# \#micom **URL:** https://forum.qiime2.org/tag/micom/228.md [Latest](https://forum.qiime2.org/latest.md) · [Categories](https://forum.qiime2.org/categories.md) · [Tags](https://forum.qiime2.org/tags.md) --- ## [MICOM ERROR:All numerical optimizations failed. This indicates a problem with the solver or numerical instabilities. Check that you have CPLEX or Gurobi installed. You may also increase the abundance cutoff to create simpler models.](https://forum.qiime2.org/t/micom-error-all-numerical-optimizations-failed-this-indicates-a-problem-with-the-solver-or-numerical-instabilities-check-that-you-have-cplex-or-gurobi-installed-you-may-also-increase-the-abundance-cutoff-to-create-simpler-models/27760)
**Author:** [@dgenc](https://forum.qiime2.org/u/dgenc)\ **Replies:** 4\ **Last updated:** [March 25, 2025, 9:38am UTC](https://forum.qiime2.org/t/micom-error-all-numerical-optimizations-failed-this-indicates-a-problem-with-the-solver-or-numerical-instabilities-check-that-you-have-cplex-or-gurobi-installed-you-may-also-increase-the-abundance-cutoff-to-create-simpler-models/27760 "2025-03-25T09:38:28Z")
Hi.. First I would like to thank you for providing such an amazing tool! I am new to computational studies and also to MICOM, so I am sorry in advance if this question is not makes much sense When I use grow function I … --- ## [IndexError: index 0 is out of bounds for axis 0 with size 0](https://forum.qiime2.org/t/indexerror-index-0-is-out-of-bounds-for-axis-0-with-size-0/30465)
**Author:** [@herrynguyen1706](https://forum.qiime2.org/u/herrynguyen1706)\ **Replies:** 6\ **Last updated:** [August 2, 2024, 8:18am UTC](https://forum.qiime2.org/t/indexerror-index-0-is-out-of-bounds-for-axis-0-with-size-0/30465 "2024-08-02T08:18:01Z")
Dear All, I am trying to run model microbiota-wide metabolism with MICOM. I upload my tax data and then I build community models. However, they solve the problem below. Could you please help me with this issue? Thank y… --- ## [Identifying primary metabolite producing taxa](https://forum.qiime2.org/t/identifying-primary-metabolite-producing-taxa/30505)
**Author:** [@Lauren\_Anderson](https://forum.qiime2.org/u/Lauren_Anderson)\ **Replies:** 0\ **Last updated:** [June 13, 2024, 10:45pm UTC](https://forum.qiime2.org/t/identifying-primary-metabolite-producing-taxa/30505 "2024-06-13T22:45:59Z")
Hi, Recently, I have been playing with MICOM within QIIME2 after seeing @cdiener present it at ISB2020. There is one feature in that notebook that I can't figure out within the q2 plugin. Is it possible to identify the … --- ## [Preparing and importing custom diets and taxonomy files for q2-MICOM](https://forum.qiime2.org/t/preparing-and-importing-custom-diets-and-taxonomy-files-for-q2-micom/19857)
**Author:** [@Mehrbod\_Estaki](https://forum.qiime2.org/u/Mehrbod_Estaki)\ **Replies:** 2\ **Last updated:** [June 11, 2021, 8:57am UTC](https://forum.qiime2.org/t/preparing-and-importing-custom-diets-and-taxonomy-files-for-q2-micom/19857 "2021-06-11T08:57:47Z")
Hi @cdiener, Finally getting a chance to check out q2-micom and it's looking really cool so far! And thanks for the excellent documentations and tutorials! I have a few quasi related questions about the starting input … --- ## [Plugin error from micom: cannot convert float NaN to integer](https://forum.qiime2.org/t/plugin-error-from-micom-cannot-convert-float-nan-to-integer/29987)
**Author:** [@Mary1](https://forum.qiime2.org/u/Mary1)\ **Replies:** 4\ **Last updated:** [May 1, 2024, 4:17pm UTC](https://forum.qiime2.org/t/plugin-error-from-micom-cannot-convert-float-nan-to-integer/29987 "2024-05-01T16:17:52Z")
Hi all, I am having a problem with running Qiime2 - MICOM I keep getting this error: Merged with the database using ranks: species Traceback (most recent call last): File "/opt/anaconda3/envs/qiime2-amplicon-2023.9/li… --- ## [medium for elasticities](https://forum.qiime2.org/t/medium-for-elasticities/29858)
**Author:** [@dgenc](https://forum.qiime2.org/u/dgenc)\ **Replies:** 0\ **Last updated:** [April 11, 2024, 2:21pm UTC](https://forum.qiime2.org/t/medium-for-elasticities/29858 "2024-04-11T14:21:46Z")
Hello! I have used the Western diet file provided at media/media at main · micom-dev/media · GitHub. I thought they were already completed mediums, but when I tried complete\_medium function, I saw the EX\_rxn number went… --- ## [Converting excel file to a sbml for community models](https://forum.qiime2.org/t/converting-excel-file-to-a-sbml-for-community-models/29594)
**Author:** [@dgenc](https://forum.qiime2.org/u/dgenc)\ **Replies:** 2\ **Last updated:** [March 21, 2024, 1:20pm UTC](https://forum.qiime2.org/t/converting-excel-file-to-a-sbml-for-community-models/29594 "2024-03-21T13:20:13Z")
Hello! I am trying to use community model for elasticities in MICOM. My taxonomy file is an excel file that has the id information, reaction and metabolite number and abundance data (same as the one I used for build and… --- ## [Modfying Virtual Metabolic Human diets to be suitible for MICOM](https://forum.qiime2.org/t/modfying-virtual-metabolic-human-diets-to-be-suitible-for-micom/29157)
**Author:** [@dgenc](https://forum.qiime2.org/u/dgenc)\ **Replies:** 13\ **Last updated:** [March 17, 2024, 1:41pm UTC](https://forum.qiime2.org/t/modfying-virtual-metabolic-human-diets-to-be-suitible-for-micom/29157 "2024-03-17T13:41:36Z")
Hello! I am currently using MICOM to observe the changes in the gut microbiota at genus level. I have used the pre-built western diet environment provided but now I am trying to shift to diets provided by VMH (I have a… --- ## [MICOM tradeoff value](https://forum.qiime2.org/t/micom-tradeoff-value/20890)
**Author:** [@Hansol-cloud](https://forum.qiime2.org/u/Hansol-cloud)\ **Replies:** 2\ **Last updated:** [November 30, 2021, 8:46am UTC](https://forum.qiime2.org/t/micom-tradeoff-value/20890 "2021-11-30T08:46:29Z")
Hi, I'm trying to build a mouse microbiome model using micom. During the process, I got a result from micom.workflows.tradeoff.tradeoff and the result show that as tradeoff value increases, the fraction of taxa growing … --- ## [Making micom genus metabolites models](https://forum.qiime2.org/t/making-micom-genus-metabolites-models/19936)
**Author:** [@Hansol-cloud](https://forum.qiime2.org/u/Hansol-cloud)\ **Replies:** 5\ **Last updated:** [June 24, 2021, 10:59pm UTC](https://forum.qiime2.org/t/making-micom-genus-metabolites-models/19936 "2021-06-24T22:59:23Z")
Hi, I'm trying to build a mouse microbiome model using micom-q2. But the AGORA file that micom tutorial provided don't have some genus included in my mouse metagenome sequences data. So I want to make a genus metabolit…