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Old 07-08-2012, 09:55 PM   #1
dmdrmagbanua
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Location: Philippines

Join Date: Jul 2012
Posts: 1
Default Problem with generating GLF files in Dindel

Hi all,

I am running dindel in our server, and I keep having the following error:

Traceback (most recent call last):
File "/home/applications/dindel-1.01-python/mergeOutputPooled.py", line 620, in <module>
main(sys.argv[1:])
File "/home/applications/dindel-1.01-python/mergeOutputPooled.py", line 613, in main
processPooledGLFFiles(glfFilesFile = options.inputFiles, maxHPLen = options.maxHPLen, refFile = options.refFile, outputVCFFile = options.outputFile, doNotFilterOnFR = (not options.filterFR), filterQual = int(options.filterQual), numSamples = int(options.numSamples), numBamFiles = int(options.numBAMFiles))
File "/home/applications/dindel-1.01-python/mergeOutputPooled.py", line 277, in processPooledGLFFiles
raise NameError("GLF files are corrupt. Could not find all required columns.")

I am new to this tool, which is why I rely heavily on the manual. I followed every thing in the instructions (changing some file names as necessary), which is why I got baffled when I got the said error. Can anybody enlighten me on this?

Thanks in advance for any help!

DM
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Old 08-07-2012, 08:09 AM   #2
clarissaboschi
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Join Date: Apr 2010
Posts: 63
Default

Which step are you running? The last?
I am trying to use the same software, and I had an error message like "GLF files are corrupt" in the last step, but my problem was because in the txt file with all glf files names I put the path and the name of the files, when I removed the paths, it worked...

I am also using the mergeOutputPooled.py option, but in the end I had a VCF file empty and I dont know what is the problem!
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Old 08-14-2012, 12:33 AM   #3
dmagbanua
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Location: Philippines

Join Date: Apr 2012
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Default

Quote:
Originally Posted by clarissaboschi View Post
Which step are you running? The last?
I am trying to use the same software, and I had an error message like "GLF files are corrupt" in the last step, but my problem was because in the txt file with all glf files names I put the path and the name of the files, when I removed the paths, it worked...

I am also using the mergeOutputPooled.py option, but in the end I had a VCF file empty and I dont know what is the problem!
Hi there. This message was sent to my SPAM folder, which is why I wasn't able to check this immediately. Anyway...

I think it was the last part? I found out that the input for the last step should contain the absolute paths of the .glf files. When I did this, dindel finally worked.
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