No /home/chencong/.ncbirc file, please fix it before using the program

[ChenCongZ]

Hi @Clémence Frioux, This question arises when I reconstruct the metabolic network. I checked my home directory with this filename. (base) chencong@chencong-QiTianM428-A606:~$ m2m recon -g /home/chencong/test -o /home/chencong/output -c 1 ######### Running metabolic network reconstruction with Pathway Tools ######### No /home/chencong/.ncbirc file, please fix it before using the program (base) chencong@chencong-QiTianM428-A606:~$ ls -a . .config output ptools-local .. Desktop output1 Public AIC-prefs Documents output2 .python_history anaconda3 Downloads output3 snap .bash_history .gnupg PathoLogic-Console-Logs .sudo_as_admin_successful .bash_logout .local .pathway-tools Templates .bashrc .mozilla pathway-tools test .cache Music Pictures Videos .conda .ncbirc .profile

[cfrioux]

Can you show the content of this file please?

https://metage2metabo.readthedocs.io/en/latest/install.html#requirements-and-installation

[ChenCongZ]

(base) chencong@chencong-QiTianM428-A606:~$ ls -l ./.ncbirc total 0

[ChenCongZ]

Hi @cfrioux, I fixed this error. However, this problem always arises. (base) chencong@chencong-QiTianM428-A606:~$ m2m recon -g /home/chencong/pitmud -o /home/chencong/output5 -c 1 ######### Running metabolic network reconstruction with Pathway Tools ######### ---------- Launching mpwt ---------- Check and delete unfinished builds of Pathway Tools. Traceback (most recent call last): File "/home/chencong/anaconda3/bin/m2m", line 8, in sys.exit(main()) File "/home/chencong/anaconda3/lib/python3.9/site-packages/metage2metabo/main.py", line 371, in main main_recon(args.genomes, args.out, args.noorphan, args.padmet, args.level, args.cpu, File "/home/chencong/anaconda3/lib/python3.9/site-packages/metage2metabo/main.py", line 401, in main_recon pgdbdir, sbmldir, padmet_folder= recon(*allargs) File "/home/chencong/anaconda3/lib/python3.9/site-packages/metage2metabo/m2m/reconstruction.py", line 62, in recon pgdb_dir = genomes_to_pgdb(inp_dir, out_dir, nb_cpu, File "/home/chencong/anaconda3/lib/python3.9/site-packages/metage2metabo/m2m/reconstruction.py", line 159, in genomes_to_pgdb multiprocess_pwt(genomes_dir, pgdb_dir, File "/home/chencong/anaconda3/lib/python3.9/site-packages/mpwt/mpwt_workflow.py", line 158, in multiprocess_pwt independent_mpwt(input_folder, output_folder, patho_inference, File "/home/chencong/anaconda3/lib/python3.9/site-packages/mpwt/mpwt_workflow.py", line 357, in independent_mpwt run_patho_flat_ids, run_flat_ids = check_input_and_existing_pgdb(run_ids, input_folder, output_folder, number_cpu_to_use) File "/home/chencong/anaconda3/lib/python3.9/site-packages/mpwt/pathologic_input.py", line 169, in check_input_and_existing_pgdb pathologic_string = pathologic_log.read() File "/home/chencong/anaconda3/lib/python3.9/codecs.py", line 322, in decode (result, consumed) = self._buffer_decode(data, self.errors, final) UnicodeDecodeError: 'utf-8' codec can't decode byte 0xb7 in position 186820: invalid start byte

[ChenCongZ]

Hi @cfrioux, @ArnaudBelcour, When I was creating pictures, I ran into this problem. Can you tell what caused this error? (base) chencong@chencong-QiTianM428-A606:~$ m2m_analysis graph -j /hone/chencong/output11/json -t /home/chencong/targets_toy.sbml -o /home/chencong/output12 Traceback (most recent call last): File "/home/chencong/anaconda3/bin/m2m_analysis", line 8, in sys.exit(main()) File "/home/chencong/anaconda3/lib/python3.9/site-packages/metage2metabo/main_analysis__.py", line 302, in main main_graph(args.json, args.targets, args.out, args.taxon, args.level) File "/home/chencong/anaconda3/lib/python3.9/site-packages/metage2metabo/main_analysis__.py", line 324, in main_graph graph_analysis(*allargs) File "/home/chencong/anaconda3/lib/python3.9/site-packages/metage2metabo/m2m_analysis/solution_graph.py", line 58, in graph_analysis create_gml(json_paths, target_paths, output_dir, taxonomy_output_file) File "/home/chencong/anaconda3/lib/python3.9/site-packages/metage2metabo/m2m_analysis/solution_graph.py", line 109, in create_gml with open(json_paths[target_category]) as json_data: KeyError: 'targets_toy'

[ChenCongZ]

I fixed it while entering. I would like to ask how this file(--oog Oog.jar) was generated, since I didn't find it in the directory I got.