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BoevaLab / FREEC

Control-FREEC: Copy number and genotype annotation in whole genome and whole exome sequencing data
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Segmentation fault (core dumped) #101

Open wyqhyrz opened 2 years ago

wyqhyrz commented 2 years ago

Hi, I'm trying to run Control-FREEC on human exome sequencing data, but I have a problem with it. Creating Pileup file to compute BAF profile... ..will increase flanking regions by 106 bp Segmentation fault (core dumped) Actually I have seen the same problem with me here, http://seqanswers.com/forums/archive/index.php/t-16803.html, but I didn't see the solution. If I remove [BAF] parameters, the error disappears. Maybe something wrong with my bed or vcf files, so I tried using your [hg19_snp142.SingleDiNucl.1based.txt.gz](actually my genome is hg38) for testing, it still reported the same error. Here are my config txt `[general] BedGraphOutput = TRUE chrLenFile = /home/wangyuqian/reference/Exon_V6/sorted.genome.fa.fai chrFiles=/home/wangyuqian/reference/hg38_ensembl104/homo_sapiens/chr_24 window = 0 degree=1 forceGCcontentNormalization=1 maxThreads=20 minCNAlength=3 minimalSubclonePresence=30 breakPointThreshold=0.8 noisyData=TRUE printNA=FALSE ploidy = 2 readCountThreshold=50 samtools=/home/wangyuqian/miniconda3/bin/samtools outputDir = /data/wangyuqian/gastric/02Data/example/CNV/freec/ID05

[sample] mateFile = /data/wangyuqian/gastric/02Data/example/bam/ID06_T/ID06_T.BQSR.bam inputFormat = BAM mateOrientation = FR

[control] mateFile = /data/wangyuqian/gastric/02Data/example/bam/ID06_N/ID06_N.BQSR.bam inputFormat = BAM mateOrientation = FR

[BAF] fastaFile=/home/wangyuqian/reference/hg38_ensembl104/homo_sapiens/with_chr/genome.fa SNPfile=/home/wangyuqian/data/gastric/02Data/example/CNV/freec/hg38_snp146.SingleDiNucl.vcf minimalCoveragePerPosition = 5 makePileup=/home/wangyuqian/data/gastric/02Data/example/CNV/freec/hg38_snp146.SingleDiNucl.bed

[target] captureRegions = /home/wangyuqian/reference/Exon_V6/sorted_ExonV6.bed ` Thank you very much in advance!

valeu commented 2 years ago

Dear Wang, Please check that: captureRegions .bed file is sorted by position, and that ID06_T.BQSR.bam and ID06_N.BQSR.bam contain 'chr' in the chromosome names. You can also try this simplified config:

[general]
BedGraphOutput = TRUE
chrLenFile = /home/wangyuqian/reference/Exon_V6/sorted.genome.fa.fai
chrFiles=/home/wangyuqian/reference/hg38_ensembl104/homo_sapiens/chr_24
window = 0
forceGCcontentNormalization=1
maxThreads=20
minCNAlength=3
breakPointThreshold=0.8
noisyData=TRUE
printNA=FALSE
ploidy = 2
readCountThreshold=50
samtools=/home/wangyuqian/miniconda3/bin/samtools
outputDir = /data/wangyuqian/gastric/02Data/example/CNV/freec/ID05

[sample]
mateFile = /data/wangyuqian/gastric/02Data/example/bam/ID06_T/ID06_T.BQSR.bam
inputFormat = BAM
mateOrientation = FR

[control]
mateFile = /data/wangyuqian/gastric/02Data/example/bam/ID06_N/ID06_N.BQSR.bam
inputFormat = BAM
mateOrientation = FR

[BAF]
fastaFile=/home/wangyuqian/reference/hg38_ensembl104/homo_sapiens/with_chr/genome.fa
SNPfile=/home/wangyuqian/data/gastric/02Data/example/CNV/freec/hg38_snp146.SingleDiNucl.vcf
minimalCoveragePerPosition = 5
makePileup=/home/wangyuqian/data/gastric/02Data/example/CNV/freec/hg38_snp146.SingleDiNucl.vcf

[target]
captureRegions = /home/wangyuqian/reference/Exon_V6/sorted_ExonV6.bed