unknown & unclassified clade

[Andrew Lang]

I'm running into issues with running MethaPhlAn2 from the docker container via singularity. I have built a singularity image file from dockerhub://biobakery/metaphlan2:2.7.7. Local install of the mpa_v20 DB using metphaln2.py --install

[alang@srv5-BOS metaphlan2]$ singularity inspect ~/Desktop/singularity_files/metaphlan2_2.7.7.sif ==labels==

org.label-schema.build-date: Thursday_21_November_2019_9:53:41_EST
org.label-schema.schema-version: 1.0
org.label-schema.usage.singularity.deffile.bootstrap: docker
org.label-schema.usage.singularity.deffile.from: biobakery/metaphlan2:2.7.7
org.label-schema.usage.singularity.version: 3.4.1-1.2.el7
[alang@srv5-BOS metaphlan2]$ singularity exec -B /home/alang/Desktop/metaphlan2:/opt/conda/bin/metaphlan_databases /home/alang/Desktop/singularity_files/metaphlan2_2.7.7.sif metaphlan2.py --version
MetaPhlAn version 2.7.7 (31 May 2018)
[alang@srv5-BOS metaphlan2]$ singularity exec -B /home/alang/Desktop/metaphlan2:/opt/conda/bin/metaphlan_databases /home/alang/Desktop/singularity_files/metaphlan2_2.7.7.sif metaphlan2.py --install
The database is installed
[alang@srv5-BOS metaphlan2]$ singularity exec -B /home/alang/Desktop/metaphlan2:/opt/conda/bin/metaphlan_databases \
/home/alang/Desktop/singularity_files/metaphlan2_2.7.7.sif metaphlan2.py /home/alang/Desktop/BRR_localfiles/shovill/SRR10375928/SRR10375928.fa \
--bowtie2out /home/alang/Desktop/BRR_localfiles/metaphlan2/SRR10375928.2.7.7.bowtie2out.txt --input_type fasta \
--nproc 30 > /home/alang/Desktop/BRR_localfiles/metaphlan2/SRR10375928_2.7.7.profile.txt
Help message for read_fastx.py
[alang@srv5-BOS metaphlan2]$ cat SRR10375928_2.7.7.profile.txt
#SampleID    Metaphlan2_Analysis
unclassified    100.0
[alang@srv5-BOS metaphlan2]$ cat SRR10375928.2.7.7.bowtie2out.txt
[alang@srv5-BOS metaphlan2]$

I have also done a build of my own container wherein I pulled the base miniconda image and used that to build a docker container of metaphlan2.9. Local install of the mpa_v295 DB using metphaln2.py --install

[alang@srv5-BOS metaphlan2]$ singularity inspect ~/Desktop/singularity_files/metaphlan2_2.sif
==labels==
org.label-schema.usage.singularity.deffile.from: andrewlangvt/metaphlan2:2
org.label-schema.usage.singularity.version: 3.4.1-1.2.el7
org.label-schema.build-date: Monday_2_December_2019_15:0:2_EST
org.label-schema.schema-version: 1.0
org.label-schema.usage.singularity.deffile.bootstrap: docker

[alang@srv5-BOS metaphlan2]$ singularity exec -B /home/alang/Desktop/metaphlan2:/opt/conda/bin/metaphlan_databases /home/alang/Desktop/singularity_files/metaphlan2_2.sif metaphlan2.py --version
MetaPhlAn version 2.9.22 (14 Oct 2019)
[alang@srv5-BOS metaphlan2]$ singularity exec -B /home/alang/Desktop/metaphlan2:/opt/conda/bin/metaphlan_databases /home/alang/Desktop/singularity_files/metaphlan2_2.sif metaphlan2.py --install
The database is installed

[alang@srv5-BOS metaphlan2]$ /home/alang/Desktop/singularity_files/metaphlan2_2.sif metaphlan2.py /home/alang/Desktop/BRR_localfiles/shovill/SRR10375928/SRR10375928.fa \
--bowtie2out /home/alang/Desktop/BRR_localfiles/metaphlan2/SRR10375928.2.9.22.bowtie2out.txt --input_type fasta \
--nproc 30 > /home/alang/Desktop/BRR_localfiles/metaphlan2/SRR10375928_2.9.22.profile.txt
Elapsed time to run MetaPhlAn2: 331.8113214969635 s
[alang@srv5-BOS metaphlan2]$ cat SRR10375928_2.9.22.profile.txt
#mpa_v295_CHOCOPhlAn_201901
#/opt/conda/bin/metaphlan2.py /home/alang/Desktop/BRR_localfiles/shovill/SRR10375928/SRR10375928.fa --bowtie2out /home/alang/Desktop/BRR_localfiles/metaphlan2/SRR10375928.2.9.22.bowtie2out.txt --input_type fasta --nproc 30
#SampleID    Metaphlan2_Analysis
#clade_name    NCBI_tax_id    relative_abundance
UNKNOWN    -1    100.0
[alang@srv5-BOS metaphlan2]$ cat SRR10375928.2.9.22.bowtie2out.txt
#nreads    57
[alang@srv5-BOS metaphlan2]$

I'm not quite sure why all I am getting from the output is "unclassified" or "UNKNOWN" as this SRR is Salmonella enterica so I would assume, if nothing else, MetaPhlAn should ID that...Any thoughts here?

Thanks,

Andrew

[Andrew Lang]

Does anyone have thoughts on this?