Open sophie-03 opened 1 year ago
if you have a command line argument that would help troubleshoot the issue. Also are there any markers missing from the output file?
On Thu, Sep 1, 2022 at 11:17 AM Sophie @.***> wrote:
Reopened #90 https://github.com/WGLab/PennCNV/issues/90.
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Thanks for your quick response. The command line argument is:
~/PennCNV/compile_pfb.pl -listfile sample_list.txt -output chr2.pfb
the list file is as below:
/mnt/data/individual_files/sample1.txt
/mnt/data/individual_files/sample2.txt
/mnt/data/individual_files/sample3.txt
/mnt/data/individual_files/sample4.txt
/mnt/data/individual_files/sample5.txt
When I run the above command, the two error lines in the initial posting continue to repeat until I force the command to stop running. The output file is empty.
Not sure whether it's relevant but I am also using the docker image to run PennCNV - as I was unable to install a local version of perl on my virtual machine.
Hi, I am running into the same problem and was wondering if you were able to solve it? I am also using a docker image to run PennCNV
I am trying to create a pfb file. When running compile_pfb.pl I get the following output:
Use of uninitialized value $snp in pattern match (m//) at /root/PennCNV/compile_pfb.pl line 128. Use of uninitialized value $snp in hash element at /root/PennCNV/compile_pfb.pl line 140.