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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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Error in rep.int(rows, nr) : invalid 'times' value #36

Closed rahulram70 closed 6 years ago

rahulram70 commented 6 years ago

Hey guys,

So I ran a the command call listed below and have continuously received the following error: Error in rep.int(rows, nr) : invalid 'times' value Calls: loadReadCountsFromWig ... standardGeneric -> eval -> eval -> eval -> rep.int -> rep.int.

Could you please help me fix this? Thank you.

Rscript /home/users/boniface/ichorCNA/scripts/runIchorCNA.R --id tumor_sample --WIG LIB180124PS_Sol8_S8.wig --ploidy "c(2)" --normal "c(0)" --maxCN 10 --gcWig /home/users/boniface/ichorCNA/inst/extdata/gc_hg19_1000kb.wig --mapWig /home/users/boniface/ichorCNA/inst/extdata/map_hg19_1000kb.wig --centromere /home/users/boniface/ichorCNA/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt --normalPanel /home/users/boniface/ichorCNA/inst/extdata/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds --includeHOMD False --chrs "c(1:22, \"X\")" --chrTrain "c(1:22)" --estimateNormal False --estimatePloidy False --estimateScPrevalence False --scStates "c(1)" --txnE 0.9999 --txnStrength 10000 --plotYLim "c(-2,3)" --outDir /home/exacloud/lustre1/SpellmanLab/ram/bash_snakemake/snakemake_scripts/output_ichor_test