An issue related to chrX when running ichorCNA.snakefile thru TitanCNA

[wenching]

Hi @gavinha,

When I ran a tumor-normal pair with chrM removed, I got the following error.

RuleException:
CalledProcessError in line 70 of /home/user/TOOL/TitanCNA/scripts/snakemake/ichorCNA.snakefile:
Command ' Rscript /home/user/TOOL/ichorCNA/scripts/runIchorCNA.R --libdir /home/user/TOOL/ichorCNA --id dummy_Tumor --WIG results/readDepth/dummy_Tumor.bin10000.wig --gcWig /home/user/TOOL/ichorCNA/inst/extdata/gc_hg19_10kb.wig --mapWig /home/user/TOOL/ichorCNA/inst/extdata/map_hg19_10kb.wig --NORMWIG results/readDepth/dummy_Normal.bin10000.wig --ploidy "c(2,3)" --normal "c(0.5)" --maxCN 8 --includeHOMD False --genomeStyle NCBI --chrs "c('chr1','chr2','chr3','chr4','chr5','chr6','chr7','chr8','chr9','chr10','chr11','chr12','chr13','chr14','chr15','chr16','chr17','chr18','chr19','chr20','chr21','chr22','chrX')" --estimateNormal True --estimatePloidy True --estimateScPrevalence True --scStates "c(1,3)" --centromere /home/user/TOOL/ichorCNA/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt --exons.bed None --txnE 0.9999 --txnStrength 10000 --fracReadsInChrYForMale 0.001 --plotFileType png --plotYLim "c(-2,4)" --outDir results/ichorCNA/dummy_Tumor/ > logs/ichorCNA/dummy_Tumor.log 2> logs/ichorCNA/dummy_Tumor.log ' returned non-zero exit status 1.
  File "/home/user/TOOL/TitanCNA/scripts/snakemake/ichorCNA.snakefile", line 70, in __rule_ichorCNA
  File "/home/user/miniconda3/envs/rnatera_py3/lib/python3.6/concurrent/futures/thread.py", line 56, in run

The error msg from the log is as follows.

logs/ichorCNA/dummy_Tumor.log

$WIG
[1] "results/readDepth/dummy_Tumor.biLoading required package: data.table
Warning message:
package ‘HMMcopy’ was built under R version 3.6.1
Loading required package: stats4
Loading required package: BiocGenerics
Loading required package: parallel

...

Sorting by decreasing chromosome size
Slurping: /home/user/TOOL/ichorCNA/inst/extdata/map_hg19_10kb.wig
Parsing: fixedStep chrom=1 start=1 step=10000 span=10000
Parsing: fixedStep chrom=2 start=1 step=10000 span=10000
Parsing: fixedStep chrom=3 start=1 step=10000 span=10000
Parsing: fixedStep chrom=4 start=1 step=10000 span=10000
Parsing: fixedStep chrom=5 start=1 step=10000 span=10000
Parsing: fixedStep chrom=6 start=1 step=10000 span=10000
Parsing: fixedStep chrom=7 start=1 step=10000 span=10000
Parsing: fixedStep chrom=8 start=1 step=10000 span=10000
Parsing: fixedStep chrom=9 start=1 step=10000 span=10000
Parsing: fixedStep chrom=10 start=1 step=10000 span=10000
Parsing: fixedStep chrom=11 start=1 step=10000 span=10000
Parsing: fixedStep chrom=12 start=1 step=10000 span=10000
Parsing: fixedStep chrom=13 start=1 step=10000 span=10000
Parsing: fixedStep chrom=14 start=1 step=10000 span=10000
Parsing: fixedStep chrom=15 start=1 step=10000 span=10000
Parsing: fixedStep chrom=16 start=1 step=10000 span=10000
Parsing: fixedStep chrom=17 start=1 step=10000 span=10000
Parsing: fixedStep chrom=18 start=1 step=10000 span=10000
Parsing: fixedStep chrom=19 start=1 step=10000 span=10000
Parsing: fixedStep chrom=20 start=1 step=10000 span=10000
Parsing: fixedStep chrom=21 start=1 step=10000 span=10000
Parsing: fixedStep chrom=22 start=1 step=10000 span=10000
Parsing: fixedStep chrom=X start=1 step=10000 span=10000
Parsing: fixedStep chrom=Y start=1 step=10000 span=10000
Sorting by decreasing chromosome size
Correcting Tumour
Removed 7383 bins near centromeres.
Applying filter on data...
Correcting for GC bias...
Correcting for mappability bias...
Filtering low uniqueness regions with mappability score < 0.9
Removed 321 bins near centromeres.
Error in if (chrXMedian < chrXMedianForMale) { :
  missing value where TRUE/FALSE needed
Calls: loadReadCountsFromWig -> getGender
In addition: Warning message:
In regularize.values(x, y, ties, missing(ties)) :
  collapsing to unique 'x' values
Execution halted

Please let me know if you need more info.

Thanks.

[BFortunato1]

@wenching @gavinha were you ever able to figure this out?