ZeroDivisionError when finding amplified intervals

[auberginekenobi]

Hi Jens, I'm getting a ZeroDivisionError while generating the [SAMPLE]_CNV_SEEDS.bed file from cnvkit results for a few of my samples. Could be a problem with the sample or the bam file but I wonder if you've seen it before.

Log: (stdout + stderr) (base) [ochapman@comet-ln3 AmpliconArchitect]$ cat [SAMPLE]/slurm-%x-33869064.out /home/ochapman/miniconda3/envs/cnvkit/lib/python3.7/site-packages/skgenome/intersect.py:15: FutureWarning: pandas.core.index is deprecated and will be removed in a future version. The public classes are available in the top-level namespace. from pandas.core.index import Int64Index CNVkit 0.9.6 Wrote /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/GRCh37_cnvkit_filtered_ref.target-tmp.bed with 565907 regions Wrote /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/GRCh37_cnvkit_filtered_ref.antitarget-tmp.bed with 0 regions Running 1 samples in 16 processes (that's 16 processes per bam) Running the CNVkit pipeline on [SAMPLE]/[SAMPLE].bam ... Processing reads in [SAMPLE].bam Time: 365.348 seconds (3206112 reads/sec, 1549 bins/sec) Summary: #bins=565907, #reads=1171346894, mean=2069.8576, min=0.0, max=111391.54455445544 Percent reads in regions: 83.248 (of 1407057807 mapped) Wrote /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/[SAMPLE].targetcoverage.cnn with 565907 regions Skip processing ICGC_MB92.bam with empty regions file /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/GRCh37_cnvkit_filtered_ref.antitarget-tmp.bed Wrote /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/[SAMPLE].antitargetcoverage.cnn with 0 regions Processing target: [SAMPLE] Keeping 565907 of 565907 bins Correcting for GC bias... Processing antitarget: [SAMPLE] Wrote /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/[SAMPLE].cnr with 565907 regions Segmenting /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/[SAMPLE].cnr ... Segmenting with method 'cbs', significance threshold 1e-06, in 16 processes Dropped 1 outlier bins: chromosome start end gene depth log2 weight 0 1 234757235 234762234 - 160.511102 1.965995 0.942141 Dropped 1 / 20650 bins on chromosome 1 Dropped 1 outlier bins: chromosome start end gene depth log2 weight 0 2 230338821 230343821 - 247.3222 2.550093 0.942329 Dropped 1 / 29186 bins on chromosome 2 Dropped 1 outlier bins: chromosome start end gene depth log2 weight 0 13 67325231 67330231 - 226.8016 2.296797 0.942329 Dropped 1 / 13448 bins on chromosome 13 /home/ochapman/miniconda3/envs/cnvkit/lib/python3.7/site-packages/skgenome/intersect.py:15: FutureWarning: pandas.core.index is deprecated and will be removed in a future version. The public classes are available in the top-level namespace. from pandas.core.index import Int64Index Segmenting with method 'cbs', significance threshold 0.0001, in 16 processes Dropped 1 outlier bins: chromosome start end gene log2 depth weight 0 1 234757235 234762234 - 1.966 160.511 0.942141 Dropped 1 / 20650 bins on chromosome 1 Dropped 1 outlier bins: chromosome start end gene log2 depth weight 0 2 230338821 230343821 - 2.55009 247.322 0.942329 Dropped 1 / 29186 bins on chromosome 2 Dropped 1 outlier bins: chromosome start end gene log2 depth weight 0 13 67325231 67330231 - 2.2968 226.802 0.942329 Dropped 1 / 13448 bins on chromosome 13 Dropped 3 outlier bins: chromosome start end gene log2 depth weight 0 Y 977526 982534 - -12.2974 0.003794 0.943837 1 Y 1269227 1274220 - -12.2999 0.004006 0.941010 2 Y 1339135 1344128 - -12.2267 0.004006 0.941010 Dropped 3 / 1971 bins on chromosome Y Wrote /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/[SAMPLE].cns with 476 regions GRCh37 Traceback (most recent call last): File "/oasis/projects/nsf/ddp360/collab/bin/AmpliconArchitect/AmpliconArchitect/src/amplified_intervals.py", line 91, in <module> rdList = hg.interval_list([r for r in rdList if float(r.info[1]) > GAIN + 2 * max(1.0, bamFileb2b.median_coverage(refi=r)[0] / bamFileb2b.median_coverage()[0]) - 2]) ZeroDivisionError: float division by zero Running PrepareAA on sample: [SAMPLE] /home/ochapman/miniconda3/envs/cnvkit/bin//python /home/ochapman/miniconda3/envs/cnvkit/bin//cnvkit.py batch -m wgs -y -r /oasis/projects/nsf/ddp360/collab/bin/AmpliconArchitect/data_repo/GRCh37/GRCh37_cnvkit_filtered_ref.cnn -p 16 -d /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/ /oasis/projects/nsf/ddp360/collab/data/icgc//[SAMPLE]/[SAMPLE].bam Set Rscript flag: --rscript-path /home/ochapman/miniconda3/envs/cnvkit/bin/Rscript /home/ochapman/miniconda3/envs/cnvkit/bin//python /home/ochapman/miniconda3/envs/cnvkit/bin//cnvkit.py segment /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/[SAMPLE].cnr --rscript-path /home/ochapman/miniconda3/envs/cnvkit/bin/Rscript -p 16 -o /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/[SAMPLE].cns Running amplified_intervals python /oasis/projects/nsf/ddp360/collab/bin/AmpliconArchitect/AmpliconArchitect/src/amplified_intervals.py --ref GRCh37 --bed /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/cnvkit_output/[SAMPLE]_CNV_GAIN.bed --bam /oasis/projects/nsf/ddp360/collab/data/icgc//[SAMPLE]/[SAMPLE].bam --gain 4.0 --cnsize_min 50000 --out /oasis/projects/nsf/ddp360/collab/projects/ecDNA/AmpliconArchitect/[SAMPLE]/[SAMPLE]_AA_CNV_SEEDS Completed

[jluebeck]

I believe we resolved this issue. Could you describe the issue/solution before I close this?

[jluebeck]

This error arose as a result of a collision in the name of two BAM files summarized in the coverage.stats file, located inside the user's AA_DATA_REPO folder. The fix is to remove the offending entry from the coverage.stats file, or clear the contents of the file entirely.