Open xiangLi3945 opened 1 year ago
GeorgescuC
commented
1 year ago Hi @xiangLi3945 ,
How big is your dataset, and how much memory (RAM) do you have available? The error looks as if R is trying to allocate some memory but cannot.
Regards, Christophe.
xiangLi3945
commented
1 year ago Thinks a lot @GeorgescuC ,I think I've figured it out, the problem is that my data is too big for memory, so I'm going to filter the number of cells in my count matrix
GeorgescuC
commented
1 year ago Hi @xiangLi3945 ,
One thing you can try is to run the Rscript in "scripts/prepare_sparsematrix.R" if you are inputing your matrix as a file. This will produce a sparsematrix object you can use as input to infercnv, which will reduce the memory requirements significantly during the first few steps. Once filtering is done the matrix dimensions will be smaller so when it ends up being converted to a dense matrix it won't require quite as much memory.
Regards, Christophe.
On Tue, Apr 25, 2023, 14:53 xiangLi3945 @.***> wrote:
Thinks a lot @GeorgescuC https://github.com/GeorgescuC ,I think I've figured it out, the problem is that my data is too big for memory, so I'm going to filter the number of cells in my count matrix
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INFO [2023-04-26 02:19:29] Parsing matrix: expFile.txt INFO [2023-04-26 02:27:53] Parsing gene order file: geneFile.txt INFO [2023-04-26 02:27:53] Parsing cell annotations file: groupFiles.txt INFO [2023-04-26 02:27:53] ::order_reduce:Start. INFO [2023-04-26 02:27:55] .order_reduce(): expr and order match. INFO [2023-04-26 02:28:01] ::process_data:order_reduce:Reduction from positional data, new dimensions (r,c) = 18250,24912 Total=52603908.8302446 Min=0 Max=9.34296659698465. INFO [2023-04-26 02:28:04] num genes removed taking into account provided gene ordering list: 682 = 3.73698630136986% removed. INFO [2023-04-26 02:28:06] -filtering out cells < 100 or > Inf, removing 0 % of cells WARN [2023-04-26 02:28:10] Please use "options(scipen = 100)" before running infercnv if you are using the analysis_mode="subclusters" option or you may encounter an error while the hclust is being generated. Error in serialize(object, connection = NULL, ascii = ascii, version = serializeVersion) : cannot allocate buffer how can i slove this problem?