# Humann 3.0 error within biobakery\_workflows wmgx

**URL:** <https://forum.biobakery.org/t/humann-3-0-error-within-biobakery-workflows-wmgx/5036>\
**Category:** bioBakery workflows\
**Created:** [March 28, 2023, 11:56am UTC](https://forum.biobakery.org/t/humann-3-0-error-within-biobakery-workflows-wmgx/5036 "2023-03-28T11:56:07Z")\
**Posts on this page:** 6\
**Page:** 1

<div class="post-metadata">

**Author:** ![bdpessem](https://avatars.discourse-cdn.com/v4/letter/b/7c8e57/32.png) [@bdpessem](https://forum.biobakery.org/u/bdpessem)\
**Post date:** [March 28, 2023, 11:56am UTC](https://forum.biobakery.org/t/humann-3-0-error-within-biobakery-workflows-wmgx/5036/1 "2023-03-28T11:56:07Z")

</div>

Dear, I was trying to run metaphlan3.0 and humann3.0 within the biobakery workflows wmgx pipeline.  
Using the following line of code:

biobakery\_workflows wmgx --input /Projects1/ **/humann\_input\_subset --output /Projects1/** /humann\_output\_subset6 --input-extension fastq --bypass-quality-control --taxonomic-profiling-options “–bowtie2db /media/ **/biobakery\_3/metaphlan3/ --stat\_q 0.1" --functional-profiling-options "–nucleotide-subject-coverage-threshold 0 --translated-subject-coverage-threshold 0 --pathways-database /media/** /biobakery\_workflows/wmgx/humann/pathways/metacyc\_reactions\_level4ec\_only.uniref.bz2,/media/\*\*\*\*/biobakery\_workflows/wmgx/humann/pathways/metacyc\_pathways\_structured\_filtered\_v24” --remove-intermediate-output --bypass-strain-profiling --threads 20

