bigomics / omicsplayground

Visual self-service analytics platform for big omics data.
http://www.bigomics.ch
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`example-data` fails to compute in `https://free.playground.bigomics.ch/`, works locally #609

Closed mauromiguelm closed 1 year ago

mauromiguelm commented 1 year ago

Computed with all extras:

image

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

ivokwee commented 1 year ago

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.