Open jwli28 opened 1 year ago
How do you solve the problem? I met the same error.
imagingtranscriptomics --input C:/Users/lena/Downloads/5-HT_atlas/resized_5-HT2A_mean_bmax.nii.gz --regions all --geneset lake pls --ncomp 1
It showed something wrong.
2024-01-24 19:34:23,707: Running the pls analysis. 2024-01-24 19:34:23,707: Permuting data. 2024-01-24 19:34:24,393: Calculating PLS with permuted data +-----------+----------------+-------+ | Component | Cumulative var | p val |
---|---|---|---|
1 | 0.466 | 0.255 |
+-----------+----------------+-------+
2024-01-24 19:34:57,818: Performing bootstrapping of the genes. 2024-01-24 19:35:33,124: Calculating statistics. 2024-01-24 19:35:33,840: Performing GSEA. 2024-01-24 19:35:33,852 Input gene rankings contains duplicated IDs, Only use the duplicated ID with highest value! Traceback (most recent call last): File "D:\anaconda\envs\transcriptomics\lib\shutil.py", line 616, in _rmtree_unsafe os.unlink(fullname) PermissionError: [WinError 32] Another program is using this file and the process cannot access it。: 'C:\Users\lena\AppData\Local\Temp\tmpstjb_our\gseapy.prerank.geneset_lake.log'
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "D:\anaconda\envs\transcriptomics\lib\tempfile.py", line 802, in onerror _os.unlink(path) PermissionError: [WinError 32] Another program is using this file and the process cannot access it: 'C:\Users\lena\AppData\Local\Temp\tmpstjb_our\gseapy.prerank.geneset_lake.log'
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "D:\anaconda\envs\transcriptomics\lib\runpy.py", line 194, in _run_module_as_main
return _run_code(code, main_globals, None,
File "D:\anaconda\envs\transcriptomics\lib\runpy.py", line 87, in _run_code
exec(code, run_globals)
File "D:\anaconda\envs\transcriptomics\Scripts\imagingtranscriptomics.exe__main__.py", line 7, in
(I am using imaging-transcriptomics V1.1.7, and python 3.8.)
Hi, apologies for this, but the issue is due to using the toolbox in Windows.
Some users already reported this and it's due the inability of one of the libraries used "under the hood" to write temporary files in the C:\
directory (even if ran as admin). I've tried to work around this but am sadly not able to resolve it. If ran in MacOS and Linux the issue doesn't persist.
Dear alegiac95,
Thanks for providing this great scripts! I am using this toolbox in my project but meeting a bug.
After PLS analysis, I obtained .pkl file. When I did imt_gsea (below),
imt_gsea –i C:\Users\jwli2\Desktop\update\Imt_PET_pls\pls_analysis.pkl --geneset lake
It showed something wrong.
(I am using imaging-transcriptomics V1.1.7) I tried to solve it but had no idea. I would appreciate your help, thanks!