CONTRA problem. It does not stop.

Question

[mafonso]

Hi,

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        : [20]
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.

Thanks

Answer 1

[Kizuna]

Regarding CONTRA,

I had exactly the same issue, have a look: CONTRA for CNV detection. troubleshooting

Answer 2

[stam]

For me the solution was to change (lower) the minimum number of exons per bins. I think this was also mentioned in one of the comments in the other thread.

CONTRA assumes a a certain number of exons to be present. Default 2000. If they are not there (like they were for me, I had only 300 exons in my targeted regions), it keeps looking indefinitely. Try changing --minExon to 100 or even less.