We are testing CNVRadar for somatic CNV calling on hybrid capture data. However, I am running into some issues in the last step when we run the "CNV_Radar.r" script. My normal cohort is build of ~90 some samples on the same ROI bedfile used to generate tumor_roiSummary.txt file.
Can you please help me understand what could be causing this error.
Thank you.
Ashini
The error I am getting is:
"""
[2021-02-24 13:34:59] - getopt - INFO - Params: useAllVars = FALSE
[2021-02-24 13:34:59] - getopt - INFO - Params: gatk = FALSE
[2021-02-24 13:34:59] - getopt - INFO - Params: sensitivity = FALSE
[2021-02-24 13:34:59] - getopt - INFO - Params: depth = DP
[2021-02-24 13:34:59] - getopt - INFO - Params: cex = 0.35
[2021-02-24 13:34:59] - getopt - INFO - Params: printChrs = all
[2021-02-24 13:34:59] - getopt - INFO - Params: omitCNVcalls = FALSE
[2021-02-24 13:34:59] - getopt - INFO - Params: plotPredDepth = FALSE
[2021-02-24 13:34:59] - getopt - INFO - Params: plotPredVAF = FALSE
[2021-02-24 13:34:59] - getopt - INFO - Params: writeFilteredVCF = FALSE
[2021-02-24 13:34:59] - readVCF - DEBUG - Reading in the vcf file tumor_ann.vcf.gz
[2021-02-24 13:34:59] - readVCF - DEBUG - 13359 total variants reported in the VCF
[2021-02-24 13:34:59] - readVCF - DEBUG - 13359 variants reported on the autosomal or sex chromosomes
[2021-02-24 13:34:59] - readVCF - DEBUG - 0 complex variants to remove from VCF
[2021-02-24 13:34:59] - readVCF - DEBUG - 0 indels to remove from VCF
[2021-02-24 13:35:00] - readVCF - DEBUG - 9880 heterozygous and 3479 homozygous variants reported
[2021-02-24 13:35:00] - readVCF - INFO - Extracting the total read depth from the VCF reported in the fields: DP
[2021-02-24 13:35:00] - readVCF - INFO - Single depth field supplied: DP
[2021-02-24 13:35:01] - readVCF - DEBUG - Filtering VCF to only 'common' variants
[2021-02-24 13:35:01] - readVCF - DEBUG - 7046 variants annotated as common
[2021-02-24 13:35:01] - readVCF - DEBUG - 7046 total heterozygous common single nucleotide variants reported in the VCF[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 1 = 525
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 2 = 597
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 3 = 507
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 4 = 460
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 5 = 428
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 6 = 497
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 7 = 493
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 8 = 320
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 9 = 315
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 10 = 294
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 11 = 249
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 12 = 293
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 13 = 283
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 14 = 155
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 15 = 184
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 16 = 194
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 17 = 260
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 18 = 141
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 19 = 215
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 20 = 175
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 21 = 114
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 22 = 94
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome X = 253
[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome Y = 0
[2021-02-24 13:35:01] - readVCF - DEBUG - VCF file tumor_ann.vcf.gz with 7046 variants took 0.039 minutes to read and parse
[2021-02-24 13:35:01] - readROI - DEBUG - Reading in the depth file tumor_roiSummary.txt
[2021-02-24 13:35:02] - readROI - DEBUG - ROI depth file tumor_roiSummary.txt with 49383 regions of interest took 0.002 minutes to read and parse
[2021-02-24 13:35:02] - main - DEBUG - Filtering to autosomes only
[2021-02-24 13:35:02] - main - DEBUG - Median normalizing iteration 1
[2021-02-24 13:35:03] - main - DEBUG - Beginning modeling for iteration 1
[2021-02-24 13:35:03] - main - DEBUG - Calculating fold change for iteration 1
[2021-02-24 13:35:03] - main - DEBUG - Analyzing Chr 1 for iteration 1
Error in smooth.spline(x = preds$Beg, y = preds$fc, nknots = iterative_fit$cknots, :
missing or infinite values in inputs are not allowed
Calls: predict -> smooth.spline
Execution halted
"""
Hi,
We are testing CNVRadar for somatic CNV calling on hybrid capture data. However, I am running into some issues in the last step when we run the "CNV_Radar.r" script. My normal cohort is build of ~90 some samples on the same ROI bedfile used to generate tumor_roiSummary.txt file.