Metaplan3.0 ran successfully.  
However, I ran into an error when Humann3.0 started which stated the following: “The MetaPhlAn2 taxonomic profile provided was not generated with the database version v30 . Please update your version of MetaPhlAn2 to v3.0.” However, when looking at the log file, the used versions of both metaphlan and humann were both 3.0. I provided the full error and the log file of one of the files underneath.  
The pipeline did ran successfully in the past, but now I am running into some errors. Do you maybe have an idea what the problem could be?  
Many thanks in advance!  
Best regards,  
Britta  
Error :  
(biobakery3) **:/Projects1/** //Biobakery/wmgx\_ **/$ biobakery\_workflows wmgx --input /Projects1/** //Biobakery/wmgx\_ **/humann\_input\_subset --output /Projects1/** /humann\_output\_subset6 --input-extension fastq --bypass-quality-control --taxonomic-profiling-options "–bowtie2db /media/ **/biobakery\_3/metaphlan3/ --stat\_q 0.1" --functional-profiling-options "–nucleotide-subject-coverage-threshold 0 --translated-subject-coverage-threshold 0 --pathways-database /media/** /biobakery\_workflows/wmgx/humann/pathways/metacyc\_reactions\_level4ec\_only.uniref.bz2,/media/**/biobakery\_workflows/wmgx/humann/pathways/metacyc\_pathways\_structured\_filtered\_v24" --remove-intermediate-output --bypass-strain-profiling --threads 20  
(Mar 28 11:49:15) [0/25 - 0.00%] \*\*Ready \*\* Task 3: metaphlan\_\_\_\_Sample1  
(Mar 28 11:49:15) [0/25 - 0.00%] \*\*Started \*\* Task 3: metaphlan\_\_\_\_Sample1  
(Mar 28 11:51:49) [1/25 - 4.00%] Completed Task 3: metaphlan\_\_\_\_Sample1  
(Mar 28 11:51:49) [1/25 - 4.00%] \*\*Ready \*\* Task 9: humann\_\_\_\_Sample1  
(Mar 28 11:51:49) [1/25 - 4.00%] \*\*Started \*\* Task 9: humann\_\_\_\_Sample1  
(Mar 28 11:52:18) [2/25 - 8.00%] \*\*Failed \*\* Task 9: humann\_\_\_\_Sample1  
(Mar 28 11:52:18) [3/25 - 12.00%] \*\*Failed \*\* Task 12: humann\_regroup\_UniRef2EC\_\_\_\_Sample1  
(Mar 28 11:52:18) [4/25 - 16.00%] \*\*Failed \*\* Task 19: humann\_renorm\_ecs\_relab\_\_\_\_Sample1  
(Mar 28 11:52:18) [5/25 - 20.00%] \*\*Failed \*\* Task 17: humann\_renorm\_genes\_relab\_\_\_\_Sample1  
(Mar 28 11:52:18) [6/25 - 24.00%] \*\*Failed \*\* Task 21: humann\_renorm\_pathways\_relab\_\_\_\_Sample1  
(Mar 28 11:52:18) [6/25 - 24.00%] \*\*Ready \*\* Task 0: metaphlan\_\_\_\_Sample2  
(Mar 28 11:52:18) [6/25 - 24.00%] \*\*Started \*\* Task 0: metaphlan\_\_\_\_Sample2  
(Mar 28 11:54:27) [7/25 - 28.00%] Completed Task 0: metaphlan\_\_\_\_Sample2  
(Mar 28 11:54:27) [7/25 - 28.00%] \*\*Ready \*\* Task 5: metaphlan\_join\_taxonomic\_profiles  
(Mar 28 11:54:27) [7/25 - 28.00%] \*\*Started \*\* Task 5: metaphlan\_join\_taxonomic\_profiles  
(Mar 28 11:54:27) [8/25 - 32.00%] Completed Task 5: metaphlan\_join\_taxonomic\_profiles  
(Mar 28 11:54:27) [8/25 - 32.00%] \*\*Ready \*\* Task 6: metaphlan\_count\_species  
(Mar 28 11:54:27) [8/25 - 32.00%] \*\*Started \*\* Task 6: metaphlan\_count\_species  
(Mar 28 11:54:27) [9/25 - 36.00%] Completed Task 6: metaphlan\_count\_species  
(Mar 28 11:54:27) [9/25 - 36.00%] \*\*Ready \*\* Task 7: humann\_\_\_\_Sample2  
(Mar 28 11:54:27) [9/25 - 36.00%] \*\*Started \*\* Task 7: humann\_\_\_\_Sample2  
(Mar 28 11:54:56) [10/25 - 40.00%] \*\*Failed \*\* Task 7: humann\_\_\_\_Sample2  
(Mar 28 11:54:56) [11/25 - 44.00%] \*\*Failed \*\* Task 10: humann\_count\_alignments\_species  
(Mar 28 11:54:56) [12/25 - 48.00%] \*\*Failed \*\* Task 11: humann\_regroup\_UniRef2EC\_\_\_\_Sample2  
(Mar 28 11:54:56) [13/25 - 52.00%] \*\*Failed \*\* Task 14: humann\_join\_tables\_ecs  
(Mar 28 11:54:56) [14/25 - 56.00%] \*\*Failed \*\* Task 18: humann\_renorm\_ecs\_relab\_\_\_\_Sample2  
(Mar 28 11:54:56) [15/25 - 60.00%] \*\*Failed \*\* Task 23: humann\_join\_tables\_ecs\_relab  
(Mar 28 11:54:56) [16/25 - 64.00%] \*\*Failed \*\* Task 26: humann\_count\_features\_ecs  
(Mar 28 11:54:56) [17/25 - 68.00%] \*\*Failed \*\* Task 13: humann\_join\_tables\_genefamilies  
(Mar 28 11:54:56) [18/25 - 72.00%] \*\*Failed \*\* Task 15: humann\_join\_tables\_pathabundance  
(Mar 28 11:54:56) [19/25 - 76.00%] \*\*Failed \*\* Task 16: humann\_renorm\_genes\_relab\_\_\_\_Sample2  
(Mar 28 11:54:56) [20/25 - 80.00%] \*\*Failed \*\* Task 22: humann\_join\_tables\_genes\_relab  
(Mar 28 11:54:56) [21/25 - 84.00%] \*\*Failed \*\* Task 25: humann\_count\_features\_genes  
(Mar 28 11:54:56) [22/25 - 88.00%] \*\*Failed \*\* Task 20: humann\_renorm\_pathways\_relab\_\_\_\_Sample2  
(Mar 28 11:54:56) [23/25 - 92.00%] \*\*Failed \*\* Task 24: humann\_join\_tables\_pathways\_relab  
(Mar 28 11:54:56) [24/25 - 96.00%] \*\*Failed \*\* Task 27: humann\_count\_features\_pathways  
