# MetaPhlAn **URL:** https://forum.biobakery.org/c/microbial-community-profiling/metaphlan/7.md [Latest](https://forum.biobakery.org/latest.md) · [Categories](https://forum.biobakery.org/categories.md) --- ## [MetaPhlAn 4.2.5 release (minor code updates and database update)](https://forum.biobakery.org/t/metaphlan-4-2-5-release-minor-code-updates-and-database-update/9002)
**Author:** [@Claudia\_Mengoni](https://forum.biobakery.org/u/Claudia_Mengoni)\ **Replies:** 1\ **Last updated:** [July 21, 2026, 10:18pm UTC](https://forum.biobakery.org/t/metaphlan-4-2-5-release-minor-code-updates-and-database-update/9002 "2026-07-21T22:18:12Z")
Announcement We are pleased to share that MetaPhlAn 4.2.5 is now available, which incorporates minor code improvements and includes a new version of the MetaPhlAn database (vJan26\_202605) containing \>13k new SGBs. For d… --- ## [MetaPhlAn 4.2.2 release (initial long-read sequencing support and database update)](https://forum.biobakery.org/t/metaphlan-4-2-2-release-initial-long-read-sequencing-support-and-database-update/8109)
**Author:** [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Replies:** 1\ **Last updated:** [June 11, 2025, 8:16am UTC](https://forum.biobakery.org/t/metaphlan-4-2-2-release-initial-long-read-sequencing-support-and-database-update/8109 "2025-06-11T08:16:57Z")
Announcement We are pleased to share that MetaPhlAn 4.2.2 is now available, which incorporates taxonomic profiling of long-read metagenomes for the first time and includes a new version of the MetaPhlAn database (vJan25\_… --- ## [Announcing MetaPhlAn 4](https://forum.biobakery.org/t/announcing-metaphlan-4/3994)
**Author:** [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Replies:** 6\ **Last updated:** [June 8, 2023, 9:57am UTC](https://forum.biobakery.org/t/announcing-metaphlan-4/3994 "2023-06-08T09:57:29Z")
MetaPhlAn 4 Release Notes The new MetaPhlAn 4 integrates information from both metagenome assemblies and microbial isolate genomes for improved and more comprehensive metagenomic taxonomic profiling (https://doi.org/10.1… --- ## [Announcing MetaPhlAn 3.1](https://forum.biobakery.org/t/announcing-metaphlan-3-1/3882)
**Author:** [@franzosa](https://forum.biobakery.org/u/franzosa)\ **Replies:** 1\ **Last updated:** [August 4, 2022, 2:00am UTC](https://forum.biobakery.org/t/announcing-metaphlan-3-1/3882 "2022-08-04T02:00:05Z")
MetaPhlAn 3.1 / HUMAnN 3.1 Release Notes MetaPhlAn 3.1 and HUMAnN 3.1 represent a moderate update to the bioBakery 3 software and databases. This update is based on improvements in our ability to align NCBI-sourced micro… --- ## [Request for updated SGB-to-GTDB mapping file for MetaPhlAn 4.2.2 Jan 2026 database](https://forum.biobakery.org/t/request-for-updated-sgb-to-gtdb-mapping-file-for-metaphlan-4-2-2-jan-2026-database/9008)
**Author:** [@young\_doktor](https://forum.biobakery.org/u/young_doktor)\ **Replies:** 3\ **Last updated:** [September 25, 2026, 7:26am UTC](https://forum.biobakery.org/t/request-for-updated-sgb-to-gtdb-mapping-file-for-metaphlan-4-2-2-jan-2026-database/9008 "2026-09-25T07:26:15Z")
Dear MetaPhlAn team, I am using MetaPhlAn 4.2.2 and the database: mpa\_vJan26\_CHOCOPhlAnSGB\_202605 to profile metagenomic samples. I would like to convert my MetaPhlAn profiles from SGB identifiers to GTDB taxonomy usi… --- ## [SGB2GTDB v232 utils script](https://forum.biobakery.org/t/sgb2gtdb-v232-utils-script/9043)
**Author:** [@chuiyang-mok](https://forum.biobakery.org/u/chuiyang-mok)\ **Replies:** 0\ **Last updated:** [August 25, 2026, 9:33am UTC](https://forum.biobakery.org/t/sgb2gtdb-v232-utils-script/9043 "2026-08-25T09:33:06Z")
Hi there, I’m writing to try to understand the sourcecode of SGB2GTDB. The latest GTDB database has been updated to version 232, and multiple MAGs-focused metagenomics tools were also updating theirs to v232. I was think… --- ## [Absolute cell counts using spike-in in MetaPhlAn](https://forum.biobakery.org/t/absolute-cell-counts-using-spike-in-in-metaphlan/9033)
