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broadinstitute / ichorCNA

Estimating tumor fraction in cell-free DNA from ultra-low-pass whole genome sequencing.
GNU General Public License v3.0
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could not find symbol "recursive" in environment of the generic function #31

Open haoziyeung opened 6 years ago

haoziyeung commented 6 years ago

Hi @gavinha , i am getting this error: /gpfs/users/yanghao/software/anaconda2/bin/Rscript /gpfs/users/yanghao/software/ichorCNA/scripts/runIchorCNA.R --id 18b0568FF.T --WIG results/readDepth/18b0568FF.T.bin1000000.wig --gcWig /gpfs/users/yanghao/software/ichorCNA/inst/extdata/gc_hg19_1000kb.wig --mapWig /gpfs/users/yanghao/software/ichorCNA/inst/extdata/map_hg19_1000kb.wig --NORMWIG results/readDepth/18b0558D1.N.bin1000000.wig --ploidy "c(2,3)" --normal "c(0.5)" --maxCN 8 --includeHOMD False --chrs "c(1:22, \"X\")" --chrTrain "c(1:22)" --estimateNormal True --estimatePloidy True --estimateScPrevalence True --scStates "c(1,3)" --centromere None --exons.bed None --txnE 0.9999 --txnStrength 10000 --fracReadsInChrYForMale 0.001 --plotFileType png --plotYLim "c(-2,4)" --outDir results/ichorCNA/18b0568FF.T/

$WIG [1] "results/readDepth/18b0568FF.T.bin1000000.wig"

$NORMWIG [1] "results/readDepth/18b0558D1.N.bin1000000.wig"

$gcWig [1] "/gpfs/users/yanghao/software/ichorCNA/inst/extdata/gc_hg19_1000kb.wig"

$mapWig [1] "/gpfs/users/yanghao/software/ichorCNA/inst/extdata/map_hg19_1000kb.wig"

$exons.bed [1] "None"

$id [1] "18b0568FF.T"

$centromere [1] "None"

$rmCentromereFlankLength [1] 1e+05

$normal [1] "c(0.5)"

$scStates [1] "c(1,3)"

$lambda [1] "NULL"

$lambdaScaleHyperParam [1] 3

$ploidy [1] "c(2,3)"

$maxCN [1] 8

$estimateNormal [1] TRUE

$estimateScPrevalence [1] TRUE

$estimatePloidy [1] TRUE

$maxFracCNASubclone [1] 0.7

$maxFracGenomeSubclone [1] 0.5

$minSegmentBins [1] 50

$altFracThreshold [1] 0.05

$chrNormalize [1] "c(1:22)"

$chrTrain [1] "c(1:22)"

$chrs [1] "c(1:22, \"X\")"

$normalizeMaleX [1] TRUE

$fracReadsInChrYForMale [1] 0.001

$includeHOMD [1] FALSE

$txnE [1] 0.9999

$txnStrength [1] 10000

$plotFileType [1] "png"

$plotYLim [1] "c(-2,4)"

$outDir [1] "results/ichorCNA/18b0568FF.T/"

$help [1] FALSE

Loading required package: IRanges Loading required package: methods Loading required package: BiocGenerics Loading required package: parallel

Attaching package: ‘BiocGenerics’

The following objects are masked from ‘package:parallel’:

clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
clusterExport, clusterMap, parApply, parCapply, parLapply,
parLapplyLB, parRapply, parSapply, parSapplyLB

The following objects are masked from ‘package:stats’:

IQR, mad, sd, var, xtabs

The following objects are masked from ‘package:base’:

anyDuplicated, append, as.data.frame, basename, cbind, colMeans,
colnames, colSums, dirname, do.call, duplicated, eval, evalq,
Filter, Find, get, grep, grepl, intersect, is.unsorted, lapply,
lengths, Map, mapply, match, mget, order, paste, pmax, pmax.int,
pmin, pmin.int, Position, rank, rbind, Reduce, rowMeans, rownames,
rowSums, sapply, setdiff, sort, table, tapply, union, unique,
unsplit, which, which.max, which.min

Loading required package: S4Vectors Loading required package: stats4

Attaching package: ‘S4Vectors’

The following object is masked from ‘package:base’:

expand.grid

Loading required package: geneplotter Loading required package: Biobase Welcome to Bioconductor

Vignettes contain introductory material; view with
'browseVignettes()'. To cite Bioconductor, see
'citation("Biobase")', and for packages 'citation("pkgname")'.

Loading required package: lattice Loading required package: annotate Loading required package: AnnotationDbi Loading required package: XML

Attaching package: ‘ichorCNA’

The following object is masked from ‘package:HMMcopy’:

HMMsegment

Loading tumour file:18b0568FF.T Slurping: results/readDepth/18b0568FF.T.bin1000000.wig Parsing: fixedStep chrom=1 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=2 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=3 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=4 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=5 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=6 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=7 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=8 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=9 start=1 step=1000000 span=1000000

▽ Parsing: fixedStep chrom=10 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=11 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=12 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=13 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=14 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=15 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=16 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=17 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=18 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=19 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=20 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=21 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=22 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=X start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=Y start=1 step=1000000 span=1000000 Sorting by decreasing chromosome size Reading GC and mappability files Slurping: /gpfs/users/yanghao/software/ichorCNA/inst/extdata/gc_hg19_1000kb.wig Parsing: fixedStep chrom=1 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=2 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=3 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=4 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=5 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=6 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=7 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=8 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=9 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=10 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=11 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=12 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=13 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=14 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=15 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=16 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=17 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=18 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=19 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=20 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=21 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=22 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=X start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=Y start=1 step=1000000 span=1000000 Sorting by decreasing chromosome size Slurping: /gpfs/users/yanghao/software/ichorCNA/inst/extdata/map_hg19_1000kb.wig Parsing: fixedStep chrom=1 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=2 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=3 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=4 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=5 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=6 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=7 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=8 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=9 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=10 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=11 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=12 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=13 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=14 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=15 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=16 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=17 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=18 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=19 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=20 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=21 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=22 start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=X start=1 step=1000000 span=1000000 Parsing: fixedStep chrom=Y start=1 step=1000000 span=1000000 Sorting by decreasing chromosome size Correcting Tumour Loading required package: GenomeInfoDb Error in c(x, value) : could not find symbol "recursive" in environment of the generic function Calls: loadReadCountsFromWig ... setListElement -> .append_list_element -> coerce2 -> coerce2 -> c Execution halted

tumor bam depth is :1048 and normal bam depth is :168 target panel is around 1M+

Thanks.

gavinha commented 6 years ago

Hi @haoziyeung

Can you provide the sessionInfo() so that we can see the version of R and other packages?

Thanks, Gavin

haoziyeung commented 6 years ago

sessionInfo() R version 3.4.1 (2017-06-30) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /gpfs/users/yanghao/software/anaconda2/lib/R/lib/libRblas.so LAPACK: /gpfs/users/yanghao/software/anaconda2/lib/R/lib/libRlapack.so

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] stats graphics grDevices utils datasets methods base

loaded via a namespace (and not attached): [1] compiler_3.4.1

gavinha commented 6 years ago

Hi @haoziyeung

We have never encountered this error. This is what I could find searching this error on Google. https://support.bioconductor.org/p/93695/ It might have something to do with R versions and packages, but I'm not sure.

Hope this helps, Gavin