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bioinfo-ibms-pumc / SCSA

SCSA: cell type annotation for single-cell RNA-seq data
GNU General Public License v3.0
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excel(ms-excel) output error #32

Open krayon4river opened 10 months ago

krayon4river commented 10 months ago

hi, i encountered an error when running the SCSA.py as following python3 /home/Group/singleCell/Software/SCSA/SCSA.py -d $dbwhole -s seurat -i $markers -k All -E -g Human -p 0.01 -f 1.5 -o $output/scCATCH$libraryID &> $output/SCSA.out

the error : Other Gene number: 411 Traceback (most recent call last): File "/home/Group/singleCell/Software/SCSA/SCSA.py", line 1284, in p.run_cmd(args) File "/home/Group/singleCell/Software/SCSA/SCSA.py", line 1250, in run_cmd outs = anno.run_detail_cmd() ^^^^^^^^^^^^^^^^^^^^^ File "/home/Group/singleCell/Software/SCSA/SCSA.py", line 1166, in run_detail_cmd outs = self.calcu_seurat_group(self.args.input,self.args.Gensymbol) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/Group/singleCell/Software/SCSA/SCSA.py", line 464, in calcu_seurat_group self.wbgo.close() File "/home/Group/singleCell/Software/anaconda3/envs/scCATCH/lib/python3.11/site-packages/pandas/io/excel/_base.py", line 1480, in close self._save() File "/home/Group/singleCell/Software/anaconda3/envs/scCATCH/lib/python3.11/site-packages/pandas/io/excel/_openpyxl.py", line 109, in _save self.book.save(self._handles.handle) File "/home/Group/singleCell/Software/anaconda3/envs/scCATCH/lib/python3.11/site-packages/openpyxl/workbook/workbook.py", line 386, in save save_workbook(self, filename) File "/home/Group/singleCell/Software/anaconda3/envs/scCATCH/lib/python3.11/site-packages/openpyxl/writer/excel.py", line 291, in save_workbook archive = ZipFile(filename, 'w', ZIP_DEFLATED, allowZip64=True) ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/Group/singleCell/Software/anaconda3/envs/scCATCH/lib/python3.11/zipfile.py", line 1308, in init self.start_dir = self.fp.tell() ^^^^^^^^^^^^^^ ValueError: I/O operation on closed file

However ，I found that it generated the excel file, but first of all,i didnt'know what led to the error when output format was excel （txt output was okay）； Secondly whether the content of the excel output was complete.

Looking forward to the reply ，thanks！！

rrllab commented 1 month ago

same problem, must set -m txt, then the output is normal