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…	7	372	November 12, 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	2169	June 20, 2025
HUMAnN 3.0 stratified KOs return paradoxical interpretations	0	4	November 12, 2025
How should I compare HUMAnN 4 “Counts” from concatenated paired-end reads to known species read abundances?	3	38	November 6, 2025
Humann=4.0.0a1 : MinPath12hmp.py:804: SyntaxWarning	0	18	November 6, 2025
Unable to download the databases in Humann4	1	52	November 4, 2025
Optimal thread count for KneadData, Bowtie2, MetaPhlAn, and HUMAnN on multi-core systems	1	39	November 4, 2025
Very low mapping rate of Hummann v4alpha	1	45	November 4, 2025
Downloading humann from HPC cluster	1	25	November 4, 2025
Big differences in results depending on type of mapping used?	5	133	November 4, 2025
Humann3 does not recognize "relative abundance" in metaphlan profile file	8	999	November 4, 2025
Discrepancies in prescreen.py script	1	13	November 4, 2025
MetaPhlAn 4.2.2 work with humann v3.0.1	8	259	October 22, 2025
Using Kraken2 with Humann3	5	564	October 8, 2025
Matching tools and database versions	4	75	September 25, 2025
Problems running Humann	2	50	September 25, 2025
READS_UNMAPPED Is Not Presented in CPM Format	1	45	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	75	September 25, 2025
Humann 3.9 conda install will not work. Please update your version of MetaPhlAn?	1	78	September 25, 2025
MetaPhlAn / CHOCOPhlAn version mismatch while doing humann 3 analysis	1	55	September 23, 2025
Can't load databases	5	49	September 23, 2025
Errors with humann-metaphlan	2	101	September 23, 2025
Ultima sequencing with BioBakery tools	1	21	September 19, 2025
HUMAnN 4.2 for long read data	7	127	September 6, 2025
Missing relative abundance and coverage error for humann4a	2	90	August 29, 2025
Humann v3.8 misinterprets non-default analysis types, ie "-t rel_ab_w_read_stats", results from metaphlan 4.1	4	71	August 28, 2025
Metaphlan-informed taxonomic stratification and its discrepancies with unirefids	2	41	August 27, 2025
Are humann_regroup_table (utility_mapping) command and flag –utility-database in HUMANnN v4.0.0.alpha.1 doing the same thing?	2	58	August 28, 2025
Statistical Approach for Comparing Functional Potential of Selected SGBs vs. Community Background	3	50	August 28, 2025
Humann3 Paired end reads	20	6145	August 27, 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…

7

372

November 12, 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…