**Author:** [@Stefano\_Cardinale](https://forum.biobakery.org/u/Stefano_Cardinale)\ **Replies:** 0\ **Last updated:** [August 12, 2026, 3:06pm UTC](https://forum.biobakery.org/t/absolute-cell-counts-using-spike-in-in-metaphlan/9033 "2026-08-12T15:06:30Z")
Hello! I would like to ask a question about the use of spiked- in species with MetaPhlAn. We used samples with spiked species in our analysis, is there support in MetaPhlAn to use spiked species to get absolute cell coun… --- ## [MetaPhlAn and GPU - BWA-mem](https://forum.biobakery.org/t/metaphlan-and-gpu-bwa-mem/9032)
**Author:** [@Stefano\_Cardinale](https://forum.biobakery.org/u/Stefano_Cardinale)\ **Replies:** 0\ **Last updated:** [August 12, 2026, 2:57pm UTC](https://forum.biobakery.org/t/metaphlan-and-gpu-bwa-mem/9032 "2026-08-12T14:57:27Z")
Hello, I was wondering whether it is possible to use a different aligner’s SAM output with MetaPhlAn now. For example, in my group we would like to use some versions of aligners (like BWA) that can run on GPU, has anyone… --- ## [Negative Values in GTDB Converted MetaPhlAn4 Result File](https://forum.biobakery.org/t/negative-values-in-gtdb-converted-metaphlan4-result-file/9017)
**Author:** [@aegreen32](https://forum.biobakery.org/u/aegreen32)\ **Replies:** 5\ **Last updated:** [August 10, 2026, 2:43pm UTC](https://forum.biobakery.org/t/negative-values-in-gtdb-converted-metaphlan4-result-file/9017 "2026-08-10T14:43:18Z")
Hello! I recently used the newest version of the sgb\_to\_gtdb\_profile.py script with the GTDB r226 updated mapping file, and as I was starting to analyze the results I realized that the conversion script added negative v… --- ## [Update for sgb to GTDB Translation File - r220](https://forum.biobakery.org/t/update-for-sgb-to-gtdb-translation-file-r220/7388)
**Author:** [@sammie](https://forum.biobakery.org/u/sammie)\ **Replies:** 9\ **Last updated:** [July 20, 2026, 1:33pm UTC](https://forum.biobakery.org/t/update-for-sgb-to-gtdb-translation-file-r220/7388 "2026-07-20T13:33:37Z")
Hi bioBakery team, The current sgb to GTDB translation file is based on GTDB r207. Earlier this year, a new version, r220, was released with significant changes—for example, the reclassification of Firmicutes to Bacillo… --- ## [Too many SGB or other unclassified species when processing mouse metagenomic samples](https://forum.biobakery.org/t/too-many-sgb-or-other-unclassified-species-when-processing-mouse-metagenomic-samples/5961)
**Author:** [@yuzhu\_chen](https://forum.biobakery.org/u/yuzhu_chen)\ **Replies:** 4\ **Last updated:** [July 15, 2026, 9:07pm UTC](https://forum.biobakery.org/t/too-many-sgb-or-other-unclassified-species-when-processing-mouse-metagenomic-samples/5961 "2026-07-15T21:07:01Z")
Hello, I have recently been using the Metaphlan4 to analyze mice fecal metagenomic samples. However, I have encountered some issues and would like to seek your advice. Taking a sample as an example, after parsing out th… --- ## [Interpretation of additional column in MetaPhlan4](https://forum.biobakery.org/t/interpretation-of-additional-column-in-metaphlan4/8991)
**Author:** [@MonicaSteffi](https://forum.biobakery.org/u/MonicaSteffi)\ **Replies:** 0\ **Last updated:** [July 8, 2026, 3:26pm UTC](https://forum.biobakery.org/t/interpretation-of-additional-column-in-metaphlan4/8991 "2026-07-08T15:26:07Z")
Hi all, I’m doing species-level functional analysis downstream of MetaPhlAn 4 (mpa\_vJan25), where organisms are mapped to functional roles (e.g. mucin degraders) by matching on species name. I’d like to check my underst… --- ## [Downloading MetaPhlAn 4 database](https://forum.biobakery.org/t/downloading-metaphlan-4-database/4732)
