smetana

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Love the tool, its been very simple to set up and use, and provides thought provoking results. This may seem a small quibble, but I thought I would at least...

winatony

Comparative Analysis of MIP and MRO Across Variable MAG Compositions and Investigating Cross-Feeding Pathways in Microbial Communities

1

Hi Daniel, I'm calculating MIP and MRO based on MAGs assembled from different samples using SMETANA. The number of MAGs assembled varies between each metagenomic sample. Can I compare MIP...

Noob-Monkey

smetana *.xml -d -c communities.tsv need much more time. So how to submit parallelized jobs to analyze? Thanks

LiZhihua1982

Adjusting the non-CarveMe GEMs to SMETANA

2

Hi Daniel, I am trying to use SMETANA with GEMs from different repositories. When I use it with CarveMe-generated GEMs, it works pretty fine. $ smetana carveme1.xml carveme2.xml carveme3.xml --flavor...

mohammadmirhakkak

(carveme) lizhihua@lizhihua-T640:/media/lizhihua/software/gapseq/gapseq/GJ89_bins$ smetana carveme/*.xml Traceback (most recent call last): File "/home/lizhihua/.local/lib/python3.8/site-packages/optlang/util.py", line 305, in __getattr__ return self._functions[item][0]() KeyError: 'optimality' During handling of the above exception, another exception occurred: Traceback (most...

LiZhihua1982

Got an empty file with only the header

3

Hi, I used smetana to build an interactive feeding model of a community of 108 strains of bacteria, using the code below: smetana *.xml -d -o model -m M9[-O2] --mediadb...

zoelwl

smetana is not is not recognized as command

1

Hi, I wanted to try smetana, the installation went really well but I can't use smetana as a command line. Do you have an idea why? (I used python 3.6...

Clem-Jos

Specifying compartment identifiers

2

Hi, I am currently trying to run smetana on some genome-scale metabolic models constructed using ModelSEED. I get an error when trying to run smetana through the command `smetana *.xml`,...

lauralmf

CarveMe Models without Gap Filling for Smetana

8

Thank you for developing smetana! I just have a general question. I'm currently building models with carveme by using the default command (`carve genome.faa`) without specifying any media via `--gapfill`....

pbelmann

Hi @cdanielmachado, I am having a issue running into it that is "RuntimeError: Model not in list: GCF_001435755". But my model is on the list. 

ChenCongZ