Ming314
commented
2 months ago Hi, I want to use OrthoFinder to study orthology relationships for all genes in multiple species. I ran orthofinder with the command : orthofinder -f prot and got this error:
Traceback (most recent call last): File "/home/ming/miniconda3/envs/orthofinder/bin/orthofinder", line 7, in main(args) File "/home/ming/miniconda3/envs/orthofinder/bin/scripts_of/main.py", line 1806, in main GetOrthologues(speciesInfoObj, options, prog_caller) File "/home/ming/miniconda3/envs/orthofinder/bin/scripts_of/main.py", line 1550, in GetOrthologues orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse, ^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^ File "/home/ming/miniconda3/envs/orthofinder/bin/scripts_of/orthologues.py", line 1061, in OrthologuesWorkflow shutil.copy(rootedSpeciesTreeFN[0], files.FileHandler.GetSpeciesTreeIDsRootedFN()) File "/home/ming/miniconda3/envs/orthofinder/lib/python3.12/shutil.py", line 436, in copy copymode(src, dst, follow_symlinks=follow_symlinks) File "/home/ming/miniconda3/envs/orthofinder/lib/python3.12/shutil.py", line 317, in copymode chmod_func(dst, stat.S_IMODE(st.st_mode)) PermissionError: [Errno 1] Operation not permitted: '/mnt/f/metagenome_analysis/SPM_namco_sjy_metagenome/data_analysis/DNRA_ANR/nrfA_MAGs/prot/OrthoFinder/Results_Sep21/WorkingDirectory/OrthoFinder/Results_Sep23/WorkingDirectory/SpeciesTree_rooted_ids.txt'
Did that happen because I am not the root user? But i ran with the command: ls -l, 'SpeciesTree_rooted_ids.txt' exists and is under root. How can I fix this? Thanks!
I've solved this problem, it seems to be due to a computer memory problem, I ran it successfully on another computer with more memory and arithmetic power
Hi, I want to use OrthoFinder to study orthology relationships for all genes in multiple species. I ran orthofinder with the command : orthofinder -f prot and got this error:
Traceback (most recent call last): File "/home/ming/miniconda3/envs/orthofinder/bin/orthofinder", line 7, in
main(args)
File "/home/ming/miniconda3/envs/orthofinder/bin/scripts_of/main.py", line 1806, in main
GetOrthologues(speciesInfoObj, options, prog_caller)
File "/home/ming/miniconda3/envs/orthofinder/bin/scripts_of/main.py", line 1550, in GetOrthologues
orthologues.OrthologuesWorkflow(speciesInfoObj.speciesToUse,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/ming/miniconda3/envs/orthofinder/bin/scripts_of/orthologues.py", line 1061, in OrthologuesWorkflow
shutil.copy(rootedSpeciesTreeFN[0], files.FileHandler.GetSpeciesTreeIDsRootedFN())
File "/home/ming/miniconda3/envs/orthofinder/lib/python3.12/shutil.py", line 436, in copy
copymode(src, dst, follow_symlinks=follow_symlinks)
File "/home/ming/miniconda3/envs/orthofinder/lib/python3.12/shutil.py", line 317, in copymode
chmod_func(dst, stat.S_IMODE(st.st_mode))
PermissionError: [Errno 1] Operation not permitted: '/mnt/f/metagenome_analysis/SPM_namco_sjy_metagenome/data_analysis/DNRA_ANR/nrfA_MAGs/prot/OrthoFinder/Results_Sep21/WorkingDirectory/OrthoFinder/Results_Sep23/WorkingDirectory/SpeciesTree_rooted_ids.txt'
Did that happen because I am not the root user? But i ran with the command: ls -l, 'SpeciesTree_rooted_ids.txt' exists and is under root. How can I fix this? Thanks!