# MelonnPan **URL:** https://forum.biobakery.org/c/microbial-community-profiling/melonnpan/27.md [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) --- ## [About the MelonnPan category](https://forum.biobakery.org/t/about-the-melonnpan-category/48)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 0
Name: MelonnPan User manual || Tutorial Description: MelonnPan is composed of two high-level workflows: MelonnPan-Predict and MelonnPan-Train . The MelonnPan-Predict workflow takes a table of microbial sequen… --- ## [Using Melonnpan wiht HUMAnN4](https://forum.biobakery.org/t/using-melonnpan-wiht-humann4/9036)
**Author:** [@Florencia\_Penalba](https://forum.biobakery.org/u/Florencia_Penalba)\ **Replies:** 0\ **Last updated:** [August 13, 2026, 7:57pm UTC](https://forum.biobakery.org/t/using-melonnpan-wiht-humann4/9036 "2026-08-13T19:57:32Z")
I have been using humann v4.0.0.alpha.1 and I have several results. I want to predict the metabolites for this samples. I have tried using melonnpan 0.99.0.predict but it returns an error “No common IDS found between tra… --- ## [Understanding melonnpan cv.enet code](https://forum.biobakery.org/t/understanding-melonnpan-cv-enet-code/8326)
**Author:** [@juliacapperella](https://forum.biobakery.org/u/juliacapperella)\ **Replies:** 0\ **Last updated:** [July 31, 2025, 11:34am UTC](https://forum.biobakery.org/t/understanding-melonnpan-cv-enet-code/8326 "2025-07-31T11:34:23Z")
Hello, I am new to melonnpan and recently ran into a dependency issue and was unable to install the R package. I am waiting for these issues to be resolved, but in the meantime I am trying to download the melonnpan code … --- ## [Running melonnpan with a single sample](https://forum.biobakery.org/t/running-melonnpan-with-a-single-sample/7520)
**Author:** [@greg00](https://forum.biobakery.org/u/greg00)\ **Replies:** 1\ **Last updated:** [December 10, 2024, 3:58pm UTC](https://forum.biobakery.org/t/running-melonnpan-with-a-single-sample/7520 "2024-12-10T15:58:40Z")
Can melonnpan predict be used with one sample only? If so, how is it possible? It works fine for 3 samples or above, but I get trait is monomorphic error when I use a single sample, or trait is binary error if I use 2 s… --- ## [System resourced needed for Melonnpan & Shortbred](https://forum.biobakery.org/t/system-resourced-needed-for-melonnpan-shortbred/7485)
**Author:** [@SC07](https://forum.biobakery.org/u/SC07)\ **Replies:** 0\ **Last updated:** [October 10, 2024, 9:56am UTC](https://forum.biobakery.org/t/system-resourced-needed-for-melonnpan-shortbred/7485 "2024-10-10T09:56:49Z")
Hi All, I am new to Melonnpan and Shortbred and planning to use these two tools for metabolites prediction and protein profiling. May I know what is the system resourced needed to install and run these two pipelines in … --- ## [Model Transferrability to Different Human Anatomic Site](https://forum.biobakery.org/t/model-transferrability-to-different-human-anatomic-site/7306)
**Author:** [@Dario](https://forum.biobakery.org/u/Dario)\ **Replies:** 0\ **Last updated:** [July 23, 2024, 12:00am UTC](https://forum.biobakery.org/t/model-transferrability-to-different-human-anatomic-site/7306 "2024-07-23T00:00:01Z")
Downloadable model is trained on gut microbiome data. Is there any evaulation of its prediction performance for oral microbiome? --- ## [Error while trying to use melonnpan for predicting metabolites from metatranscriptome data](https://forum.biobakery.org/t/error-while-trying-to-use-melonnpan-for-predicting-metabolites-from-metatranscriptome-data/6810)
