mct_plot_region running out of memory

[yonatans2]

> devtools::load_all("~/src/mcATAC/")
ℹ Parallelization enabled. Using 77 threads.
> setwd('/net/mraid14/export/tgdata/users/yonshap/proj/mmcortex')
> my_genome <- "mm10"
> gset_genome(my_genome)
> options(gmax.data.size = 1e+9)
> mctracks <- readRDS('./data/mmcortex_mctracks.rds')
> exons <- gintervals.load('intervs.global.exon')
> gene <- 'Satb2'
> gene_exons <- dplyr::filter(exons, geneSymbol == gene)
> gene_intervals <- dplyr::summarise(gene_exons, chrom = unique(chrom), start = min(start), end = max(end))
> mct_plot_region(mct = mctracks, intervals = gene_intervals, downsample_n = 1e+5)
→ Extracting region chr1:56793980-56971340
Error: Failed to allocate shared memory: Cannot allocate memory
Memory usage of the library can be controlled via gmax.data.size option (see options, getOptions).

[aviezerl]

Try setting:

options(gmultitasking = FALSE)

?

On Mon, Sep 5, 2022 at 11:49 AM Yonatan Shapira @.***> wrote:

devtools::load_all("~/src/mcATAC/")

ℹ Parallelization enabled. Using 77 threads.

setwd('/net/mraid14/export/tgdata/users/yonshap/proj/mmcortex') my_genome <- "mm10" gset_genome(my_genome) options(gmax.data.size = 1e+9) mctracks <- readRDS('./data/mmcortex_mctracks.rds') exons <- gintervals.load('intervs.global.exon') gene <- 'Satb2' gene_exons <- dplyr::filter(exons, geneSymbol == gene) gene_intervals <- dplyr::summarise(gene_exons, chrom = unique(chrom), start = min(start), end = max(end)) mct_plot_region(mct = mctracks, intervals = gene_intervals, downsample_n = 1e+5)

→ Extracting region chr1:56793980-56971340 Error: Failed to allocate shared memory: Cannot allocate memory Memory usage of the library can be controlled via gmax.data.size option (see options, getOptions).

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[yonatans2]

That worked

[yonatans2]

> mct_plot_region(mct = mctracks, intervals = gene_intervals, detect_dca=TRUE)
ℹ Using 5th percentile of the total coverage as the downsample threshold: 1494186
→ Extracting region chr1:56543980-57221340
! 23 metacells were removed from the downsampled matrix
Error in as.character.default(new("McTracks", metacells = c("1", "2",  :
no method for coercing this S4 class to a vector

> mctracks
<McTracks> object with 454 metacells from mm10.
Loaded from: /net/mraid14/export/tgdata/users/yonshap/proj/mmcortex/data/mmcortex_mcc
resolution: 10
window_size: 100
Slots include:
• `@tracks`: a vector with track names
• `@total_cov`: a vector with total coverage per track
• `@genome`: genome assembly of the peaks
• `@metacells`: a character vector with metacell ids
Tracks (only first are shown):
• "mmcortex_mct.mc1"
• "mmcortex_mct.mc10"
• "mmcortex_mct.mc100"
• "mmcortex_mct.mc101"
• "mmcortex_mct.mc102"