wasade
commented
8 years ago Just to check, when you indicate the files produced are nonsense and not human-readable, are they being output as BIOM 2.1? It's built on top of HDF5 and is binary. Are you receiving any error output?
On Sat, Jun 25, 2016 at 7:39 PM, danchurch notifications@github.com wrote:
I am doing an ITS region fungal study. I used the usearch v8.1 pipeline, without any qiime scripts, to get me to the point of a biom table with taxonomic assignments. As far as I can tell, the json biom table that was outputted by usearch is not readable by any downstream applications, including biom, either python scripts or in R environment. I believe this may be due to the structure of the taxonomic metadata. So I edited them to try to match examples on the biom website. However, the taxonomic info is still not reading correctly.
The original output from usearch 8.1:
""" { "id":"otu_95_sub.biom", "format": "Biological Observation Matrix 1.0", "format_url": "http://biom-format.org", "generated_by": "usearch8.11803", "type": "OTU table", "date": "Thu Jun 23 20:38:04 2016", "matrix_type": "sparse", "matrix_element_type": "float", "shape": [767176,98], "rows":[ {"id":"OTU1575410:M01498:244:000000000-ANT97:1:1101:18025:5338:160", "metadata":{"taxonomy":"d:Fungi(0.9991),p:Ascomycota(0.5394),c:Sordariomycetes(0.3516),o:Xylariales(0.1885),f:Xylariaceae(0.0879),g:Xylaria(0.0105)"}},
"""
After my scripting, rows look like this:
""" "shape": [767176,98], "rows":[ {"id":"OTU1575410", "metadata":{"taxonomy": ["kFungi", "pAscomycota", "cSordariomycetes", "oXylariales", "fXylariaceae", "gXylaria"]}},
"""
I believe all brackets have been properly closed. Biom will happily convert to a classical OTU table from this for me when I do not include taxonomic info, but every other biom command generates a nonsense file, not human-readable, and not readable by phyloseq. No error message is returned.
Let me know if this row format seems erroneous, please. If it does not, I will look elsewhere for the source of the error. If you are curious, I am keeping a log of my pipeline on my own github account.
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danchurch
joey711
I am doing an ITS region fungal study. I used the usearch v8.1 pipeline, without any qiime scripts, to get me to the point of a biom table with taxonomic assignments. As far as I can tell, the json biom table that was outputted by usearch is not readable by any downstream applications, including biom, either python scripts or in R environment. I believe this may be due to the structure of the taxonomic metadata. So I edited them to try to match examples on the biom website. However, the taxonomic info is still not reading correctly.
The original output from usearch 8.1:
After my scripting, rows look like this:
I believe all brackets have been properly closed. Biom will happily convert to a classical OTU table from this for me when I do not include taxonomic info, but every other biom command generates a nonsense file, not human-readable, and not readable by phyloseq. No error message is returned.
Let me know if this row format seems erroneous, please. If it does not, I will look elsewhere for the source of the error. If you are curious, I am keeping a log of my pipeline on my own github account.