**Author:** [@Rishav\_Sahil](https://forum.biobakery.org/u/Rishav_Sahil)\ **Replies:** 1\ **Last updated:** [March 21, 2024, 6:50am UTC](https://forum.biobakery.org/t/error-while-trying-to-use-melonnpan-for-predicting-metabolites-from-metatranscriptome-data/6810 "2024-03-21T06:50:16Z")
Hello sir, I am trying to use melonnpan for predicting metabolites using this command Rscript /home/sahil/Documents/manuscript/melonnpan/predict\_metabolites.R -i data\_dyadobacter.txt -o Output/ from the metatranscri… --- ## [Is acetate a predicted metabolite for Melonpann?](https://forum.biobakery.org/t/is-acetate-a-predicted-metabolite-for-melonpann/6452)
**Author:** [@Jwright](https://forum.biobakery.org/u/Jwright)\ **Replies:** 0\ **Last updated:** [January 11, 2024, 9:18pm UTC](https://forum.biobakery.org/t/is-acetate-a-predicted-metabolite-for-melonpann/6452 "2024-01-11T21:18:14Z")
Hello I am running melonpann and was expected to observe acetate as one of the predicted metabolites, but it was not. Is there a list of metabolites that melonpann predicts? Just wanted to confirm if that was outside th… --- ## [Usage of "train.metag" function in melonnpan](https://forum.biobakery.org/t/usage-of-train-metag-function-in-melonnpan/5960)
**Author:** [@DEEPCHANDA7](https://forum.biobakery.org/u/DEEPCHANDA7)\ **Replies:** 1\ **Last updated:** [November 7, 2023, 12:50am UTC](https://forum.biobakery.org/t/usage-of-train-metag-function-in-melonnpan/5960 "2023-11-07T00:50:20Z")
Hi @himel.mallick - I have trained paired metagenome-metabolome data which resulted into 3 outputs: MelonnPan\_Trained\_Metabolites.txt MelonnPan\_Training\_Summary.txt MelonnPan\_Trained\_Weights.txt For the prediction pur… --- ## [Error in FUN(newX\[, i\], ...) : trait is binary?](https://forum.biobakery.org/t/error-in-fun-newx-i-trait-is-binary/5467)
**Author:** [@Rachael](https://forum.biobakery.org/u/Rachael)\ **Replies:** 2\ **Last updated:** [June 23, 2023, 7:10pm UTC](https://forum.biobakery.org/t/error-in-fun-newx-i-trait-is-binary/5467 "2023-06-23T19:10:00Z")
test-transposed\_copy.txt (4.5 MB) Hello, I am attempting to run melonpann predict on my own UniRef90 annotation data (produced via Humann3) that I (believe) I have formatted correctly (see attachment). The file looks … --- ## [Point in melonnpan output](https://forum.biobakery.org/t/point-in-melonnpan-output/5288)
**Author:** [@xiaoafei](https://forum.biobakery.org/u/xiaoafei)\ **Replies:** 1\ **Last updated:** [May 24, 2023, 7:17pm UTC](https://forum.biobakery.org/t/point-in-melonnpan-output/5288 "2023-05-24T19:17:10Z")
i notice that there are many metabolite’name contain point, such as C16.0.ceramide…d18.1. ; butyrate…isobutytare. ; methylbutyric.aid…valeric…isovaleric. ; i want to know what that point represent？ --- ## [Can melonnpan used for soil?](https://forum.biobakery.org/t/can-melonnpan-used-for-soil/5324)
**Author:** [@xiaoafei](https://forum.biobakery.org/u/xiaoafei)\ **Replies:** 1\ **Last updated:** [May 24, 2023, 7:15pm UTC](https://forum.biobakery.org/t/can-melonnpan-used-for-soil/5324 "2023-05-24T19:15:15Z")
can melonnpan used for soil? or only for gut? --- ## [Annotation of 16S sequences to UniRef90](https://forum.biobakery.org/t/annotation-of-16s-sequences-to-uniref90/4796)
**Author:** [@seibikobara](https://forum.biobakery.org/u/seibikobara)\ **Replies:** 4\ **Last updated:** [February 28, 2023, 2:27am UTC](https://forum.biobakery.org/t/annotation-of-16s-sequences-to-uniref90/4796 "2023-02-28T02:27:53Z")
Hello, we would like to perform metabolite prediction using MelonnPan. Our data is an OTU table with 16S nucleotide sequences, and I would like to use this table for metabolite prediction. I have learned from the tutori… --- ## [Variability in melonnpan result](https://forum.biobakery.org/t/variability-in-melonnpan-result/4829)
