correctGCbias error

[LavanyaRanganathan95]

Hello,

version: deeptools 3.5.4.post1 python version: Python 3.9.16

I am trying to run correctGCbias as a part of a CNV calling pipeline. As mentioned in your manual, I used computeGCbias to generate GC_freq.txt. computeGCBias -b sample.bam --effectiveGenomeSize 2701495761 -l 300 --genome hg38.2bit --GCbiasFrequenciesFile gc_freq.txt --biasPlot gc_sample.svg -v

The output from computeGCbias was as follows: gc_freq.txt

I then used the GC_freq.txt for correctGCbias as follows; correctGCBias -b sample.bam --effectiveGenomeSize 2701495761 --genome hg38.2bit -freq GC_freq.txt -o sample.bg -p 3 -v I have attached the output as a log file here. log_correctGCbias.txt

Do you have any idea as to why I get such an error message?

Looking forward to hearing from you Thanks and regards Lavanya

[dpryan79]

Do you really need to run GC bias correction? This generally hasn't been needed in many years and this GC bias tools are deprecated.

[WardDeb]

Closing due to inactivity.