I have a couple of tumor-germline paired samples and I tried running cnvkit this way:
cnvkit.py batch *Tumor.bam --normal *Normal.bam \ --targets my_baits.bed \ --fasta hg19.fasta --access data/access-5kb-mappable.hg19.bed \ --output-reference my_reference.cnn --output-dir results/ \ --diagram --scatter
When I do this, I get the following output and the analysis stops with the creation of a cnr file. I do not see a cns file/the scatter and diagram pdfs being produced.
> Correcting for GC bias... Correcting for RepeatMasker bias... > Loading sampleA_Normal.antitargetcoverage.cnn > Correcting for GC bias... Correcting for RepeatMasker bias... > Loading sampleA_Normal.antitargetcoverage.cnn > Correcting for GC bias... Correcting for RepeatMasker bias... > ....local/lib/python3.6/site-packages/pandas/core/frame.py:7116: > FutureWarning: Sorting because non-concatenation axis is not aligned. > A future version of pandas will change to not sort by default. > To accept the future behavior, pass 'sort=False'. > To retain the current behavior and silence the warning, pass > 'sort=True'. > > sort=sort, Calculating average bin coverages Calculating bin spreads > Targets: 1162 (13.7499%) bins failed filters (log2 < -5.0, log2 > 5.0,> spread > 1.0) > Antitargets: 19439 (100.0000%) bins failed filters > Wrote my_reference.cnn with 27890 regions > Running 1 samples in 8 processes (that's 8 processes per bam) > Running the CNVkit pipeline on SampleB_Tumor.bam > ... Processing reads in SampleB_Tumor.bam > Time: 76.712 seconds > (63585 reads/sec, 110 bins/sec) > Summary: #bins=8451, #reads=4877720, mean=577.1767, min=0.0, max=3535.910891089109 > Percent reads in regions: 92.246 (of 5287755 mapped) > Wrote SampleB_Tumor.targetcoverage.cnn with 8451 regions > Processing reads in SampleB_Tumor.bam > Time: 2.223 seconds (0 reads/sec, 8746 bins/sec) > Summary: #bins=19439, #reads=0, mean=0.0000, min=0.0, max=0.0 > Percent reads in regions: 0.000 (of 5287755 mapped) > Wrote SampleB_Tumor.antitargetcoverage.cnn with 19439 regions > Processing target: SampleB_Tumor > Keeping 7289 of 8451 bins Correcting for GC bias... > Correcting for density bias... > Processing antitarget: SampleB_Tumor > Keeping 0 of 19439 bins > WARNING: most bins have no or very low coverage; check that the right BED file was used > Wrote SampleB_Tumor.cnr with 7289 regions > Segmenting SampleB_Tumor.cnr > ... Segmenting with method 'cbs', significance threshold 0.0001, in 8 processes > .../cnvkit/cnvlib/smoothing.py:197: > RuntimeWarning: invalid value encountered in greater bad_idx = (y > > x.max()) | (y < x.min()) > .../cnvkit/cnvlib/smoothing.py:197: > RuntimeWarning: invalid value encountered in less bad_idx = (y > > x.max()) | (y < x.min())
I see the RuntimeWarnings repeat several times and the command ends with no other output being produced. Has anyone else experienced this?
Any input is appreciated! My cnvkitversion is 0.9.6.dev0 and python version is 3.6.1 . Thank you.