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gao-lab / Cell_BLAST

A BLAST-like toolkit for large-scale scRNA-seq data querying and annotation.
http://cblast.gao-lab.org
MIT License
82 stars 13 forks source link

snakemake CPU question #8

Closed caiquanyou closed 4 years ago

caiquanyou commented 4 years ago

the snakemake runs no other problem ,but in this step run_ZIFA.py,it took 100%CPU occupied. timeout 12h python -u run_ZIFA.py -i ../Datasets/data/Bach/data.h5 -o ../Results/ZIFA/Bach/dim_20/seed_15/result.h5 -g seurat_genes -d 20 -s 15 --clean cell_ontology_class > ../Results/ZIFA/Bach/dim_20/seed_15/log.txt 2>&1 few hours no output,is it something wrong?

Jeff1995 commented 4 years ago

I observed the same thing. It should be normal. ZIFA indeed seems slow on large datasets like "Bach".

caiquanyou commented 4 years ago

Ok,then i just keep it running and wait for output ,thx!

caiqy

 

------------------ 原始邮件 ------------------ 发件人: "gao-lab/Cell_BLAST" <notifications@github.com>; 发送时间: 2020年8月28日(星期五) 下午4:58 收件人: "gao-lab/Cell_BLAST"<Cell_BLAST@noreply.github.com>; 抄送: "xianmao"<951463554@qq.com>;"Author"<author@noreply.github.com>; 主题: Re: [gao-lab/Cell_BLAST] snakemake CPU question (#8)

I observed the same thing. It should be normal. ZIFA indeed seems slow on large datasets like "Bach".

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