# Feature/Pull Request **URL:** https://forum.biobakery.org/c/pull-request/39.md [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) --- ## [Missing \`mpa\_vOct22\_CHOCOPhlAnSGB\_202403.tsv\` in HUMAnN 4 utility\_mapping database](https://forum.biobakery.org/t/missing-mpa-voct22-chocophlansgb-202403-tsv-in-humann-4-utility-mapping-database/8643)
**Author:** [@fmerinocasallo](https://forum.biobakery.org/u/fmerinocasallo)\ **Replies:** 4\ **Last updated:** [September 25, 2026, 7:11am UTC](https://forum.biobakery.org/t/missing-mpa-voct22-chocophlansgb-202403-tsv-in-humann-4-utility-mapping-database/8643 "2026-09-25T07:11:55Z")
Hello, fellow bioBakers! :waving\_hand: I’m currently working with HUMAnN v4.0.0.alpha.1 and MetaPhlAn v4.1.1 (11 Mar 2024) for metatranscriptomics analysis, and I’ve encountered an issue with the utility mapping files. … --- ## [Implement download resumption in \`humann\_databases\`](https://forum.biobakery.org/t/implement-download-resumption-in-humann-databases/6208)
**Author:** [@kmlhpk](https://forum.biobakery.org/u/kmlhpk)\ **Replies:** 3\ **Last updated:** [November 21, 2023, 11:02am UTC](https://forum.biobakery.org/t/implement-download-resumption-in-humann-databases/6208 "2023-11-21T11:02:48Z")
I tried to follow Step 5 of “Initial Installation”, and ran into an issue with the command humann\_databases --download chocophlan full \. Namely, after ~15m of downloading the download failed with the following erro… --- ## [Reduce storage requirements when running HUMAnN](https://forum.biobakery.org/t/reduce-storage-requirements-when-running-humann/3642)
**Author:** [@alienzj](https://forum.biobakery.org/u/alienzj)\ **Replies:** 1\ **Last updated:** [May 26, 2022, 10:13am UTC](https://forum.biobakery.org/t/reduce-storage-requirements-when-running-humann/3642 "2022-05-26T10:13:59Z")
PR: --- ## [Update HUMAnN for MetaPhlAn 4.2 compatability](https://forum.biobakery.org/t/update-humann-for-metaphlan-4-2-compatability/8117)
**Author:** [@zzkt](https://forum.biobakery.org/u/zzkt)\ **Replies:** 3\ **Last updated:** [June 16, 2025, 5:34pm UTC](https://forum.biobakery.org/t/update-humann-for-metaphlan-4-2-compatability/8117 "2025-06-16T17:34:41Z")
I’ve recently upgraded to humann v3.9 & MetaPhlAn version 4.2.2 and it appears that the way MetaPhlAn handles map files has changed, so the ‘–bowtie2out’ arg is now ‘–mapout’ (as mentioned in the release announcement) A… --- ## [Use nvBowtie instead of bowtie2](https://forum.biobakery.org/t/use-nvbowtie-instead-of-bowtie2/3650)
**Author:** [@bobdoulz](https://forum.biobakery.org/u/bobdoulz)\ **Replies:** 0\ **Last updated:** [May 27, 2022, 11:05am UTC](https://forum.biobakery.org/t/use-nvbowtie-instead-of-bowtie2/3650 "2022-05-27T11:05:47Z")
Hi, I am currently helping some research teams to optimize their current workflow which involves kneaddata and humann running on our local HPC. I recently discovered the nvBio / nvBowtie project and I wondered if kneadd… --- ## [Add metaphlan database location to humann3 log file](https://forum.biobakery.org/t/add-metaphlan-database-location-to-humann3-log-file/3853)
**Author:** [@cdeanj](https://forum.biobakery.org/u/cdeanj)\ **Replies:** 0\ **Last updated:** [July 19, 2022, 6:49pm UTC](https://forum.biobakery.org/t/add-metaphlan-database-location-to-humann3-log-file/3853 "2022-07-19T18:49:18Z")
Feature Request Name: Add metaphlan database location to humann3 log file Detailed Description: It remains unclear what database is being used during the prescreening process within Humann3. The log file output from t… --- ## [Performance of HUMAnN Custom Database Creation](https://forum.biobakery.org/t/performance-of-humann-custom-database-creation/7091)
