dape start keyerror u'rn:R08266C07108C16545'

[Marta Potrykus]

Dear Marco,

During the analysis of a mutant versus wildtype strain I encounter such a key error (in the topic) at the end of analysis ('dape start'). Also I encounter some (minor?) errors in the meantime like this:

Traceback (most recent call last):
  File "/usr/local/bin/dape", line 1013, in <module>
    ret = options.func(options, wdir, project)
  File "/usr/local/bin/dape", line 103, in dstart
    if not dNet(project, options.all, options.paths):
  File "/usr/local/lib/python2.7/dist-packages/ductape/actions.py", line 3390, in dNet
    ref_rpairs[ref_id] = kegg.getExclusiveRPairsReactMutants(ref_id, muts)
  File "/usr/local/lib/python2.7/dist-packages/ductape/storage/SQLite/database.py", line 2287, in getExclusiveRPairsReactMutants
    del ref_temp[k]
KeyError: u'rn:R08266C07108C16545'


Can you elaborate on that type of errors? Why do I encounter them?

The mutant is the deletion mutant where one gene is inactivated and I have deleted its accession in the KO database and in the faa file as well.

Thank you very much.
Best
Marta

[Marco Galardini]

Hi Marta,

I believe you might have found a bug, actually, so please accept my apologies for that. If you could send me your "ductape.db" file I could look into the details and come up with a fix.

Thanks,
Marco

[Marta Potrykus]

Hi,

I do not know how but I missed your answer. I get this kind of problem in many analysis, wildtype versus mutant. Please find here enclosed the log and db files, of another analysis but the problem is the same.

https://drive.google.com/file/d/0BxG8qFcu8sqleWtpSnBCdGp3RzA/view?usp=sharing

Thank you!

Marta

[Marta Potrykus]

Dear Marco,

Were you able to fix the problem with mutant versus wildtype comparison?

Thank you very much!

Best,

Marta

[Marco Galardini]

Hi Marta!

Sorry for the very late reply! Yes, I think I found the problem, thanks for reporting it. Can you try the following?

    git clone https://github.com/combogenomics/DuctApe.git
    cd DuctApe
    [copy your database here]
    ./dape start

Best,
Marco

[Marta Potrykus]

Dear Marco,

I will try it this week and let you know.

Best,

Marta

Thank you!

[Marta Potrykus]

Dear Marco,

I still find the same problem. Please find attached the log file, for my exemplary analysis. I performed the 'mutant' analysis from scratch, taking the wildtype and the mutant. I have also question for gene annotation. The mutant differs from the wildtype with just one gene (deletion), however the annotation tool found much less (about 70 less positions) for the mutant, Is it correct?

Best,
Marta

[Marco Galardini]

Hi Marta,

I can confirm that the fix works fine for me; may I remind you that if you have downloaded the fix (for instance here: https://github.com/combogenomics/DuctApe/archive/master.zip) you should run the analysis from inside the downloaded directory, calling the scripts by prefixing them with "pythoh". In your case you can just transfer the "ductape.db" file inside the downloaded directory and then type:

python dape start

Hope this helps,
Marco

p.s. what do you mean by "gene annotation"?

[Marta Potrykus]

Dear Marco,

Thank you for thorough desrciption of what to do. I have used the commands inside the directory but have not prefixed the command with python.

Now it works for me as well,

Thanks

Marta