The bioBakery help forum

100 Unknown raw reads

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

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

Hi,

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

Luc,

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.

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!

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.