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  • #76
    Segmentation fault (core dumped)

    Hi,

    I'm trying to run Control-FREEC on cancer whole genome sequencing data, but I get the error "Segmentation fault (core dumped)". thanks for any help!


    config file :

    Code:
    [general]

chrLenFile = /public1/users/ruanys/human_genome/ref/b37.len
chrFiles= /public1/users/ruanys/human_genome/ref/b37_chrfa
ploidy = 2,3,4
BedGraphOutput=TRUE
coefficientOfVariation = 0.062
outputDir = ./
sex=XX

#minCNAlength=1


[sample]

mateFile = /public2/users/chenbj/called/HCC2.pileup
inputFormat = pileup
mateOrientation = FR


[control]

mateFile = /public2/users/chenbj/called/CRN.pileup
inputFormat = pileup
mateOrientation = FR


[BAF]

minimalCoveragePerPosition=0
SNPfile=/public1/users/ruanys/software/FREEC-9.5/download/hg19_snp142.SingleDiNucl.1based.txt.gz
shiftInQuality = 33
    full output while running Control-FREEC:
    Code:
    Control-FREEC v9.6 : a method for automatic detection of copy number alterations, subclones and for accurate estimation of contamination and main ploidy using deep-sequencing data
Non MT-mode
..consider the sample being female
..Breakpoint threshold for segmentation of copy number profiles is 0.8
..telocenromeric set to 50000
..FREEC is not going to adjust profiles for a possible contamination by normal cells
..Coefficient Of Variation set equal to 0.062
..it will be used to evaluate window size
..Output directory: ./
..Directory with files containing chromosome sequences: /public1/users/ruanys/human_genome/ref/b37_chrfa
..Sample file:  /public2/users/chenbj/called/HCC2.pileup
..Sample input format:  pileup
..Control file: /public2/users/chenbj/called/CRN.pileup
..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
..Polynomial degree for "ReadCount ~ GC-content" normalization is 3 or 4: will try both
..Minimal CNA length (in windows) is 1
..File with chromosome lengths: /public1/users/ruanys/human_genome/ref/b37.len
..Using the default minimal mappability value of 0.85
..uniqueMatch = FALSE
..FREEC will try to guess the correct ploidy(for each ploidy specified in 'ploidy' parameter)
..It will try ploidies: 2
3
4
..break-point type set to 2
..noisyData set to 0
..minimal number of reads per window in the control sample is set to 10
..Control-FREEC will not look for subclones
Warning: we recommend setting "window=0" for exome sequencing data
..will use SNP positions from /public1/users/ruanys/software/FREEC-9.5/download/hg19_snp142.SingleDiNucl.1based.txt.gz to calculate BAF profiles
..Starting reading /public1/users/ruanys/software/FREEC-9.5/download/hg19_snp142.SingleDiNucl.1based.txt.gz to get SNP positions
..read 101778434 SNP positions
PROFILING [tid=139713552041760]: /public1/users/ruanys/software/FREEC-9.5/download/hg19_snp142.SingleDiNucl.1based.txt.gz read in 1329 seconds [readSNPs]
..use "pileup" format of reads to calculate BAF profiles
..Starting reading /public2/users/chenbj/called/HCC2.pileup to calculate BAF profiles
will skip chrMT
will skip chrGL000207.1
will skip chrGL000226.1
will skip chrGL000229.1
will skip chrGL000231.1
will skip chrGL000210.1
will skip chrGL000239.1
will skip chrGL000235.1
will skip chrGL000201.1
will skip chrGL000247.1
will skip chrGL000245.1
will skip chrGL000197.1
will skip chrGL000203.1
will skip chrGL000246.1
will skip chrGL000249.1
will skip chrGL000196.1
will skip chrGL000248.1
will skip chrGL000244.1
will skip chrGL000238.1
will skip chrGL000202.1
will skip chrGL000234.1
will skip chrGL000232.1
will skip chrGL000206.1
will skip chrGL000240.1
will skip chrGL000236.1
will skip chrGL000241.1
will skip chrGL000243.1
will skip chrGL000242.1
will skip chrGL000230.1
will skip chrGL000237.1
will skip chrGL000233.1
will skip chrGL000204.1
will skip chrGL000198.1
will skip chrGL000208.1
will skip chrGL000191.1
will skip chrGL000227.1
will skip chrGL000228.1
will skip chrGL000214.1
will skip chrGL000221.1
will skip chrGL000209.1
will skip chrGL000218.1
will skip chrGL000220.1
will skip chrGL000213.1
will skip chrGL000211.1
will skip chrGL000199.1
will skip chrGL000217.1
will skip chrGL000216.1
will skip chrGL000215.1
will skip chrGL000205.1
will skip chrGL000219.1
will skip chrGL000224.1
will skip chrGL000223.1
will skip chrGL000195.1
will skip chrGL000212.1
will skip chrGL000222.1
will skip chrGL000200.1
will skip chrGL000193.1
will skip chrGL000194.1
will skip chrGL000225.1
will skip chrGL000192.1
2842829201 lines read
PROFILING [tid=139713552033536]: /public2/users/chenbj/called/HCC2.pileup read in 2400 seconds [assignValues]
..use "pileup" format of reads to calculate BAF profiles
..Starting reading /public2/users/chenbj/called/CRN.pileup to calculate BAF profiles