(Mar 28 11:54:56) [25/25 - 100.00%] \*\*Failed \*\* Task 28: humann\_merge\_feature\_counts  
Run Finished  
Task 9 failed  
Name: humann\_\_\_\_Sample1  
Original error:  
Error executing action 0. Original Exception:  
Traceback (most recent call last):  
File “/usr/local/bin/miniconda3/envs/biobakery3/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally  
action\_func(task)  
File “/usr/local/bin/miniconda3/envs/biobakery3/lib/python3.7/site-packages/anadama2/helpers.py”, line 89, in actually\_sh  
ret = \_sh(s, \*\*kwargs)  
File “/usr/local/bin/miniconda3/envs/biobakery3/lib/python3.7/site-packages/anadama2/util/init.py”, line 320, in sh  
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))  
anadama2.util.ShellException: [Errno 1] Command `humann --input /Projects1/ **/humann\_input\_subset/Sample1.fastq --output /Projects1/** /humann\_output\_subset6/humann/main --o-log /Projects1/ **/humann\_output\_subset6/humann/main/Sample1.log --threads 20 --taxonomic-profile /Projects1/** /humann\_output\_subset6/metaphlan/main/Sample1\_taxonomic\_profile.tsv --remove-temp-output --nucleotide-subject-coverage-threshold 0 --translated-subject-coverage-threshold 0 --pathways-database /media/ **/biobakery\_workflows/wmgx/humann/pathways/metacyc\_reactions\_level4ec\_only.uniref.bz2,/media/** /biobakery\_workflows/wmgx/humann/pathways/metacyc\_pathways\_structured\_filtered\_v24 ’ failed.  
Out: b’Output files will be written to: /Projects1/**/Biobakery/wmgx\_\*\*\*\*/humann\_output\_subset6/humann/main\nFound g\_\_Cutibacterium.s\_\_Cutibacterium\_acnes : 78.67% of mapped reads\nFound g\_\_Corynebacterium.s\_\_Corynebacterium\_otitidis : 12.31% of mapped reads\nFound g\_\_Malassezia.s\_\_Malassezia\_globosa : 2.04% of mapped reads\nFound g\_\_Cutibacterium.s\_\_Propionibacterium\_namnetense : 1.86% of mapped reads\nFound g\_\_Staphylococcus.s\_\_Staphylococcus\_epidermidis : 0.77% of mapped reads\nFound g\_\_Streptococcus.s\_\_Streptococcus\_mitis : 0.59% of mapped reads\nFound g\_\_Morococcus.s\_\_Morococcus\_cerebrosus : 0.38% of mapped reads\nFound g\_\_Cutibacterium.s\_\_Cutibacterium\_granulosum : 0.30% of mapped reads\nFound g\_\_Streptococcus.s\_\_Streptococcus\_gordonii : 0.27% of mapped reads\nFound g\_\_Lactococcus.s\_\_Lactococcus\_lactis : 0.27% of mapped reads\nFound g\_\_Micrococcus.s\_\_Micrococcus\_luteus : 0.26% of mapped reads\nFound g\_\_Dermacoccus.s\_\_Dermacoccus\_nishinomiyaensis : 0.24% of mapped reads\nFound g\_\_Micrococcus.s\_\_Micrococcus\_aloeverae : 0.22% of mapped reads\nFound g\_\_Actinomyces.s\_\_Actinomyces\_odontolyticus : 0.21% of mapped reads\nFound g\_\_Streptococcus.s\_\_Streptococcus\_thermophilus : 0.18% of mapped reads\nFound g\_\_Streptococcus.s\_\_Streptococcus\_oralis : 0.16% of mapped reads\nFound g\_\_Veillonella.s\_\_Veillonella\_parvula : 0.16% of mapped reads\nFound g\_\_Rothia.s\_\_Rothia\_dentocariosa : 0.15% of mapped reads\nFound g\_\_Rothia.s\_\_Rothia\_mucilaginosa : 0.13% of mapped reads\nFound g\_\_Abiotrophia.s\_\_Abiotrophia\_defectiva : 0.11% of mapped reads\nFound g\_\_Staphylococcus.s\_\_Staphylococcus\_saccharolyticus : 0.10% of mapped reads\nFound g\_\_Prevotella.s\_\_Prevotella\_intermedia : 0.08% of mapped reads\nFound g\_\_Actinomyces.s\_\_Actinomyces\_oris : 0.08% of mapped reads\nFound g\_\_Streptococcus.s\_\_Streptococcus\_sanguinis : 0.07% of mapped reads\nFound g\_\_Corynebacterium.s\_\_Corynebacterium\_pseudogenitalium : 0.05% of mapped reads\nFound g\_\_Haemophilus.s\_\_Haemophilus\_influenzae : 0.05% of mapped reads\nFound g\_\_Neisseria.s\_\_Neisseria\_subflava : 0.04% of mapped reads\nFound g\_\_Neisseria.s\_\_Neisseria\_macacae : 0.03% of mapped reads\nFound g\_\_Streptococcus.s\_\_Streptococcus\_sp\_A12 : 0.03% of mapped reads\nFound g\_\_Neisseria.s\_\_Neisseria\_flavescens : 0.03% of mapped reads\nFound g\_\_Haemophilus.s\_\_Haemophilus\_parainfluenzae : 0.03% of mapped reads\nFound g\_\_Porphyromonas.s\_\_Porphyromonas\_somerae : 0.02% of mapped reads\nFound g\_\_Moraxella.s\_\_Moraxella\_osloensis : 0.02% of mapped reads\nFound g\_\_Neisseria.s\_\_Neisseria\_polysaccharea : 0.01% of mapped reads\nFound g\_\_Bradyrhizobium.s\_\_Bradyrhizobium\_sp\_MOS004 : 0.01% of mapped reads\nFound g\_\_Actinomyces.s\_\_Actinomyces\_viscosus : 0.01% of mapped reads\nFound g\_\_Bacteria\_unclassified.s\_\_bacterium\_HR18 : 0.01% of mapped reads\nFound g\_\_Abiotrophia.s\_\_Abiotrophia\_sp\_HMSC24B09 : 0.01% of mapped reads\n’  
Err: b’\n\nERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the database version v30 . Please update your version of MetaPhlAn2 to v3.0.\n’

