Metaphlan(4.0.6) reported an error while running humann(3.6.1)

Microbial community profiling HUMAnN
1

I’m a novice.

humann -i demo.fastq -o lx
Output files will be written to: /home/zhoujian/02.SoftWare/humann/examples/lx

Running metaphlan …

ERROR: The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJan21 . Please update your version of MetaPhlAn to at least v3.0 or if you are using MetaPhlAn v4 please use the database vJan21.

my humann and metaphlan version

humann --version
humann v3.6.1

metaphlan -v
MetaPhlAn version 4.0.6 (1 Mar 2023)

I am install humann with conda .And I can run metaphaln alone.

metaphlan demo.fastq --input_type fastq -o pro.txt
WARNING: The metagenome profile contains clades that represent multiple species merged into a single representant.
An additional column listing the merged species is added to the MetaPhlAn output.

run metaphlan I can get result. But run humann, I get a error. So what should I do

2 
$ humann --version
humann v3.6.1
$ metaphlan --version
MetaPhlAn version 4.0.6 (1 Mar 2023)
$ biobakery_workflows --version
biobakery_workflows v3.1

I seem to have the same problem, here are some of the specific (which I posted previously on hte biobakery mailing list):

When running:

humann --input /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data3/kneaddata/main/HD32R1_subsample.fastq.gz --output /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data3/humann/main --o-log /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data3/humann/main/HD32R1_subsample.log --threads 1 --taxonomic-profile /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data3/metaphlan/main/HD32R1_subsample_taxonomic_profile.tsv

I get:

ERROR: The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJan21 . Please update your version of MetaPhlAn to at least v3.0 or if you are using MetaPhlAn v4 please use the database vJan21.

Indeed when downloading the metaphlan DB with:

metaphlan --install

the db installed is: vOct22

this is a consequence of: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/mpa_latest containing:

mpa_vOct22_CHOCOPhlAnSGB_202212

I downloaded the precomputed version of the bt2 database from: http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/mpa_vJan21_CHOCOPhlAnSGB_202103_bt2.tar (as suggested in How to install the latest metaphlan reference DB? - #13 by aitor.blancomiguez and I untarred the file and placed the bt2l files in the methaplan_databases directory but even after doing so I still get the same error.

Question: I see that vJan21 is hardcoded in many files humann and metaphlan (e.g., humann/config.py, humann-3.6.1-py3.9.egg-info/SOURCES.txt, MetaPhlAn-4.0.6.dist-info/METADATA, etc.), shouldn’t accordingly mpa_latest in Index of /biobakery4/metaphlan_databases point to vJan21 and not vOct22 or the version be updated in humann and metaphlan?

Even after downloading the DB with the --index, the step:

$ humann --input /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/kneaddata/main/HD32R1_subsample.fastq.gz --output /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/humann/main --o-log /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/humann/main/HD32R1_subsample.log --threads 1 --taxonomic-profile /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/metaphlan/main/HD32R1_subsample_taxonomic_profile.tsv

still fails with error:

ERROR: The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJan21 . Please update your version of MetaPhlAn to at least v3.0 or if you are using MetaPhlAn v4 please use the database vJan21.

I think is caused by the fact that when computing the taxonomic profile metaphlan chooses the version of the DB as declared in mpa_latest, I am not sure how to correct this step (especially when it occurs from within biobakery_workflow).

Please see below the first few lines of the tsv file:

$ head /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/metaphlan/main/HD32R1_subsample_taxonomic_profile.tsv
#mpa_vOct22_CHOCOPhlAnSGB_202212
#/u/local/apps/PYTHON-VIRT-ENVS/3.9.6/biobakery/bin/metaphlan /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/kneaddata/main/HD32R1_subsample.fastq.gz --input_type fastq --output_file /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/metaphlan/main/HD32R1_subsample_taxonomic_profile.tsv --samout /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/metaphlan/main/HD32R1_subsample_bowtie2.sam --nproc 1 --no_map --tmp_dir /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/metaphlan/main
#34596 reads processed
#SampleID	Metaphlan_Analysis
#clade_name	NCBI_tax_id	relative_abundance	additional_species
k__Bacteria	2	100.0	
k__Bacteria|p__Bacteroidetes	2|976	76.7975	
k__Bacteria|p__Firmicutes	2|1239	18.81751	
k__Bacteria|p__Actinobacteria	2|201174	4.38499	
k__Bacteria|p__Bacteroidetes|c__Bacteroidia	2|976|200643	76.7975

Any suggestion would be appreciated.

