Error Calls: ATACRunSeurat ... CreateSeuratObject.default -> CreateSeuratObject -> CreateSeuratObject.Assay
jphe opened this issue · 3 comments
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::.__C__GenomicRanges_OR_GenomicRangesList' by 'rtracklayer::.__C__GenomicRanges_OR_GenomicRangesList' 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
Attached is the details for the log file.
you should install Seurat V4.0
if you installed the latest v1.4 MAESTRO, Seurat will be https://github.com/liulab-dfci/MAESTRO/blob/master/conda/MAESTRO/meta.yaml#L42