Hello,
Thank you so much for your work on Metaphlan! I am encountering an issue with the Metaphlan --biom option that I have not been able to resolve on my own. In my test runs, Metaphlan is producing biom files containing total relative counts > 100% due to what appears to be extra entries in the biom file.
I am testing Metaphlan 4.0.6 on one publicly available sample with paired-end FASTQ files:
I used the following line to run Metaphlan:
metaphlan
–nproc 8
–input_type fastq
SAMEA8614982_run1.unmapped_1.fastq.gz,SAMEA8614982_run1.unmapped_2.fastq.gz
–bowtie2out SAMEA8614982_pe_db1.metaphlan4.bowtie2out.txt
–bowtie2db $BT2_DB
–biom SAMEA8614982_pe_db1.metaphlan4.biom
–output_file SAMEA8614982_pe_db1.metaphlan4_profile.txt
The biom file Metaphlan generated has a total relative count of 103.96769%. The BIOM file has additional entries that are not at the sample level. These are the first six entries in the BIOM file and have a total relative count of 3.96771%. I have copy pasted the IDs and their corresponding metadata and data entries below.
{“id”: “MetaPhlAn_Analysis”, “format”: “Biological Observation Matrix 1.0.0”,“format_url”: “http://biom-format.org”,“generated_by”: “MetaPhlAn”,“date”: “2023-04-26T01:51:34.908174”,“matrix_element_type”: “float”,“shape”: [132, 1],“type”: null,“matrix_type”: “sparse”,“data”: [[0,0,0.45889],[1,0,0.28211],[2,0,2.36258],[3,0,0.07014],[4,0,0.07103],[5,0,0.72296]],“rows”: [{“id”: “k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales”, “metadata”: {“taxonomy”: [“k__Bacteria”, “p__Firmicutes”, “c__Clostridia”, “o__Eubacteriales”]}},{“id”: “k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Clostridiaceae”, “metadata”: {“taxonomy”: [“k__Bacteria”, “p__Firmicutes”, “c__Clostridia”, “o__Eubacteriales”, “f__Clostridiaceae”]}},{“id”: “k__Bacteria|p__Firmicutes|c__Erysipelotrichia|o__Erysipelotrichales|f__Erysipelotrichaceae”, “metadata”: {“taxonomy”: [“k__Bacteria”, “p__Firmicutes”, “c__Erysipelotrichia”, “o__Erysipelotrichales”, “f__Erysipelotrichaceae”]}},{“id”: “k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales_Family_XIII_Incertae_Sedis”, “metadata”: {“taxonomy”: [“k__Bacteria”, “p__Firmicutes”, “c__Clostridia”, “o__Eubacteriales”, “f__Eubacteriales_Family_XIII_Incertae_Sedis”]}},{“id”: “k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Eubacteriales_unclassified”, “metadata”: {“taxonomy”: [“k__Bacteria”, “p__Firmicutes”, “c__Clostridia”, “o__Eubacteriales”, “f__Eubacteriales_unclassified”]}},{“id”: “k__Bacteria|p__Firmicutes|c__Clostridia|o__Eubacteriales|f__Lachnospiraceae”, “metadata”: {“taxonomy”: [“k__Bacteria”, “p__Firmicutes”, “c__Clostridia”, “o__Eubacteriales”, “f__Lachnospiraceae”]}}
Any help/clarification with this issue would be greatly appreciated. Thank you so much.