Task 12 failed  
Name: humann\_regroup\_UniRef2EC\_\_\_\_Sample1  
Original error:  
Task failed because parent task `9' failed Task 19 failed Name: humann_renorm_ecs_relab ____ Sample1 Original error: Task failed because parent task `12’ failed  
Task 17 failed  
Name: humann\_renorm\_genes\_relab\_\_\_\_Sample1  
Original error:  
Task failed because parent task `9' failed Task 21 failed Name: humann_renorm_pathways_relab ____ Sample1 Original error: Task failed because parent task `9’ failed  
Task 7 failed  
Name: humann\_\_\_\_Sample2  
Original error:  
Error executing action 0. Original Exception:  
Traceback (most recent call last):  
File “/usr/local/bin/miniconda3/envs/biobakery3/lib/python3.7/site-packages/anadama2/runners.py”, line 201, in \_run\_task\_locally  
action\_func(task)  
File “/usr/local/bin/miniconda3/envs/biobakery3/lib/python3.7/site-packages/anadama2/helpers.py”, line 89, in actually\_sh  
ret = \_sh(s, \*\*kwargs)  
File “/usr/local/bin/miniconda3/envs/biobakery3/lib/python3.7/site-packages/anadama2/util/ **init**.py”, line 320, in sh  
raise ShellException(proc.returncode, msg.format(cmd, ret[0], ret[1]))  
anadama2.util.ShellException: [Errno 1] Command `humann --input /Projects1/ **/humann\_input\_subset/Sample2.fastq --output /Projects1/** /humann\_output\_subset6/humann/main --o-log /Projects1/ **/humann\_output\_subset6/humann/main/Sample2.log --threads 20 --taxonomic-profile /Projects1/** /humann\_output\_subset6/metaphlan/main/Sample2\_taxonomic\_profile.tsv --remove-temp-output --nucleotide-subject-coverage-threshold 0 --translated-subject-coverage-threshold 0 --pathways-database /media/ **/biobakery\_workflows/wmgx/humann/pathways/metacyc\_reactions\_level4ec\_only.uniref.bz2,/media/** /biobakery\_workflows/wmgx/humann/pathways/metacyc\_pathways\_structured\_filtered\_v24 ’ failed.  
Out: b’Output files will be written to: /Projects1/\*\*\*\*/humann\_output\_subset6/humann/main\nFound g\_\_Cutibacterium.s\_\_Propionibacterium\_namnetense : 51.63% of mapped reads\nFound g\_\_Cutibacterium.s\_\_Cutibacterium\_acnes : 43.49% of mapped reads\nFound g\_\_Corynebacterium.s\_\_Corynebacterium\_otitidis : 3.03% of mapped reads\nFound g\_\_Morococcus.s\_\_Morococcus\_cerebrosus : 1.28% of mapped reads\nFound g\_\_Staphylococcus.s\_\_Staphylococcus\_epidermidis : 0.57% of mapped reads\n’  
Err: b’\n\nERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the database version v30 . Please update your version of MetaPhlAn2 to v3.0.\n’

