compile_pfb.pl issue

[sophie-03]

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.

[kaichop]

if you have a command line argument that would help troubleshoot the issue. Also are there any markers missing from the output file?

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On Thu, Sep 1, 2022 at 11:17 AM Sophie ***@***.***> wrote: Reopened #90 <#90>. — Reply to this email directly, view it on GitHub <#90 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/ABNG3OFYBRQVGK2A5HR4FILV4DCHLANCNFSM57W7AHIQ> . You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[sophie-03]

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.

[SinjaH]

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

[aress212]

Same issue here, then I tried just suppressing warnings and the code has been running with 15 hrs with 106 samples, which I assume is incorrect, even if i am running it locally. did anyone get this solved?