kaichop
commented
2 years ago you can try install a different version such as 5.8 or 5.10, or use one of the docker builds of PennCNV, if there is a compilation error. I think it is likely a GCC problem, not perl problem, that you have compilation error.
On Sun, Jan 30, 2022 at 9:07 PM Apprentice2 @.***> wrote:
The OS of my PC is CentOS 8 and I followed the steps described in last resort to compile from the PennCNV source code. However, there was a problem with the source code of perl v5.14.2, so I installed perl v5.14.2 after applying a patch from the following site. ( https://groups.google.com/group/perl.perl5.porters/attach/320ae2ab8fdfd/0001-pp-Guard-fix-for-really-old-bug-in-glibc-libcrypt.patch?part=0.1 )
Using PennCNV, I ran the following command. $ detect_cnv.pl -test -hmm ~/PennCNV-1.0.5/lib/hhall.hmm -pfb out.pfb sample.split* -log ex1.log -out ex1.rawcnv
Then I got the following RuntimeError. How can I fix the problem?
NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file ex1.log NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from out.pfb ... Done with 962312 records (1881 records in chr 0,MT,XY were discarded) NOTICE: Reading LRR and BAF values for from sample.split1 ... Done with 962312 records in 24 chromosomes (1881 records are discarded due to lack of PFB information for the markers) NOTICE: Adjusting LRR by GC model: WF changes from 0.0382 to -0.0146, GCWF changes from 0.0336 to -0.0038 NOTICE: Data from chromosome X,Y will not be used in analysis NOTICE: Median-adjusting LRR values for all autosome markers from sample.split1 by 0.0232 NOTICE: Median-adjusting BAF values for all autosome markers from sample.split1 by 0.0133 NOTICE: quality summary for sample.split1: LRR_mean=-0.0311 LRR_median=0.0000 LRR_SD=0.1995 BAF_mean=0.5070 BAF_median=0.5000 BAF_SD=0.0499 BAF_DRIFT=0.000257 WF=-0.0146 GCWF=-0.0038 RuntimeError Usage: ReadCHMM(filename); at /home/myuser/PennCNV-1.0.5/ detect_cnv.pl line 872.
— Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/77, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3ODYX4HS4EQFSMEZLVDUYXVFPANCNFSM5NFBXUTA . You are receiving this because you are subscribed to this thread.Message ID: @.***>
Apprentice2
The OS of my PC is CentOS 8 and I followed the steps described in last resort to compile from the PennCNV source code. However, there was a problem with the source code of perl v5.14.2, so I installed perl v5.14.2 after applying a patch from the following site. (https://groups.google.com/group/perl.perl5.porters/attach/320ae2ab8fdfd/0001-pp-Guard-fix-for-really-old-bug-in-glibc-libcrypt.patch?part=0.1)
Using PennCNV, I ran the following command. $ detect_cnv.pl -test -hmm ~/PennCNV-1.0.5/lib/hhall.hmm -pfb out.pfb sample.split* -log ex1.log -out ex1.rawcnv
Then I got the following RuntimeError. How can I fix the problem?
NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file ex1.log NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from out.pfb ... Done with 962312 records (1881 records in chr 0,MT,XY were discarded) NOTICE: Reading LRR and BAF values for from sample.split1 ... Done with 962312 records in 24 chromosomes (1881 records are discarded due to lack of PFB information for the markers) NOTICE: Adjusting LRR by GC model: WF changes from 0.0382 to -0.0146, GCWF changes from 0.0336 to -0.0038 NOTICE: Data from chromosome X,Y will not be used in analysis NOTICE: Median-adjusting LRR values for all autosome markers from sample.split1 by 0.0232 NOTICE: Median-adjusting BAF values for all autosome markers from sample.split1 by 0.0133 NOTICE: quality summary for sample.split1: LRR_mean=-0.0311 LRR_median=0.0000 LRR_SD=0.1995 BAF_mean=0.5070 BAF_median=0.5000 BAF_SD=0.0499 BAF_DRIFT=0.000257 WF=-0.0146 GCWF=-0.0038 RuntimeError Usage: ReadCHMM(filename); at /home/myuser/PennCNV-1.0.5/detect_cnv.pl line 872.