Issue at step4: Missing allmcl.out.OGs.group

Thanks for the tool!

I am running the program and i am encountering this error at step 4 File "/home/samuelG/.conda/envs/python38/bin/Tree2gd", line 33, in sys.exit(load_entry_point('Tree2gd==1.0.38', 'console_scripts', 'Tree2gd')()) File "/home/samuelG/.conda/envs/python38/lib/python3.8/site-packages/Tree2gd-1.0.38-py3.8.egg/tree2gd_main.py", line 235, in main run_tree2gd(step1out,args,cf,step2out,step4out) File "/home/samuelG/.conda/envs/python38/lib/python3.8/site-packages/Tree2gd-1.0.38-py3.8.egg/tree2gd/wgd.py", line 118, in run_tree2gd fa_list=mcl2fasta(int(minimal_taxa),os.sep.join([step4out,'all_fa/']),step2out,step1out,args) File "/home/samuelG/.conda/envs/python38/lib/python3.8/site-packages/Tree2gd-1.0.38-py3.8.egg/tree2gd/wgd.py", line 24, in mcl2fasta with open(os.sep.join([step2out,'allmcl.out.OGs.group']),"rU") as infile: FileNotFoundError: [Errno 2] No such file or directory: '/mnt/HDD2/WH_revision/Tree2GD_try/Tree2gd/output/step2.MCL/allmcl.out.OGs.group'

and my MCL log is empty and there is no segmentation fault reported at the time of run

2024-04-18 19:35:04: INFO ALL step1 blastp has done. 2024-04-18 19:35:04: INFO Start sorting results.. 2024-04-18 19:35:08: INFO pep all2all diamond done. 2024-04-18 19:35:08: INFO The Step2 output dir :/mnt/HDD2/WH_revision/Tree2GD_try/Tree2gd/output/step2.MCL does not exist,will create it. 2024-04-18 19:35:08: INFO Writing step2 script files... 2024-04-18 19:35:08: INFO Start runing step2 MCL: /mnt/HDD2/WH_revision/Tree2GD_try/Tree2gd/output/step2.MCL/step2.sh.. 2024-04-18 19:35:50: INFO step2 mcl has done. 2024-04-18 19:35:50: INFO The Step3 output dir :/mnt/HDD2/WH_revision/Tree2GD_try/Tree2gd/output/step3.dollop does not exist,will create

Please provide inputs to resolve the issue.

Thanks

Dee-chen / Tree2gd

Issue at step4: Missing allmcl.out.OGs.group #21