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When using the RCTD package for single-cell spatial transcriptome data analysis. Therun.RCTDfunction is trapped in an infinite loop. Specifically, after the function runs, multiple worker processes start, but the computation process seems to have no progress and continues to run without any signs of ending.
Here is my code example:
# set up reference
ref <- readRDS("../data/mouse_hippocampus_reference.rds")
ref <- UpdateSeuratObject(ref)
Idents(ref) <- "celltype"
# extract information to pass to the RCTD Reference function
counts <- ref[["RNA"]]$counts
cluster <- as.factor(ref$celltype)
names(cluster) <- colnames(ref)
nUMI <- ref$nCount_RNA
names(nUMI) <- colnames(ref)
reference <- Reference(counts, cluster, nUMI,
n_max_cells = 10000)#设置每类细胞的最大数目
# set up query with the RCTD function SpatialRNA
slide.seq <- SeuratData::LoadData("ssHippo")
counts <- slide.seq[["Spatial"]]$counts
coords <- GetTissueCoordinates(slide.seq)
colnames(coords) <- c("x", "y")
coords[is.na(colnames(coords))] <- NULL
query <- SpatialRNA(coords, counts, colSums(counts))
RCTD <- create.RCTD(query, reference, max_cores = 60)
RCTD <- run.RCTD(RCTD, doublet_mode = "doublet")
#The following is the output text of the terminal
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Likelihood value: 1002895.50152005
Sigma value: 0.69
starting worker pid=1888651 on localhost:11865 at 14:23:12.711
starting worker pid=1888739 on localhost:11865 at 14:23:12.982
starting worker pid=1888828 on localhost:11865 at 14:23:13.317
starting worker pid=1888917 on localhost:11865 at 14:23:13.582
starting worker pid=1889002 on localhost:11865 at 14:23:13.842
starting worker pid=1889087 on localhost:11865 at 14:23:14.100
starting worker pid=1889174 on localhost:11865 at 14:23:14.359
starting worker pid=1889259 on localhost:11865 at 14:23:14.653
starting worker pid=1889346 on localhost:11865 at 14:23:14.942
starting worker pid=1889433 on localhost:11865 at 14:23:15.212
starting worker pid=1889519 on localhost:11865 at 14:23:15.477
starting worker pid=1889604 on localhost:11865 at 14:23:15.758
starting worker pid=1889693 on localhost:11865 at 14:23:16.032
starting worker pid=1889781 on localhost:11865 at 14:23:16.314
starting worker pid=1889866 on localhost:11865 at 14:23:16.613
starting worker pid=1889954 on localhost:11865 at 14:23:16.913
starting worker pid=1890040 on localhost:11865 at 14:23:17.191
starting worker pid=1890128 on localhost:11865 at 14:23:17.461
starting worker pid=1890215 on localhost:11865 at 14:23:17.716
starting worker pid=1890300 on localhost:11865 at 14:23:17.982
starting worker pid=1890389 on localhost:11865 at 14:23:18.242
starting worker pid=1890474 on localhost:11865 at 14:23:18.508
starting worker pid=1890559 on localhost:11865 at 14:23:18.767
starting worker pid=1890644 on localhost:11865 at 14:23:19.025
starting worker pid=1890729 on localhost:11865 at 14:23:19.282
starting worker pid=1890818 on localhost:11865 at 14:23:19.540
starting worker pid=1890905 on localhost:11865 at 14:23:19.796
starting worker pid=1890990 on localhost:11865 at 14:23:20.072
starting worker pid=1891078 on localhost:11865 at 14:23:20.331
starting worker pid=1891164 on localhost:11865 at 14:23:20.619
starting worker pid=1891252 on localhost:11865 at 14:23:20.903
starting worker pid=1891337 on localhost:11865 at 14:23:21.183
starting worker pid=1891422 on localhost:11865 at 14:23:21.442
starting worker pid=1891508 on localhost:11865 at 14:23:21.720
starting worker pid=1891596 on localhost:11865 at 14:23:22.078
starting worker pid=1891684 on localhost:11865 at 14:23:22.340
starting worker pid=1891774 on localhost:11865 at 14:23:22.609
starting worker pid=1891860 on localhost:11865 at 14:23:22.872
starting worker pid=1891945 on localhost:11865 at 14:23:23.129
starting worker pid=1892030 on localhost:11865 at 14:23:23.388
starting worker pid=1892115 on localhost:11865 at 14:23:23.650
starting worker pid=1892204 on localhost:11865 at 14:23:23.913
starting worker pid=1892289 on localhost:11865 at 14:23:24.199
starting worker pid=1892375 on localhost:11865 at 14:23:24.461
starting worker pid=1892463 on localhost:11865 at 14:23:24.724
starting worker pid=1892548 on localhost:11865 at 14:23:25.008
starting worker pid=1892637 on localhost:11865 at 14:23:25.287
starting worker pid=1892724 on localhost:11865 at 14:23:25.538
starting worker pid=1892814 on localhost:11865 at 14:23:25.900
starting worker pid=1892905 on localhost:11865 at 14:23:26.175
starting worker pid=1892994 on localhost:11865 at 14:23:26.439
starting worker pid=1893079 on localhost:11865 at 14:23:26.717
starting worker pid=1893164 on localhost:11865 at 14:23:27.035
starting worker pid=1893252 on localhost:11865 at 14:23:27.338
starting worker pid=1893343 on localhost:11865 at 14:23:27.602
starting worker pid=1893428 on localhost:11865 at 14:23:27.891
starting worker pid=1893516 on localhost:11865 at 14:23:28.158
starting worker pid=1893601 on localhost:11865 at 14:23:28.419
starting worker pid=1893687 on localhost:11865 at 14:23:28.693
starting worker pid=1893775 on localhost:11865 at 14:23:28.963
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
Loading required package: spacexr
loaded spacexr and set parent environment
........again and again
I am running on a server, so I allow the core of 63 to work without any memory related errors. At the same time, I also considered potential conflicts with the future package, and this situation did not change after the future package was detached.
Looking forward to your attention and answers,THANKS~~
The text was updated successfully, but these errors were encountered:
When using the RCTD package for single-cell spatial transcriptome data analysis. The
run.RCTD
function is trapped in an infinite loop. Specifically, after the function runs, multiple worker processes start, but the computation process seems to have no progress and continues to run without any signs of ending.Here is my code example:
I am running on a server, so I allow the core of 63 to work without any memory related errors. At the same time, I also considered potential conflicts with the
future
package, and this situation did not change after the future package was detached.Looking forward to your attention and answers,THANKS~~
The text was updated successfully, but these errors were encountered: