Question: PennCNV Segmentation Fault
3.9 years ago by

I'm running PennCNV on a CentOS cluster with Perl 5.10.1 and I keep getting a segmentation fault error. Even with the example scripts for

I tried using perlbrew and downloaded Perl 5.8.8 and explicity defined it in the she-bang line. Still same segmenatation fault.

Running make in the kext directory works without any errors. I tried PennCNV versions 1.0.2 and 1.0.3 on two different clusters (CentOS same version of Perl) and keep getting a segfault

What do?

../ -test -hmm example.hmm -pfb example.pfb -log ex3.log -out ex3.rawcnv  -conf -list inputlist


NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file ex3.log
NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from example.pfb ... Done with 93129 records
NOTICE: Reading LRR and BAF values for from father.txt ... Done with 93129 records in 4 chromosomes
NOTICE: Data from chromosome X will not be used in analysis
NOTICE: Median-adjusting LRR values for all autosome markers from father.txt by 0.0221
NOTICE: Median-adjusting BAF values for all autosome markers from father.txt by 0.0029
NOTICE: quality summary for father.txt: LRR_mean=0.0027 LRR_median=0.0000 LRR_SD=0.1335 BAF_mean=0.5063 BAF_median=0.5000 BAF_SD=0.0390 BAF_DRIFT=0.000037 WF=0.0184 GCWF=0.0136
Segmentation fault
penncnv • 1.7k views
ADD COMMENTlink modified 10 months ago by RamRS24k • written 3.9 years ago by QVINTVS_FABIVS_MAXIMVS2.3k

After looking at the code (C/XS and dependent on version-specific Perl API), I don't think anyone other than the author would be able to help with this issue. I would file an issue on github

ADD REPLYlink modified 10 months ago by RamRS24k • written 3.9 years ago by SES8.2k
gravatar for Irina Astrovskaya
2.3 years ago by
Irina Astrovskaya20 wrote:

I got the same problem with perl 5.14.2 on CentOS. We managed to make it work after we rebuild it with gcc44 4.4.7 (compatibility compiler instead of default gcc 4.8.5) (

ADD COMMENTlink modified 2.3 years ago • written 2.3 years ago by Irina Astrovskaya20
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