PennCNV and segfault error

Question

[kiminsigne]

I'm trying to use PennCNV to call CNVs in Affymetrix arrays (Axiom BioBank). After finally compiling the code, I get a segfault error and have no idea where it could be coming from or where to even start. My output is listed below. It seems to run normally for the first file, decides the file doesn't pass quality control, then all of a sudden quits. Any insights would be much appreciated!

$ perl detect_cnv.pl -test -hmm gw6/lib/affygw6.hmm -pfb AxiomBioBank1.pfb -list sigfile_list.txt -log Axiom.log -out Axiom.rawcnv
NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file Axiom.log
NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from AxiomBioBank1.pfb ... Done with 628576 records (101 records in chr MT were discarded)
NOTICE: Reading LRR and BAF values for from C:/Users/Kimberly/Documents/2014_Fall/Kruglyak Lab/familyCNV/pennCNV/Axiom_CNV/sig_files/01_8000094320_8007536673_9999_3_40_1_A1.cnv.txt ... Done with 628576 records in 24 chromosomes (101 records are discarded due to lack of PFB information for the markers)
NOTICE: Data from chromosome X,Y will not be used in analysis
NOTICE: Median-adjusting LRR values for all autosome markers from C:/Users/Kimberly/Documents/2014_Fall/Kruglyak Lab/familyCNV/pennCNV/Axiom_CNV/sig_files/01_8000094320_8007536673_9999_3_40_1_A1.cnv.txt by 0.0274
NOTICE: Median-adjusting BAF values for all autosome markers from C:/Users/Kimberly/Documents/2014_Fall/Kruglyak Lab/familyCNV/pennCNV/Axiom_CNV/sig_files/01_8000094320_8007536673_9999_3_40_1_A1.cnv.txt by -0.0123
NOTICE: quality summary for C:/Users/Kimberly/Documents/2014_Fall/Kruglyak Lab/familyCNV/pennCNV/Axiom_CNV/sig_files/01_8000094320_8007536673_9999_3_40_1_A1.cnv.txt: LRR_mean=-0.0016 LRR_median=0.0000 LRR_SD=0.3312 BAF_mean=0.4983 BAF_median=0.5000 BAF_SD=0.0915 BAF_DRIFT=0.008258 WF=0.0198 GCWF=0.0008
WARNING: Sample from C:/Users/Kimberly/Documents/2014_Fall/Kruglyak Lab/familyCNV/pennCNV/Axiom_CNV/sig_files/01_8000094320_8007536673_9999_3_40_1_A1.cnv.txt does not pass default quality control criteria due to its large SD for LRR (0.331152390801654)!
WARNING: Sample from C:/Users/Kimberly/Documents/2014_Fall/Kruglyak Lab/familyCNV/pennCNV/Axiom_CNV/sig_files/01_8000094320_8007536673_9999_3_40_1_A1.cnv.txt does not pass default quality control criteria due to its drifting BAF values (drift=0.0082584572428637)!
WARNING: Small-sized CNV calls may not be reliable and should be interpreted with caution!
Segmentation fault (core dumped)

[cruzpedro]

Hi, sorry I cannot help, but I would like to ask you if there's a link for this script pf yours, I am currently trying to use PennCNV for Axiom arrays. Thank in advance. :)

Kind regards

Answer 1

[Matt Shirley]

I vaguely remember this problem happening for me. I think the perl script calls a binary file, and that binary might need to be re-compiled on your computer. Change to the kext directory and then type make.

Answer 2

[yogacacarolom]

I had the same problem and I solved installing a compatible perl version and replacing the first row of the detec_cnv.pl function to specify my new perl version.

## INSTALL compatible version of perl with the perlbrew utility
# install perlbrew
\wget -O - http://install.perlbrew.pl | bash
source ~/perl5/perlbrew/etc/bashrc

# install perl 5.8.8
perlbrew install perl-5.8.8 --thread --multi # says that installation failed because 1 test failed
cd /home/yourhomename/perl5/perlbrew/build/perl-5.8.8; make install # force install anyway

# replace the first line of detect_cnv.pl : #!/usr/bin/perl
# by the location where perlbrew installed perl-5.8.8 : #!/home/yourhomename/perl5/perlbrew/perls/perl-5.8.8/bin/perl
# then the following command works (if the pennCNV folder is in your $PATH):
detect_cnv.pl --test --hmm example.hmm --pfb example.pfb father.txt mother.txt offspring.txt

You can find more details in the end of the PennCNV install guide

Answer 3

[Robert Sicko]

Are you running in cygwin or with ActivePerl? Also it sounds like you compiled pennCNV and did not use the pre-compiled executable... did you use 32 bit perl?

From the pennCNV website

If you see a "core dumped" error message, or see a "cannot locate loadable object" error message, when running detect_cnv.pl program, it means that the executable is not compatible with your system architecture.

[kiminsigne]

I'm running in cygwin. I was getting that "cannot locate loadable object" error before I recompiled with make and then I got the core dumped error. I emailed the author and he thinks it may be a memory issue!