Task 10 failed  
Name: humann\_count\_alignments\_species  
Original error:  
Task failed because parent task `9' failed Task 11 failed Name: humann_regroup_UniRef2EC ____ Sample2 Original error: Task failed because parent task `7’ failed  
Task 14 failed  
Name: humann\_join\_tables\_ecs  
Original error:  
Task failed because parent task `11' failed Task 18 failed Name: humann_renorm_ecs_relab ____ Sample2 Original error: Task failed because parent task `11’ failed  
Task 23 failed  
Name: humann\_join\_tables\_ecs\_relab  
Original error:  
Task failed because parent task `18' failed Task 26 failed Name: humann_count_features_ecs Original error: Task failed because parent task `23’ failed  
Task 13 failed  
Name: humann\_join\_tables\_genefamilies  
Original error:  
Task failed because parent task `9' failed Task 15 failed Name: humann_join_tables_pathabundance Original error: Task failed because parent task `9’ failed  
Task 16 failed  
Name: humann\_renorm\_genes\_relab\_\_\_\_Sample2  
Original error:  
Task failed because parent task `7' failed Task 22 failed Name: humann_join_tables_genes_relab Original error: Task failed because parent task `16’ failed  
Task 25 failed  
Name: humann\_count\_features\_genes  
Original error:  
Task failed because parent task `22' failed Task 20 failed Name: humann_renorm_pathways_relab ____ Sample2 Original error: Task failed because parent task `7’ failed  
Task 24 failed  
Name: humann\_join\_tables\_pathways\_relab  
Original error:  
Task failed because parent task `20' failed Task 27 failed Name: humann_count_features_pathways Original error: Task failed because parent task `24’ failed  
Task 28 failed  
Name: humann\_merge\_feature\_counts  
Original error:  
Task failed because parent task `25’ failed  
Traceback (most recent call last):  
File “/usr/local/bin/miniconda3/envs/biobakery3/bin/wmgx.py”, line 184, in   
workflow.go()  
File “/usr/local/bin/miniconda3/envs/biobakery3/lib/python3.7/site-packages/anadama2/workflow.py”, line 800, in go  
self.\_handle\_finished()  
File “/usr/local/bin/miniconda3/envs/biobakery3/lib/python3.7/site-packages/anadama2/workflow.py”, line 832, in \_handle\_finished  
raise RunFailed()  
anadama2.workflow.RunFailed

