HUMAnN

Topic	Replies	Views	Activity
MetaPhlAn 4 + HUMAnN 4 compatibility HUMAnN users - I’m making a quick pinned post about MetaPhlAn 4 + HUMAnN 4 compatibility since we’re seeing a lot of posts raising similar issues. We will follow up with more detailed information in the short term, and l…	10	582	November 30, 2025
Announcing HUMAnN 4.0 (alpha) Dear HUMAnN users: HUMAnN 4.0 (alpha) has arrived! Many thanks for your patience—we know there have been a lot of users looking forward to this release for a long time. Since a lot is changing in this version, we’re tryi…	3	2277	June 20, 2025
Humann4 not recognizing relab column in metaphlan4 table	0	7	December 2, 2025
Zero community-level pathways detected despite gene families present	0	19	November 18, 2025
Humann biocontainer: Unable to write to the HUMAnN config file	3	760	November 14, 2025
Absent tryptophan pathway in all metagenomic results	0	13	November 13, 2025
HUMAnN 3.0 stratified KOs return paradoxical interpretations	0	28	November 12, 2025
How should I compare HUMAnN 4 “Counts” from concatenated paired-end reads to known species read abundances?	3	58	November 6, 2025
Humann=4.0.0a1 : MinPath12hmp.py:804: SyntaxWarning	0	36	November 6, 2025
Unable to download the databases in Humann4	1	69	November 4, 2025
Optimal thread count for KneadData, Bowtie2, MetaPhlAn, and HUMAnN on multi-core systems	1	50	November 4, 2025
Very low mapping rate of Hummann v4alpha	1	56	November 4, 2025
Downloading humann from HPC cluster	1	31	November 4, 2025
Big differences in results depending on type of mapping used?	5	146	November 4, 2025
Humann3 does not recognize "relative abundance" in metaphlan profile file	8	1012	November 4, 2025
Discrepancies in prescreen.py script	1	16	November 4, 2025
MetaPhlAn 4.2.2 work with humann v3.0.1	8	292	October 22, 2025
Using Kraken2 with Humann3	5	591	October 8, 2025
Matching tools and database versions	4	87	September 25, 2025
Problems running Humann	2	66	September 25, 2025
READS_UNMAPPED Is Not Presented in CPM Format	1	56	September 25, 2025
ERROR: The MetaPhlAn taxonomic profile provided was not generated with the expected database version. Please update your version of MetaPhlAn to at least v3.0	1	85	September 25, 2025
Humann 3.9 conda install will not work. Please update your version of MetaPhlAn?	1	92	September 25, 2025
MetaPhlAn / CHOCOPhlAn version mismatch while doing humann 3 analysis	1	65	September 23, 2025
Can't load databases	5	58	September 23, 2025
Errors with humann-metaphlan	2	113	September 23, 2025
Ultima sequencing with BioBakery tools	1	22	September 19, 2025
HUMAnN 4.2 for long read data	7	146	September 6, 2025
Missing relative abundance and coverage error for humann4a	2	101	August 29, 2025
Humann v3.8 misinterprets non-default analysis types, ie "-t rel_ab_w_read_stats", results from metaphlan 4.1	4	77	August 28, 2025

MetaPhlAn 4 + HUMAnN 4 compatibility

HUMAnN users - I’m making a quick pinned post about MetaPhlAn 4 + HUMAnN 4 compatibility since we’re seeing a lot of posts raising similar issues. We will follow up with more detailed information in the short term, and l…

10

582

November 30, 2025

Announcing HUMAnN 4.0 (alpha)

Dear HUMAnN users: HUMAnN 4.0 (alpha) has arrived! Many thanks for your patience—we know there have been a lot of users looking forward to this release for a long time. Since a lot is changing in this version, we’re tryi…