errors in version 1.7.53
1
0
Entering edit mode
@xiaoqiaoliu-14074
Last seen 3.6 years ago

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

 

 

 

PureCN • 440 views
ADD COMMENT
0
Entering edit mode
@markusriester-9875
Last seen 28 days ago

If your VCF is generated by Mutect2, then this might be related to a bug in filterVcfMuTect2 that I just fixed yesterday in GitHub. This function is new and is supposed to filter variants by various Mutect2 flags, but wrongly removed all variants when unfiltered VCF was provided. Please note that only tumor-only Mutect2 VCF will work.

Can you try updating with biocLite("lima1/PureCN") and try again?

 

 

 

ADD COMMENT
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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.

ADD REPLY
0
Entering edit mode

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

ADD REPLY
0
Entering edit mode

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")?

ADD REPLY
0
Entering edit mode

i have updated the PureCN. the version number is still PureCN_1.7.55? no change?

ADD REPLY
0
Entering edit mode

Hi, I didn't increase in the version number because 1.7.55 wasn't build yet in Bioconductor 3.6. 

ADD REPLY
0
Entering edit mode

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

 

 

ADD REPLY
0
Entering edit mode

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)

 

ADD REPLY

Login before adding your answer.

Traffic: 544 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6