100 Unknown raw reads

Microbial community profiling MetaPhlAn
1

Dear Metaphlan2 team,

When I use metaphlan2 on raw illumina reads, I have the following results.

#mpa_v296_CHOCOPhlAn_201901.
#/opt/miniconda/bin/metaphlan2.py P1030_R1.paired.fastq --input_type fastq --nproc 15 --bowtie2db bowtie2db/mpa --mpa_pkl mpa_v296_CHOCOPhlAn_201901.pkl --unknown_estimation.
#SampleID Metaphlan2_Analysis.
#clade_name NCBI_tax_id relative_abundance.
UNKNOWN -1 100.0.

metaphlan2 semis to work on example dataset (see below), but I found strange to found 100 Unknown. Did I miss something or do something wrong ?

On an example provided in Bitbucket :
#mpa_v296_CHOCOPhlAn_201901
#/opt/miniconda/bin/metaphlan2.py SRS014476-Supragingival_plaque.fasta --input_type fasta --nproc 15 --bowtie2db bowtie2db/mpa --mpa_pkl mpa_v296_CHOCOPhlAn_201901.pkl
#SampleID Metaphlan2_Analysis
#clade_name NCBI_tax_id relative_abundance
k__Bacteria 2 100.0
k__Bacteria|p__Actinobacteria 2|201174 100.0
k__Bacteria|p__Actinobacteria|c__Actinobacteria 2|201174|1760 100.0
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales 2|201174|1760|85007 65.25681
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales 2|201174|1760|85006 34.74319
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae 2|201174|1760|85007|1653 65.25681
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae 2|201174|1760|85006|1268 34.74319
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium 2|201174|1760|85007|1653|1716 65.25681
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia 2|201174|1760|85006|1268|32207 34.74319
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Corynebacteriales|f__Corynebacteriaceae|g__Corynebacterium|s__Corynebacterium_matruchotii 2|201174|1760|85007|1653|1716|43768 65.25681
k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia_dentocariosa 2|201174|1760|85006|1268|32207|2047 34.74319
#Additional species represented by this clade: k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia_sp_HMSC071F11,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia_sp_HMSC069C01,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia_sp_HMSC08A08,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia_sp_HMSC036D11,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia_sp_HMSC067H10,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia_sp_HMSC065D02,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia_sp_HMSC058E10,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia_sp_HMSC065G12,k__Bacteria|p__Actinobacteria|c__Actinobacteria|o__Micrococcales|f__Micrococcaceae|g__Rothia|s__Rothia_sp_HMSC064D08

2

Hi,
Have you tried to update MetaPhlAn to the latest available version? Which kind of sample are you trying to profile?

3

Hi,

Yes I retry the whole pipeline with a few days ago, same result.
It is lichens whole métagenomes, quite rare samples.

Luc,

4

Hi Luc,

In this case, the bacterial community associated with lichen probably has no reference genomes present in the MetaPhlAn database. Currently, the database includes human-associated species and we have expanded with murine and some soil associated species.

5

Hi,
When I use metaphlan2 on raw illumina reads, I have the following results.
No MetaPhlAn BowTie2 database found (–index option)!
Expecting location /home/ftz/anaconda3/envs/mpa/lib/python3.7/site-packages/metaphlan/metaphlan_databases/mpa_v296_CHOCOPhlAn_201901

I think the reason is my mpa_v296_CHOCOPhlAn_201901.tar which has some problems.
Can you support all metaphlan_database file for me?
Just like this :mpa_v20_m200.1.bt2
mpa_v20_m200.2.bt2
mpa_v20_m200.3.bt2
mpa_v20_m200.4.bt2
mpa_v20_m200.rev.1.bt2
mpa_v20_m200.rev.2.bt2
If you can I will be extremely grateful.Thank you very much!

6

I have received the same results “UNKNOWN -1 100.0” when I tried the latest version for samples from a mice MGX dataset. It would be a great resource if there is a pipeline or pre-generated MetaPhlAn databases for different types of host/niche.

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