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bioinfo-ibms-pumc / SCSA

SCSA: cell type annotation for single-cell RNA-seq data
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Zero marker sets found -- error #3

Closed jhb1980 closed 4 years ago

jhb1980 commented 4 years ago

Hi! I have tried SCSA on a Seurat 'FindAllMarkers' output from a public PBMC dataset. SCSA starts well into Cluster 0 (-> Monocytes), but crashes out on Cluster 1. Attaching the culprit csv seurat-markers.csv.zip

Command line: SCSA.py -d /Users/Husband/SCSA/whole.db -s seurat -i SCT-20_seu-markers.csv -o SCT-20_seu-annotation -k All -E -g Human -p 0.01 -f 1.5

Error output and stop at Cluster 1 >>>

############################## Cluster 1 ##############################

!WARNING3:Zero marker sets found, type:marker !WARNING3:Change the threshold or tissue name and try again? !WARNING3:EnsemblID or GeneID,try '-E' command? Traceback (most recent call last): File "/Users/Husband/SCSA/SCSA.py", line 1111, in p.run_cmd(args) File "/Users/Husband/SCSA/SCSA.py", line 1077, in run_cmd outs = anno.run_detail_cmd() File "/Users/Husband/SCSA/SCSA.py", line 1012, in run_detail_cmd outs = self.calcu_seurat_group(self.args.input,self.args.Gensymbol) File "/Users/Husband/SCSA/SCSA.py", line 428, in calcu_seurat_group h_values,colnames = self.get_cell_matrix(newexps,ltitle,fid,gcol,ccol,abs_tag) File "/Users/Husband/SCSA/SCSA.py", line 836, in get_cell_matrix return DataFrame(),set(colnames) TypeError: 'NoneType' object is not iterable

bioinfo-ibms-pumc commented 4 years ago

Sorry for the inconvenience. I have just fix the error. In addition, there seems to be no significant marker gene in the cluster 1 under the certain filter. You may change the -f command or reanalysis from seurat.