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liulab-dfci / MAESTRO

Single-cell Transcriptome and Regulome Analysis Pipeline
GNU General Public License v3.0
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Error Calls: ATACRunSeurat ... CreateSeuratObject.default -> CreateSeuratObject -> CreateSeuratObject.Assay #121

Closed jphe closed 3 years ago

jphe commented 3 years ago

Hi,

Thanks for update MAESTRO, I have installed the latest MAESTRO but it reports an error:

Seems it is Seurat problem? My Seurat version is 3.99

Registered S3 method overwritten by 'GGally': method from +.gg ggplot2 Registered S3 methods overwritten by 'SeuratObject': method from $.JackStrawData Seurat $.Seurat Seurat $.SeuratCommand Seurat $<-.Seurat Seurat [.Assay Seurat [.DimReduc Seurat [.Seurat Seurat [.SeuratCommand Seurat [.SpatialImage Seurat [[.Assay Seurat [[.DimReduc Seurat [[.Seurat Seurat levels<-.Seurat Seurat .DollarNames.JackStrawData Seurat .DollarNames.Seurat Seurat .DollarNames.SeuratCommand Seurat as.list.SeuratCommand Seurat as.logical.JackStrawData Seurat dim.Assay Seurat dim.DimReduc Seurat dim.Neighbor Seurat dim.Seurat Seurat dim.SpatialImage Seurat dimnames.Assay Seurat dimnames.DimReduc Seurat dimnames.Seurat Seurat droplevels.Seurat Seurat length.DimReduc Seurat levels.Seurat Seurat merge.Assay Seurat merge.DimReduc Seurat merge.Seurat Seurat names.DimReduc Seurat names.Seurat Seurat print.DimReduc Seurat subset.Assay Seurat subset.DimReduc Seurat subset.Seurat Seurat subset.SpatialImage Seurat Registered S3 method overwritten by 'cli': method from print.boxx spatstat Warning message: replacing previous import 'GenomicRanges::.CGenomicRanges_OR_GenomicRangesList' by 'rtracklayer::.CGenomicRanges_ORGenomicRangesList' when loading 'BSgenome' Warning: Feature names cannot have underscores (''), replacing with dashes ('-') Error in [[<-(*tmp*, "orig.ident", value = idents) : [[<- defined for objects of type "S4" only for subclasses of environment Calls: ATACRunSeurat ... CreateSeuratObject.default -> CreateSeuratObject -> CreateSeuratObject.Assay Execution halted [Thu Mar 11 20:33:25 2021] Error in rule scatac_analysis: jobid: 5 output: Result/Analysis/10X_PBMC_10k_DiffPeaks.tsv, Result/Analysis/10X_PBMC_10k_cluster.png, Result/Analysis/10X_PBMC_10k.PredictedTFTop10.txt, Result/Analysis/10X_PBMC_10k_cell_cluster.txt shell: Rscript /public/home/jphe/anaconda3/envs/scanpy/lib/python3.6/site-packages/MAESTRO-1.4.0-py3.6.egg/MAESTRO/R/scATACseq_pipe.R --peakcount ../QC/10X_PBMC_10k_filtered_peak_count.h5 --rpmatrix 10X_PBMC_10k_gene_score.h5 --species GRCh38 --prefix 10X_PBMC_10k --annotation True --method both --signature human.immune.CIBERSORT --gigglelib /public/home/jphe/ATACseq/hg38/scATAC/PBMC/giggle.all --fragment ../minimap2/fragments_corrected_count.tsv.gz --outdir Result/Analysis --thread 10 (one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)

Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: /public/home/jphe/ATACseq/hg38/scATAC/PBMC/MEASTRO/PBMC_10k_MAESTRO_bam/.snakemake/log/2021-03-11T202306.024792.snakemake.log

jphe commented 3 years ago

Attached is the details for the log file.

10X_PBMC_10k.txt

crazyhottommy commented 3 years ago

you should install Seurat V4.0

crazyhottommy commented 3 years ago

if you installed the latest v1.4 MAESTRO, Seurat will be https://github.com/liulab-dfci/MAESTRO/blob/master/conda/MAESTRO/meta.yaml#L42