chr prefix

[hidehitofukushima]

Hi.
I'm using Battenberg recently and facing a little situation I seriously can't cope with, so I need your help.

I used the docker image from quay.io/wtsicgp/cgpbattenberg:3.7.1 , pulled it in a singularity image(singuarity pull docker://quay.io/wtsicgp/cgpbattenberg:3.7.1) and tried this command, and got these error.

####################################################################################
#$ -S /bin/bash
#$ -cwd
#$ -pe def_slot 16
#$ -l s_vmem=32G

singularity exec -e --bind /share/xxx/:/share/xxx/ /home/xxxx/database/images/cgpbattenberg_3.7.1.sif
battenberg.pl
-o ${OUTPUT_DIR}
-r ${FASTA}.fai
-tb ${TUMOR_BAM}
-nb ${NORMAL_BAM}
-e /home/xxxx/BATTENBERG/tmp2/reference_hg38/impute_info.txt
-u /home/xxxx/BATTENBERG/tmp2/reference_hg38/1000G_loci_hg38/
-ig /home/xxxx/BATTENBERG/tmp2/reference_hg38/ignore_contigs.wtchr
-gc /home/xxxx/BATTENBERG/tmp2/reference_hg38/GC_correction_hg38/
-t 16
-c /home/xxxx/BATTENBERG/tmp2/reference_hg38/probloci/probloci.txt.gz
-pr WGS
-ge XY
-ra 38

xxxxxxxxxxxxxxxx_allelecount.1.err:

• /opt/wtsi-cgp/bin/alleleCounter -l /home/xxxxx/BATTENBERG/result/sample2/xxxxxxxxxxx/tmpBattenberg/1000genomesloci2012_chr1_split1.txt -b /home/xxxxxx/database/links/xxxxxx/result/wgs/xxxxxxxxxxxxxx/bam/yyyyyyyyyyyyyyyyyyyy/yyyyyyyyyyyyyyyyyyyyyyy.markdup.bam -o /home/xxxx/BATTENBERG/result/sample2/xxxxxxxxxxxxxxxxxx/tmpBattenberg/yyyyyyyyyyyyyyyyyyyyyyyyy_alleleFrequencies_chr1_split1.txt -m 20 -r /home/xxxx/database/reference/Homo_sapiens_assembly38.fasta.fai -d
  Reading locis
  Done reading locis
  Multi pos start:
  1054.64user 14.98system 17:53.85elapsed 99%CPU (0avgtext+0avgdata 4563196maxresident)k
  521476inputs+119296outputs (9major+1137847minor)pagefaults 0swaps

xxxxxxxxxxxxxxxx_runbaflog.0.err:

• cd /home/xxxx/some_directory/tmpBattenberg
• /usr/bin/Rscript -e 'library(Battenberg); getBAFsAndLogRs(tumourAlleleCountsFile.prefix="87336744-255b-42a1-a1ff-0eded2655d8f_alleleFrequencies_chr", normalAlleleCountsFile.prefix="dace3db7-74a8-408c-9872-d424ee7429bb_alleleFrequencies_chr", figuresFile.prefix="87336744-255b-42a1-a1ff-0eded2655d8f_", BAFnormalFile="87336744-255b-42a1-a1ff-0eded2655d8f_normalBAF.tab", BAFmutantFile="87336744-255b-42a1-a1ff-0eded2655d8f_mutantBAF.tab", logRnormalFile="87336744-255b-42a1-a1ff-0eded2655d8f_normalLogR.tab", logRmutantFile="87336744-255b-42a1-a1ff-0eded2655d8f_mutantLogR.tab", combinedAlleleCountsFile="87336744-255b-42a1-a1ff-0eded2655d8f_alleleCounts.tab", chr_names=as.vector(c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X")), g1000file.prefix="/home/xxxx/BATTENBERG/tmp2/reference_hg38/1000G_loci_hg38/1000genomesAlleles2012_chr", minCounts=10, samplename="87336744-255b-42a1-a1ff-0eded2655d8f", seed=1488823153) '
  511.57user 12.36system 10:01.43elapsed 87%CPU (0avgtext+0avgdata 19791232maxresident)k
  785890inputs+5320592outputs (122major+2178229minor)pagefaults 0swaps

xxxxxxxxxxxxxxxx_gc_correct.0.err:

