CNVnator need help

[jchoo]

I am using CNVnator recently, preparing to call CNV in a 200 samples with 6X average coverage population, here is the command I used:
cnvnator -root m.root -genome hg19 -chrom 22 -tree 210099.chr22.bam 210103.chr22.bam
cnvnator -root m.root -genome hg19 -chrom 22 -d /dir_contain_chr22.fa -his 500
cnvnator -root m.root -chrom 22 -stat 500
cnvnator -root m.root -chrom 22 -partition 500
cnvnator -root m.root -chrom 22 -call 500
all command up goes well, some call set I can got too,
but while I tried
cnvnator -root m.root -chrom 22 -genotype 500
and then type chr22:1-200
heres what I got :
Can't find directory 'bin_1000'.
Can't find directory 'bin_1000'.
Genotype chr22:1-200 210099.chr22.root 0 -1
nomatter bin size I type , the programe could not found bin_1000.
Could guys give any suggestion? thanks so much

[Alicia B]

Hi Jchoo. Did you ever find an solution to that problem? I'm running into the very same at the moment. Thanks!

[SES]

I think the problem is the way that the fasta directory is specified and also the read IDs. Note that "22" and "chr22" are different and not compatible. Other than that, the order of the commands looks correct to me.

[Alicia B]

Hi SES, thanks for taking the time to answer. I've gone through my commands and they all seem correct, however I am still getting the
'Can't find directory 'bin_1000'.
Can't find directory 'bin_1000'.

this is what I've typed:
./cnvnator -root out.root -genome ref.fa -chrom chr5 -genotype 100
>chr5 37601 47300
Can't find directory 'bin_1000'.
Can't find directory 'bin_1000'.
Genotype chr5:37601-47300 out.root 2.6292 -1

When I type the exact same command for -view instead of -genotype I have no problems.

Any ideas on what is going on? I've found the question posted a few times in different forums but no answers. Any help/suggestions greatly appreciated!

[Alicia B]

Ok so I found an answer to this issue on github by the cnvnator creator:


warnings are not the issue. By default CNVnator estimates CN (last two number in each line) using bin size that you provided and bins of 1 kbp. If histogram for 1 kbp bins don’t exist then the software prints the warning.

So in the output you see. The first number given is the copy number based on the bin size you used and -1 is for the 1000bp bin since it doesn't exist.