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broadinstitute / infercnv

Inferring CNV from Single-Cell RNA-Seq
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The pdf draw step error when running the 120 thousand cell by infercnv #453

Open honghh2018 opened 2 years ago

honghh2018 commented 2 years ago

Hi @developer, The pdf plotting using the memory size startle me with 18446744071839307776 byte. it was so horrible that no computer can allocate that size of memory to draw the pdf. had any solution to fix this bug? Any advices would be appreciated. Best, hanhuihong

The error showing below: INFO [2022-08-30 05:19:58] plot_cnv_references:Start INFO [2022-08-30 05:19:58] Reference data size: Cells= 14149 Genes= 7260 INFO [2022-08-30 07:58:32] plot_cnv_references:Number reference groups= 2 INFO [2022-08-30 07:58:33] plot_cnv_references:Plotting heatmap. INFO [2022-08-30 07:58:57] Colors for breaks: #00008B,#24249B,#4848AB,#6D6DBC,#9191CC,#B6B6DD,#DADAEE,#FFFFFF,#EEDADA,#DDB6B6,#CC9191,#BC6D6D,#AB4848,#9B2424,#8B0000 INFO [2022-08-30 07:58:57] Quantiles of plotted data range: 0.808958341791289,0.976262396215306,1,1.021929970991,1.19996400639478 INFO [2022-08-30 07:59:08] plot_cnv_references:Writing reference data to /share/home/hhhong/yuanxin_bio/yx_personality/yx_disk4_personality/2021-5-12/xuyu2022-8-26/01.infercnv/result/infercnv.preliminary.references.txt Error in dev.off() : 'Calloc' could not allocate memory (18446744071839307776 of 1 bytes) Calls: two_steps_inferCNV -> -> plot_cnv -> dev.off Execution halted PDF error: Couldn't find trailer dictionary PDF error: Couldn't find trailer dictionary PDF error: Couldn't read xref table Error in poppler_pdf_info(loadfile(pdf), opw, upw) : PDF parsing failure. Calls: -> pdf_info -> poppler_pdf_info Execution halted

GeorgescuC commented 2 years ago

Hi @honghh2018 ,

This memory error pops up every so often and seems to be an internal error with R as it sometimes pop with a subsample of bigger datasets. There is unfortunately no obvious workaround as it is not a predictible error, but you can try a few things:

You could also try changing the output format to PNG and the "bitmapType" option in R but I am not sure if those can get around the issue.

Regards, Christophe.