Cnvnator *** Break *** Segmentation Violation

Question

[siyu]

Is there anyone who meets the problem as follows when using CNVnator to discovery CNVs ?

when I run the step 3 of CNVnator: ./CNVnator_v0.2.7/src/cnvnator -genome GRCh37 -root H9.root -chrom 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 x -stat 100

the error is :

---

There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x00007fa9da718dde in waitpid () from /lib64/libc.so.6
#1  0x00007fa9da6a0099 in ?? () from /lib64/libc.so.6
#2  0x00007fa9df5d75f5 in TUnixSystem::StackTrace() () from /usr/lib64/root/libCore.so
#3  0x00007fa9df5d9773 in TUnixSystem::DispatchSignals(ESignals) () from /usr/lib64/root/libCore.so
#4  <signal handler="" called="">
#5  0x00007fa9da7b2e81 in ?? () from /lib64/libc.so.6
#6  0x00007fa9df50fcb4 in TString::TString(char const*) () from /usr/lib64/root/libCore.so
#7  0x00007fa9ddcda7a4 in TH1::DoIntegral(int, int, int, int, int, int, double&, char const*, bool) const () from /usr/lib64/root/libHist.so
#8  0x00007fa9ddcd462f in TH1::Integral(int, int, char const*) const () from /usr/lib64/root/libHist.so
#9  0x0000000000411f18 in HisMaker::getMeanSigma(TH1*, double&, double&) ()
#10 0x000000000041944c in HisMaker::stat(std::string*, int, bool) ()
#11 0x0000000000408bd1 in main ()
===========================================================
The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug report at
http://root.cern.ch/bugs. Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#5  0x00007fa9da7b2e81 in ?? () from /lib64/libc.so.6
#6  0x00007fa9df50fcb4 in TString::TString(char const*) () from /usr/lib64/root/libCore.so
#7  0x00007fa9ddcda7a4 in TH1::DoIntegral(int, int, int, int, int, int, double&, char const*, bool) const () from /usr/lib64/root/libHist.so
#8  0x00007fa9ddcd462f in TH1::Integral(int, int, char const*) const () from /usr/lib64/root/libHist.so
#9  0x0000000000411f18 in HisMaker::getMeanSigma(TH1*, double&, double&) ()
#10 0x000000000041944c in HisMaker::stat(std::string*, int, bool) ()
#11 0x0000000000408bd1 in main ()
===========================================================

---

Can anyone help me ?

[brentp]

can you give the previous commands that you ran? does it run on a subset of the data (just chr1?).

[siyu]

./CNVnator_v0.2.7/src/cnvnator -genome GRCh37 -unique -root H9.root -chrom 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 x -tree H9_merge_L3L4L5.bam.prefix.bam
./CNVnator_v0.2.7/src/cnvnator -genome GRCh37 -root H9.root -chrom 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 x -his 100
./CNVnator_v0.2.7/src/cnvnator -genome GRCh37 -root H9.root -chrom 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 x -stat 100

It also can't run on a subset of the data.

[drashu_11]

