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	852	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	2492	June 20, 2025
No SGBs in humann3.9 genefamily.tsv	2	14	January 12, 2026
Pathway abundance stratification	0	4	January 9, 2026
How to handle transferred and split EC numbers in humann outputs	1	9	January 9, 2026
HUMAnN targeted functional analysis?	2	37	January 9, 2026
Humann (v3.9) returning 100% unaligned reads on demo data	1	12	January 9, 2026
Dereplicating and normalizing reads for humann and metaphlan	2	20	January 9, 2026
HUMAnN4 Support for MetaPhlAn vJan25 Database	1	44	January 9, 2026
HUMAnN 4 database downloads inaccessible due to Globus (data.globus.org) domain blocking	2	32	December 9, 2025
Humann3 Database errors	7	51	December 8, 2025
HUMAnN (v3.6) a new db update issue - CHOCOPhlAnSGB_202103	6	154	December 7, 2025
How to silence database download message from Metaphlan 4.0.6 within Humann 3.8	4	132	December 7, 2025
HUMAnN 4 prescreen issue and input file format clarification	2	31	December 7, 2025
Combine Output from Separate Runs of Single Sample	3	20	December 5, 2025
Trouble running HUMAnN with updated metaphlan database	3	174	December 5, 2025
Humann4 not recognizing relab column in metaphlan4 table	1	39	December 5, 2025
Zero community-level pathways detected despite gene families present	1	42	December 5, 2025
Absent tryptophan pathway in all metagenomic results	1	30	December 5, 2025
Humann=4.0.0a1 : MinPath12hmp.py:804: SyntaxWarning	1	51	December 5, 2025
HUMAnN 3.0 stratified KOs return paradoxical interpretations	1	44	December 4, 2025
Humann biocontainer: Unable to write to the HUMAnN config file	3	772	November 14, 2025
How should I compare HUMAnN 4 “Counts” from concatenated paired-end reads to known species read abundances?	3	86	November 6, 2025
Unable to download the databases in Humann4	1	95	November 4, 2025
Optimal thread count for KneadData, Bowtie2, MetaPhlAn, and HUMAnN on multi-core systems	1	61	November 4, 2025
Very low mapping rate of Hummann v4alpha	1	64	November 4, 2025
Downloading humann from HPC cluster	1	42	November 4, 2025
Big differences in results depending on type of mapping used?	5	157	November 4, 2025
Humann3 does not recognize "relative abundance" in metaphlan profile file	8	1018	November 4, 2025
Discrepancies in prescreen.py script	1	18	November 4, 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

852

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…