kaichop
commented
6 years ago 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 notifications@github.com 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/formattedreports/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.
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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.