Closed Tianqi-Ma closed 2 years ago
Hi, scMAGIC team
I was playing around this package with the data provided in tutorial (Tasic.Rdata and Campbell_2k.Rdata) in a docker image in Linux. An error occoured says:
[1] "Sum single cell counts matrix:" Warning: Feature names cannot have underscores ('_'), replacing with dashes ('-') [1] "Number of overlapped genes:" [1] 17131 [1] "Start clustering :" sh: 1: /usr/local/R/lib/R/bin/Rscript: Permission denied sh: 1: /usr/local/R/lib/R/bin/Rscript: Permission denied sh: 1: /usr/local/R/lib/R/bin/Rscript: Permission denied sh: 1: /usr/local/R/lib/R/bin/Rscript: Permission denied Error in makePSOCKcluster(names = spec, ...) : Cluster setup failed. 4 of 4 workers failed to connect. Calls: scMAGIC ... .cluster_increase_speed -> makeCluster -> makePSOCKcluster
It seems come from the parallel thread. Here is the code i used:
# load reference dataset list.Ref <- readRDS('Tasic.Rdata') ref.mtx <- list.Ref$mat_exp ref.labels <-list.Ref$label[, 1] # load target dataset list.demo <- readRDS('Campbell_2k.Rdata') exp_sc_mat <- list.demo$mat_exp label_sc <-list.demo$label output.scMAGIC <- scMAGIC(exp_sc_mat, ref.mtx, ref.labels, atlas = 'MCA', num_threads = 4)
Hope get reply from you soon.
It seems that this error is related to the permission.
Yes, you are right. I've figured it out and thanks a lot.
Hi, scMAGIC team
I was playing around this package with the data provided in tutorial (Tasic.Rdata and Campbell_2k.Rdata) in a docker image in Linux. An error occoured says:
It seems come from the parallel thread. Here is the code i used:
Hope get reply from you soon.