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Old 07-03-2013, 01:44 PM   #52
Junior Member
Location: California

Join Date: Mar 2011
Posts: 3
Default SegFault when running Freec

Hi all. First, I wanted to say thanks to valeu for taking the time to answer questions on here, I've found some of the advice to be very useful.

Second, I've been having a problem with segmentation faults when trying to use Freec to compute BAF. I had previously been using Freec to analyze exome samples without calculating BAF, and had success calling CNVs from the .bam files. However, when I tried to compute BAF (which required converting the .bams into pileup files, as well as using a file of known SNPs) I ran into some problems.
Specifically, the program dies after about 1 second of runtime with the following as the specific error:

line 13: 269410 Segmentation fault

This occurs after the program outputs the following:

..Starting reading /home/sf062971/resources/ucsc_snps/snp137.no_dashes.freec_baf.txt to get SNP positions

Which suggests that it might be something with my SNP file. However, I have omitted this file and still get a segfault when it tries to read my sample pileups.

My configuration file is below. Any help on what may be causing this would be appreciated.


window = 5000
step = 1000

ploidy = 2

samtools = /home/sf062971/programs/samtools-0.1.18/samtools

minCNAlength = 4

BedGraphOutput = TRUE

chrLenFile = /home/sf062971/resources/freec_resources/mm10.len

chrFiles = /data/sf062971/data/reference/chr_files

noisyData = TRUE


outputDir = 1148T_1205N_V3

contamination = 0.5
contaminationAdjustment = TRUE


mateFile = /data/sf062971/LUNG_BAMS/SC_GCIM5351148/1148_ALIGN_RECAL_V3/1148_EXOME.mpileup

inputFormat = pileup

mateOrientation = 0


mateFile = /data/sf062971/LUNG_BAMS/SC_GCIM5351205/1205_ALIGN_RECAL_V3/1205_EXOME.mpileup

inputFormat = pileup

mateOrientation = 0


SNPfile = /home/sf062971/resources/ucsc_snps/snp137.no_dashes.freec_baf.txt

minimalCoveragePerPosition = 10


captureRegions = /home/sf062971/resources/agilent_data/covered_regions_mm10_merged_sorted.bed
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