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.
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！！