior Member
Location: Basel

Join Date: Jun 2009
Posts: 6

Hi Cole,

I had a disk quote problem too. TopHat produced: >1.5TB!

I use v1.1.4 with the default setting to map ~1M SE total RNA reads which are 20-37 nt long. The huge file is produced by long_spanning_reads after junction mapping step.

Any ideas?

biterbilen is offline   Reply With Quote
Old 12-02-2010, 03:46 AM   #4
Location: College Park

Join Date: Oct 2010
Posts: 27

This is a bug due to variable read length, which we fixed, the next version will include the fix.
Daehwan is offline   Reply With Quote

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