Question: Cnvnator *** Break *** Segmentation Violation
0
gravatar for siyu
6.8 years ago by
siyu130
China
siyu130 wrote:

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 ?

• 3.9k views
ADD COMMENTlink modified 5.2 years ago by drashu_110 • written 6.8 years ago by siyu130

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

ADD REPLYlink written 6.8 years ago by brentp23k

./CNVnatorv0.2.7/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 H9mergeL3L4L5.bam.prefix.bam ./CNVnatorv0.2.7/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 .

ADD REPLYlink modified 6.8 years ago • written 6.8 years ago by siyu130
0
gravatar for Vivek
6.8 years ago by
Vivek2.3k
Denmark
Vivek2.3k wrote:

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.

ADD COMMENTlink written 6.8 years ago by Vivek2.3k

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

ADD REPLYlink written 6.8 years ago by siyu130

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?

ADD REPLYlink written 5.7 years ago by Nima0
0
gravatar for drashu_11
5.2 years ago by
drashu_110
Denmark
drashu_110 wrote:

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 

 

ADD COMMENTlink written 5.2 years ago by drashu_110
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