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chrisamiller / copyCat

a parallel R package for detecting copy-number alterations from short sequencing reads
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Error in hist.default( #3

Open zhaoming159753 opened 8 years ago

zhaoming159753 commented 8 years ago

I use samtools and bcftools call SNVs of tumor and normal bam, and got the VCF file for earch sample

when running copyCat I meet this error

[1] "inferred that samtools file format is: VCF" Error in hist.default(adjReadDepths, breaks = 100, col = "darkgreen", : 'x' must be numeric Calls: runPairedSampleAnalysis -> cnNeutralDepthFromHetSites -> hist -> hist.default Execution halted

chrisamiller commented 8 years ago

Does your VCF contain the DP and AF1 fields in your info column? Can you paste a few lines from your VCF file for troubleshooting?

udp3f commented 6 years ago

Running copyCat version 1.6.12, I have a similar error and my VCF has the DP and AF fields. Any suggestions?

chrisamiller commented 6 years ago

Can you paste a few lines from your VCF file for troubleshooting?

udp3f commented 6 years ago

Hi Chris,

Attached are a smaller version of the two vcf files I used.

Thanks,

Uma

From: Chris Miller notifications@github.com Sent: Wednesday, June 13, 2018 12:38:32 PM To: chrisamiller/copyCat Cc: Paila, Uma Devi (udp3f); Comment Subject: Re: [chrisamiller/copyCat] Error in hist.default( (#3)

Can you paste a few lines from your VCF file for troubleshooting?

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udp3f commented 6 years ago

Did you get a chance to look into this?

-Uma

chrisamiller commented 6 years ago

Attachments don't come through in github via email replies, AFAIK. Can you either email me directly or attach it to this issue? The head plus the first few lines of the body should be sufficient. (please don't send me the whole germline VCF and run afoul of privacy regulations!)

qotjrud3 commented 3 years ago

Has this problem been solved? I made the vcf file in the same way and got the same error.

chrisamiller commented 3 years ago

As above, I'd need more info to troubleshoot. Can you paste the first few lines of the body of your VCF here?

qotjrud3 commented 3 years ago

Thanks for the quick response.

The vcf file below is the file with the problem,

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AML02_CR

1 564520 . C T 11.1139 . DP=6;VDB=0.02;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;DP4=0,0,2,0;MQ=23;FQ=-32.9882 GT:PL 1/1:42,6,0 1 564731 . A AA 26.4408 . INDEL;IDV=3;IMF=0.5;DP=3;VDB=0.0249187;SGB=-0.511536;MQ0F=0;AF1=1;AC1=2;DP4=0,0,3,0;MQ=26;FQ=-43.5253 GT:PL 1/1:66,9,0 1 567242 . G A 57.1325 . DP=7;VDB=0.00740154;SGB=-0.616816;MQ0F=0;AF1=1;AC1=2;DP4=0,0,6,0;MQ=24;FQ=-44.9861 GT:PL 1/1:90,18,0 1 569717 . T C 49.2632 . DP=7;VDB=0.00376034;SGB=-0.590765;MQ0F=0;AF1=1;AC1=2;DP4=0,0,5,0;MQ=24;FQ=-41.9862 GT:PL 1/1:82,15,0 1 570178 . G A 4.12858 . DP=44;VDB=0.18;SGB=-0.453602;RPB=1;MQB=0;BQB=0.5;MQ0F=0;AF1=0.499862;AC1=1;DP4=2,0,2,0;MQ=26;FQ=5.81863;PV4=1,1,0.047733,1 GT:PL 0/1:32,0,41 1 775426 . G A 26.9806 . DP=3;VDB=0.839668;SGB=-0.511536;MQ0F=0;AF1=1;AC1=2;DP4=0,0,3,0;MQ=24;FQ=-35.9869 GT:PL 1/1:59,9,0 1 777122 . A T 12.9881 . DP=2;VDB=0.58;SGB=-0.453602;MQ0F=0;AF1=1;AC1=2;DP4=0,0,2,0;MQ=24;FQ=-32.9881 GT:PL 1/1:44,6,0

The vcf file below this did not cause the above problem.

