I was trying to use the demo data to run CellBin pipeline and got the same error on both Mac and Linux. Not sure what the problem is. please find the code and error info below:
python pipeline.py --tiles_path /Users/fanya562/Downloads/STO_demo --gene_exp_data /Users/fanya562/Downloads/STO_demo/SS200000135TL_D1.gem.gz --output_path /Users/fanya562/Downloads/ --chip_no SS200000135TL_D1
I0810 18:09:31.766294 21042 pipeline.py:205] Start RUN StereoCell analysis pipeline
I0810 18:09:31.766386 21042 pipeline.py:83] Anchor point positioning for subsequent registration process
/Users/fanya562/anaconda3/envs/CellBin/bin/python ../cellbin/iqc/qc_util.py -i /Users/fanya562/Downloads/STO_demo -o /Users/fanya562/Downloads/ -c SS200000135TL_D1 -n test -e fanya562
W0810 18:09:34.973216 21044 motic_reader.py:59] File /Users/fanya562/Downloads/STO_demo/info.ini does not exist.
Traceback (most recent call last):
File "../cellbin/iqc/qc_util.py", line 536, in
main()
File "../cellbin/iqc/qc_util.py", line 529, in main
ret = qc_entry(para)
File "../cellbin/iqc/qc_util.py", line 432, in qc_entry
ret = qual.run()
File "../cellbin/iqc/qc_util.py", line 147, in run
MR = motic_reader.MoticReader(self.input_path)
File "/Users/fanya562/Downloads/CellBin-dev/cellbin/iqc/image_reader/read/motic_reader.py", line 61, in init
assert len(dirs) == 1
AssertionError
Traceback (most recent call last):
File "pipeline.py", line 261, in
para.func(para, args)
File "pipeline.py", line 243, in main
p.run(image=input, output=output, stereo_chip=chip_no, gem=gem_file)
File "pipeline.py", line 207, in run
if self.is_QC_pass():
File "pipeline.py", line 74, in is_QC_pass
json_path = glob.glob(os.path.join(self._output_path, '*.json'))[0]
IndexError: list index out of range
Hi,
I was trying to use the demo data to run CellBin pipeline and got the same error on both Mac and Linux. Not sure what the problem is. please find the code and error info below:
python pipeline.py --tiles_path /Users/fanya562/Downloads/STO_demo --gene_exp_data /Users/fanya562/Downloads/STO_demo/SS200000135TL_D1.gem.gz --output_path /Users/fanya562/Downloads/ --chip_no SS200000135TL_D1 I0810 18:09:31.766294 21042 pipeline.py:205] Start RUN StereoCell analysis pipeline I0810 18:09:31.766386 21042 pipeline.py:83] Anchor point positioning for subsequent registration process /Users/fanya562/anaconda3/envs/CellBin/bin/python ../cellbin/iqc/qc_util.py -i /Users/fanya562/Downloads/STO_demo -o /Users/fanya562/Downloads/ -c SS200000135TL_D1 -n test -e fanya562 W0810 18:09:34.973216 21044 motic_reader.py:59] File /Users/fanya562/Downloads/STO_demo/info.ini does not exist. Traceback (most recent call last): File "../cellbin/iqc/qc_util.py", line 536, in
main()
File "../cellbin/iqc/qc_util.py", line 529, in main
ret = qc_entry(para)
File "../cellbin/iqc/qc_util.py", line 432, in qc_entry
ret = qual.run()
File "../cellbin/iqc/qc_util.py", line 147, in run
MR = motic_reader.MoticReader(self.input_path)
File "/Users/fanya562/Downloads/CellBin-dev/cellbin/iqc/image_reader/read/motic_reader.py", line 61, in init
assert len(dirs) == 1
AssertionError
Traceback (most recent call last):
File "pipeline.py", line 261, in
para.func(para, args)
File "pipeline.py", line 243, in main
p.run(image=input, output=output, stereo_chip=chip_no, gem=gem_file)
File "pipeline.py", line 207, in run
if self.is_QC_pass():
File "pipeline.py", line 74, in is_QC_pass
json_path = glob.glob(os.path.join(self._output_path, '*.json'))[0]
IndexError: list index out of range