Hi,
I’m encountering an issue while running HUMAnN v3.9 alongside MetaPhlAn v4.0.6 (installed and confirmed via metaphlan --version) and recent database mpa_vJun23_CHOCOPhlAnSGB_202403.
During the prescreen step, HUMAnN throws an error when the -t flag (e.g., -t rel_ab) is used via the --metaphlan-options parameter. Here’s the relevant part of the command:
‘’’
–index mpa_vJun23_CHOCOPhlAnSGB_202403 -t re
l_ab_w_read_stats --bowtie2db=/well/kir-scratch/kir-ocms/metaphlan
And here is the error message:
ERROR ::
05/19/2025 12:30:42 PM - humann.store - DEBUG: Initialize Alignments class instance to minimize memory use
05/19/2025 12:30:42 PM - humann.store - DEBUG: Initialize Reads class instance to minimize memory use
05/19/2025 12:31:03 PM - humann.humann - INFO: Load pathways database part 1: /gpfs3/well/kir-ocms/shared/apps/apps/humann-3.9/lib/python3.10/site-packages/humann/data/pathways/metacyc_reactions_l
evel4ec_only.uniref.bz2
05/19/2025 12:31:03 PM - humann.humann - INFO: Load pathways database part 2: /gpfs3/well/kir-ocms/shared/apps/apps/humann-3.9/lib/python3.10/site-packages/humann/data/pathways/metacyc_pathways_st
ructured_filtered_v24_subreactions
05/19/2025 12:31:03 PM - humann.search.prescreen - INFO: Running metaphlan …
05/19/2025 12:31:03 PM - humann.utilities - DEBUG: Using software: /gpfs3/well/kir-ocms/users/pqm791/devel/venv/Python-3.10.8-GCCcore-12.2.0/skylake/bin/metaphlan
05/19/2025 12:31:03 PM - humann.utilities - DEBUG: Remove file: /gpfs3/well/kir-scratch/kir-ocms/Humann3.9_test/testing_new_version/humann3.dir/Pred_IBD13295963.50176_2_6_masked/Pred_IBD13295963.5
0176_2_6_masked_humann_temp/Pred_IBD13295963.50176_2_6_masked_metaphlan_bowtie2.txt
05/19/2025 12:31:03 PM - humann.utilities - INFO: Execute command: /gpfs3/well/kir-ocms/users/pqm791/devel/venv/Python-3.10.8-GCCcore-12.2.0/skylake/bin/metaphlan /gpfs3/well/kir-scratch/kir-ocms/
Humann3.9_test/testing_new_version/humann3.dir/Pred_IBD13295963.50176_2_6_masked/Pred_IBD13295963.50176_2_6_masked_humann_temp/tmp5p9_tigv/tmp11vk_9si --index mpa_vJun23_CHOCOPhlAnSGB_202403 -t re
l_ab_w_read_stats --bowtie2db=/well/kir-scratch/kir-ocms/metaphlan -o /gpfs3/well/kir-scratch/kir-ocms/Humann3.9_test/testing_new_version/humann3.dir/Pred_IBD13295963.50176_2_6_masked/Pred_IBD1329
5963.50176_2_6_masked_humann_temp/Pred_IBD13295963.50176_2_6_masked_metaphlan_bugs_list.tsv --input_type fastq --bowtie2out /gpfs3/well/kir-scratch/kir-ocms/Humann3.9_test/testing_new_version/huma
nn3.dir/Pred_IBD13295963.50176_2_6_masked/Pred_IBD13295963.50176_2_6_masked_humann_temp/Pred_IBD13295963.50176_2_6_masked_metaphlan_bowtie2.txt --nproc 8
05/19/2025 12:44:10 PM - humann.utilities - DEBUG: b’’
05/19/2025 12:44:10 PM - humann.humann - INFO: TIMESTAMP: Completed prescreen : 786 seconds
05/19/2025 12:44:10 PM - humann.search.prescreen - 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.
‘’’
Running the same MetaPhlAn command manually outside HUMAnN works as expected. This suggests that HUMAnN may not be handling or validating the MetaPhlAn version correctly when constructing the prescreen command, or is imposing version checks that are no longer appropriate for MetaPhlAn v4.0.6+.
Is this a known issue, or is there a workaround you would recommend?
Happy to provide logs, environment details, or test patches if helpful.
Thanks for your support!