**Author:** [@diecasfranco](https://forum.biobakery.org/u/diecasfranco)\ **Replies:** 6\ **Last updated:** [June 11, 2026, 7:27am UTC](https://forum.biobakery.org/t/downloading-metaphlan-4-database/4732 "2026-06-11T07:27:38Z")
MetaPhlAn version 4.0.4 (17 Jan 2023) metaphlan --install After 20%, download process stopped. I tried using screen command, and after two days nothing. Also, I’ve tried using wget directly from the repository without… --- ## [Error in downloading metaphlan database](https://forum.biobakery.org/t/error-in-downloading-metaphlan-database/8966)
**Author:** [@Shourish\_Das](https://forum.biobakery.org/u/Shourish_Das)\ **Replies:** 0\ **Last updated:** [June 11, 2026, 5:03am UTC](https://forum.biobakery.org/t/error-in-downloading-metaphlan-database/8966 "2026-06-11T05:03:46Z")
metaphlan --install Thu Jun 11 10:07:40 2026: Downloading http://cmprod1.cibio.unitn.it/biobakery4/metaphlan\_databases/mpa\_latest Thu Jun 11 10:07:40 2026: Downloading file of size: 0.0000 MB Thu Jun 11 10:07:40 2026:… --- ## [Metaphlan 4.2.4: TypeError: stat: path should be string, bytes, os.PathLike or integer, not NoneType](https://forum.biobakery.org/t/metaphlan-4-2-4-typeerror-stat-path-should-be-string-bytes-os-pathlike-or-integer-not-nonetype/8934)
**Author:** [@db61](https://forum.biobakery.org/u/db61)\ **Replies:** 2\ **Last updated:** [May 27, 2026, 5:16pm UTC](https://forum.biobakery.org/t/metaphlan-4-2-4-typeerror-stat-path-should-be-string-bytes-os-pathlike-or-integer-not-nonetype/8934 "2026-05-27T17:16:25Z")
I am getting a TypeError when trying to run metaphlan and I suspect that its a bug. Version: metaphlan 4.2.4 installed through conda. Python 3.11.15 Command: metaphlan mysample.fastq --input\_type fastq --db\_dir meta… --- ## [Getting split reads from MetaPhlAn 4.2.4?](https://forum.biobakery.org/t/getting-split-reads-from-metaphlan-4-2-4/8929)
**Author:** [@idak](https://forum.biobakery.org/u/idak)\ **Replies:** 0\ **Last updated:** [May 26, 2026, 9:27am UTC](https://forum.biobakery.org/t/getting-split-reads-from-metaphlan-4-2-4/8929 "2026-05-26T09:27:25Z")
Hi, I understand from the discussions on the forum that there is not yet support for long reads in HUMAnN. However, I have run MetaPhlAn 4.2.4 with the option split\_reads on nanopore data and I was wondering if it woul… --- ## [Downloading metaphlan4 SGB genomes](https://forum.biobakery.org/t/downloading-metaphlan4-sgb-genomes/7513)
**Author:** [@anashank97](https://forum.biobakery.org/u/anashank97)\ **Replies:** 9\ **Last updated:** [May 25, 2026, 6:02pm UTC](https://forum.biobakery.org/t/downloading-metaphlan4-sgb-genomes/7513 "2026-05-25T18:02:40Z")
Hi all, Can you please suggest a method to download all the SGB genomes used to construct the metaphlan4 database? If I understand correctly, the links on the Segata Lab website (Segata Lab - Computational Metagenomics) … --- ## [Difference in sequencing depth](https://forum.biobakery.org/t/difference-in-sequencing-depth/8757)
**Author:** [@KSK](https://forum.biobakery.org/u/KSK)\ **Replies:** 3\ **Last updated:** [May 25, 2026, 5:21am UTC](https://forum.biobakery.org/t/difference-in-sequencing-depth/8757 "2026-05-25T05:21:15Z")
I have two batch of shotgun metagenomic sequences. Batch one has 20 samples with avg depth of 10 million sequences and batch 2 has 50 samples with avg depth of 25 million sequences. Will this difference in the sequencing… --- ## [Total Bacteria species relative abundance no longer sums to 1 after converting the SGB profile to GTDB](https://forum.biobakery.org/t/total-bacteria-species-relative-abundance-no-longer-sums-to-1-after-converting-the-sgb-profile-to-gtdb/4913)
