dindel: stage 4 crach

[ndiaye]

Hi All,

I've successfully went through first three stages of dindel variant calling, but getting the following error message when using mergeOutputPooled.py to generate the final vcf file. Note that cases_A.gene.ABCA1.glf.txt contain the name of my 10 glf.txt files.
Thank you for helping me to fix that.

[ndiayea@topaz] /shares/data/illumina_datastore/MI_20100215/analyses/Indels_calling/BAM_files/vcf_cases $ python /shares/home/ndiayea/programs/dindel-1.01-python/mergeOutputPooled.py --inputFiles ABCA1_cases_outputfiles.txt --outputFile ABCA1_cases_variantCalls.VCF --ref /shares/data/genome_datastore/homo_sapiens/Homo_sapiens_assembly18.fasta --numSamples 500 --numBamFiles 10
Reading cases_A.gene.ABCA1.glf.txt
An error occurred!
Traceback (most recent call last):
File "/shares/home/ndiayea/programs/dindel-1.01-python/mergeOutputPooled.py", line 620, in ?
main(sys.argv[1:])
File "/shares/home/ndiayea/programs/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 "/shares/home/ndiayea/programs/dindel-1.01-python/mergeOutputPooled.py", line 336, in processPooledGLFFiles
raise NameError('Inconsistent glf files! Is the number of BAM files correctly specified?')
NameError: Inconsistent glf files! Is the number of BAM files correctly specified?

[nilshomer]

Note that you posted the same question in three different places (two new threads). Please do not spam the different forums like this; please have patience.

[ndiaye]

Sorry I thought I was not in the wright category