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Old 05-23-2011, 01:34 AM   #1
sphil
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Location: Stuttgart, Germany

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Default Strange Tophat crash

Hey guys,

i'm going to align 50nt illumina paired end with TopHat.
When i start the run with : tophat -r 100 -p 2 bowtie index readfiles all looks quite nice.
The first output i get is:

[Mon May 23 10:31:32 2011] Beginning TopHat run (v1.2.0)
-----------------------------------------------
[Mon May 23 10:31:32 2011] Preparing output location ./tophat_out/
[Mon May 23 10:31:32 2011] Checking for Bowtie index files
[Mon May 23 10:31:32 2011] Checking for reference FASTA file
[Mon May 23 10:31:32 2011] Checking for Bowtie
Bowtie version: 0.12.7.0
[Mon May 23 10:31:32 2011] Checking for Samtools
Samtools Version: 0.1.16
[Mon May 23 10:31:32 2011] Checking reads
min read length: 50bp, max read length: 50bp
format: fastq
quality scale: phred33 (default)

BUT: after that the programm terminates and no computation was done. Any hints how to solve the problem?


Thanks in advance,

Philip
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Old 05-23-2011, 02:14 AM   #2
darked89
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1) what was the command line you used to run tophat?
2) tophat creates (unless modified) tophat_out directory with logs/ and tmp/ subdirs.
What is the content of tophat_out/logs/run.log?
3) kindly list the content (= file names) of all stuff in tophat_out
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Old 05-23-2011, 03:11 AM   #3
sphil
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1) what was the command line you used to run tophat?

tophat -r 100 -p 2 ~/HSmtDNAIndex ~/HSmtDNAReads

2) tophat creates (unless modified) tophat_out directory with logs/ and tmp/ subdirs.
What is the content of tophat_out/logs/run.log?

just the command line. No other output there

3) kindly list the content (= file names) of all stuff in tophat_out

almost empty. clearly no files which could contain a result. (i am not in my office right now, will reply one more time when i am back....)
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Old 05-23-2011, 08:15 AM   #4
sphil
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Hey folks,

as said before. The output folder are completly empty...
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Old 06-03-2011, 08:49 AM   #5
DocWalsh
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I am having the same problem. Has anybody found a solution yet?
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Old 06-07-2011, 02:55 AM   #6
sphil
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installing ubuntu 10.4 again (and not using newest version) solved the problem....
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