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Old 03-11-2011, 01:56 PM   #1
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Location: San Francisco, CA

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Default Error joing segment hits in tophat

Can anyone offer advice on what to do about this error -11, or even what it means:

[Fri Mar 11 15:54:38 2011] Beginning TopHat run (v1.2.0)
[Fri Mar 11 15:54:38 2011] Preparing output location tophat_out/cDNA/organ/
[Fri Mar 11 15:54:38 2011] Checking for Bowtie index files
[Fri Mar 11 15:54:38 2011] Checking for reference FASTA file
[Fri Mar 11 15:54:38 2011] Checking for Bowtie
Bowtie version:
[Fri Mar 11 15:54:38 2011] Checking for Samtools
Samtools Version: 0.1.12a
[Fri Mar 11 15:54:40 2011] Checking reads
min read length: 21bp, max read length: 991bp
format: fasta
[Fri Mar 11 15:54:41 2011] Mapping reads against Anocarol2.0.61_toplevel with Bowtie
[Fri Mar 11 15:55:05 2011] Joining segment hits
Error: Segment join failed with err = -11

Last edited by Wallysb01; 03-11-2011 at 02:43 PM.
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Old 03-18-2011, 07:40 AM   #2
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Location: Sao Paulo, Brazil

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We are experiencing exactly the same error mentioned in the post above running a particular batch of 454 RNAseq. The same version of TopHat (v1.2.0) was used.
I could not find a list with details of TopHat error codes. That would be useful for troubleshooting.
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