compile_pfb.pl not working

[lsheffield]

I am trying to compile my own pfb file from my signal files.
Here is the command I'm passing it:
compile_pfb.pl -listfile /gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/signal_file_list_02.txt -output /gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/pfb_files/pop_b_freq.pfb

The list file looks as follows:
/gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/4770-MA-1651_202566700099_R01C01_formatted_02.txt
/gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/4770-MA-1635_202524980055_R06C01_formatted_02.txt
/gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/4770-MA-1659_202566700099_R08C01_formatted_02.txt

The files it is trying to read look as follows:
SNP Name Chr Pos BFreq LogR
1:100292476 1 100292476 0.0 -1.02807
1:101064936 1 101064936 0.0728731 0.0350392
1:103380393 1 103380393 1.0 0.0676645

The following are the outputs/errors that are produced when I attempt to run the command:
NOTICE: A total of 1686 input signal files is specified in /gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/signal_file_list_02.txt
WARNING: Skipping the file /gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/4770-MA-0212_201131650106_R08C01_formatted_02.txt that cannot be read by the current program
Use of uninitialized value $baf_index in addition (+) at /gpfs/gpfs2/software/PennCNV-1.0.4/compile_pfb.pl line 99.
NOTICE: The B Allele Freq information is annotated as column 1 in input files
NOTICE: A total of 0 input files will be used for compiling PFB values
Use of uninitialized value $snp in pattern match (m//) at /gpfs/gpfs2/software/PennCNV-1.0.4/compile_pfb.pl line 128.
Use of uninitialized value $snp in hash element at /gpfs/gpfs2/software/PennCNV-1.0.4/compile_pfb.pl line 140.

[kaichop]

The error message below basically says that /gpfs/gpfs2/home/lsheffield/ AGHI/formatted_reports/4770-MA-0212_201131650106_R08C01_formatted_02.txt cannot be read. Did you check whether there are permission issues (for example just do a simple "head /gpfs/gpfs2/home/lsheffield/ AGHI/formatted_reports/4770-MA-0212_201131650106_R08C01_formatted_02.txt "). Basically " A total of 0 input files will be used for compiling PFB values " so your output is empty. It looks like a simple file reading problem. Make sure there is no unintended white space, tab character or weird characters in the list file.

…

On Thu, Jun 14, 2018 at 5:01 PM, lsheffield ***@***.***> wrote: I am trying to compile my own pfb file from my signal files. Here is the command I'm passing it: compile_pfb.pl -listfile /gpfs/gpfs2/home/lsheffield/ AGHI/formatted_reports/signal_file_list_02.txt -output /gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/pfb_ files/pop_b_freq.pfb The list file looks as follows: /gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/4770- MA-1651_202566700099_R01C01_formatted_02.txt /gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/4770- MA-1635_202524980055_R06C01_formatted_02.txt /gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/4770- MA-1659_202566700099_R08C01_formatted_02.txt The files it is trying to read look as follows: SNP Name Chr Pos BFreq LogR 1:100292476 1 100292476 0.0 -1.02807 1:101064936 1 101064936 0.0728731 0.0350392 1:103380393 1 103380393 1.0 0.0676645 The following are the outputs/errors that are produced when I attempt to run the command: NOTICE: A total of 1686 input signal files is specified in /gpfs/gpfs2/home/lsheffield/AGHI/formatted_reports/signal_file_list_02.txt WARNING: Skipping the file /gpfs/gpfs2/home/lsheffield/ AGHI/formatted_reports/4770-MA-0212_201131650106_R08C01_formatted_02.txt that cannot be read by the current program Use of uninitialized value $baf_index in addition (+) at /gpfs/gpfs2/software/PennCNV-1.0.4/compile_pfb.pl line 99. NOTICE: The B Allele Freq information is annotated as column 1 in input files NOTICE: A total of 0 input files will be used for compiling PFB values Use of uninitialized value $snp in pattern match (m//) at /gpfs/gpfs2/software/PennCNV-1.0.4/compile_pfb.pl line 128. Use of uninitialized value $snp in hash element at /gpfs/gpfs2/software/PennCNV-1.0.4/compile_pfb.pl line 140. — You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub <#27>, or mute the thread <https://github.com/notifications/unsubscribe-auth/AFptuD_9B9Wtg6Xma1UcW2oKWllC7caJks5t8s8OgaJpZM4Uop7J> .

[lsheffield]

Thank you