Thanks

RD

3

Hello,
Run metaphlan separately and provide the metaphlan output while running humann3.
More importantly, download the vJan21 version of chocophlan,

metaphlan --install --index mpa_vJan21_CHOCOPhlAnSGB_202103

save it to a folder and provide the path to the database in the metaphlan command with

–bowtie2db DIRECTORY_PATH --index mpa_vJan21_CHOCOPhlAnSGB_202103

I hope this helps.

1 Like
4

Hello,

Thanks for the explanation. Same here tried running humann (version 3.6.1 with metaphlan 4.0.6 and chocophlan vJan21) without success, get the error message

The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJan21 . Please update your version of MetaPhlAn to at least v3.0 or if you are using MetaPhlAn v4 please use the database vJan21.

So you run independently Metaphlan and then humann3. As argument to Humann you add

 --bypass-prescreen

Thanks for the helps.

5

@Vikas thanks for your answer, to be cleat I did install the DB with: --index mpa_vJan21_CHOCOPhlAnSGB_202103, as from below:

$ metaphlan --install --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db /u/local/apps/PYTHON-VIRT-ENVS/3.9.6/biobakery/lib/python3.9/site-packages/metaphlan/metaphlan_databases

but the problem persists.

@nbat64 adding --bypass-prescreen did not seem to help either:

$ humann --bypass-prescreen --input /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/kneaddata/main/HD32R1_subsample.fastq.gz --output /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/humann/main --o-log /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/humann/main/HD32R1_subsample.log --threads 1 --taxonomic-profile /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/metaphlan/main/HD32R1_subsample_taxonomic_profile.tsv

but I still get:

Output files will be written to: /u/home/staff1/cusgunx/ATS-TEST/biobakery/output_data4/humann/main
Decompressing gzipped file ...



ERROR: The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJan21 . Please update your version of MetaPhlAn to at least v3.0 or if you are using MetaPhlAn v4 please use the database vJan21.

Also, I am trying to use biobakery_workflows so adding a flag to humann would not be practical in that context.

Any ideas?

Thanks

6

Hi,
I was able to run the demo.fastq data using this:

Conda env with MetaPhlan_v4.0.6 HUMAnN_v3.6.1 Diamond_v2.0.5

code

humann  -i $INPUTFILE1 \
--metaphlan-options "-t rel_ab --index mpa_vJan21_CHOCOPhlAnSGB_202103 --bowtie2db $DB/MetaPhlAn_mpa_vJan21" \
-o ${RUN}_Humann3/ \
--threads 24 \
--nucleotide-database $DBHNuc \
--protein-database $DBHPro \
--verbose \
--o-log ${INPUTFILE1%.*}_humann3.log
7

thank you very much,I I have downloaded metaphlan(3.0) in conda virtual environment,and then run metaphlan,they will download the database theivef.in this enveronment donwnloaded humann.That solves the problem.

8

Try downloading and running metaphlan3.0 first

9

@rda Hello, has your problem been solved? I also encountered the same problem, but I still don’t know where the root of the problem lies. Can you give me your help?
MetaPhlAn version 4.0.6 (1 Mar 2023)
humann v3.6
ERROR: The MetaPhlAn taxonomic profile provided was not generated with the database version v3 or vJan21 . Please update your version of MetaPhlAn to at least v3.0 or if you are using MetaPhlAn v4 please use the database vJan21.