Please increase the window size. Coverage is too low! error

[rezenman]

Hey all, I am working with a genome of the yeast Saccharomyces cerevisiae, it is a specific strain so I need to build my own mappability map. I followed the pipeline in the faq and everything looks well but when running the following command: delly cnv -a -y 1 -g $ref -m $map $bam_file > cnv.vcf I get the error: Please increase the window size. Coverage is too low! I tried modifying the parameters: -ijw but it didn't work for any number up to 1000000 I know that the coverage in my bam file is good, and I think the mappability map also make sense, just to make sure I counted A,C and N bases in my contigs:

NC_001133: Size=230225 A=10255 N=21551 C=198419 G=0 T=0 NC_001134: Size=813166 A=6527 N=29442 C=777197 G=0 T=0 NC_001135: Size=316615 A=4805 N=18115 C=293695 G=0 T=0 NC_001136: Size=1532214 A=18763 N=84345 C=1429106 G=0 T=0 NC_001137: Size=575776 A=3781 N=26610 C=545385 G=0 T=0 NC_001138: Size=270165 A=3542 N=13827 C=252796 G=0 T=0 NC_001139: Size=1090945 A=6778 N=44766 C=1039401 G=0 T=0 NC_001140: Size=562642 A=12664 N=33545 C=516433 G=0 T=0 NC_001141: Size=439890 A=9366 N=20179 C=410345 G=0 T=0 NC_001142: Size=745757 A=15890 N=42467 C=687400 G=0 T=0 NC_001143: Size=666817 A=2487 N=5650 C=658680 G=0 T=0 NC_001144: Size=1075784 A=19062 N=80427 C=976295 G=0 T=0 NC_001145: Size=924434 A=4877 N=36268 C=883289 G=0 T=0 NC_001146: Size=784503 A=8410 N=33207 C=742886 G=0 T=0 NC_001147: Size=1091098 A=9315 N=40339 C=1041444 G=0 T=0 NC_001148: Size=948056 A=9286 N=49074 C=889696 G=0 T=0 NC_001224: Size=85779 A=83 N=710 C=84986 G=0 T=0

Any help will be appreciated! Shahar