dgenome start problems: protein present as duplicate

[Marta Potrykus]

Dear Marco,

I have another problem with Ductape and have no clue why it is so.

I initialize the programme, add organisms, add faa files, add tab files and command "dgenome start"
then it shows failure. The IFB00223 strain was uploaded as a second strain.

Please comment on that.

Log file:

marta@marta-desktop:~/Desktop/Omnilog_data_storage/Omnilog_comparisons_to_make/all_strains_22C$ dgenome start
14:17:51 - 6 organisms are present
14:17:52 - 1 - Making room
14:17:52 - 2 - Creating Blast DBs
                               Creating Blast DBs                              
 33% [=======================-----------------------------------------------]
                               Item 2 on 6 total                              
14:17:52 - Protein IFB_0223_00001 present as duplicate!
14:17:52 - Failure! Create DBs failure!
14:17:52 - PanGenome could not be calculated!

[Marco Galardini]

Hi Marta,

sorry to hear that you encountered this error; could you please send over the ductape.log file, so that I can inspect the error more precisely?

Also, could you indicate which version of DuctApe you are using?

Another thing you could try is to re-run the same analysis from scratch in a different directory.

Best,

Marco

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[ata...@gmail.com]

Hi Marco,
I am running into the same problem. All my strain are different, so is not a duplication of the same file. I attached my log, but I will like to understand why the error is generated, if you have the time to explain, please.

On a different topic, BioPython removed "Bio.Alphabet" module and that create an error in the software (https://biopython.org/wiki/Alphabet) 
I personally fixed for myself simply removing line 708 and 714 from database.py, but I am sure is not the correct way to patch it.

Best regards
Davide