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 detect_cnv.pl
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
../detect_cnv.pl -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