**Author:** [@Fangxi\_Xu](https://forum.biobakery.org/u/Fangxi_Xu)\ **Replies:** 18\ **Last updated:** [May 24, 2026, 9:50pm UTC](https://forum.biobakery.org/t/total-bacteria-species-relative-abundance-no-longer-sums-to-1-after-converting-the-sgb-profile-to-gtdb/4913 "2026-05-24T21:50:31Z")
Hi, I used MetaPhlAn version 4.0.4 (17 Jan 2023) to perform taxonomy profiling on our shotgun metagenomic samples and after getting the metaphlan profiles (SGB level), I used the sgb\_to\_gtdb\_profile.py command to conver… --- ## [Strain taxonomic level Identification](https://forum.biobakery.org/t/strain-taxonomic-level-identification/8558)
**Author:** [@Serna\_Blasco](https://forum.biobakery.org/u/Serna_Blasco)\ **Replies:** 4\ **Last updated:** [May 22, 2026, 1:50pm UTC](https://forum.biobakery.org/t/strain-taxonomic-level-identification/8558 "2026-05-22T13:50:39Z")
Hi everyone, I’m relatively new to metagenomic analysis and currently using MetaPhlAn 4 for taxonomic profiling. While reviewing the output, I noticed that some bacteria are annotated up to the strain level (see example… --- ## [SGB Newick file labels](https://forum.biobakery.org/t/sgb-newick-file-labels/8222)
**Author:** [@Che](https://forum.biobakery.org/u/Che)\ **Replies:** 3\ **Last updated:** [May 22, 2026, 1:19pm UTC](https://forum.biobakery.org/t/sgb-newick-file-labels/8222 "2026-05-22T13:19:14Z")
Hi I was going through the Metaphlan databases and wanted to make use of the newick files used for unifrac distances. I am a little unclear on how the newick file is labeled and wanted to confirm here. Are the leaves of … --- ## [MetaPhlAn4 (mpa\_vJun23\_CHOCOPhlAnSGB\_202307): unexpected behavior with fix\_relab\_mpa4.py](https://forum.biobakery.org/t/metaphlan4-mpa-vjun23-chocophlansgb-202307-unexpected-behavior-with-fix-relab-mpa4-py/8835)
**Author:** [@Saharb](https://forum.biobakery.org/u/Saharb)\ **Replies:** 6\ **Last updated:** [May 22, 2026, 1:11pm UTC](https://forum.biobakery.org/t/metaphlan4-mpa-vjun23-chocophlansgb-202307-unexpected-behavior-with-fix-relab-mpa4-py/8835 "2026-05-22T13:11:13Z")
Hi, I used metaphlan 4.1 using mpa\_vJun23\_CHOCOPhlAnSGB\_202307 version of the DB for taxonomy profiling. Then I learnt about the fix\_relab\_mpa4.py script to fix the RA of taxa at each rank. But my results show that the … --- ## [Beta diversity in metaphlan 4.2.4 doesn't work becuase of rbiom upgrade?](https://forum.biobakery.org/t/beta-diversity-in-metaphlan-4-2-4-doesnt-work-becuase-of-rbiom-upgrade/8911)
**Author:** [@Irc47](https://forum.biobakery.org/u/Irc47)\ **Replies:** 1\ **Last updated:** [May 22, 2026, 12:58pm UTC](https://forum.biobakery.org/t/beta-diversity-in-metaphlan-4-2-4-doesnt-work-becuase-of-rbiom-upgrade/8911 "2026-05-22T12:58:15Z")
Hello! I’m using metphlan 4.2.4 to profile long reads and things are going well, but I’m trying to use the provided tool to calculate beta diversity and get the error “beta.div’ is not an exported object from ‘namespace… --- ## [Correupt bowtie2 index file? metaphlan error](https://forum.biobakery.org/t/correupt-bowtie2-index-file-metaphlan-error/8917)
**Author:** [@lfreund](https://forum.biobakery.org/u/lfreund)\ **Replies:** 1\ **Last updated:** [May 22, 2026, 10:40am UTC](https://forum.biobakery.org/t/correupt-bowtie2-index-file-metaphlan-error/8917 "2026-05-22T10:40:53Z")
Hi there, I am trying to run metaphlan both within humann and separately, and am receiving the same error. Here is a screenshot of the error: However, we downloaded the necessary index files from here. Here is a s… --- ## [Nanopore long-reads analysis with Metaphlan4.2.2](https://forum.biobakery.org/t/nanopore-long-reads-analysis-with-metaphlan4-2-2/8916)
