Dear Dr. Khozoie, thanks for your previous help. I used Docker and it worked. However now, there are errors in the packages have functions with the same names, and unused argument. I also tried test dataset on other systems and on my desktop in scflow-docker container, but all of them returned same errors. Additionally, I wanted explore nfcore/scflow container, but it seems It hasn't released yet at docker hub.
executor > local (17)
[56/fc7bc4] process > SCFLOW:SCFLOW_CHECKINPUTS (SCFLOW_CHECKINPUTS) [100%] 1 of 1 ✔
[73/f77f90] process > SCFLOW:SCFLOW_QC (finov) [100%] 6 of 6 ✔
[4b/0a8107] process > SCFLOW:SCFLOW_MERGEQCTABLES (MERGEQCTABLES) [100%] 1 of 1 ✔
[27/69b5a5] process > SCFLOW:SCFLOW_MERGE (MERGED) [100%] 1 of 1 ✔
[72/58ad73] process > SCFLOW:SCFLOW_INTEGRATE (MERGED) [100%] 1 of 1 ✔
[f9/69935e] process > SCFLOW:SCFLOW_REDUCEDIMS (MERGED) [100%] 1 of 1 ✔
[91/8201fb] process > SCFLOW:SCFLOW_CLUSTER (MERGED) [100%] 1 of 1 ✔
[66/5a4db6] process > SCFLOW:SCFLOW_REPORTINTEGRATED (MERGED) [100%] 1 of 1 ✔
[e5/f33209] process > SCFLOW:SCFLOW_MAPCELLTYPES (MERGED) [100%] 1 of 1 ✔
[ee/448b5d] process > SCFLOW:SCFLOW_FINALIZE (MERGED) [100%] 1 of 1, failed: 1 ✘
[- ] process > SCFLOW:SCFLOW_DGE -
[- ] process > SCFLOW:SCFLOW_IPA -
[- ] process > SCFLOW:SCFLOW_DIRICHLET -
[56/0db475] process > SCFLOW:SCFLOW_PLOTREDDIMGENES (MERGED) [100%] 1 of 1 ✔
[3e/d1f397] process > SCFLOW:GET_SOFTWARE_VERSIONS (Version Info) [100%] 1 of 1 ✔
Execution cancelled -- Finishing pending tasks before exit
-[nf-core/scflow] Pipeline completed with errors-
Error executing process > 'SCFLOW:SCFLOW_FINALIZE (MERGED)'
Caused by:
Process `SCFLOW:SCFLOW_FINALIZE (MERGED)` terminated with an error exit status (1)
Command executed:
export MC_CORES=2
scflow_finalize_sce.r --clusters_colname clusters --celltype_var cluster_celltype --unique_id_var manifest --facet_vars manifest,diagnosis,sex --input_reduced_dim UMAP_Liger --metric_vars pc_mito,pc_ribo,total_counts,total_features_by_counts --top_n 5 --reddimplot_pointsize 1 --reddimplot_alpha 0.8 --sce_path celltype_mapped_sce --celltype_mappings celltype_mappings.tsv
scflow_version=$(Rscript -e 'cat(as.character(utils::packageVersion("scFlow")))'); echo "scFlow ${scflow_version}" > "scFlow_${scflow_version}.version.txt"
Command exit status:
1
Command output:
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Command error:
Attaching package: ‘DelayedArray’
The following objects are masked from ‘package:matrixStats’:
colMaxs, colMins, colRanges, rowMaxs, rowMins, rowRanges
The following objects are masked from ‘package:base’:
aperm, apply, rowsum
── Reading SingleCellExperiment ────────────────────────────────────────────────
── Reading feature-barcode matrix ──
Reading: 'celltype_mapped_sce/barcodes.tsv.gz'
Reading: 'celltype_mapped_sce/features.tsv.gz'
Reading: 'celltype_mapped_sce/matrix.mtx.gz'
✔ Imported sparse matrix: 1332 cols x 3484 rows.
── Reading colData/rowData ──
Reading: 'celltype_mapped_sce/sce-rowdata.tsv'
Reading: 'celltype_mapped_sce/scecoldata_classes.tsv'
Reading: 'celltype_mapped_sce/sce-coldata.tsv'
Generating SingleCellExperiment
Reading: 'ReducedDim_Liger.tsv'
Reading: 'ReducedDim_PCA_PB.tsv'
Reading: 'ReducedDim_PCA.tsv'
Reading: 'ReducedDim_tSNE_Liger.tsv'
Reading: 'ReducedDim_tSNE_PCA.tsv'
Reading: 'ReducedDim_UMAP_Liger.tsv'
Reading: 'ReducedDim_UMAP_PCA_PB.tsv'
Reading: 'ReducedDim_UMAP_PCA.tsv'
Reading: 'ReducedDim_UMAP3D_Liger.tsv'
Reading: 'ReducedDim_UMAP3D_PCA.tsv'
✔ Imported SingleCellExperiment.
── Finding Top Marker Genes ────────────────────────────────────────────────────
→ Finding markers for cells grouped by `cluster_celltype`
→ Finding markers for cells grouped by `clusters`
Error in (function (sce, feature_dim = "Cluster", reduced_dim = "UMAP", :
unused argument (top_n = 5)
Calls: annotate_celltype_metrics -> do.call
In addition: Warning messages:
1: In if (axis_order == "marker_group") { :
the condition has length > 1 and only the first element will be used
2: In if (axis_order == "marker_group") { :
the condition has length > 1 and only the first element will be used
Execution halted
Check Documentation
I have checked the following places for your error:
Description of the bug
Dear Dr. Khozoie, thanks for your previous help. I used Docker and it worked. However now, there are errors in the packages have functions with the same names, and unused argument. I also tried test dataset on other systems and on my desktop in scflow-docker container, but all of them returned same errors. Additionally, I wanted explore nfcore/scflow container, but it seems It hasn't released yet at docker hub.
Steps to reproduce
Steps to reproduce the behaviour:
nextflow run nf-core/scflow -profile test -r dev ,dockerSystem
Nextflow Installation
Container engine