Gu mode error

Question

Gu mode error

freitasla opened this issue 5 years ago · comments

Hello,

I am using ZOMBI to simulate some genomes in the Gu mode and I got this error message:

Simulating genomes. Time 0.0
Traceback (most recent call last):
  File "/data/software/ZOMBI/Zombi.py", line 365, in <module>
    Z.G(parameters_file, experiment_folder, advanced_mode)
  File "/data/software/ZOMBI/Zombi.py", line 130, in G
    gss.run_u()
  File "/data/software/ZOMBI/GenomeSimulator.py", line 679, in run_u
    self.advanced_evolve_genomes(current_time)
  File "/data/software/ZOMBI/GenomeSimulator.py", line 1106, in advanced_evolve_genomes
    self.make_inversion(i_e, lineage, time)
  File "/data/software/ZOMBI/GenomeSimulator.py", line 2217, in make_inversion
    affected_genes = chromosome.obtain_affected_genes(p)
  File "/data/software/ZOMBI/GenomeSimulator.py", line 3182, in obtain_affected_genes
    length = self.select_random_length(p_extension)
  File "/data/software/ZOMBI/GenomeSimulator.py", line 3072, in select_random_length
    return int(af.obtain_value(p))
  File "/data/software/ZOMBI/AuxiliarFunctions.py", line 94, in obtain_value
    handle = value.split(":")
AttributeError: 'float' object has no attribute 'split'

First I've simulated a species tree:

python Zombi.py T SpeciesTreeParameters.tsv Test1

Then I used this command to create the genome rates files:

python RateCustomizer.py G GenomeParameters.tsv Test1

Finally, the command who gave the error:

python Zombi.py Gu GenomeParameters.tsv Test1

Thanks!

Theo Tricou · Answer 1 · Tue Oct 15 2019 21:12:55 GMT+0800 (China Standard Time)

Hello,
I just run those commands with the default SpeciesTreeParameters and GenomeParameters and it works fine.
Have you made modifications to any file in the CustomRates directory ?

Théo

freitasla · Answer 2 · Tue Oct 15 2019 21:29:08 GMT+0800 (China Standard Time)

Hello,

Thanks for your quick reply.

I did not change anything in the CustomRates directory. Also, I've used the same commands both in CentOS/MacOS and they returned the same previous error.

Thanks!

Theo Tricou · Answer 3 · Tue Oct 15 2019 21:37:02 GMT+0800 (China Standard Time)

Could you show me the SpeciesTreeParameters.tvs and GenomeParameters.tsv files you are using ?
And did you clobe the last version of Zombi ?

Théo

freitasla · Answer 4 · Tue Oct 15 2019 21:52:45 GMT+0800 (China Standard Time)

Hello,

I cloned ZOMBI today and I am using the parameters files that came with ZOMBI. I just changed the extension to upload here.

GenomeParameters.txt and SpeciesTreeParameters.txt

Theo Tricou · Answer 5 · Tue Oct 15 2019 22:14:50 GMT+0800 (China Standard Time)

hello,
Ok I found the issue. Contrary to what is stated in the wiki, geometric and exponential distribution are not implemented.
For now you can only use f fixed, u uniform, n normal and l log-normal distribution.
I will send a mail to the main developer to see the reason.

Théo

Theo Tricou · Answer 6 · Tue Oct 15 2019 22:25:53 GMT+0800 (China Standard Time)

Hello,

I've made a modification in the code.
This should fix the issue.

Théo

Adrián A. Davín · Answer 7 · Wed Oct 16 2019 09:14:06 GMT+0800 (China Standard Time)

Thanks for the prompt response Théo!

freitasla · Answer 8 · Wed Oct 16 2019 17:08:42 GMT+0800 (China Standard Time)

Hello again,

Sorry but I am still having the issue. Just cloned the repository and did everything from scratch:

Thanks!

Adrián A. Davín · Answer 9 · Wed Oct 16 2019 17:22:55 GMT+0800 (China Standard Time)

Hi! Can you attach the parameters file you are using? Or is the one that comes with Zombi? I'll have a look into this tomorrow Le mercredi 16 octobre 2019, freitasla <notifications@github.com> a écrit :

…

Hello again, Sorry but I am still having the issue. Just cloned the repository and did everything from scratch: [image: GuZOMBI] <https://user-images.githubusercontent.com/56592549/66904899-c5276080-effc-11e9-9e54-0bfdde665322.png> Thanks! — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#5>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIPUBWLHNLXHHAIEDE7OQS3QO3KZXANCNFSM4JA4EGUA> .

-- Adrián A. Davín, PhD Postdoc researcher at Queensland University

freitasla · Answer 10 · Wed Oct 16 2019 17:30:48 GMT+0800 (China Standard Time)

Hello,

It is the same that comes with ZOMBI.

Thank you!

Adrián A. Davín · Answer 11 · Thu Oct 17 2019 13:56:25 GMT+0800 (China Standard Time)

There was indeed a bug. It should work now. Let me know if you find any other problems Cheers! Le mer. 16 oct. 2019 à 19:08, freitasla <notifications@github.com> a écrit :

…

Hello again, Sorry but I am still having the issue. Just cloned the repository and did everything from scratch: [image: GuZOMBI] <https://user-images.githubusercontent.com/56592549/66904899-c5276080-effc-11e9-9e54-0bfdde665322.png> Thanks! — You are receiving this because you modified the open/close state. Reply to this email directly, view it on GitHub <#5>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AIPUBWLHNLXHHAIEDE7OQS3QO3KZXANCNFSM4JA4EGUA> .

-- Adrián A. Davín, PhD Postdoc researcher at Queensland University

freitasla · Answer 12 · Fri Oct 18 2019 17:17:22 GMT+0800 (China Standard Time)

Thank you! It's working now.