will skip chrMT
will skip chrGL000207.1
will skip chrGL000226.1
will skip chrGL000229.1
will skip chrGL000231.1
will skip chrGL000210.1
will skip chrGL000239.1
will skip chrGL000235.1
will skip chrGL000201.1
will skip chrGL000247.1
will skip chrGL000245.1
will skip chrGL000197.1
will skip chrGL000203.1
will skip chrGL000246.1
will skip chrGL000249.1
will skip chrGL000196.1
will skip chrGL000248.1
will skip chrGL000244.1
will skip chrGL000238.1
will skip chrGL000202.1
will skip chrGL000234.1
will skip chrGL000232.1
will skip chrGL000206.1
will skip chrGL000240.1
will skip chrGL000236.1
will skip chrGL000241.1
will skip chrGL000243.1
will skip chrGL000242.1
will skip chrGL000230.1
will skip chrGL000237.1
will skip chrGL000233.1
will skip chrGL000204.1
will skip chrGL000198.1
will skip chrGL000208.1
will skip chrGL000191.1
will skip chrGL000227.1
will skip chrGL000228.1
will skip chrGL000214.1
will skip chrGL000221.1
will skip chrGL000209.1
will skip chrGL000218.1
will skip chrGL000220.1
will skip chrGL000213.1
will skip chrGL000211.1
will skip chrGL000199.1
will skip chrGL000217.1
will skip chrGL000216.1
will skip chrGL000215.1
will skip chrGL000205.1
will skip chrGL000219.1
will skip chrGL000224.1
will skip chrGL000223.1
will skip chrGL000195.1
will skip chrGL000212.1
will skip chrGL000222.1
will skip chrGL000200.1
will skip chrGL000193.1
will skip chrGL000194.1
will skip chrGL000225.1
will skip chrGL000192.1
2841735157 lines read
PROFILING [tid=139713541543680]: /public2/users/chenbj/called/CRN.pileup read in 1730 seconds [assignValues]
..File /public1/users/ruanys/human_genome/ref/b37.len was read
total genome size: 3.1018e+09
PROFILING [tid=139713552041760]: /public2/users/chenbj/called/HCC2.pileup read in 10471 seconds [getReadNumberFromPileup]
read number:   1246830993
coefficientOfVariation:    0.062
 evaluated window size: 647
 ..Starting reading /public2/users/chenbj/called/HCC2.pileup
 PROFILING [tid=139713552041760]: /public2/users/chenbj/called/HCC2.pileup read in 3551 seconds [fillMyHash]
 2842829201 lines read..
 1246830993 reads used to compute copy number profile
 printing counts into ./HCC2.pileup_sample.cpn
 ..Window size: 647
 ..Will not consider chrY..
 ..Erased chrY from the list of chromosomes
 ..File /public1/users/ruanys/human_genome/ref/b37.len was read
 ..Starting reading /public2/users/chenbj/called/CRN.pileup
 PROFILING [tid=139713552041760]: /public2/users/chenbj/called/CRN.pileup read in 2893 seconds [fillMyHash]
 2841735157 lines read..
 880018556 reads used to compute copy number profile
 printing counts into ./CRN.pileup_control.cpn
 ..Will not consider chrY..
 ..Erased chrY from the list of chromosomes
 ..using GC-content to normalize copy number profiles
 CG-content printed into ./GC_profile.cnp
 ..using GC-content to normalize the control profile
 file ./GC_profile.cnp is read
 ..will remove all windows with read count in the control less than 10
 Warning: control length is not equal to the sample length for chromosome MT
 Warning: control length is not equal to the sample length for chromosome GL000207.1
 Warning: control length is not equal to the sample length for chromosome GL000226.1
 Warning: control length is not equal to the sample length for chromosome GL000229.1
 Warning: control length is not equal to the sample length for chromosome GL000210.1
 Warning: control length is not equal to the sample length for chromosome GL000239.1
 Warning: control length is not equal to the sample length for chromosome GL000235.1
 Warning: control length is not equal to the sample length for chromosome GL000201.1
 Warning: control length is not equal to the sample length for chromosome GL000245.1
 Warning: control length is not equal to the sample length for chromosome GL000203.1
 Warning: control length is not equal to the sample length for chromosome GL000246.1
 Warning: control length is not equal to the sample length for chromosome GL000249.1
 Warning: control length is not equal to the sample length for chromosome GL000196.1
 Warning: control length is not equal to the sample length for chromosome GL000202.1
 Warning: control length is not equal to the sample length for chromosome GL000232.1
 Warning: control length is not equal to the sample length for chromosome GL000206.1
 Warning: control length is not equal to the sample length for chromosome GL000236.1
 Warning: control length is not equal to the sample length for chromosome GL000241.1
 Warning: control length is not equal to the sample length for chromosome GL000243.1
 Warning: control length is not equal to the sample length for chromosome GL000230.1
