consensus.py fails to write output file

[bharat1912]

I. Ran the following successfully with the proteins in the example file: $python corecruncher_master.py -in example -out out_folder1 -ext .prot -align muscle -ref Serratia_oryzae_J11-6.prot -score 60 AND $python corecruncher_master.py -in example -out out_folder2 -ext .prot -align muscle -ref Serratia_grimesii_A2.prot -score 60

II. However, the consensus.py on the above two folders failed. $python consensus.py -folders out_folder1 out_folder2 -in example/ -out /media/bharat/volume1/Folder_consensus

(2, ' folders will be analyzed:', ['out_folder1/', 'out_folder2/']) ('Core genome of ', 'out_folder2/', 1973) ('Core genome of ', 'out_folder1/', 1996) (77, 1919) (1915, 4) ('partial=', 1996) ['out_folder1/'] out_folder2/ ('new genes', 54) ('CONSENSUS CORE GENOME:', 2050) ('Writing output file consensus_core.txt in ', '/media/bharat/volume1/Folder_consensus/') Traceback (most recent call last): File "consensus.py", line 313, in f=open(outpath + "consensus_core.txt","w") IOError: [Errno 2] No such file or directory: '/media/bharat/volume1/Folder_consensus/consensus_core.txt'

Assistance to resolve this error appreciated.

Thanks Bharat

[lbobay]

It looks like a path issue. Have you checked that the path is working and that you have permission to write in it?On Sep 3, 2023, at 06:03, bharat1912 @.***> wrote: I. Ran the following successfully with the proteins in the example file: $python corecruncher_master.py -in example -out out_folder1 -ext .prot -align muscle -ref Serratia_oryzae_J11-6.prot -score 60 AND $python corecruncher_master.py -in example -out out_folder2 -ext .prot -align muscle -ref Serratia_grimesii_A2.prot -score 60 II. However, the consensus.py on the above two folders failed. $python consensus.py -folders out_folder1 out_folder2 -in example/ -out /media/bharat/volume1/Folder_consensus (2, ' folders will be analyzed:', ['out_folder1/', 'out_folder2/']) ('Core genome of ', 'out_folder2/', 1973) ('Core genome of ', 'out_folder1/', 1996) (77, 1919) (1915, 4) ('partial=', 1996) ['out_folder1/'] out_folder2/ ('new genes', 54) ('CONSENSUS CORE GENOME:', 2050) ('Writing output file consensus_core.txt in ', '/media/bharat/volume1/Folder_consensus/') Traceback (most recent call last): File "consensus.py", line 313, in f=open(outpath + "consensus_core.txt","w") IOError: [Errno 2] No such file or directory: '/media/bharat/volume1/Folder_consensus/consensus_core.txt' Assistance to resolve this error appreciated. Thanks Bharat

—Reply to this email directly, view it on GitHub, or unsubscribe.You are receiving this because you are subscribed to this thread.Message ID: @.***>