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…	22	1201	February 4, 2026
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…	4	2756	February 2, 2026
Humann3 --metaphlan-options error	0	2	February 18, 2026
READS_UNMAPPED Is Not Presented in CPM Format	2	96	February 18, 2026
Dereplicating and normalizing reads for humann and metaphlan	6	69	January 30, 2026
Failure Downloading HUMAnN UniRef90 DIAMOND Database via WSL	0	9	January 28, 2026
Unable to download ChocoPhlAn and UniRef databases (connection error)	0	18	January 21, 2026
Glitch in humann4 genefamilies file creation	0	21	January 15, 2026
No SGBs in humann3.9 genefamily.tsv	2	28	January 12, 2026
Pathway abundance stratification	0	28	January 9, 2026
How to handle transferred and split EC numbers in humann outputs	1	14	January 9, 2026
HUMAnN targeted functional analysis?	2	64	January 9, 2026
Humann (v3.9) returning 100% unaligned reads on demo data	1	30	January 9, 2026
HUMAnN4 Support for MetaPhlAn vJan25 Database	1	104	January 9, 2026
HUMAnN 4 database downloads inaccessible due to Globus (data.globus.org) domain blocking	2	50	December 9, 2025
Humann3 Database errors	7	123	December 8, 2025
HUMAnN (v3.6) a new db update issue - CHOCOPhlAnSGB_202103	6	160	December 7, 2025
How to silence database download message from Metaphlan 4.0.6 within Humann 3.8	4	151	December 7, 2025
HUMAnN 4 prescreen issue and input file format clarification	2	50	December 7, 2025
Combine Output from Separate Runs of Single Sample	3	50	December 5, 2025
Trouble running HUMAnN with updated metaphlan database	3	223	December 5, 2025
Humann4 not recognizing relab column in metaphlan4 table	1	51	December 5, 2025
Zero community-level pathways detected despite gene families present	1	50	December 5, 2025
Absent tryptophan pathway in all metagenomic results	1	36	December 5, 2025
Humann=4.0.0a1 : MinPath12hmp.py:804: SyntaxWarning	1	53	December 5, 2025
HUMAnN 3.0 stratified KOs return paradoxical interpretations	1	58	December 4, 2025
Humann biocontainer: Unable to write to the HUMAnN config file	3	775	November 14, 2025
How should I compare HUMAnN 4 “Counts” from concatenated paired-end reads to known species read abundances?	3	99	November 6, 2025
Unable to download the databases in Humann4	1	106	November 4, 2025
Optimal thread count for KneadData, Bowtie2, MetaPhlAn, and HUMAnN on multi-core systems	1	71	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…

22

1201

February 4, 2026

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…