 Warning: control length is not equal to the sample length for chromosome GL000237.1
 Warning: control length is not equal to the sample length for chromosome GL000233.1
 Warning: control length is not equal to the sample length for chromosome GL000204.1
 Warning: control length is not equal to the sample length for chromosome GL000198.1
 Warning: control length is not equal to the sample length for chromosome GL000208.1
 Warning: control length is not equal to the sample length for chromosome GL000191.1
 Warning: control length is not equal to the sample length for chromosome GL000227.1
 Warning: control length is not equal to the sample length for chromosome GL000228.1
 Warning: control length is not equal to the sample length for chromosome GL000214.1
 Warning: control length is not equal to the sample length for chromosome GL000221.1
 Warning: control length is not equal to the sample length for chromosome GL000209.1
 Warning: control length is not equal to the sample length for chromosome GL000218.1
 Warning: control length is not equal to the sample length for chromosome GL000220.1
 Warning: control length is not equal to the sample length for chromosome GL000213.1
 Warning: control length is not equal to the sample length for chromosome GL000211.1
 Warning: control length is not equal to the sample length for chromosome GL000199.1
 Warning: control length is not equal to the sample length for chromosome GL000215.1
 Warning: control length is not equal to the sample length for chromosome GL000205.1
 Warning: control length is not equal to the sample length for chromosome GL000219.1
 Warning: control length is not equal to the sample length for chromosome GL000224.1
 Warning: control length is not equal to the sample length for chromosome GL000223.1
 Warning: control length is not equal to the sample length for chromosome GL000195.1
 Warning: control length is not equal to the sample length for chromosome GL000222.1
 Warning: control length is not equal to the sample length for chromosome GL000200.1
 Warning: control length is not equal to the sample length for chromosome GL000193.1
 Warning: control length is not equal to the sample length for chromosome GL000194.1
 Warning: control length is not equal to the sample length for chromosome GL000225.1
 Warning: control length is not equal to the sample length for chromosome GL000192.1
 ..will process the control file as well: removing all windows with read count in the control less than 10
 ..Set ploidy for the control genome equal to 2
 ..Running FREEC with ploidy set to 2
 2645.86    -3376.64    1406.51 -189.551
 1256.67    -1598.41    661.752 -88.7931
 642.334    -822.065    341.75  -46.061
 334.722    -432.897    181.612 -24.6936
 172.978    -225.899    95.6776 -13.1404
 87.9735    -114.832    48.6472 -6.68335
 41.8822    -55.0312    23.4134 -3.22546
 20.4673    -27.3629    11.8648 -1.66627
 13.0201    -17.4558    7.57621 -1.0632
 3.97755    -5.10018    2.12297 -0.28691
 2.15448    -2.89124    1.26563 -0.180688
 0.620571   -0.747793   0.292975    -0.0372971
 0  0   0   0
 Number of EM iterations :12
 root mean square error = 27.3447
 -9154.09   19731.4 -15436.1    5205.91 -638.203
 -4604.52   9828.18 -7620.35    2547.45 -309.835
 -2104.57   4427.19 -3386.03    1116.97 -134.13
 -959.901   1981.09 -1487.84    482.197 -56.9187
 -448.968   902.816 -662.002    209.83  -24.2583
 -236.815   466.895 -336.011    104.598 -11.8814
 -116.556   225.078 -159.085    48.7493 -5.4619
 -82.6468   155.462 -106.854    31.7517 -3.43634
 -47.7307   87.0257 -58.1954    16.9145 -1.80325
 -36.084    63.2147 -40.7236    11.4445 -1.18504
 -28.2197   50.9987 -33.7152    9.6528  -1.0098
 -23.3177   42.3226 -28.1507    8.10278 -0.846576
 -8.77687   15.6185 -10.1197    2.82089 -0.284334
 -8.45886   14.7795 -9.41635    2.59205 -0.260067
 -4.2932    7.44233 -4.73822    1.31233 -0.133346
 -0.497625  0.879831    -0.552636   0.14733 -0.0141353
 -0.404366  0.650716    -0.360985   0.0819369   -0.00635136
 0  0   0   0   0
 Number of EM iterations :17
 root mean square error = 27.3093
 2645.86    -3376.64    1406.51 -189.551
 1256.67    -1598.41    661.752 -88.7931
 642.334    -822.065    341.75  -46.061
 334.722    -432.897    181.612 -24.6936
 q172.978   -225.899    95.6776 -13.1404
 87.9735    -114.832    48.6472 -6.68335
 41.8822    -55.0312    23.4134 -3.22546
 20.4673    -27.3629    11.8648 -1.66627
 13.0201    -17.4558    7.57621 -1.0632
 3.97755    -5.10018    2.12297 -0.28691
 2.15448    -2.89124    1.26563 -0.180688
 0.620571   -0.747793   0.292975    -0.0372971
 0  0   0   0
 Number of EM iterations :12
 root mean square error = 27.3447
 Y = 110.664*x*x*x+-749.239*x*x+769.89*x+71.4395
 Segmentation fault (core dumped)