**Author:** [@Maria\_Gomez](https://forum.biobakery.org/u/Maria_Gomez)\ **Replies:** 0\ **Last updated:** [May 12, 2026, 3:54pm UTC](https://forum.biobakery.org/t/nanopore-long-reads-analysis-with-metaphlan4-2-2/8916 "2026-05-12T15:54:43Z")
Hi. I use the previous version of metaphlan for analyzing Illumina reads. Now I’m going to analyze Nanopore sequences, and I found this new update of metaphlan. However, I’d like to know about other people’s experienc… --- ## [mpa\_vJan25\_CHOCOPhlAnSGB\_202503.fna not downloaded in the .tar file](https://forum.biobakery.org/t/mpa-vjan25-chocophlansgb-202503-fna-not-downloaded-in-the-tar-file/8854)
**Author:** [@melparker101](https://forum.biobakery.org/u/melparker101)\ **Replies:** 2\ **Last updated:** [May 11, 2026, 3:09am UTC](https://forum.biobakery.org/t/mpa-vjan25-chocophlansgb-202503-fna-not-downloaded-in-the-tar-file/8854 "2026-05-11T03:09:57Z")
Hello, I’ve been recommended your tool and I am looking forward to using it. However, I am having issues downloading the 2025 database. My command was metaphlan --install --index mpa\_vJan25\_CHOCOPhlAnSGB\_202503 --db\_di… --- ## [Matching/linking profiled species using MetaPhlAn3 (v3.0.1) to MetaPhlAn (4.2.4),database: mpa\_vJan25\_CHOCOPhlAnSGB\_202503](https://forum.biobakery.org/t/matching-linking-profiled-species-using-metaphlan3-v3-0-1-to-metaphlan-4-2-4-database-mpa-vjan25-chocophlansgb-202503/8864)
**Author:** [@Lord\_Azkaban](https://forum.biobakery.org/u/Lord_Azkaban)\ **Replies:** 0\ **Last updated:** [April 9, 2026, 10:50pm UTC](https://forum.biobakery.org/t/matching-linking-profiled-species-using-metaphlan3-v3-0-1-to-metaphlan-4-2-4-database-mpa-vjan25-chocophlansgb-202503/8864 "2026-04-09T22:50:47Z")
Hi there, I am working with a couple of microbes that were initially profiled using Metaphlan3 (v3.0.1). I am currently profiling my samples to gauge the abundance ( and later do strainphlan analysis) of those exact s… --- ## [Metaphlan 3.0.7 related problem with deep sequenced wgs file](https://forum.biobakery.org/t/metaphlan-3-0-7-related-problem-with-deep-sequenced-wgs-file/8857)
**Author:** [@Jayeeta](https://forum.biobakery.org/u/Jayeeta)\ **Replies:** 0\ **Last updated:** [April 3, 2026, 8:39pm UTC](https://forum.biobakery.org/t/metaphlan-3-0-7-related-problem-with-deep-sequenced-wgs-file/8857 "2026-04-03T20:39:59Z")
I am using MetaPhlAn 3.0.7 for microbial community profiling. As input, I am providing FASTQ files generated after removing host-derived sequences using KneadData. Each input file is approximately 15–19 GB in size. My sy… --- ## [Inquiry regarding qPCR primer design for uncharacterized SGBs using the CHOCOPhlAn marker database](https://forum.biobakery.org/t/inquiry-regarding-qpcr-primer-design-for-uncharacterized-sgbs-using-the-chocophlan-marker-database/8852)
**Author:** [@Wen1](https://forum.biobakery.org/u/Wen1)\ **Replies:** 0\ **Last updated:** [April 1, 2026, 11:49am UTC](https://forum.biobakery.org/t/inquiry-regarding-qpcr-primer-design-for-uncharacterized-sgbs-using-the-chocophlan-marker-database/8852 "2026-04-01T11:49:20Z")
Dear MetaPhlAn Developers and Community, First, thank you for developing and maintaining MetaPhlAn4; it has been incredibly useful for our research. I have recently been using MetaPhlAn4 for the taxonomic profiling of … --- ## [HUMANN3.9 cannot recognize MetaPhlAn 4.2.2 output file](https://forum.biobakery.org/t/humann3-9-cannot-recognize-metaphlan-4-2-2-output-file/8264)
**Author:** [@YUNPENG](https://forum.biobakery.org/u/YUNPENG)\ **Replies:** 11\ **Last updated:** [April 1, 2026, 8:56am UTC](https://forum.biobakery.org/t/humann3-9-cannot-recognize-metaphlan-4-2-2-output-file/8264 "2026-04-01T08:56:13Z")
Dear team of Humann/Metaphlan: During the process of metagenomic data analysis, I encountered several technical challenges. Upon obtaining the raw sequencing data, I initially performed quality control and host sequence… [Next page](https://forum.biobakery.org/c/microbial-community-profiling/metaphlan/7.md?page=1)