Hi

I am using CNVnator to call cnvs from the bam files. my code was like this

/cnvnator -root Chr23.root -genome .chr1-29.X.fa -chrom Chr23 -stat 100

and I am geeting similar error message like what Siyu have got with his run

Info in <TCanvas::MakeDefCanvas>:  created default TCanvas with name c1

 *** Break *** segmentation violation

===========================================================

There was a crash.
This is the entire stack trace of all threads:
===========================================================
#0  0x0000003373abd3be in waitpid () from /lib64/libc.so.6
#1  0x0000003373a4210e in do_system () from /lib64/libc.so.6
#2  0x00007f4fdb2bebf0 in TUnixSystem::StackTrace() () from /home/asda/software/root/lib/libCore.so
#3  0x00007f4fdb2c1443 in TUnixSystem::DispatchSignals(ESignals) () from /home/asda/software/root/lib/libCore.so
#4  <signal handler called>
#5  0x00007f4fd50c2e3a in asim_parse_argb_color () from /home/asda/software/root/lib/libASImage.so
#6  0x00007f4fd5108cb5 in build_xpm_colormap () from /home/asda/software/root/lib/libASImage.so
#7  0x00007f4fd50ed5eb in xpm_file2ASImage () from /home/asda/software/root/lib/libASImage.so
#8  0x00007f4fd50ed787 in xpm2ASImage () from /home/asda/software/root/lib/libASImage.so
#9  0x00007f4fd50ef95b in file2ASImage_extra () from /home/asda/software/root/lib/libASImage.so
#10 0x00007f4fd50aee62 in TASImage::ReadImage(char const*, TImage::EImageFileTypes) () from /home/asda/software/root/lib/libASImage.so
#11 0x00007f4fd94ce201 in TImage::Open(char const*, TImage::EImageFileTypes) () from /home/asda/software/root/lib/libGraf.so
#12 0x00007f4fd72d99ea in TGPicturePool::GetPicture(char const*) () from /home/asda/software/root/lib/libGui.so
#13 0x00007f4fd72a014f in TGComboBox::Init() () from /home/asda/software/root/lib/libGui.so
#14 0x00007f4fd72a14a9 in TGComboBox::TGComboBox(TGWindow const*, int, unsigned int, unsigned long) () from /home/asda/software/root/lib/libGui.so
#15 0x00007f4fd53dafab in TFitEditor::TFitEditor(TVirtualPad*, TObject*) () from /home/asda/software/root/lib/libFitPanel.so
#16 0x00007f4fd53dbd99 in TFitEditor::GetInstance(TVirtualPad*, TObject*) () from /home/asda/software/root/lib/libFitPanel.so
#17 0x00007f4fd53ebba8 in G__G__FitPanel_402_0_22(G__value*, char const*, G__param*, int) () from /home/asda/software/root/lib/libFitPanel.so
#18 0x00007f4fda8432bf in Cint::G__CallFunc::Execute(void*) () from /home/asda/software/root/lib/libCint.so
#19 0x00007f4fdb287981 in TCint::CallFunc_ExecInt(void*, void*) const () from /home/asda/software/root/lib/libCore.so
#20 0x00007f4fdb2857b7 in TMethodCall::Execute(void*, long&) () from /home/asda/software/root/lib/libCore.so
#21 0x00007f4fdb215063 in TPluginHandler::ExecPlugin(int, ...) () from /home/asda/software/root/lib/libCore.so
#22 0x00007f4fd993e335 in TH1::FitPanel() () from /home/asda/software/root/lib/libHist.so
#23 0x0000000000412985 in HisMaker::getMeanSigma(TH1*, double&, double&) ()
#24 0x0000000000419bca in HisMaker::stat(std::string*, int, bool) ()
#25 0x0000000000408b5a in main ()
===========================================================

The lines below might hint at the cause of the crash.
If they do not help you then please submit a bug report at
http://root.cern.ch/bugs. Please post the ENTIRE stack trace
from above as an attachment in addition to anything else
that might help us fixing this issue.
===========================================================
#5  0x00007f4fd50c2e3a in asim_parse_argb_color () from /home/asda/software/root/lib/libASImage.so
#6  0x00007f4fd5108cb5 in build_xpm_colormap () from /home/asda/software/root/lib/libASImage.so
#7  0x00007f4fd50ed5eb in xpm_file2ASImage () from /home/asda/software/root/lib/libASImage.so
#8  0x00007f4fd50ed787 in xpm2ASImage () from /home/asda/software/root/lib/libASImage.so
#9  0x00007f4fd50ef95b in file2ASImage_extra () from /home/asda/software/root/lib/libASImage.so
#10 0x00007f4fd50aee62 in TASImage::ReadImage(char const*, TImage::EImageFileTypes) () from /home/asda/software/root/lib/libASImage.so
#11 0x00007f4fd94ce201 in TImage::Open(char const*, TImage::EImageFileTypes) () from /home/asda/software/root/lib/libGraf.so
#12 0x00007f4fd72d99ea in TGPicturePool::GetPicture(char const*) () from /home/asda/software/root/lib/libGui.so
#13 0x00007f4fd72a014f in TGComboBox::Init() () from /home/asda/software/root/lib/libGui.so
#14 0x00007f4fd72a14a9 in TGComboBox::TGComboBox(TGWindow const*, int, unsigned int, unsigned long) () from /home/asda/software/root/lib/libGui.so
#15 0x00007f4fd53dafab in TFitEditor::TFitEditor(TVirtualPad*, TObject*) () from /home/asda/software/root/lib/libFitPanel.so
#16 0x00007f4fd53dbd99 in TFitEditor::GetInstance(TVirtualPad*, TObject*) () from /home/asda/software/root/lib/libFitPanel.so
===========================================================

Siyu could you got it worked? If so please help me if any solution of this

Thanks in advance

Answer 1

[Vivek]

You could check if your reference fasta file has more than 60 bases per line. I had a segmentation fault error when I used such file.

[siyu]

yes，there are 60 bases per line in my reference fasta file. is there another problem you know?

[Nima]

Hej, my reference.fa is 60 bp per line but still receiving the same error as you posted. Iwas wondering to know if you had chance to solve the problem?