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Old 07-14-2014, 04:48 AM   #60
Location: Milan

Join Date: May 2013
Posts: 40

Dear Velntina,

Please find the output for the above call, I have made 6 such calls but all had the same problem. Below am attaching the log of the output run and at what stage I get the segmentation fault.

/scratch/GT/softwares/FREEC_Linux64/freec -conf config_ctrl5.txt
Control-FREEC v7.0 : calling copy number alterations and LOH regions using deep-sequencing data
MT-mode using 6 threads
..Minimal CNA length (in windows) is 1
..Breakpoint threshold for segmentation of copy number profiles is 1.5
..Polynomial degree for "ReadCount ~ GC-content" or "Sample ReadCount ~ Control ReadCount" is 3
..telocenromeric set to 50000
..FREEC is not going to adjust profiles for a possible contamination by normal cells
..Window = 50000 was set
..Step: 250
..Output directory: /scratch/GT/vdas/pietro/exome_seq/test_Control_FREEC/CNA_LOH/out1/
..Directory with files containing chromosome sequences: /scratch/GT/vdas/test_exome/exome/
..will use a threshold of 5 read(s) per SNP position to calculate beta allel frequency (BAF) values
..Sample file: /scratch/GT/vdas/pietro/exome_seq/results/T_S7999/T_S7999.realigned.recal.pileup.gz
..Sample input format: pileup
..Control file: /scratch/GT/vdas/pietro/exome_seq/results/N_S8981/N_S8981.realigned.recal.pileup.gz
..Input format for the control file: pileup
..minimal expected GC-content (general parameter "minExpectedGC") was set to 0.35
..maximal expected GC-content (general parameter "maxExpectedGC") was set to 0.55
..File with chromosome lengths: /scratch/GT/vdas/pietro/exome_seq/test_Control_FREEC/hs19_chr.len
..Using the default minimal mappability value of 0.85
..uniqueMatch = FALSE
..average ploidy set to 2
..break-point type set to 4
Warning: I would not recommend using '[general] noisyData=true' for whole genome data; you can miss some real CNAs in this case
..minimal number of reads per window in the control sample is set to 10
..will use SNP positions from /scratch/GT/vdas/pietro/exome_seq/test_Control_FREEC/hg19_snp137.SingleDiNucl.1based.txt to calculate BAF profiles
..Starting reading /scratch/GT/vdas/pietro/exome_seq/test_Control_FREEC/hg19_snp137.SingleDiNucl.1based.txt to get SNP positions
Segmentation fault
Just after the Segmentation fault it stops and I do not get any outputs in the directory where I have mentioned. Do you want to me to mail again the log status?
vd4mindia is offline   Reply With Quote