FileNotFoundError: [Errno 2] 01.KEGG_Regular_Module_Information.pickle

[rzhan186]

Dear MicrobeAnnotator developers,

I tried to annotate two bins with the light mode using blast as my search method, however, it returned a FIleNotFoundError with “01.KEGG_Regular_Module_Information.pickle” being the missing file. The software was used in a virtual python environment in a cluster instead of using Conda. I thought KEGG is not freely available, is it possible that the error was caused by the fact that I do not a KEGG subscription?

Could you help with this? Thank you!

Rui

2021-05-10 02:33:22,505 [INFO]: ---- This is MicrobeAnnotator v2.0.4 ---- 2021-05-10 02:33:22,505 [INFO]: Validating user inputs 2021-05-10 02:33:22,543 [INFO]: Passed 2021-05-10 02:33:22,544 [INFO]: Processing 2 files. I will run 2 files in parallel with 24 threads per file. 2021-05-10 02:33:22,544 [INFO]: Running in light mode. Searching only KOfam and Swissprot using blast. 2021-05-10 02:33:23,270 [INFO]: Searching proteins against KOfam profiles 2021-05-10 02:33:23,270 [INFO]: Parsing HMM profile metadata 2021-05-10 02:33:38,597 [INFO]: Filtering and saving results... 2021-05-10 02:33:38,697 [INFO]: Search against KOfam done! 2021-05-10 02:34:36,306 [INFO]: Filtering and saving results... 2021-05-10 02:34:36,475 [INFO]: Search against KOfam done! 2021-05-10 02:34:37,122 [INFO]: Searching proteins against Swissprot 2021-05-10 03:28:36,327 [INFO]: Extracting Swissprot annotation data 2021-05-10 03:28:49,720 [INFO]: MicrobeAnnotator annotation has finished succesfully! 2021-05-10 03:28:49,721 [INFO]: Summarizing results 2021-05-10 03:28:49,724 [INFO]: Extracting ko numbers and summarizing results Importing data... Traceback (most recent call last): File "/home/ruizhang/microbe_annotator/bin/microbeannotator", line 981, in main() File "/home/ruizhang/microbe_annotator/bin/microbeannotator", line 969, in main module_information, metabolism_matrix, module_group_matrix = ko_mapper.module_information_importer(annotation_files) File "/home/ruizhang/microbe_annotator/lib/python3.7/site-packages/microbeannotator/pipeline/ko_mapper.py", line 93, in module_information_importer regular_modules = import_module_dict(data_folder / "01.KEGG_Regular_Module_Information.pickle") File "/home/ruizhang/microbe_annotator/lib/python3.7/site-packages/microbeannotator/pipeline/ko_mapper.py", line 83, in import_module_dict pickle_in = open(dictionary_location,"rb") FileNotFoundError: [Errno 2] No such file or directory: '/home/ruizhang/microbe_annotator/lib/python3.7/site-packages/microbeannotator/data/01.KEGG_Regular_Module_Information.pickle'

[cruizperez]

Hi @Rui-Zzhang, It seems we are having some issues with the associated data when MicrobeAnnotator is installed using pip. Can you confirm this is the case? If so, you could try installing it from Conda and it should work. Let me know if it does not.

[ashuiit]

@cruizperez, I have installed microbeannotator on conda but still getting the same error of '01.KEGG_Regular_Module_Information.pickle'. If anyone has solved it please share the debugging technique.

[Julboteroc]

Hey, first, thank you for making MicrobeAnnotator. I had the same problem and I solved by copying and pasting the files that are missing inside the anaconda environment. git clone https://github.com/cruizperez/MicrobeAnnotator then the missing files are going to be in /home/user/MicrobeAnnotator/microbeannotator/data/01.KEGG_Regular_Module_Information.pickle then you just have to copy and paste the file cd /home/cd/microbe_annotator/lib/python3.7/site-packages/microbeannotator/data/ cp /home/user/MicrobeAnnotator/microbeannotator/data/01.KEGG_Regular_Module_Information.pickle .