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WGLab / PennCNV

Copy number vaiation detection from SNP arrays
http://penncnv.openbioinformatics.org
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Error: input to reg_linear() should be two reference to arrays #108

Open sahwa opened 1 year ago

sahwa commented 1 year ago

I am trying to use the gcmodel file /PennCNV-1.0.5/gc_file/hg38.gc5Base.txt which is distributed with PennCNV.

However, when I run the command:

perl ${source_dir}/detect_cnv.pl \
        -test \
        -gcmodelfile ${gcfile} \
        -hmm ${hmm} \
        -pfb ${plate}/${bname}_pfb.txt \
        -list pdb_input_files_${bname}.txt \
        -log ${bname}.log \
        -out ${bname}.rawcnv

I get the output:

NOTICE: All program notification/warning messages that appear in STDERR will be also written to log file plates1-53_cnv.log
NOTICE: Reading marker coordinates and population frequency of B allele (PFB) from ../data/plates1-53_cnv/plates1-53_cnv_pfb.txt ... Done with 781390 records (416 records in chr MT were discarded)
NOTICE: Reading LRR and BAF values for from `gunzip -c ../data/plates1-53_cnv/56_14110603_CK24916489G_H07.penncnv.cnv.txt.gz` ... Done with 781390 records in 24 chromosomes (416 records are discarded due to lack of PFB information for the markers)
Error: input to reg_linear() should be two reference to arrays

The program runs fine without including the gcmodel file. What might be causing this error?