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combiz / nf-core-scflow

Complete analysis workflow for single-cell/nuclei RNA-sequencing data.
MIT License
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Unused argument and Packages have functions with the same names errors #4

Open MEFarhadieh opened 2 years ago

MEFarhadieh commented 2 years ago

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:

  1. Command line: nextflow run nf-core/scflow -profile test -r dev ,docker
  2. See error: 
    
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 ${scflowversion}" > "scFlow${scflow_version}.version.txt"

Command exit status: 1

Command output: |======================================================== | 51%, ETA 00:05 |========================================================= | 52%, ETA 00:05 |========================================================== | 53%, ETA 00:05 |=========================================================== | 54%, ETA 00:05 |============================================================ | 55%, ETA 00:05 |============================================================= | 56%, ETA 00:05 |============================================================== | 57%, ETA 00:05 |=============================================================== | 58%, ETA 00:05 |================================================================ | 59%, ETA 00:04 |================================================================= | 60%, ETA 00:04 |================================================================== | 61%, ETA 00:04 |==================================================================== | 62%, ETA 00:04 |===================================================================== | 63%, ETA 00:04 |====================================================================== | 64%, ETA 00:04 |======================================================================= | 65%, ETA 00:04 |======================================================================== | 66%, ETA 00:04 |========================================================================= | 67%, ETA 00:04 |========================================================================== | 68%, ETA 00:03 |=========================================================================== | 69%, ETA 00:03 |============================================================================ | 70%, ETA 00:03 |============================================================================= | 71%, ETA 00:03 |============================================================================== | 72%, ETA 00:03 |================================================================================ | 73%, ETA 00:03 |================================================================================= | 74%, ETA 00:03 |================================================================================== | 75%, ETA 00:03 |=================================================================================== | 76%, ETA 00:03 |==================================================================================== | 77%, ETA 00:02 |===================================================================================== | 78%, ETA 00:02 |====================================================================================== | 79%, ETA 00:02 |======================================================================================= | 80%, ETA 00:02 |======================================================================================== | 81%, ETA 00:02 |========================================================================================= | 82%, ETA 00:02 |========================================================================================== | 83%, ETA 00:02 |============================================================================================ | 84%, ETA 00:02 |============================================================================================= | 85%, ETA 00:02 |============================================================================================== | 86%, ETA 00:01 |=============================================================================================== | 87%, ETA 00:01 |================================================================================================ | 88%, ETA 00:01 |================================================================================================= | 89%, ETA 00:01 |================================================================================================== | 90%, ETA 00:01 |=================================================================================================== | 91%, ETA 00:01 |==================================================================================================== | 92%, ETA 00:01 |===================================================================================================== | 93%, ETA 00:01 |====================================================================================================== | 94%, ETA 00:01 |======================================================================================================== | 95%, ETA 00:01 |========================================================================================================= | 96%, ETA 00:00 |========================================================================================================== | 97%, ETA 00:00 |=========================================================================================================== | 98%, ETA 00:00 |============================================================================================================ | 99%, ETA 00:00 |=========================================================================================================| 100%, Elapsed 00:11

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



## System

- Hardware: Cloud
- Executor:  local
- OS: Ubuntu Linux
- Version: 20.04

## Nextflow Installation

- Version: 22.04.0

## Container engine

- Engine: Docker
- version:  20.10.14
combiz commented 2 years ago

Could you please share your scflow_analysis.config file and the column names from your sample sheet? This looks like a parameter issue.

MEFarhadieh commented 2 years ago

Thanks for your reply.

I did my analysis with scFlow package in R. Everything was perfect. Thanks for developing these great tools.