mixcr downsample error: "Require clnx file type, got ./clns"

[jvpon]

Dear mixcr people,

After running
mixcr analyze takara-mouse-tcr-cdr3
I have only .clns files, which I link to the folder ./clns

I'd like to obtain normalized read counts for clonotypes.

I am trying to run
mixcr downsample \ --chains TRA,TRB \ --downsampling count-reads-auto \ --only-productive \ --summary summary.tsv \ ./clns
and get an error
Require clnx file type, got ./clns

Thanks,

Julia

[mizraelson]

Hi,
if you have .clns files in the clns folder the command should be:

mixcr downsample \ 
--chains TRA,TRB \ 
--downsampling count-reads-auto \
--only-productive \
--summary summary.tsv \
 ./clns/*.clns