Metaphla4 rel_ab_w_read_stats issue

Microbial community profiling MetaPhlAn
1

Hi metaphlan author,

I used metaphlan4 (4.0.1) to generate profile. The following few lines are attached below. My issue is checking bacteria count (59839072). It is more than bowtie2 input reads (15148903). I also run the similar command using metaphlan 3.0.6. It doesn’t have this issue. I notice in another thread, someone claim there is issue to run using rel_ab_w_read_stats. Do you have a solution? Thanks a lot!

“#/opt/conda/bin/metaphlan results/metaphlan3/HND0022_un.fastq.bowtie2out.txt --input_type bowtie2out --nproc 8 --bowtie2db /data/wany/MGS_test/database/metaphlan4 -t rel_ab_w_read_stats --unclassified_estimation
#SampleID Metaphlan_Analysis
#estimated_reads_mapped_to_known_clades:59839072
#clade_name clade_taxid relative_abundance coverage estimated_number_of_reads_from_the_clade
UNCLASSIFIED -1 41.75627 - 0
k__Bacteria 2 58.24373 3.19643 59839072
k__Bacteria|p__Firmicutes 2|1239 20.53348 1.12688 16203915
k__Bacteria|p__Actinobacteria 2|201174 15.97619 0.87678 14740033
k__Bacteria|p__Proteobacteria 2|1224 11.54269 0.63347 10348415”

2

Hi @mentorwan
Thanks for reporting this issue. We will have a look at it and try to include a fix in the next version (4.0.3)

3

Hi @mentorwan
The new 4.0.3 version is now available in conda and should solve this issue

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4

Thanks for updating. I will check.

5

Any idea when the official BioBakery container for this version will be released?
I could create one myself, but if possible, we prefer to use containers created by the developers of the particular tool.

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6

Same – would love to have official versions available. @MalbertR you can use the one we build here if you want in the meantime. It’s got humann3.6 and metaphlan 4.0.3. docker pull ghcr.io/vdblab/biobakery-profiler:20221107

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7

Hi @MalbertR and @nickp60 for version 4, we are not currently planning to mantain the docker images but only the pip and conda installations. However, when most of the biobakery tools move to version 4 (using the SGB system) this might change

8

I’m happy to help set up the CI/CD if you’d like. The process has been simplified dirastically with GitHub Container Registry, so you no longer have to manually push things to dockerhub or set up auth tokens between GitHub and DockerHub. Having docker containers is invaluable, especially given the number of dependencies in these tools.

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