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chrisamiller / copyCat

a parallel R package for detecting copy-number alterations from short sequencing reads
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Error in { : task 1 failed - "cannot open the connection" #16

Open Li-Rui091 opened 3 years ago

Li-Rui091 commented 3 years ago

When I use copyCat. I met this error: Using copyCat version 1.6.12 [1] "inferred bin size: 10000" [1] "calculating mapability content for read length 100 Fri Oct 22 14:59:56 2021" Error in { : task 1 failed - "cannot open the connection" In addition: Warning message: package ‘stringr’ was built under R version 4.1.0

My code is as follows: library(copyCat)

run copyCat in paired mode

runPairedSampleAnalysis(annotationDirectory="/home/ruil/PMB/somatic/copycat_WGS/copyCat_annotation", outputDirectory="/home/ruil/PMB/somatic/copycat_WGS", normal="/home/ruil/PMB/somatic/copycat_WGS/WGS_Norm.mosdepth.regions.2.bed", tumor="/home/ruil/PMB/somatic/copycat_WGS/WGS_Tumor.mosdepth.regions.2.bed", inputType="bins", maxCores=0, binSize=0, perLibrary=1, perReadLength=1, verbose=TRUE, minWidth=3, minMapability=0.6, dumpBins=TRUE, doGcCorrection=TRUE, samtoolsFileFormat="unknown", purity=1, normalSamtoolsFile=NULL, tumorSamtoolsFile=NULL) Do you know how to fix it?

pengweixing commented 3 years ago

In the "/annotation/mapability directory", each file's name should start with "chr". For example, change the "1.dat.gz" to "chr1.dat.gz". It will be work.

pengweixing commented 3 years ago

Also for the "/annotation/gcWinds/"