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gavinha / TitanCNA

Analysis of subclonal copy number alterations (CNA) and loss of heterozygosity (LOH) in cancer
GNU General Public License v3.0
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problem with ichorCNA in snakemake #93

Closed thek71 closed 3 years ago

thek71 commented 3 years ago

Hi all, I am trying to run for the first time TitanCNA and I am stuck in an error that is probably something small that I cannot see. I get an error in this step Rscript /home/R/x86_64-pc-linux-gnu-library/4.1/ichorCNA/R/ichorCNA --libdir /home/R/x86_64-pc-linux-gnu-library/4.1/ichorCNA --id tumor_sample_1 --WIG results/readDepth/tumor_sample_1.bin10000.wig --gcWig /home/katia/R/x86_64-pc-linux-gnu-library/4.1/ichorCNA/extdata/gc_hg38_10kb.wig --mapWig /home/R/x86_64-pc-linux-gnu-library/4.1/ichorCNA/extdata/map_hg38_10kb.wig --NORMWIG results/readDepth/normal_sample_1.bin10000.wig --ploidy "c(2,3)" --normal "c(0.5)" --maxCN 8 --includeHOMD False --genomeStyle UCSC --chrs "c(1:22, \"X\")" --estimateNormal True --estimatePloidy True --estimateScPrevalence True --scStates "c(1,3)" --centromere /home/R/x86_64-pc-linux-gnu-library/4.1/ichorCNA/extdata/GRCh38.GCA_000001405.2_centromere_acen.txt --exons.bed /home/Reference/exome_targets/S30409818_Regions.bed --txnE 0.9999 --txnStrength 10000 --fracReadsInChrYForMale 0.001 --plotFileType png --plotYLim "c(-2,4)" --outDir results/ichorCNA/tumor_sample_1/ > logs/ichorCNA/tumor_sample_1.log 2> logs/ichorCNA/tumor_sample_1.log (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

When I run the same command in bash to get a better description of the error I get Error in dynGet("LoadingNamespaceInfo", stop("not loading a namespace")) : not loading a namespace Calls: local ... eval -> eval -> eval -> loadingNamespaceInfo -> dynGet Execution halted

So something is not loading correctly. I have installed ichorCNA as in the github page and within R is loading. I am not an R person, so I would really appreciate any help.

Thanks in advance