CHROM POS ID REF ALT QUAL FILTER INFO FORMAT AML02_Dx

1 14677 . G A 26.0177 . DP=58;VDB=2.29379e-06;SGB=-0.670168;RPB=0.440413;MQB=4.53999e-05;BQB=0.920678;MQ0F=0;AF1=0.499999;AC1=1;DP4=0,22,0,10;MQ=28;FQ=29.0205;PV4=1,1,5.32681e-38,0.375763 GT:PL 0/1:56,0,120 1 16495 . G C 14.176 . DP=6;VDB=0.0249187;SGB=-0.511536;RPB=0.28717;MQB=0.28717;BQB=0.861511;MQ0F=0;AF1=0.49999;AC1=1;DP4=0,3,0,3;MQ=27;FQ=16.9342;PV4=1,1,3.51053e-05,1 GT:PL 0/1:44,0,58 1 564520 . C T 74.0058 . DP=35;VDB=0.0561217;SGB=-0.670168;MQ0F=0;AF1=1;AC1=2;DP4=0,0,10,0;MQ=23;FQ=-56.9861 GT:PL 1/1:107,30,0 1 564654 . G A 52.0072 . DP=141;VDB=1.04896e-14;SGB=-0.693145;RPB=4.71147e-09;MQB=1.76123e-11;BQB=5.55535e-06;MQ0F=0;AF1=0.5;AC1=1;DP4=32,0,41,0;MQ=27;FQ=55.0099;PV4=1,3.56407e-07,1.34497e-41,2.13661e-16 GT:PL 0/1:82,0,111 1 564731 . A AA 16.3491 . INDEL;IDV=58;IMF=0.659091;DP=67;VDB=2.29532e-29;SGB=-0.693147;MQ0F=0;AF1=1;AC1=2;DP4=10,0,57,0;MQ=26;FQ=-44.5252;PV4=1,1,8.92969e-08,0.327038 GT:PL 1/1:56,10,0 1 565282 . A G 16.8548 . DP=5;VDB=0.38;SGB=-0.453602;MQSB=1;MQ0F=0;AF1=1;AC1=2;DP4=0,0,1,1;MQ=24;FQ=-32.988 GT:PL 1/1:48,6,0

chrisamiller commented 3 years ago

Thanks. Can you please drop the outputs of sessionInfo() and then also traceback() (run immediately after the error) here?

qotjrud3 commented 3 years ago

sessionINfo()

R version 3.6.0 (2019-04-26) Platform: x86_64-redhat-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/lib64/R/lib/libRblas.so

Random number generation: RNG: Mersenne-Twister Normal: Inversion Sample: Rounding

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] grid splines parallel stats4 stats graphics grDevices utils datasets methods base

other attached packages: [1] copyCat_1.6.12 stringr_1.4.0 DNAcopy_1.60.0 doMC_1.3.7 iterators_1.0.12
[6] foreach_1.4.8 sciClone_1.1.0 TeachingDemos_2.12 MKmisc_1.6 plotrix_3.7-8
[11] RColorBrewer_1.1-2 rgl_0.100.54 bmm_0.3.1 NORMT3_1.0-3 biomaRt_2.42.1
[16] monocle_2.14.0 DDRTree_0.1.5 irlba_2.3.3 VGAM_1.1-3 ggplot2_3.3.0
[21] Matrix_1.2-18 fishplot_0.5 DESeq2_1.26.0 SummarizedExperiment_1.16.1 DelayedArray_0.12.2
[26] BiocParallel_1.20.1 matrixStats_0.56.0 Biobase_2.46.0 GenomicRanges_1.38.0 GenomeInfoDb_1.22.0
[31] IRanges_2.20.1 S4Vectors_0.24.3 BiocGenerics_0.32.0

