program interrupted without any error information

[victor0104]

Hi All,

A seqz data(around 0.9Gb) were generated from WGS data. I used it as input for scarHRD. Unfortunately，program were interrupted automatically without any error information on Rstudio Server v1.3.1073. The scarHRD version is 0.1.1. Any suggestion for this situation?

Regards,
Victor

[victor0104]

Hi all,

Here is the update for this problem.
I used following command to generate sequenza.gz file for scarHRD.An error message were generated by scarHRD. Any idea for this situation? Thanks in advance.
command:
sequenza-utils bam2seqz -S /home/biosoft/samtools/1.9/bin/samtools -gc /home/test/HRD/data/hg19.gc50Base.txt.gz -F /home/test/HRD/data/hg19.fasta -n /home/test/HRD/sh/data/HRD-01N.sorted.bam -t /home/test/HRD/sh/data/HRD-01T.sorted.bam -C chr1 chr2 chr3 chr4 chr5 chr6 chr7 chr8 chr9 chr10 chr11 chr12 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr20 chr21 chr22 chrX -T /home/biosoft/tabix_bgzip/0.2.5/tabix | sequenza-utils seqz_binning -w 50 -s - | gzip > /home/test/HRD/sh/HRD-01.test1.seqz.gz
error message:Warning:
1 parsing failure.
row col expected actual file
1992800 -- 14 columns 2 columns '/home/test/HRD/wgs/HRD-01.test1.seqz.gz'

Error in data.frame(chrom, pos, wins.data, stringsAsFactors = FALSE) :
arguments imply differing number of rows: 49773, 49772
Error in data.frame(base.count = as.integer(n.base.mut), maj.base.freq = as.numeric(max.freqs[, :
arguments imply differing number of rows: 182, 181

Regards,
Victor