    Comment

    • #77
      Please send me the generated .cnp files and your config: valentina . boeva at inserm . fr
      Valentina

      Comment

      • #78
        Hi, I am trying to run controlfreec on WGS cancer cell line data I received from a collaborator. However, I am hitting an error for all of them:

        Code:
        ..failed to run segmentation on chrGL000207.1
terminate called after throwing an instance of 'std::bad_alloc'
  what():  std::bad_alloc
        It is the same error in all cases, though not necessarily at the same stage - in most cases the last output generated is:

        Code:
        Will continue with contamination = 0
..Identified contamination by normal cells: 0%
Seeking eventual subclones...
        But in some cases, this step runs to completion:
        Code:
        Seeking eventual subclones...-> Done!
Total proportion of unexplained regions: 165470 out of 4.47446e+06 = 0.036981
        Attaching an example config file:
        Code:
        [general]

## parameters chrLenFile and ploidy are required.
BedGraphOutput=TRUE
breakPointType = 4
chrFiles = /projects/wtsspipeline/resources/Homo_sapiens/bfa_NCBI-37-TCGA/hg19a_per_chr_fastas/
chrLenFile = /projects/wtsspipeline/programs/code/Control-FREEC_1.0.0/resources/hg19_control_FreeC_chr_length.txt
coefficientOfVariation = 0.062
contaminationAdjustment=TRUE
forceGCcontentNormalization = 2
gemMappabilityFile = /projects/wtsspipeline/resources/Homo_sapiens/bfa_NCBI-37-TCGA/out100m1_hg19.gem
minCNAlength = 2
minimalSubclonePresence = 0.05
maxThreads=8
outputDir = /projects/ccg_capture_panel/cmay_dev/projects/CLINGEN-5870_LSARP/CLINGEN-6122_Run_CNV_analysis_on_cell_line_BAMS/freec_run1/A12438
ploidy = 2,3,4,5,6
sambamba = /gsc/software/linux-x86_64/sambamba-0.5.5/sambamba_v0.5.5
samtools = /home/rcorbett/aligners/samtools-1.2/samtools
telocentromeric = 75000


[sample]

mateFile = /projects/analysis/analysis19/A12438/merge_bwa-0.5.7/100nt/hg19a/A12438_3_lanes_dupsFlagged.bam
inputFormat = BAM
mateOrientation = FR
        I had seen elsewhere that this could be because the chromosome lengths file doesn't match the chromosome lengths in the bam files, however these all match. Any insight would be helpful! Thanks.

        Comment

        • #79
          Hi Valentina! How are you?
          I was hopping you could help me with the following:
          I have a human tumor sample from WES which has also been analyzed by cytogenetists and they concluded it is near-tetraploid. I also have its matching normal sample, with regular diploidy.
          When running Control-FREEC should I set ploidy to 3 or 2? In other words, does the plody entered refer to the tumor ploidy, the normal ploidy or it assumes both samples have the same one?
          Thank you very much in advance,
          Best,
          Daiana

          Comment

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