$ 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