**Author:** [@ChristianRomberg](https://forum.biobakery.org/u/ChristianRomberg)\ **Replies:** 2\ **Last updated:** [June 20, 2024, 9:03pm UTC](https://forum.biobakery.org/t/performance-of-humann-custom-database-creation/7091 "2024-06-20T21:03:46Z")
Hi, I am currently in the process of writing my bachelor thesis and I am using HUMAnN3 in the process. I noticed that the custom database creation step is quite slow for what is seems to be doing and decided to profile … --- ## [Support for SummarizedExperiment assays](https://forum.biobakery.org/t/support-for-summarizedexperiment-assays/7772)
**Author:** [@antagomir](https://forum.biobakery.org/u/antagomir)\ **Replies:** 3\ **Last updated:** [January 31, 2025, 6:19pm UTC](https://forum.biobakery.org/t/support-for-summarizedexperiment-assays/7772 "2025-01-31T18:19:48Z")
Maaslin3 0.99.3 Thanks for adding SummarizedExperiment support for Maaslin3, and soon Bioconductor availability. SummarizedExperiment supports multiple abundance tables (e.g. counts, relative abundances, log, clr etc) … --- ## [Check for downloaded db](https://forum.biobakery.org/t/check-for-downloaded-db/6825)
**Author:** [@alouyakis](https://forum.biobakery.org/u/alouyakis)\ **Replies:** 0\ **Last updated:** [March 20, 2024, 6:13pm UTC](https://forum.biobakery.org/t/check-for-downloaded-db/6825 "2024-03-20T18:13:31Z")
MetaPhlAn version 4.1.0 (23 Aug 2023) metaphlan --install --index mpa\_vJun23\_CHOCOPhlAnSGB\_202403 --bowtie2db metaphlan\_db/ After downloading the db, command quit because I hadn’t installed bowtie2 in the conda env. Fi… --- ## [LICENSE file for BAQLaVA is placeholder](https://forum.biobakery.org/t/license-file-for-baqlava-is-placeholder/8848)
**Author:** [@Matt-BF](https://forum.biobakery.org/u/Matt-BF)\ **Replies:** 0\ **Last updated:** [March 28, 2026, 5:16pm UTC](https://forum.biobakery.org/t/license-file-for-baqlava-is-placeholder/8848 "2026-03-28T17:16:27Z")
I’m adding the BAQLaVA package to bioconda, but the PR reviewer noted that the LICENSE file is a placeholder license for now. Is there any plans to update it? Thanks in advance --- ## [ FIX: metaphlan4 bowtie2-build --threads flag bug #229 ](https://forum.biobakery.org/t/fix-metaphlan4-bowtie2-build-threads-flag-bug-229/7395)
**Author:** [@heloint](https://forum.biobakery.org/u/heloint)\ **Replies:** 0\ **Last updated:** [August 22, 2024, 5:37pm UTC](https://forum.biobakery.org/t/fix-metaphlan4-bowtie2-build-threads-flag-bug-229/7395 "2024-08-22T17:37:43Z")
metaphlan4 bowtie2-build “–threads” flag bug Software details metaphlan4 version: MetaPhlAn version 4.1.1 (11 Mar 2024) bowtie2-build version: bowtie2-build version 2.2.3 64-bit, compiled with gcc version 4.1.2 20080704… --- ## [Fixing broken links in readme.md from HUMAnN GitHub repository](https://forum.biobakery.org/t/fixing-broken-links-in-readme-md-from-humann-github-repository/8667)
**Author:** [@fmerinocasallo](https://forum.biobakery.org/u/fmerinocasallo)\ **Replies:** 2\ **Last updated:** [January 20, 2026, 11:19pm UTC](https://forum.biobakery.org/t/fixing-broken-links-in-readme-md-from-humann-github-repository/8667 "2026-01-20T23:19:47Z")
Hello, fellow bioBakers! :waving\_hand: I took the opportunity to submit a harmless PR that fixes some broken links from the readme.md in the HUMAnN GitHub repository. Also, in that readme.md, there is a broken referenc… --- ## [Chocophlan version](https://forum.biobakery.org/t/chocophlan-version/8042)
**Author:** [@brockels](https://forum.biobakery.org/u/brockels)\ **Replies:** 0\ **Last updated:** [May 8, 2025, 12:35am UTC](https://forum.biobakery.org/t/chocophlan-version/8042 "2025-05-08T00:35:39Z")
full\_chocophlan.v201901\_v31.tar.gz but there is a newer version? Is it possible to have access to the newer one? Likewise the uniref90 version is from 2019 but I believe there is a newer one however this is not availab… --- ## [Multithreading blasting of unaligned reads](https://forum.biobakery.org/t/multithreading-blasting-of-unaligned-reads/7349)
