I can run PureCN v1.6.3 successfully, but the same runAbsoluteCN command failed for v1.7.53. Could you please help? Thanks.
below is the warning message
Error in if (fractionContaminated > 0) { :
missing value where TRUE/FALSE needed
Calls: runAbsoluteCN ... do.call -> <Anonymous> -> filterVcfMuTect2 -> filterVcfBasic
Execution halted
below is the sessionInfo
R version 3.3.1 Patched (2016-08-12 r71089)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server release 6.3 (Santiago)
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] PureCN_1.7.53 VariantAnnotation_1.20.3
[3] Rsamtools_1.24.0 Biostrings_2.40.2
[5] XVector_0.12.1 SummarizedExperiment_1.2.3
[7] Biobase_2.32.0 GenomicRanges_1.26.4
[9] GenomeInfoDb_1.10.3 IRanges_2.8.2
[11] S4Vectors_0.12.2 BiocGenerics_0.20.0
[13] DNAcopy_1.48.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.12 RColorBrewer_1.1-2 futile.logger_1.4.3
[4] plyr_1.8.4 GenomicFeatures_1.24.5 bitops_1.0-6
[7] futile.options_1.0.0 tools_3.3.1 zlibbioc_1.18.0
[10] biomaRt_2.28.0 RSQLite_1.0.0 gtable_0.2.0
[13] BSgenome_1.40.1 DBI_0.7 rtracklayer_1.32.2
[16] grid_3.3.1 data.table_1.10.4 AnnotationDbi_1.34.4
[19] XML_3.98-1.4 BiocParallel_1.6.6 VGAM_1.0-3
[22] ggplot2_2.1.0 lambda.r_1.1.9 scales_0.4.1
[25] GenomicAlignments_1.8.4 splines_3.3.1 colorspace_1.2-6
[28] RCurl_1.95-4.8 munsell_0.4.3
Hi Riester,
Actually i generated all the VCF by Mutect 1, not Mutect 2, but it seems that PureCN wrongly output "Detected MuTect2 VCF." in stdout. is this also a bug?
anyway, i will update PureCN and then try again.
thanks a lot.
Okay, never seen this before, but yes, looks like a bug. I'll try to reproduce. If you can share an example VCF (even if it only contains a single variant) that would be helpful. Thanks for the report.
Hi Riester,
below is one variant example extracted from Mutect 1 output. is this helpful?
1 99671 rs146209971 A T . PASS DB;SOMATIC;VT=SNP GT:AD:BQ:DP:FA:SS 0:0,0:.:0:0.00:0 0/1:0,2:34:2:1.00:2
I hope this fixed now. The Mutect2 detection should be more robust and is not attempted at all if you provide the Mutect1 stats file.
Can you re-try after biocLite("lima1/PureCN")?
i have updated the PureCN. the version number is still PureCN_1.7.55? no change?
Hi, I didn't increase in the version number because 1.7.55 wasn't build yet in Bioconductor 3.6.
Hi Riester,
I updated to latest version, v1.7.55. for several samples, there are still some errors come out for several samples. could you please help?
Error in .isAllZero(counts) : negative counts not supported
Calls: runAbsoluteCN ... .addVoomToGeneCalls -> .voomTargets -> <Anonymous>
In addition: Warning messages:
1: In calculateLogRatio(normal, tumor) : NaNs produced
2: In .bcfHeaderAsSimpleList(header) :
duplicate keys in header will be forced to unique rownames
Execution halted
Sorry to hear that. Negative counts shouldn't happen, it could be an integer overflow. We can debug offline via email (markus.riester at novartis com).
If you can send me an example coverage file (loess normalized) plus the gc.gene.file, that would be great. If this is from a custom panel you don't want to send out, would you mind sending me the output of:
tumor <- readCoverageFile(coverage.file)
summary(tumor$counts)