**Author:** [@paramartha\_banerjee](https://forum.biobakery.org/u/paramartha_banerjee)\ **Replies:** 3\ **Last updated:** [February 28, 2023, 2:27am UTC](https://forum.biobakery.org/t/variability-in-melonnpan-result/4829 "2023-02-28T02:27:17Z")
Hello!! I have trained the melonnpan model using the input metabolomic and gene family files provided in the tutorial. However now when I am attempting to test the melonnpan predict workflow using the same gene family fi… --- ## [Metatranscriptomics + MelonnPan](https://forum.biobakery.org/t/metatranscriptomics-melonnpan/4760)
**Author:** [@pad](https://forum.biobakery.org/u/pad)\ **Replies:** 2\ **Last updated:** [February 15, 2023, 11:16pm UTC](https://forum.biobakery.org/t/metatranscriptomics-melonnpan/4760 "2023-02-15T23:16:54Z")
Hi all – I am curious as to whether MelonnPan has been tested with metatranscriptomes.If so, what are the recommended changes (if any at all) that should be made to the mtg-based pipeline? Thanks. --- ## [Melonnpan predict result interpretation](https://forum.biobakery.org/t/melonnpan-predict-result-interpretation/4783)
**Author:** [@paramartha\_banerjee](https://forum.biobakery.org/u/paramartha_banerjee)\ **Replies:** 2\ **Last updated:** [February 15, 2023, 1:40am UTC](https://forum.biobakery.org/t/melonnpan-predict-result-interpretation/4783 "2023-02-15T01:40:14Z")
Hello!! I have trained the melonnpan model using my own paired data and then I have executed the melonnpan predict workflow and am getting the following file containing the relative abundances of the predicted metabolite… --- ## [Filtering of gene family and metabolite abundance file](https://forum.biobakery.org/t/filtering-of-gene-family-and-metabolite-abundance-file/4756)
**Author:** [@paramartha\_banerjee](https://forum.biobakery.org/u/paramartha_banerjee)\ **Replies:** 1\ **Last updated:** [February 7, 2023, 3:55pm UTC](https://forum.biobakery.org/t/filtering-of-gene-family-and-metabolite-abundance-file/4756 "2023-02-07T15:55:31Z")
Hello!! I have successfully obtained the gene family abundance file which contains about 5346 features. Is it necessary to do filtering of low abundant and low prevalent features? Also, I have performed log transformat… --- ## [Gene Ontology (GO) file as an alternative to UniRef90 for Melonnpan training](https://forum.biobakery.org/t/gene-ontology-go-file-as-an-alternative-to-uniref90-for-melonnpan-training/4703)
**Author:** [@paramartha\_banerjee](https://forum.biobakery.org/u/paramartha_banerjee)\ **Replies:** 2\ **Last updated:** [January 29, 2023, 10:03am UTC](https://forum.biobakery.org/t/gene-ontology-go-file-as-an-alternative-to-uniref90-for-melonnpan-training/4703 "2023-01-29T10:03:29Z")
Hello!! Can we use gene family files regrouped to Gene Ontology(GO) as an input during Melonnpan training workflow as an alternative to Uniref90? (since Uniref90 gene family files are much larger in size and hence may … --- ## [Request for clarification regarding error during Melonnpan-Train workflow execution](https://forum.biobakery.org/t/request-for-clarification-regarding-error-during-melonnpan-train-workflow-execution/387)
