genemetrics is reporting genes from first chromosome only

[npojo]

Hi,
I am running cnvkit.py genemetrics -o results.txt S.cnr;
S.cnr includes 24 chromosomes but results.txt reports only chr1 genes.
I have tested a mock cnr file:

chromosome start end gene depth log2 weight
chr1 10000 11000 A 500 2 0.5
chr1 12000 13000 A 500 2 0.5
chr1 14000 15000 A 500 2 0.5
chr1 16000 17000 A 500 2 0.5
chr1 20000 21000 B 500 2 0.5
chr1 22000 23000 B 500 2 0.5
chr1 24000 25000 B 500 2 0.5
chr1 26000 27000 B 500 2 0.5
chrX 26000 27000 C 500 2 0.5

Which reports genes A and B.

However, the following cnr file reports only gene A:

chromosome start end gene depth log2 weight
chr1 10000 11000 A 500 2 0.5
chr1 12000 13000 A 500 2 0.5
chr1 14000 15000 A 500 2 0.5
chr1 16000 17000 A 500 2 0.5
chr2 20000 21000 B 500 2 0.5
chr2 22000 23000 B 500 2 0.5
chr2 24000 25000 B 500 2 0.5
chr2 26000 27000 B 500 2 0.5
chrX 26000 27000 C 500 2 0.5

I have tested several other cnr files leading to the same conclusion.
If chr1 is missing, the next chromosome in line is reported (e.g. chr2).
Version is 0.9.8.
Any ideas?
Thanks

[tetedange13]

Hi @npojo,

It is a known bug of CNVkit (see section "bug fixes" subsection called genemetrics, diagram, scatter)
=> Has been fixed with CNVkit v0.9.9, so please update to latest release and tell us if this solved your problem?

Hope this helps.
Have a nice day.
Felix.

[npojo]

Thank you Felix!
Just tested with V0.9.9 and now it works fine.

[tetedange13]

Nice ! So could you please close this issue @npojo ?

Have a nice day.
Kind regards.
Felix.