Hi Biostars Users,

I would like to know if you have encountered this issue while working with [CONTRA tool][1] for detecting CNVs in targeted NGS.

 [1]: http://sourceforge.net/apps/mediawiki/contra-cnv/index.php?title=CONTRA:_Copy_Number_Analysis_for_Targeted_Resequencing#Examples

In fact, my analysis is "stopping" at the binning process with no error message, I have checked all the required arguments and they seem to be ok : 

```
contra apple$ python contra.py --target ngs1_probes.bed --test cic04668.bam --control  baseline_ngs1.bed --bed --fasta human_ref.fasta --outFolder ~/contrases

target              : ngs1_probes.bed
test                  : cic04668.bam
control                        : baseline_ngs1.bed
fasta                : human_ref.fasta
outfolder        : /Users/apple/contrases
numBin                       : [20]
minreaddepth            : 10
minNBases     : 10
sam                 : False
pval                 : 0.05
sampleName  : No-SampleName
nomultimapped         : False
plot                 : False
bedInput                    : True
minExon                     : 2000
largeDeletion : False
Creating Output Folder :  Done.
Converting TEST Sample...
DEBUG 123 genomeCoverageBed -ibam cic04668.bam -bga -g /Users/apple/contrases/buf/sample.Genome
Converting CONTROL Sample...
Getting targeted regions DOC...
chr1
chr10
chr11
chr12
chr14
chr15
chr16
chr17
chr19
chr2
chr20
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrX
Targeted regions pre-processing: Done
Getting targeted regions DOC...
chr1
chr10
chr11
chr12
chr14
chr15
chr16
chr17
chr19
chr2
chr20
chr3
chr4
chr5
chr6
chr7
chr8
chr9
chrX
Targeted regions pre-processing: Done
Test file read depth =  97323185
Control file read depth         =  98289477
Pre-processing Completed.
Getting the Log Ratio
Binning....
```

Do you have any idea why?

Thank you for your help

Kiz
Hello Kizauna,

I am new to CONTRA and I am facing the same problem. I have no idea what is wrong as there is no error message. I am sure the thread is not stopped but it is running in my server for a couple of days. Were you able to resolve this.

Thanks in advance