I am trying to run an algorithm for CNV detection and was testing CONTRA.
The test file works but using my own files the program never ends. This is what I get:
python contra.py --target pnpd2-280113_1_Covered.bed --test test.bam --control control.bam --fasta hg19.fasta --outFolder OUT_folderx target : pnpd2-280113_1_Covered.bed test : test.bam control : control.bam fasta : hg19.fasta outfolder : OUT_folderx numBin :  minreaddepth : 10 minNBases : 10 sam : False pval : 0.05 sampleName : No-SampleName nomultimapped : False plot : False bedInput : False minExon : 2000 largeDeletion : False Creating Output Folder : Done. Converting TEST Sample... Converting CONTROL Sample... Getting targeted regions DOC... chr1 Getting targeted regions DOC... chr1 chr10 chr10 chr11 chr11 chr12 chr13 chr12 chr14 chr15 chr13 chr14 chr15 chr16 chr17 chr18 chr19 chr16 chr2 chr17 chr20 chr21 chr22 chr3 chr18 chr4 chr19 chr5 chr2 chr6 chr20 chr7 chr21 chr22 chr8 chr3 chr4 chr9 chr5 chrX Targeted regions pre-processing: Done chr6 chr7 chr8 chr9 chrX Targeted regions pre-processing: Done Test file read depth = 12863030 Control file read depth = 10708005 Pre-processing Completed. Getting the Log Ratio ... Binning ...
I left it all night and still did not finish. About 12 hours. Is there any solution for this issue? I am using Ubuntu 14.04.