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GregorySchwartz / too-many-cells

Cluster single cells and analyze cell clade relationships with colorful visualizations.

Home Page:https://gregoryschwartz.github.io/too-many-cells/

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Runing too-many-cell's Docker 'gregoryschwartz/too-many-cells' occurred error on the middle of procedure

honghh2018 opened this issue · comments

commented

Hi @GregorySchwartz
Thanks for developing the great tools for single cell analysis.
The error would be triggered when running the docker of gregoryschwartz/too-many-cells using following command 'docker run -it --rm -v //share/nas1/Data/Users/user/Personalization/20191206_ana/20200319_mainline/result/integrated/vst/subtypes/T_cells/TooManyCells/:/input_matrix gregoryschwartz/too-many-cells:0.2.2.0 make-tree --matrix-path /input_matrix/T_cells.csv -l /input_matrix/T_cells_ann.csv -o ./out'
The error picture showing below:

image
I am confusing utterly that why the error just broke down in middle step of runing on 70% but the begin of the runing of docker.
That whether It was meaning that the inputted file i provided was right, so what happen to my
running of this situation.
Thanks
Any advice would be appreciated
System:
CentOS Linux release 7.3.1611 (Core)
the input file format display below:
cell annotation :
image
expression matrix:

image

commented

That just means that the cell barcode specified was not assigned a label. As a result, too-many-cells lets you know that the clumpiness measure can't be calculated, but that's optional. You should still see the output, just no clumpiness plot. You might want to change your docker mounts, though, as you did not mount . so you are outputting to ./out when you probably want ./input_matrix/out or something like that.

commented

Did this solve your issue?

commented

Hi @GregorySchwartz
The problem i posted before had solved yet.
But i had a question that the too-many-cell docker runing single cell data,size 32001x43111 matrix, have last for a few day and now it remained on runing status but stop. the picture showing below:
Is this norm? or abnormal.
Your advices would be appreciated.
Thanks
image

commented

I don't know the stats of your computer, but I would let it run to completion. If you want a faster result, I would recommend dimensionality reduction (as I could get millions of cells in the tree in an hour on my setup with fewer features).