Issue with running battenberg

[gaitat]

I have R v4.2.2 and I installed Battenberg v2.2.10 using

R -q -e 'BiocManager::install(c("devtools", "splines", "readr", "doParallel", "ggplot2", "RColorBrewer", "gridExtra", "gtools", "parallel", "igordot/copynumber", "VariantAnnotation"))'
R -q -e 'devtools::install_github("Wedge-lab/battenberg")'

I have downloaded the hg38 reference files and unzipped the *_chr.zip files as my data contains the chr prefix.

I have copied the battenberg_wgs.R from the installation to my working directory.
I had to modify the entry

# from
        G1000LOCIPREFIX = file.path(BEAGLE_BASEDIR, "1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_loci_chr")
# to
        G1000LOCIPREFIX = file.path(BEAGLE_BASEDIR, "1000G_loci_hg38/1kg.phase3.v5a_GRCh38nounref_loci_")

as otherwise allelecounting would not run.
I changed the analysis to paired as I have tumor/normal pairs and also supplied the correct path to ALLELECOUNTER

My script for running the algorithm is pretty simple:

#!/usr/bin/env bash

tumorName=$1
tumorFile=$2
normalName=$3
normalFile=$4

mkdir -p $tumorName

Rscript battenberg_wgs.R \
  --tumourname $tumorName \
  --tb $tumorFile \
  --normalname $normalName \
  --nb $normalFile \
  --sex female \ # I am actually not sure about this
  --output $tumorName \
  --cpu 24

exit 0

After allele counting is done, the files written to my output folder have the format (note the double chr)

51328 -rw-rw-r-- 1 user group 52522894 Dec  7 12:06 TCGA-24-0982-01A_alleleFrequencies_chrchr1.txt
55040 -rw-rw-r-- 1 user group 56313535 Dec  7 12:13 TCGA-24-0982-10C_alleleFrequencies_chrchr1.txt

And then I get the error message:

Error in `[.data.frame`(allele_data, , 1) : undefined columns selected
Calls: battenberg ... prepare_wgs -> getBAFsAndLogRs -> paste -> [ -> [.data.frame
Execution halted

Any help would be greatly appreciated.

[gaitat]

Update: After installing the 'dev' branch, I get the same error message and more:

Error in `[.data.frame`(allele_data, , 1) : undefined columns selected
Calls: battenberg ... getBAFsAndLogRs -> gsub -> is.factor -> [ -> [.data.frame
Execution halted
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Error in unserialize(node$con) : error reading from connection
Calls: <Anonymous> ... doTryCatch -> recvData -> recvData.SOCKnode -> unserialize
Execution halted