loaded via a namespace (and not attached): [1] reticulate_1.15 tidyselect_1.0.0 RSQLite_2.2.0 AnnotationDbi_1.48.0 htmlwidgets_1.5.1 combinat_0.0-8
[7] docopt_0.6.1 Rtsne_0.15 devtools_2.3.1 munsell_0.5.0 codetools_0.2-18 ica_1.0-2
[13] DT_0.16 future_1.17.0 miniUI_0.1.1.1 withr_2.3.0 colorspace_1.4-1 fastICA_1.2-2
[19] knitr_1.30 rstudioapi_0.11 Seurat_3.2.1 ROCR_1.0-11 robustbase_0.93-6 tensor_1.5
[25] listenv_0.8.0 slam_0.1-47 GenomeInfoDbData_1.2.2 polyclip_1.10-0 bit64_0.9-7 pheatmap_1.0.12
[31] rprojroot_1.3-2 vctrs_0.2.4 xfun_0.19 BiocFileCache_1.10.2 R6_2.4.1 rsvd_1.0.3
[37] locfit_1.5-9.4 manipulateWidget_0.10.1 bitops_1.0-6 spatstat.utils_1.17-0 assertthat_0.2.1 promises_1.1.0
[43] scales_1.1.1.9000 nnet_7.3-13 gtable_0.3.0 npsurv_0.4-0 globals_0.12.5 processx_3.4.5
[49] goftest_1.2-2 rlang_0.4.7 genefilter_1.68.0 lazyeval_0.2.2 checkmate_2.0.0 reshape2_1.4.4
[55] abind_1.4-5 crosstalk_1.1.0.1 backports_1.1.6 httpuv_1.5.2 Hmisc_4.4-2 usethis_1.5.1
[61] tools_3.6.0 ellipsis_0.3.0 sessioninfo_1.1.1 ggridges_0.5.2 Rcpp_1.0.5 plyr_1.8.6
[67] base64enc_0.1-3 progress_1.2.2 zlibbioc_1.32.0 purrr_0.3.4 RCurl_1.98-1.2 densityClust_0.3
[73] ps_1.3.2 prettyunits_1.1.1 rpart_4.1-15 openssl_1.4.1 deldir_0.1-25 pbapply_1.4-2
[79] viridis_0.5.1 cowplot_1.0.0 zoo_1.8-8 ggrepel_0.8.2 cluster_2.1.0 fs_1.4.1
[85] magrittr_1.5 data.table_1.12.8 lmtest_0.9-37 RANN_2.6.1 fitdistrplus_1.0-14 pkgload_1.1.0
[91] hms_0.5.3 patchwork_1.0.1 lsei_1.2-0 mime_0.9 xtable_1.8-4 XML_3.99-0.3
[97] jpeg_0.1-8.1 sparsesvd_0.2 gridExtra_2.3 testthat_2.3.2 HSMMSingleCell_1.6.0 compiler_3.6.0
[103] tibble_3.0.1 KernSmooth_2.23-17 crayon_1.3.4 htmltools_0.4.0 mgcv_1.8-32 later_1.0.0
[109] Formula_1.2-4 tidyr_1.0.2 geneplotter_1.64.0 DBI_1.1.0 dbplyr_1.4.2 MASS_7.3-51.5
[115] rappdirs_0.3.1 cli_2.0.2 igraph_1.2.5 pkgconfig_2.0.3 foreign_0.8-74 plotly_4.9.2.1
[121] annotate_1.64.0 webshot_0.5.2 XVector_0.26.0 callr_3.5.1 digest_0.6.25 sctransform_0.2.1
[127] RcppAnnoy_0.0.16 spatstat.data_1.4-3 leiden_0.3.3 htmlTable_2.1.0 uwot_0.1.8 curl_4.3
[133] shiny_1.4.0.2 lifecycle_0.2.0 nlme_3.1-148 jsonlite_1.7.2 desc_1.2.0 fansi_0.4.1
[139] viridisLite_0.3.0 askpass_1.1 limma_3.42.2 pillar_1.4.4 lattice_0.20-41 pkgbuild_1.1.0
[145] DEoptimR_1.0-8 fastmap_1.0.1 httr_1.4.1 survival_3.2-7 remotes_2.2.0 glue_1.4.0
[151] qlcMatrix_0.9.7 FNN_1.1.3 spatstat_1.64-1 png_0.1-7 bit_1.1-15.2 stringi_1.4.6
[157] blob_1.2.1 latticeExtra_0.6-29 memoise_1.1.0 dplyr_0.8.5 future.apply_1.5.0

It's just after running it.

[1] "inferred bin size: 1000" [1] "calculating mapability content for read length 91 Thu Dec 17 15:37:48 2020" [1] "WARNING: annotations for read length of 91 don't exist" [1] "using annotations for read length of 85 which are close enough" correcting for GC bias Thu Dec 17 15:38:02 2020 [1] "calculating GC content for read length 91 Thu Dec 17 15:38:02 2020" [1] "WARNING: annotations for read length of 91 don't exist" [1] "using annotations for read length of 85 which are close enough" Correcting read depth for GC-content bias: Thu Dec 17 15:38:16 2020 [1] "correcting library 1 (rd.X0.1.91)" Error in hist.default(adjReadDepths, breaks = 100, col = "darkgreen", : 'x' must be numeric

traceback() 5: stop("'x' must be numeric") 4: hist.default(adjReadDepths, breaks = 100, col = "darkgreen", xlim = c(0, (mean(adjReadDepths, na.rm = TRUE) 2))) 3: hist(adjReadDepths, breaks = 100, col = "darkgreen", xlim = c(0, (mean(adjReadDepths, na.rm = TRUE) 2))) 2: cnNeutralDepthFromHetSites(rdo2, tumorSamtoolsFile, 2000000, peakWiggle = 4, plot = TRUE, samtoolsFileFormat = samtoolsFileFormat) at #66 1: runPairedSampleAnalysis(annotationDirectory = "/home/bseo/AML_3_bam/copyCat/hg19/", outputDirectory = "/home/bseo/AML_3_bam/copyCat/aml02cr/", normal = "/home/bseo/AML_3_bam/parsing/parsed/con01_cluster_1_20.bamwindow", tumor = "/home/bseo/AML_3_bam/parsing/parsed/aml02cr_cluster_1_20.bamwindow", inputType = "bins", maxCores = 10, binSize = 0, verbose = TRUE, minWidth = 2, minMapability = 0.6, dumpBins = TRUE, doGcCorrection = TRUE, samtoolsFileFormat = "VCF", purity = 1, normalSamtoolsFile = "/home/bseo/AML_3_bam/parsing/parsed/con01_cluster_1_20.vcf", tumorSamtoolsFile = "/home/bseo/AML_3_bam/parsing/parsed/aml02cr_cluster_1_20.vcf")

Thank you