**Author:** [@sagunmaharjann](https://forum.biobakery.org/u/sagunmaharjann)\ **Replies:** 4\ **Last updated:** [January 9, 2023, 4:41pm UTC](https://forum.biobakery.org/t/request-for-clarification-regarding-error-during-melonnpan-train-workflow-execution/387 "2023-01-09T16:41:54Z")
I am an undergraduate student who is working on a project involving the metabolomic profile of lactobacillus and its interaction with the human metabolome. I have the metagenome of the organism and am very keen on using … --- ## [Different outputs of RTSI scores and metabolite abundances using the same input file](https://forum.biobakery.org/t/different-outputs-of-rtsi-scores-and-metabolite-abundances-using-the-same-input-file/4595)
**Author:** [@paramartha\_banerjee](https://forum.biobakery.org/u/paramartha_banerjee)\ **Replies:** 4\ **Last updated:** [January 9, 2023, 4:15pm UTC](https://forum.biobakery.org/t/different-outputs-of-rtsi-scores-and-metabolite-abundances-using-the-same-input-file/4595 "2023-01-09T16:15:59Z")
Hello!! I am running melonnpan predict using the melonnpan.test.data.txt file provided in the tutorial. However, I am getting different outputs of RTSI and relative abundances of the metabolites when I repeat the proces… --- ## [Metabolite Prediction using 16S microbiome data](https://forum.biobakery.org/t/metabolite-prediction-using-16s-microbiome-data/261)
**Author:** [@Aditya\_Bajaj](https://forum.biobakery.org/u/Aditya_Bajaj)\ **Replies:** 3\ **Last updated:** [December 27, 2022, 6:42pm UTC](https://forum.biobakery.org/t/metabolite-prediction-using-16s-microbiome-data/261 "2022-12-27T18:42:32Z")
Hello. We tried to perform the melonnpan-based metabolite prediction on our 16s sequencing raw data and we have come across a few doubts. Does Melonnpan accept the output from Picrust or from Humann2? If Melonnpan acce… --- ## [Transformation of preprocessed metabolomic data for using as MelonnPan input file](https://forum.biobakery.org/t/transformation-of-preprocessed-metabolomic-data-for-using-as-melonnpan-input-file/4392)
**Author:** [@DEEPCHANDA7](https://forum.biobakery.org/u/DEEPCHANDA7)\ **Replies:** 1\ **Last updated:** [November 20, 2022, 2:40am UTC](https://forum.biobakery.org/t/transformation-of-preprocessed-metabolomic-data-for-using-as-melonnpan-input-file/4392 "2022-11-20T02:40:15Z")
Hi community and Dr @himel.mallick !!! I have preprocessed raw metabolomic spectra to get an output containing abundance values of each metabolite within a sample in terms of mass spec peak area. However, mass spec expe… --- ## [Error installing GenABEL package](https://forum.biobakery.org/t/error-installing-genabel-package/4173)
**Author:** [@AndreaGatti](https://forum.biobakery.org/u/AndreaGatti)\ **Replies:** 8\ **Last updated:** [October 11, 2022, 3:02pm UTC](https://forum.biobakery.org/t/error-installing-genabel-package/4173 "2022-10-11T15:02:15Z")
Hi, I’ve installed all packages and their dependencies on R (version 4.2.1) needed for MelonnPan, aside from GenABEL package (version 1.8-0 as suggested in the installation tutorial), and when I try to install it I get … --- ## [Error,Dependencies](https://forum.biobakery.org/t/error-dependencies/97)
**Author:** [@CHALEAMKWAN\_POONPANA](https://forum.biobakery.org/u/CHALEAMKWAN_POONPANA)\ **Replies:** 6\ **Last updated:** [June 22, 2022, 11:58am UTC](https://forum.biobakery.org/t/error-dependencies/97 "2022-06-22T11:58:32Z")
Hello, When I try to install MelonnPan on R version 3.5 I got a problem which about " ERROR: dependencies ‘glmnet’, ‘GenABEL’, ‘GenABEL.data’ are not available for package ‘melonnpan’ removing ‘/Users/chalaemkwan/Lib… --- ## [MelonnPan installation on ubuntu 20.04 issues](https://forum.biobakery.org/t/melonnpan-installation-on-ubuntu-20-04-issues/4133)
