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EDePasquale / DoubletDecon

A tool for removing doublets from single-cell RNA-seq data
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all connections are in use error #17

Open pengyu1608 opened 4 years ago

pengyu1608 commented 4 years ago

Hi, I got the following error when running DoubletDecon, could anyone give some suggestion? Thanks.

Combining similar clusters... Creating synthetic doublet profiles... Step 1: Removing possible doublets... Step 2: Re-clustering possible doublets... Step 3: Rescuing cells with unique gene expression... Error in socketConnection("localhost", port = port, server = TRUE, blocking = TRUE, : all connections are in use

sessionInfo() R version 3.6.1 (2019-07-05) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS: /bioware/source/R-3.6.1/lib/libRblas.so LAPACK: /bioware/source/R-3.6.1/lib/libRlapack.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C [3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8 [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 [7] LC_PAPER=en_US.UTF-8 LC_NAME=C [9] LC_ADDRESS=C LC_TELEPHONE=C [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages: [1] stats4 grid parallel stats graphics grDevices utils [8] datasets methods base

other attached packages: [1] stringr_1.4.0 doParallel_1.0.15 iterators_1.0.12 [4] foreach_1.4.7 R.utils_2.9.0 R.oo_1.23.0 [7] R.methodsS3_1.7.1 tidyr_1.0.0 MCL_1.0 [10] plyr_1.8.4 gplots_3.0.1.1 mygene_1.22.0 [13] GenomicFeatures_1.38.0 AnnotationDbi_1.48.0 GenomicRanges_1.38.0 [16] GenomeInfoDb_1.22.0 IRanges_2.20.1 S4Vectors_0.24.0 [19] hopach_2.46.0 cluster_2.1.0 clusterProfiler_3.14.0 [22] DeconRNASeq_1.28.0 ggplot2_3.2.1 pcaMethods_1.78.0 [25] Biobase_2.46.0 BiocGenerics_0.32.0 limSolve_1.5.6 [28] dplyr_0.8.3 DoubletDecon_1.1.3 Seurat_3.1.1

EDePasquale commented 4 years ago

Hi pengyu1608,

Apologies for the late response, I've asked the developer in charge of Step 3 to review this error and see what we can figure out. He thinks the error is due to the automatic detection of cores that the function uses, which may cause problems when working on a computational cluster, or in some cases, on a normal computer. I plan to allow the user to set the number of processors they wish to use while keeping the automatic detection as the default. This fix will be pushed in the next update, which will be coming out very soon.

Best, Erica

pengyu1608 commented 4 years ago

Hi Erica,

Thanks for the reply and efforts. Good Luck.

From: EDePasquale Date: 2019-12-20 04:07 To: EDePasquale/DoubletDecon CC: Peng Yu; Author Subject: Re: [EDePasquale/DoubletDecon] all connections are in use error (#17) Hi pengyu1608, Apologies for the late response, I've asked the developer in charge of Step 3 to review this error and see what we can figure out. He thinks the error is due to the automatic detection of cores that the function uses, which may cause problems when working on a computational cluster, or in some cases, on a normal computer. I plan to allow the user to set the number of processors they wish to use while keeping the automatic detection as the default. This fix will be pushed in the next update, which will be coming out very soon. Best, Erica — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub, or unsubscribe.