Log file of Sample 2:

03/28/2023 11:54:27 AM - humann.humann - INFO: Running humann v3.0.1  
03/28/2023 11:54:27 AM - humann.humann - INFO: Output files will be written to: /Projects1/**/humann\_output\_subset6/humann/main  
03/28/2023 11:54:27 AM - humann.humann - INFO: Writing temp files to directory: /Projects1/**/humann\_output\_subset6/humann/main/Sample2\_humann\_temp\_xc2ni\_ed  
03/28/2023 11:54:27 AM - humann.utilities - INFO: File ( /Projects1/\*\*\*\*/humann\_input\_subset/Sample2.fastq ) is of format: fastq  
03/28/2023 11:54:27 AM - humann.utilities - DEBUG: Check software, metaphlan, for required version, 3.0  
03/28/2023 11:54:28 AM - humann.utilities - INFO: Using metaphlan version 3.0  
03/28/2023 11:54:28 AM - humann.utilities - DEBUG: Check software, bowtie2, for required version, 2.2  
03/28/2023 11:54:28 AM - humann.utilities - INFO: Using bowtie2 version 2.4  
03/28/2023 11:54:28 AM - humann.humann - INFO: Search mode set to uniref90 because a uniref90 translated search database is selected  
03/28/2023 11:54:28 AM - humann.utilities - DEBUG: Check software, diamond, for required version, 0.9.36  
03/28/2023 11:54:28 AM - humann.utilities - INFO: Using diamond version 2.0.14  
03/28/2023 11:54:28 AM - humann.config - INFO:  
Run config settings:

DATABASE SETTINGS  
nucleotide database folder = /media/**/biobakery\_workflows/wmgx/humann/chocophlan  
protein database folder = /media/**/biobakery\_workflows/wmgx/humann/uniref  
pathways database file 1 = /media/**/biobakery\_workflows/wmgx/humann/pathways/metacyc\_reactions\_level4ec\_only.uniref.bz2  
pathways database file 2 = /media/**/biobakery\_workflows/wmgx/humann/pathways/metacyc\_pathways\_structured\_filtered\_v24  
utility mapping database folder = /media/\*\*\*\*/biobakery\_workflows/wmgx/humann/utility\_mapping

RUN MODES  
resume = False  
verbose = False  
bypass prescreen = False  
bypass nucleotide index = False  
bypass nucleotide search = False  
bypass translated search = False  
translated search = diamond  
threads = 20

SEARCH MODE  
search mode = uniref90  
nucleotide identity threshold = 0.0  
translated identity threshold = 80.0

ALIGNMENT SETTINGS  
bowtie2 options = --very-sensitive  
diamond options = --top 1 --outfmt 6  
evalue threshold = 1.0  
prescreen threshold = 0.01  
translated subject coverage threshold = 0.0  
translated query coverage threshold = 90.0  
nucleotide subject coverage threshold = 0.0  
nucleotide query coverage threshold = 90.0

PATHWAYS SETTINGS  
minpath = on  
xipe = off  
gap fill = on

INPUT AND OUTPUT FORMATS  
input file format = fastq  
output file format = tsv  
output max decimals = 10  
remove stratified output = False  
remove column description output = False  
log level = DEBUG

03/28/2023 11:54:28 AM - humann.store - DEBUG: Initialize Alignments class instance to minimize memory use  
03/28/2023 11:54:28 AM - humann.store - DEBUG: Initialize Reads class instance to minimize memory use  
03/28/2023 11:54:55 AM - humann.humann - INFO: Load pathways database part 1: /media/**/biobakery\_workflows/wmgx/humann/pathways/metacyc\_reactions\_level4ec\_only.uniref.bz2  
03/28/2023 11:54:55 AM - humann.humann - INFO: Load pathways database part 2: /media/**/biobakery\_workflows/wmgx/humann/pathways/metacyc\_pathways\_structured\_filtered\_v24  
03/28/2023 11:54:55 AM - humann.search.prescreen - INFO: Found g\_\_Cutibacterium.s\_\_Propionibacterium\_namnetense : 51.63% of mapped reads  
03/28/2023 11:54:55 AM - humann.search.prescreen - INFO: Found g\_\_Cutibacterium.s\_\_Cutibacterium\_acnes : 43.49% of mapped reads  
03/28/2023 11:54:55 AM - humann.search.prescreen - INFO: Found g\_\_Corynebacterium.s\_\_Corynebacterium\_otitidis : 3.03% of mapped reads  
03/28/2023 11:54:55 AM - humann.search.prescreen - INFO: Found g\_\_Morococcus.s\_\_Morococcus\_cerebrosus : 1.28% of mapped reads  
03/28/2023 11:54:55 AM - humann.search.prescreen - INFO: Found g\_\_Staphylococcus.s\_\_Staphylococcus\_epidermidis : 0.57% of mapped reads  
03/28/2023 11:54:55 AM - humann.search.prescreen - ERROR: The MetaPhlAn2 taxonomic profile provided was not generated with the database version v30 . Please update your version of MetaPhlAn2 to v3.0.