• cd /home/some_directory/tmpBattenberg
• /usr/bin/Rscript -e 'library(Battenberg); gc.correct.wgs(Tumour_LogR_file="87336744-255b-42a1-a1ff-0eded2655d8f_mutantLogR.tab", outfile="87336744-255b-42a1-a1ff-0eded2655d8f_mutantLogR_gcCorrected.tab", correlations_outfile="87336744-255b-42a1-a1ff-0eded2655d8f_GCwindowCorrelations.txt", gc_content_file_prefix="/home/xxxx/BATTENBERG/tmp2/reference_hg38/GC_correction_hg38/1000_genomes_GC_corr_chr_",replic_timing_file_prefix=NULL, chrom_names=as.vector(c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X"))) '
  Warning message:
  The path argument of write_tsv() is deprecated as of readr 1.4.0.
  Please use the file argument instead.
  This warning is displayed once every 8 hours.
  Call lifecycle::last_warnings() to see where this warning was generated.
  220.29user 28.44system 4:26.97elapsed 93%CPU (0avgtext+0avgdata 21400400maxresident)k
  2455614inputs+10494816outputs (3major+3085355minor)pagefaults 0swaps

xxxxxxxxxxxxxxxxxx_imputefromaf.7.err:

• cd /home/some_directory/result/sample2/hogehoge/tmpBattenberg
• /usr/bin/Rscript -e 'library(Battenberg); generate.impute.input.wgs(chrom="chr7", tumour.allele.counts.file="87336744-255b-42a1-a1ff-0eded2655d8f_alleleFrequencies_chrchr7.txt", normal.allele.counts.file="dace3db7-74a8-408c-9872-d424ee7429bb_alleleFrequencies_chrchr7.txt", output.file="87336744-255b-42a1-a1ff-0eded2655d8f_impute_input_chrchr7.txt", imputeinfofile="/home/ny1fh/BATTENBERG/tmp2/reference_hg38/impute_info.txt", is.male="TRUE", problemLociFile="/home/ny1fh/BATTENBERG/tmp2/reference_hg38/probloci/probloci.txt.gz", useLociFile=NA, heterozygousFilter=0.1) '
  Error in file(file, "rt") : invalid 'description' argument
  Calls: generate.impute.input.wgs -> read.table -> file
  0.26user 0.04system 0:00.30elapsed 99%CPU (0avgtext+0avgdata 73864maxresident)k
  0inputs+48outputs (0major+18718minor)pagefaults 0swaps

####################################################################################

Apparently allelecount process completed with no error, and with complete set of xxxxxx_alleleFrequencies_chrZZZZ.txt.
Runbaflog.err file and gc.correct.err file seemed okay, but in the imputefromaf.err file I found the error above.

The 'chrom_names' variable first had no 'chr' prefix inside as you can see in the runbaflog.err file and gc.correct.file.
(chrom_names=as.vector(c("1","2","3","4","5","6","7","8","9","10","11","12","13","14","15","16","17","18","19","20","21","22","X"))
However, I also noticed 'chrom' variable in generate.impute.input.wgs function has 'chr'. and this function required 'xxxx_alleleFrequencies_chrchr7.txt' as inputfile. (in my result folder there's 'xxxx_alleleFrequencies_chr7.txt')

I believe the battenberg.R file has only one site defining chrom_names variable(line145-150) , and subsequent functions are called with each 'chrom' from 'chrom_names', so I wonder why chrom_names variable suddenly changed from without chr prefix to WITH chrom prefix.

Just so you know, the bam files are alinged with hg38, and has 'chr' prefix

I also tried recent versions of distributed source including dev branch with battenberg R package, as well as all previous images from quay:io, and they all got stuck in the getBAFsAndLogRs function, with empty xxxxx_mutantBAF.tab files (just as someone mentioned in the issue, even though I tried with more cores, more memory(eg, 128G+10core). So I gave these versions up.
ANY help would be appreciated.
thanks in advance!