**Author:** [@AndreaGatti](https://forum.biobakery.org/u/AndreaGatti)\ **Replies:** 2\ **Last updated:** [October 3, 2022, 1:53pm UTC](https://forum.biobakery.org/t/melonnpan-installation-on-ubuntu-20-04-issues/4133 "2022-10-03T13:53:15Z")
Hello, I tried to install MelonnPan on ubuntu 20.04 subsystem for Windows following the instructions presented in the tutorial (melonnpan · biobakery/biobakery Wiki · GitHub), trying with both R versions 4.1.2 and 3.6.1… --- ## [Input uniref90 IDs from humann3 not recognized by melonnpan](https://forum.biobakery.org/t/input-uniref90-ids-from-humann3-not-recognized-by-melonnpan/2047)
**Author:** [@hshcao](https://forum.biobakery.org/u/hshcao)\ **Replies:** 4\ **Last updated:** [May 7, 2022, 4:47pm UTC](https://forum.biobakery.org/t/input-uniref90-ids-from-humann3-not-recognized-by-melonnpan/2047 "2022-05-07T16:47:01Z")
I used humann3 to get the uniref90 gene IDs and feed melonnpan with them. As melonnpan works with humann2, will you update melonnpan to use uniref90 IDs from humann3? thanks, Huansheng --- ## [We can’t find our metabolite of interest (S-equol) among the predicted metabolites](https://forum.biobakery.org/t/we-can-t-find-our-metabolite-of-interest-s-equol-among-the-predicted-metabolites/3402)
**Author:** [@lastfirefly6](https://forum.biobakery.org/u/lastfirefly6)\ **Replies:** 0\ **Last updated:** [April 5, 2022, 6:20am UTC](https://forum.biobakery.org/t/we-can-t-find-our-metabolite-of-interest-s-equol-among-the-predicted-metabolites/3402 "2022-04-05T06:20:24Z")
We have been using MelonnPan on microbial sequence features collected and sequenced from mouse skin. In these samples, we have already identified some bacteria in high frequencies that are capable of producing S-equol (w… --- ## [Where is the melonnpan tutorial?](https://forum.biobakery.org/t/where-is-the-melonnpan-tutorial/2897)
**Author:** [@Cheng\_Guo](https://forum.biobakery.org/u/Cheng_Guo)\ **Replies:** 4\ **Last updated:** [December 17, 2021, 6:36am UTC](https://forum.biobakery.org/t/where-is-the-melonnpan-tutorial/2897 "2021-12-17T06:36:03Z")
Dear Melonnpan developer, Thanks for providing the tool. I have installed the melonnpan in the R studio, and also downloaded the Github repository. However, I am very confused with the Melonnpan tutorial. Where should I… --- ## [Input for Trainning MelonnPan](https://forum.biobakery.org/t/input-for-trainning-melonnpan/2905)
**Author:** [@y3zhu](https://forum.biobakery.org/u/y3zhu)\ **Replies:** 0\ **Last updated:** [December 16, 2021, 1:16am UTC](https://forum.biobakery.org/t/input-for-trainning-melonnpan/2905 "2021-12-16T01:16:04Z")
Hi there, @himel.mallick I am working on metagenomic samples from patients with a disease other than IBD. I want to get the predicted metabolome of the samples. What input do I need to give MelonnPan to train the model:… --- ## [Can I use default trained (IBD data) MelonnPan for prediction of Obesity associated metabolome prediction?](https://forum.biobakery.org/t/can-i-use-default-trained-ibd-data-melonnpan-for-prediction-of-obesity-associated-metabolome-prediction/2613)
**Author:** [@DEEPCHANDA7](https://forum.biobakery.org/u/DEEPCHANDA7)\ **Replies:** 1\ **Last updated:** [September 22, 2021, 10:11pm UTC](https://forum.biobakery.org/t/can-i-use-default-trained-ibd-data-melonnpan-for-prediction-of-obesity-associated-metabolome-prediction/2613 "2021-09-22T22:11:30Z")
Hi Sir- @himel.mallick , I have human control and obese samples. I want to get the predicted metabolome of the samples. Can I use the default trained model (i.e. dataset predicted with IBD and non-IBD datasets) for my pr… [Next page](https://forum.biobakery.org/c/microbial-community-profiling/melonnpan/27.md?page=1)