Closed mauromiguelm closed 1 year ago
Computed with all extras:
console:
free_app.5.te2m7kgre7qo@ip-172-31-21-2 | [INFO][2023-07-31 15:39:09][1843MB] --- [computePGX:on_process_error] ERROR: process 1 completed with an error! free_app.5.te2m7kgre7qo@ip-172-31-21-2 | Standard error from processx: free_app.5.te2m7kgre7qo@ip-172-31-21-2 | [processx.1:stderr] [ngs.fitContrastsWithAllMethods] correcting AveExpr values... free_app.5.te2m7kgre7qo@ip-172-31-21-2 | [processx.1:stderr] [ngs.fitContrastsWithAllMethods] calculating statistics... free_app.5.te2m7kgre7qo@ip-172-31-21-2 | [processx.1:stderr] [ngs.fitContrastsWithAllMethods] reshape matrices... free_app.5.te2m7kgre7qo@ip-172-31-21-2 | [processx.1:stderr] [ngs.fitContrastsWithAllMethods] aggregating p-values... free_app.5.te2m7kgre7qo@ip-172-31-21-2 | [processx.1:stderr] [compute_testGenesSingleOmics] 13 : fitting done! free_app.5.te2m7kgre7qo@ip-172-31-21-2 | [processx.1:stderr] [compute_testGenesSingleOmics] done! free_app.5.te2m7kgre7qo@ip-172-31-21-2 | [processx.1:stderr] [pgx.computePGX] testing genesets...
cat processx-error.log
cat processx-error.log [compute PGX process] : starting process [createPGX] input: dim(counts) = 7053x18 [createPGX] input: dim(samples) = 18x6 [createPGX] input: dim(contrasts) = 18x6 [createPGX] conforming matrices... [createPGX] final: dim(counts) = 7053x18 [createPGX] final: dim(samples) = 18x6 [createPGX] final: dim(contrasts) = 18x6 [createPGX] check logarithm/linear... [createPGX] scaling counts... [createPGX] converting probes to symbol... [probe2symbol] mapped 100% of probes [createPGX] creating pgx object... [createPGX] converting to HUGO symbols... [createPGX] annotating genes... detected organism: human [createPGX] filtering out not-expressed genes... [createPGX] detected organism: human [createPGX] filtering genes... estimating cell cycle (using Seurat)... estimating gender... [createPGX] clustering samples... using logCPM(pgx$counts)... [logCPM] setting column sums to = 1e+06 Reducing to 1000 max SD features... Reducing to 17 PCA dimenstions... calculating PCA 2D/3D... calculating t-SNE 2D... calculating t-SNE 3D... calculating UMAP 2D... calculating UMAP 3D... [pgx.clusterSamples2] update tsne2d/tsne3d and 'cluster' pheno... [pgx.clusterSamples2] done! Finding clusters using Louvain... Found 3 clusters... [createPGX] calculating log-expression matrix X... [createPGX] clustering genes... using expression gene X matrix... Reducing to 17 PCA dimenstions... calculating UMAP 2D... calculating UMAP 3D... [pgx.clusterGenes] done! [pgx.computePGX] testing genes... [compute_testGenesSingleOmics] detecting stat groups... [compute_testGenesSingleOmics] contrasts on groups (use design) replacing contrast matrix... [compute_testGenesSingleOmics] pruning unused contrasts [compute_testGenesSingleOmics] normalizing contrasts [compute_testGenesSingleOmics] 6 : creating model design matrix [compute_testGenesSingleOmics] 12 : start fitting... [ngs.fitContrastsWithAllMethods] using input log-expression matrix X... [ngs.fitContrastsWithAllMethods] fitting using LIMMA trend [ngs.fitContrastsWithLIMMA] fitting LIMMA contrasts using design matrix [ngs.fitContrastsWithAllMethods] fitting edgeR using QL F-test [ngs.fitContrastsWithEDGER] fitting EDGER contrasts using design matrix [ngs.fitContrastsWithAllMethods] fitting using DESeq2 (Wald test) [ngs.fitContrastsWithDESEQ2] fitting DESEQ2 using design matrix [ngs.fitContrastsWithDESEQ2] using model design: ~0 + group converting counts to integer mode estimating size factors estimating dispersions gene-wise dispersion estimates mean-dispersion relationship final dispersion estimates fitting model and testing -- replacing outliers and refitting for 4964 genes -- DESeq argument 'minReplicatesForReplace' = 7 -- original counts are preserved in counts(dds) estimating dispersions fitting model and testing[ngs.fitContrastsWithAllMethods] correcting AveExpr values... [ngs.fitContrastsWithAllMethods] calculating statistics... [ngs.fitContrastsWithAllMethods] reshape matrices... [ngs.fitContrastsWithAllMethods] aggregating p-values... [compute_testGenesSingleOmics] 13 : fitting done! [compute_testGenesSingleOmics] done! [pgx.computePGX] testing genesets...
cat processx-output.log
[createPGX] input assumed counts (not logarithm) [createPGX:autoscale] count_multiplier= 1 [probe2symbol] organism = human [probe2symbol] probe.type = symbol probe2symbol: probe is already symbol>>> computing gene tests for SINGLE-OMICS filtering for low-expressed genes: > 1 CPM in >= 2 samples filtering out 64 low-expressed genes keeping 6974 expressed genes >>> Testing differential expressed genes (DEG) with methods: trend.limma deseq2.wald edger.qlf
I do not get the error locally.. likely extra package/missing/additional db
I just tested it. You are right, it got stuck at test genesets somehow without error. I have built and deployed v3.2.17. I tested this build and computing works now again. Please test. Marked as solved.
Computed with all extras:
console:
cat processx-error.log
cat processx-output.log
I do not get the error locally.. likely extra package/missing/additional db