mendessoares / mminte Goto Github PK

Good morning!
I am trying to use your scripts (adapting them to python3.6) for my metabolic models created by carveme (https://github.com/cdanielmachado/carveme) instead of ModelSEED so starting from widget4. I was wondering whether it is a problem or your scripts work also with carveme models.

Sincerely,
Arianna Basile

-Under Widget 1: "You can check this file by going to the CaseStudy1 folder and opening the corrsFlat.txt file in any text editor. Here is what the header and first five lines of dat this file looks like:" ->
--Maybe correct to this: "You can check this file by going to the CaseStudy1 folder and opening the corrs.txt file in any text editor. Here is what the header and first five lines of data in this file look like:"
--also maybe say how to find the corrs.txt file: "go to the userFiles folder inside the CaseStudy1 folder"

-Resuls tab is written twice instead of Results tab

-"You can check this file by going to the CaseStudy1 folder and opening the rep_set.fna file in any text editor. Here is what this file looks like:"
--I think that the file name that corresponds to this line is seqs.fasta
--maybe also mention that this file is inside the userFiles folder

Hello,

I'm trying to run getModels() from widget 3 running independently of anything else, however I'm getting an internal server error.

`---> 46 if response.status_code != requests.codes.OK:
47 response.raise_for_status()
48

HTTPError: 500 Server Error: Internal Server Error`

Is there an updated URL for the active ProbModelSEED server?

Thanks,
Greg

Hello!
I like your source, I was wondering if you are planning to switch to python3 since python2 is now considered obsolete and many dependencies have already dropped support.

Faithfully,
Arianna

Hello
Please,
I am receiving this error message every time that I try to install the program
Command "python setup.py egg_info" failed with error code 1 in /tmp/pip-install-gj6wjqbr/matplotlib/
How can I fix it?

Summary: Not having unique names in the headers may cause mismatches between PctSim and e-value/bitscore, blastn output issue more than a MMinte issue.

Background:
Building my own blast databases, I am encountering issues with match assignments.

For example, with the current 16Sdb a given OTU is matching with 100 percent identity, 0 mismatch, 2e-120 bitscore ; but when the database is augmented with new sequences the best match switches to a genomeid with 27 percent identity, 170 mismatch. The effect is observed when a database is constructed of the new sequences alone. Re-testing with the new sequences alone, I find the 27% identity anomaly is definitely associated with the new sequences

Below: BLAST results before pre-processing names to make them unique:
denovo830 59620 27.35 234 170 0 1 234 523 756 5e-124 433
denovo830 59620 27.35 234 170 0 1 234 523 756 5e-124 433
denovo830 59620 27.35 234 170 0 1 234 523 756 5e-124 433
denovo830 59620 27.35 234 170 0 1 234 523 756 5e-124 433
denovo830 59620 21.84 206 147 12 1 199 540 738 3e-46 174

(inspection of the alignment from blast output shows a very bad alignment closer to 27% identity/170 mismatch than 5e-124 evalue and 433 bitscore)

Analysis of the sequence headers in the new set suggest that 38 of them share a taxa_id, thus they also share a header, which appears to mess with parsing:
(

59620
...
59620
...
)

After correcting names into uniqueness:

denovo830 59620.37 100.00 234 0 0 1 234 523 756 5e-124 433
denovo830 59620.14 100.00 234 0 0 1 234 523 756 5e-124 433
denovo830 59620.8 100.00 234 0 0 1 234 523 756 5e-124 433
denovo830 59620.7 100.00 234 0 0 1 234 523 756 5e-124 433
denovo830 59620.23 83.01 206 21 12 1 199 540 738 3e-46 174

At this point, the >59620 sequence that was a mere 27% identity is no longer highly ranked.

If this particular issue is driven by how e-value/bitscore et al are assigned in the case of duplicate headers, then there is a possibility that when a given OTU representative has a strong match to one of a set, results might not always be reported for the representative. In the above case, 59620 does have a high-evalue and high bitscore match, but reported a 27 percent identity, which is passed into MMinte as PctSim. This may have an effect on components of MMinte that rely on the PctSim value.

Edit: This would probably have the most effect in cases where a given taxa has multiple associated genomeIDs, and said genomeID's have 16S sufficiently distinct such that a query sequence would produce different percent identity for each of the similar sequences.

Hi
I have been trying to install MMinte in virtual box on Windows. I am unable to install the dependencies for MMinte. It keeps giving me an error for BLAST. I am not really good at command line can you please help me with the issue, I am attaching a screen shot of the error.

Installation of MMinte using pip as described fails due to not being able to find cobra=0.5.11. Not trying to install in qime box.

good evening!
I am trying to reproduce the tutorial for interactions you posted on interactions.ipynb but I stop at

growth_rates = mminte.calculate_growth_rates(pair_model_filenames, western_diet)

I get this error:

AttributeError: 'Solution' object has no attribute 'x_dict'

How can I manage it?

Sincerly,
Arianna

Greetings,
I'm trying to use MMinte with a personal 16s rDNA sequencing project. Everything goes well until I reach thw Widget 3, which gives me the following error:

ServerError: 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) line 232"

What kind of issue is that?
Best regards