Hi,
I am trying to visualize cnv calls from example1 of PennCNV but I have two problems. First, when I run visualize_cnv.pl -format plot -signal offspring.txt ex1.rawcnv I get this output
NOTICE: Signal values for 4 CNV regions are found in offspring.txt
NOTICE: Processing sample offspring.txt CNV chr11:55603545-55669650 with copy number of 0 ... written to offspring.txt.chr11.55603545.JPG
NOTICE: Processing sample offspring.txt CNV chr11:81792950-81806219 with copy number of 1 ... Use of uninitialized value in numeric gt (>) at C:\Users\andsav\Desktop\PennCNV-1.0.5\PennCNV-1.0.5\visualize_cnv.pl line 204.
written to offspring.txt.chr11.81792950.JPG
NOTICE: Processing sample offspring.txt CNV chr20:10511631-10583260 with copy number of 1 ... written to offspring.txt.chr20.10511631.JPG
NOTICE: Processing sample offspring.txt CNV chr3:3957986-4054960 with copy number of 1 ... written to offspring.txt.chr3.3957986.JPG
I wonder, what does this mean Use of uninitialized value in numeric gt (>) at C:\Users\andsav\Desktop\PennCNV-1.0.5\PennCNV-1.0.5\visualize_cnv.pl line 204. and how does it affect me?
Then, when I want to look at the generated plots, I was under the impresion that they will exist in jpg format in the folder. instead I have this
If I open one of them (.Rout file) using notepad, it gives me the following error
Error: /undefinedfilename in (C:\Users\Dell\AppData\Local\Temp\Rtmps9N0pB\Rbit11243a9665ae)
Operand stack:
Execution stack:
%interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push
Dictionary stack:
--dict:766/1123(ro)(G)-- --dict:0/20(G)-- --dict:75/200(L)--
Current allocation mode is local
Last OS error: No such file or directory
GPL Ghostscript 9.55.0: Unrecoverable error, exit code 1
Any ideas on what could be wrong and what I need to do to fix this?
System INFO
I use windows 10 x64, installed ActivePerl 5.8 x32 and have R 3.6.0
Hi, I am trying to visualize cnv calls from example1 of PennCNV but I have two problems. First, when I run visualize_cnv.pl -format plot -signal offspring.txt ex1.rawcnv I get this output
NOTICE: Signal values for 4 CNV regions are found in offspring.txt NOTICE: Processing sample offspring.txt CNV chr11:55603545-55669650 with copy number of 0 ... written to offspring.txt.chr11.55603545.JPG NOTICE: Processing sample offspring.txt CNV chr11:81792950-81806219 with copy number of 1 ... Use of uninitialized value in numeric gt (>) at C:\Users\andsav\Desktop\PennCNV-1.0.5\PennCNV-1.0.5\visualize_cnv.pl line 204. written to offspring.txt.chr11.81792950.JPG NOTICE: Processing sample offspring.txt CNV chr20:10511631-10583260 with copy number of 1 ... written to offspring.txt.chr20.10511631.JPG NOTICE: Processing sample offspring.txt CNV chr3:3957986-4054960 with copy number of 1 ... written to offspring.txt.chr3.3957986.JPG
I wonder, what does this mean Use of uninitialized value in numeric gt (>) at C:\Users\andsav\Desktop\PennCNV-1.0.5\PennCNV-1.0.5\visualize_cnv.pl line 204. and how does it affect me?
Then, when I want to look at the generated plots, I was under the impresion that they will exist in jpg format in the folder. instead I have this
If I open one of them (.Rout file) using notepad, it gives me the following error
Error: /undefinedfilename in (C:\Users\Dell\AppData\Local\Temp\Rtmps9N0pB\Rbit11243a9665ae) Operand stack:
Execution stack: %interp_exit .runexec2 --nostringval-- --nostringval-- --nostringval-- 2 %stopped_push --nostringval-- --nostringval-- --nostringval-- false 1 %stopped_push Dictionary stack: --dict:766/1123(ro)(G)-- --dict:0/20(G)-- --dict:75/200(L)-- Current allocation mode is local Last OS error: No such file or directory GPL Ghostscript 9.55.0: Unrecoverable error, exit code 1
Any ideas on what could be wrong and what I need to do to fix this?
System INFO I use windows 10 x64, installed ActivePerl 5.8 x32 and have R 3.6.0