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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 parse_args(parseobj) #61

Closed vipultodarwal closed 5 years ago

vipultodarwal commented 5 years ago

Hi I am Getting error after running following command :+1:

sudo Rscript /opt/installers/ichorCNA/scripts/runIchorCNA.R --id sample_id --WIG sample_id.wig --ploidy "c(2,3)" --normal "c(0.5,0.6,0.7,0.8,0.9)" --maxCN 5 -gcWig /opt/installers/ichorCNA/inst/extdata/gc_hg19_1000kb.wig --mapWig /opt/installers/ichorCNA/inst/extdata/map_hg19_1000kb.wig --centromere /opt/installers/ichorCNA/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt --normalPanel /opt/installers/ichorCNA/inst/extdata/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds --includeHOMD False --chrs "c(1:22, \"X\")" --chrTrain "c(1:22)" --estimateNormal True --estimatePloidy True --estimateScPrevalence True --scStates "c(1,3)" --txnE 0.9999 --txnStrength 10000 --outDir ./

Error in parse_args(parseobj) : Error in getopt(spec = spec, opt = args) : short flag "g" is invalid Execution halted

gavinha commented 5 years ago

sudo Rscript /opt/installers/ichorCNA/scripts/runIchorCNA.R --id sample_id --WIG sample_id.wig --ploidy "c(2,3)" --normal "c(0.5,0.6,0.7,0.8,0.9)" --maxCN 5 -gcWig /opt/installers/ichorCNA/inst/extdata/gc_hg19_1000kb.wig --mapWig /opt/installers/ichorCNA/inst/extdata/map_hg19_1000kb.wig --centromere /opt/installers/ichorCNA/inst/extdata/GRCh37.p13_centromere_UCSC-gapTable.txt --normalPanel /opt/installers/ichorCNA/inst/extdata/HD_ULP_PoN_1Mb_median_normAutosome_mapScoreFiltered_median.rds --includeHOMD False --chrs "c(1:22, "X")" --chrTrain "c(1:22)" --estimateNormal True --estimatePloidy True --estimateScPrevalence True --scStates "c(1,3)" --txnE 0.9999 --txnStrength 10000 --outDir ./

Error in parse_args(parseobj) : Error in getopt(spec = spec, opt = args) : short flag "g" is invalid Execution halted

Hi @vipuljain123

You need to use --gcWig for the argument flag. You only used -gcWig with one dash.

Best, Gavin