**Author:** [@rroutsong](https://forum.biobakery.org/u/rroutsong)\ **Replies:** 1\ **Last updated:** [August 13, 2024, 2:36pm UTC](https://forum.biobakery.org/t/multithreading-blasting-of-unaligned-reads/7349 "2024-08-13T14:36:08Z")
humann v3.9 Running data with humann3 with many unaligned reads increases the time of execution significantly. Recently I have used cProfiler to show that this time is primarily spent in the unaligned blastx portion of … --- ## [Feature request: phylophlan\_write\_config\_file, force generation of config, despite the lack of a program at PATH](https://forum.biobakery.org/t/feature-request-phylophlan-write-config-file-force-generation-of-config-despite-the-lack-of-a-program-at-path/8230)
**Author:** [@Alexiy\_Boyko](https://forum.biobakery.org/u/Alexiy_Boyko)\ **Replies:** 0\ **Last updated:** [July 4, 2025, 9:59am UTC](https://forum.biobakery.org/t/feature-request-phylophlan-write-config-file-force-generation-of-config-despite-the-lack-of-a-program-at-path/8230 "2025-07-04T09:59:49Z")
v3.1.1 If I have non-standard binary name or hasn’t binary at PATH, I also want to can create the config file. I am using phylophlan for the first time and yesterday the behavior of this script caused me a lot of pain. … --- ## [A question about the Intermediate results and abundance in MetaPhlAn](https://forum.biobakery.org/t/a-question-about-the-intermediate-results-and-abundance-in-metaphlan/7882)
**Author:** [@guo\_zhenhao](https://forum.biobakery.org/u/guo_zhenhao)\ **Replies:** 0\ **Last updated:** [March 3, 2025, 3:46pm UTC](https://forum.biobakery.org/t/a-question-about-the-intermediate-results-and-abundance-in-metaphlan/7882 "2025-03-03T15:46:13Z")
Tool name: MetaPhlAn v4.0.6 I want to establish the relationship between reads and abundance, so I used the hyperparameter --bowtie2out metagenome.bowtie2.bz2 to save the Bowtie2 results. Each line is an ID and UniRef90… --- ## [KneadData setup.py update to URL reference for TRF.exe](https://forum.biobakery.org/t/kneaddata-setup-py-update-to-url-reference-for-trf-exe/7576)
**Author:** [@Kborg000](https://forum.biobakery.org/u/Kborg000)\ **Replies:** 0\ **Last updated:** [November 11, 2024, 9:09pm UTC](https://forum.biobakery.org/t/kneaddata-setup-py-update-to-url-reference-for-trf-exe/7576 "2024-11-11T21:09:52Z")
In the GitHub repository for KneadData, the setup.py script references two URLs for retrieving the TRF executable download on lines #246 & 248 (shown below). trf\_exe = “trf” if mac\_os: url = "http://tandem.bu.edu/t… --- ## [Bioconductor build fail](https://forum.biobakery.org/t/bioconductor-build-fail/8711)
**Author:** [@TuomasBorman](https://forum.biobakery.org/u/TuomasBorman)\ **Replies:** 0\ **Last updated:** [January 15, 2026, 9:31am UTC](https://forum.biobakery.org/t/bioconductor-build-fail/8711 "2026-01-15T09:31:53Z")
Hi, it seems that Bioconductor builds are failing. The problem seems to be fixed by the following commit, but the updated version is not pushed to Bioconductor? -Tuomas --- ## [Feature request: allow to put fraction with some parameters](https://forum.biobakery.org/t/feature-request-allow-to-put-fraction-with-some-parameters/8231)
**Author:** [@Alexiy\_Boyko](https://forum.biobakery.org/u/Alexiy_Boyko)\ **Replies:** 0\ **Last updated:** [July 4, 2025, 10:09am UTC](https://forum.biobakery.org/t/feature-request-allow-to-put-fraction-with-some-parameters/8231 "2025-07-04T10:09:19Z")
v3.3.1 Is I don’t know about my species, it genus, number of markers within their genomes, quality of their genomes, or number of markers at database, but I don’t want include in analysis genomes with high number of mis… --- ## [Toy dataset name/link](https://forum.biobakery.org/t/toy-dataset-name-link/8886)
**Author:** [@artur.sannikov](https://forum.biobakery.org/u/artur.sannikov)\ **Replies:** 0\ **Last updated:** [April 27, 2026, 7:02am UTC](https://forum.biobakery.org/t/toy-dataset-name-link/8886 "2026-04-27T07:02:49Z")
Hello, is it possible to provide the direct link to the toy dataset that’s mentioned on the Wiki page? This tutorial has been updated to work with version 4.1.1 and the Oct22 toy database (Made by Franzosa May 28 2025…