Hello,
I am using to call indels from cancer data. So far I have been successfull with Stage 1, 2 & 3. When I try to use the mergeOutpuDiploid in stage 4, I get the following error:
./mergeOutputDiploid.py --inputFiles /home/ryajnik/binaries/ERR035488_cutfile.dindel_stage2_output_windows.2.glf.txt --outputFile v
ariantCalls.VCF --ref /home/ryajnik/samtools-0.1.18/genome.fa
WARNING: additional columns in line 1 of file /home/ryajnik/binaries/ERR035488_cutfile.dindel_stage2_output_windows.2.glf.txt were ignored
File msg does not exist
. Aborting.
An error occurred!
Can anyone point me on how to troubleshoot?
Thanks,
I am using to call indels from cancer data. So far I have been successfull with Stage 1, 2 & 3. When I try to use the mergeOutpuDiploid in stage 4, I get the following error:
./mergeOutputDiploid.py --inputFiles /home/ryajnik/binaries/ERR035488_cutfile.dindel_stage2_output_windows.2.glf.txt --outputFile v
ariantCalls.VCF --ref /home/ryajnik/samtools-0.1.18/genome.fa
WARNING: additional columns in line 1 of file /home/ryajnik/binaries/ERR035488_cutfile.dindel_stage2_output_windows.2.glf.txt were ignored
File msg does not exist
. Aborting.
An error occurred!
Can anyone point me on how to troubleshoot?
Thanks,
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