Can you please help me understand what could be causing this error.
Thank you. Ashini
The error I am getting is:
""" [2021-02-24 13:34:59] - getopt - INFO - Params: useAllVars = FALSE [2021-02-24 13:34:59] - getopt - INFO - Params: gatk = FALSE [2021-02-24 13:34:59] - getopt - INFO - Params: sensitivity = FALSE [2021-02-24 13:34:59] - getopt - INFO - Params: depth = DP [2021-02-24 13:34:59] - getopt - INFO - Params: cex = 0.35 [2021-02-24 13:34:59] - getopt - INFO - Params: printChrs = all [2021-02-24 13:34:59] - getopt - INFO - Params: omitCNVcalls = FALSE [2021-02-24 13:34:59] - getopt - INFO - Params: plotPredDepth = FALSE [2021-02-24 13:34:59] - getopt - INFO - Params: plotPredVAF = FALSE [2021-02-24 13:34:59] - getopt - INFO - Params: writeFilteredVCF = FALSE [2021-02-24 13:34:59] - readVCF - DEBUG - Reading in the vcf file tumor_ann.vcf.gz [2021-02-24 13:34:59] - readVCF - DEBUG - 13359 total variants reported in the VCF [2021-02-24 13:34:59] - readVCF - DEBUG - 13359 variants reported on the autosomal or sex chromosomes [2021-02-24 13:34:59] - readVCF - DEBUG - 0 complex variants to remove from VCF [2021-02-24 13:34:59] - readVCF - DEBUG - 0 indels to remove from VCF [2021-02-24 13:35:00] - readVCF - DEBUG - 9880 heterozygous and 3479 homozygous variants reported [2021-02-24 13:35:00] - readVCF - INFO - Extracting the total read depth from the VCF reported in the fields: DP [2021-02-24 13:35:00] - readVCF - INFO - Single depth field supplied: DP [2021-02-24 13:35:01] - readVCF - DEBUG - Filtering VCF to only 'common' variants [2021-02-24 13:35:01] - readVCF - DEBUG - 7046 variants annotated as common [2021-02-24 13:35:01] - readVCF - DEBUG - 7046 total heterozygous common single nucleotide variants reported in the VCF[2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 1 = 525 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 2 = 597 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 3 = 507 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 4 = 460 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 5 = 428 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 6 = 497 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 7 = 493 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 8 = 320 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 9 = 315 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 10 = 294 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 11 = 249 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 12 = 293 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 13 = 283 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 14 = 155 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 15 = 184 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 16 = 194 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 17 = 260 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 18 = 141 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 19 = 215 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 20 = 175 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 21 = 114 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome 22 = 94 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome X = 253 [2021-02-24 13:35:01] - readVCF - DEBUG - Variants reported on chromosome Y = 0 [2021-02-24 13:35:01] - readVCF - DEBUG - VCF file tumor_ann.vcf.gz with 7046 variants took 0.039 minutes to read and parse [2021-02-24 13:35:01] - readROI - DEBUG - Reading in the depth file tumor_roiSummary.txt [2021-02-24 13:35:02] - readROI - DEBUG - ROI depth file tumor_roiSummary.txt with 49383 regions of interest took 0.002 minutes to read and parse [2021-02-24 13:35:02] - main - DEBUG - Filtering to autosomes only [2021-02-24 13:35:02] - main - DEBUG - Median normalizing iteration 1 [2021-02-24 13:35:03] - main - DEBUG - Beginning modeling for iteration 1 [2021-02-24 13:35:03] - main - DEBUG - Calculating fold change for iteration 1 [2021-02-24 13:35:03] - main - DEBUG - Analyzing Chr 1 for iteration 1 Error in smooth.spline(x = preds$Beg, y = preds$fc, nknots = iterative_fit$cknots, : missing or infinite values in inputs are not allowed Calls: predict -> smooth.spline Execution halted """