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Error in { : task 1 failed - "cannot open the connection" #16

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Li-Rui091 opened this issue Oct 22, 2021 · 2 comments
Open

Error in { : task 1 failed - "cannot open the connection" #16

Li-Rui091 opened this issue Oct 22, 2021 · 2 comments

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@Li-Rui091
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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
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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
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Also for the "/annotation/gcWinds/"

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