---

<div class="post-metadata">

**Author:** ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)\
**Post date:** [March 29, 2023, 5:29pm UTC](https://forum.biobakery.org/t/humann-3-0-error-within-biobakery-workflows-wmgx/5036/2 "2023-03-29T17:29:48Z")

</div>

Hello, Thank you for providing so many details! Can you also post the first couple of lines of one MetaPhlAN output file? This is what HUMAnN searches to determine if the databases are compatible.

Thank you!  
Lauren

---

<div class="post-metadata">

**Author:** ![bdpessem](https://avatars.discourse-cdn.com/v4/letter/b/7c8e57/32.png) [@bdpessem](https://forum.biobakery.org/u/bdpessem)\
**Post date:** [March 29, 2023, 6:35pm UTC](https://forum.biobakery.org/t/humann-3-0-error-within-biobakery-workflows-wmgx/5036/3 "2023-03-29T18:35:03Z")

</div>

Hi!  
Many thanks for your quick reply!  
These are the first few lines from the metaphlan output file.  
#mpa\_v31\_CHOCOPhlAn\_201901  
#/usr/local/bin/miniconda3/envs/biobakery3/bin/metaphlan /Projects1/ **/humann\_input\_subset/P059\_CP04272\_S337\_L001.fastq --input\_type fastq --output\_file /Projects1/** /humann\_output\_subset6/metaphlan/main/P059\_CP04272\_S337\_L001\_taxonomic\_profile.tsv --samout /Projects1/ **/humann\_output\_subset6/metaphlan/main/sample2 --nproc 20 --no\_map --tmp\_dir /Projects1/** /humann\_output\_subset6/metaphlan/main --bowtie2db /media/\*\*\*\*/biobakery\_3/metaphlan3/ --stat\_q 0.1  
#SampleID Metaphlan\_Analysis  
#clade\_name NCBI\_tax\_id relative\_abundance additional\_species

Many thanks in advance!

Britta

---

<div class="post-metadata">

**Author:** ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)\
**Post date:** [March 29, 2023, 8:41pm UTC](https://forum.biobakery.org/t/humann-3-0-error-within-biobakery-workflows-wmgx/5036/4 "2023-03-29T20:41:23Z")

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Sure thing! That output looks good. You are using a newer MetaPhlAn database version than is expected by that version of HUMAnN. If you update HUMAnN to the latest version it should resolve the error you are seeing.

Thanks!  
Lauren

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<div class="post-metadata">

**Author:** ![bdpessem](https://avatars.discourse-cdn.com/v4/letter/b/7c8e57/32.png) [@bdpessem](https://forum.biobakery.org/u/bdpessem)\
**Post date:** [April 13, 2023, 7:44pm UTC](https://forum.biobakery.org/t/humann-3-0-error-within-biobakery-workflows-wmgx/5036/5 "2023-04-13T19:44:11Z")

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Thanks Lauren! It worked! 🙂

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<div class="post-metadata">

**Author:** ![lauren.j.mciver](https://avatars.discourse-cdn.com/v4/letter/l/f05b48/32.png) [@lauren.j.mciver](https://forum.biobakery.org/u/lauren.j.mciver)\
**Post date:** [April 13, 2023, 8:58pm UTC](https://forum.biobakery.org/t/humann-3-0-error-within-biobakery-workflows-wmgx/5036/6 "2023-04-13T20:58:23Z")

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Glad to hear it! Please post if you run into any other issues!

Thanks!  
Lauren