kaichop
commented
3 years ago It is likely a memory issue (at least 8G required for modern arrays with
500K markers). I will make another docker image that it is best that you just run in docker instead.
On Tue, Jan 19, 2021 at 9:24 PM Qidi Feng notifications@github.com wrote:
Hi Kai,
I was trying to do cnv comparison with a previous paper which used PennCNV v2010May. So I got package from the author and tried to install this older PennCNV version. I used perl 5.14.2 and gcc 8.3.0 (Debian 8.3.0-6). There is no error when "make" under ./kext file. But it shows "Segmentation fault" when running the example data. I am wonder do you have any suggestions? Pls feel free to ask if you need more information.
perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "UTF-8", LANG = "C.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "UTF-8", LANG = "C.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). 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 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
Best regards, Qidi
— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub https://github.com/WGLab/PennCNV/issues/65, or unsubscribe https://github.com/notifications/unsubscribe-auth/ABNG3OELNYM5FMRJ4UIUDHTS2Y5GXANCNFSM4WJ6XYHQ .
QidiFeng
Hi Kai,
I was trying to do cnv comparison with a previous paper which used PennCNV v2010May. So I got package from the author and tried to install this older PennCNV version. I used perl 5.14.2 and gcc 8.3.0 (Debian 8.3.0-6). There is no error when "make" under ./kext file. But it shows "Segmentation fault" when running the example data. I am wonder do you have any suggestions? Pls feel free to ask if you need more information.
perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "UTF-8", LANG = "C.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). perl: warning: Setting locale failed. perl: warning: Please check that your locale settings: LANGUAGE = (unset), LC_ALL = (unset), LC_CTYPE = "UTF-8", LANG = "C.UTF-8" are supported and installed on your system. perl: warning: Falling back to the standard locale ("C"). 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 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
Best regards, Qidi