mmundy42 / mackinac Goto Github PK

Hello,

I can successfully create reconstructions with, for example:

modelseed.reconstruct_modelseed_model('1133568.3')

but any function meant to use this model (e.g. optimize_modelseed_model(), gapfill_modelseed_model()) raises a ServerError, such as:

ServerError: Can't call method "genome" without a package or object reference at /disks/p3dev2/deployment/lib/Bio/KBase/ObjectAPI/functions.pm line 521.

however, calling these functions on a model I made through the modelseed GUI works fine.

when I call modelseed.list_modelseed_models() using my folder ('/username/modelseed/'), the only models listed are those created in the GUI.

Any help is appreciated!

Thanks,
Greg

I generated a metabolic reconstruction using Mackinac and found that the objective values obtained between Mackinac (mackinac.optimize_modelseed_model) and Cobra (model.optimize()) are different. The former gives 1.66 while the latter gives 38.65. Does anyone know what causes this inconsistency? Thanks very much.

Using mackinac 0.8.0, When attempting the following:

mackinac.gapfill_modelseed_model('97138.3',likelihood=True)

my system returns the following error:

Traceback (most recent call last):
File "", line 1, in
File "/usr/local/lib/python3.5/site-packages/mackinac-0.8.0-py3.5.egg/mackinac/modelseed.py", line 105, in gapfill_modelseed_model
_wait_for_job(job_id)
File "/usr/local/lib/python3.5/site-packages/mackinac-0.8.0-py3.5.egg/mackinac/modelseed.py", line 926, in _wait_for_job
raise ServerError(task['error'])
KeyError: 'error'

Appears to be on the ModelSEED side, so I tried both of the client urls in the readme to no avail. With likelihood=False, the gapfill is successful.

Thanks!

Hi, I was trying to reconstruct a model from a PATRIC genome ID with the mackinac.reconstruct_modelseed_model() function but mackinac seems to have issues connecting to PATRIC as it returned this error:

Is there a newer version of mackinac available that circumvents this issue? Otherwise can the user input a model retrieved from ModelSEED server instead instead of going through PATRIC?

This line is a cause of my error in _wait_for_job(jobid) function modelseed.py file:
jobs = ms_client.call('CheckJobs', {})

While trying to get model from ModelSeed via API http://p3.theseed.org/services/ProbModelSEED/
(http://modelseed.org/about/version)
I've got a error:
Error creating models: Attribute (host) does not pass the type constraint because: Validation failed for 'Str' with value undef at constructor MongoDB::MongoClient::new (defined at /disks/patric-common/runtime/lib/perl5/site_perl/5.20.2/x86_64-linux/MongoDB/MongoClient.pm line 1069)

--

Looks like empty dict causes the problem, but I can't find any documentation at ModelSeed to repair this problem. Could you help me, please?

Hi I'm using the current version of mackinac from the devel branch and I tried creating a reconstruction using the following:

recon_info = mackinac.create_patric_model('239935.2','Akkermansia muciniphila')

and I get the following error:

Traceback (most recent call last)
in
---> 12 recon_info = mackinac.create_patric_model(species_id,species)

c:\users\lilym\box\capstone\mackinac\mackinac\patric.py in create_patric_model(genome_id, model_id, media_reference, template_reference, output_folder)
--> 108 get_genome_summary(genome_id)

c:\users\lilym\box\capstone\mackinac\mackinac\genome.py in get_genome_summary(genome_id)
25 if response.status_code != requests.codes.OK:
26 if response.status_code == 404:
---> 27 raise ValueError('Genome ID {0} not found in PATRIC'.format(genome_id))
28 response.raise_for_status()
29 return response.json()

ValueError: Genome ID 239935.2132 not found in PATRIC

I'm able to find the genome information when I search the genome ID in PATRIC's web interface and I was able to create a model using the PATRIC web interface to check if it was an issue with the server being down. I also tried going to the url used in the code to retrieve the genome summary and it says that the site is either temporarily down or it moved to a different location. So I was wondering if it's possible if the service url in PATRIC has changed or if it's something else?

Thanks!

Hi
I'm not able to genereat/retrieve models in PATRICK using mackinac. Any help would be appreciated.

This is what I've done:
-installed mackinac 0.8.4 in a virtual environment with python 3.5.0
-uploeaded a genome to PATRICK and annotated it.
-uploaded the geome to RAST and annotated it (and made metabolic model)
-made a metabolic model in modelseed with genome retrieved from RAST.
-made a metabolic model in PATRICK.

attempts to use mackinac

mackinac.reconstruct_modelseed_model('928852.5') ## this is the id listed for my genome in PATRICK
Output: nothing happens for a long time until I get a long error meassage which ends with: read timeout=1800. Besides, I see that a job has been qued in my patrick workspace (RunProbModelSeedjob).

mackinac.reconstruct_modelseed_model('928852.3') ## this is the id of my genome in RAST
Output: same as for 1)

mackinac.reconstruct_modelseed_model('226186.12') ## this is the id for a publically avilable genome in PATRICK
Output: same as for 1)

4. various attemts using
   mackinac.create_cobra_model_from_modelseed_model(id) # where id is the id listed in http://modelseed.org/my-models/, or RAST id or PATRICK id
   Output: long error message ending with "mackinac.SeedClient.ObjectNotFoundError: An object was not found in workspace: "/[email protected]/modelseed/id"
   (so how do I get my model into /[email protected]/modelseed?)

What am I doing wrong?

Cheers
Hakonda