Strange Tophat crash

sphil · 05-23-2011, 01:34 AM

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

darked89 · 05-23-2011, 02:14 AM

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

sphil · 05-23-2011, 03:11 AM

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....)

sphil · 05-23-2011, 08:15 AM

Hey folks,

as said before. The output folder are completly empty...

DocWalsh · 06-03-2011, 08:49 AM

I am having the same problem. Has anybody found a solution yet?

sphil · 06-07-2011, 02:55 AM

installing ubuntu 10.4 again (and not using newest version) solved the problem....

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05-23-2011, 01:34 AM	#1
sphil Senior Member Location: Stuttgart, Germany Join Date: Apr 2010 Posts: 192	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

05-23-2011, 02:14 AM	#2
darked89 Member Location: Barcelona, Spain Join Date: Jun 2009 Posts: 36	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

05-23-2011, 03:11 AM	#3
sphil Senior Member Location: Stuttgart, Germany Join Date: Apr 2010 Posts: 192	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....)

05-23-2011, 08:15 AM	#4
sphil Senior Member Location: Stuttgart, Germany Join Date: Apr 2010 Posts: 192	Hey folks, as said before. The output folder are completly empty...

06-03-2011, 08:49 AM	#5
DocWalsh Junior Member Location: Jacksonville Florida Join Date: May 2011 Posts: 1	I am having the same problem. Has anybody found a solution yet?

06-07-2011, 02:55 AM	#6
sphil Senior Member Location: Stuttgart, Germany Join Date: Apr 2010 Posts: 192	installing ubuntu 10.4 again (and not using newest version) solved the problem....