tophat 1.2 multi thread mode error

altodor · 01-26-2011, 12:03 PM

Hi all,
running tophat 1.2 with 8 threads the following errors occur

srun: error: q44: tasks 0-6: Exited with exit code 1
And one thread continues running.

Also it seems like there is a conflict between threads in creating outputdirectory:
:
[Wed Jan 26 21:17:51 2011] Preparing output location tophat_04/
Traceback (most recent call last):
File "/soft/tophat-1.2.0/tophat", line 2347, in ?
sys.exit(main())

OSError: [Errno 17] File exists: '/tophat_04/'
os.mkdir(output_dir)
File "/soft/tophat-1.2.0/tophat", line 2230, in main
sys.exit(main())

Have anyone got the same problems?

Jon_Keats · 01-26-2011, 02:31 PM

I've been using this version with 8 threads for a week now with no problems. did you build from source or download a binary? When in doubt build from source

altodor · 02-16-2011, 12:02 AM

Hello, thank you!
It really worked with 8 threads. First problem was, that I ran 16 treads of tophat on 8 cores and they tried to read to the same folder.
Second problem, as appeared later, was the empty reference file. They say at tophat manual, that reference.fa will be built automatically with the first run of tophat. Nut I built in manually using bowtie-inspect. Now tophat produces junction database!

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01-26-2011, 12:03 PM	#1
altodor Member Location: Sweden Join Date: Nov 2009 Posts: 12	tophat 1.2 multi thread mode error Hi all, running tophat 1.2 with 8 threads the following errors occur srun: error: q44: tasks 0-6: Exited with exit code 1 And one thread continues running. Also it seems like there is a conflict between threads in creating outputdirectory: : [Wed Jan 26 21:17:51 2011] Preparing output location tophat_04/ Traceback (most recent call last): File "/soft/tophat-1.2.0/tophat", line 2347, in ? sys.exit(main()) OSError: [Errno 17] File exists: '/tophat_04/' os.mkdir(output_dir) File "/soft/tophat-1.2.0/tophat", line 2230, in main sys.exit(main()) Have anyone got the same problems? Last edited by altodor; 01-27-2011 at 12:23 AM.

02-16-2011, 12:02 AM	#3
altodor Member Location: Sweden Join Date: Nov 2009 Posts: 12	Problem solved Hello, thank you! It really worked with 8 threads. First problem was, that I ran 16 treads of tophat on 8 cores and they tried to read to the same folder. Second problem, as appeared later, was the empty reference file. They say at tophat manual, that reference.fa will be built automatically with the first run of tophat. Nut I built in manually using bowtie-inspect. Now tophat produces junction database!

01-26-2011, 02:31 PM	#2
Jon_Keats Senior Member Location: Phoenix, AZ Join Date: Mar 2010 Posts: 279	I've been using this version with 8 threads for a week now with no problems. did you build from source or download a binary? When in doubt build from source