error in biom convert: Unsupported matrix data type

Good morning.

I have a feature table in the .txt format, and I’m trying to convert it to JSON .biom format using the biom-format package.

biom convert -i featured_converted.txt -o OTU.biom --to-json \
--process-obs-metadata sc_separated --table-type "OTU table"

And I get this error:

Traceback (most recent call last):
  File "/Users/bris469/miniconda3/envs/hundo-dev/bin/biom", line 11, in <module>
    sys.exit(cli())
  File "/Users/bris469/miniconda3/envs/hundo-dev/lib/python3.6/site-packages/click/core.py", line 764, in __call__
    return self.main(*args, **kwargs)
  File "/Users/bris469/miniconda3/envs/hundo-dev/lib/python3.6/site-packages/click/core.py", line 717, in main
    rv = self.invoke(ctx)
  File "/Users/bris469/miniconda3/envs/hundo-dev/lib/python3.6/site-packages/click/core.py", line 1137, in invoke
    return _process_result(sub_ctx.command.invoke(sub_ctx))
  File "/Users/bris469/miniconda3/envs/hundo-dev/lib/python3.6/site-packages/click/core.py", line 956, in invoke
    return ctx.invoke(self.callback, **ctx.params)
  File "/Users/bris469/miniconda3/envs/hundo-dev/lib/python3.6/site-packages/click/core.py", line 555, in invoke
    return callback(*args, **kwargs)
  File "/Users/bris469/miniconda3/envs/hundo-dev/lib/python3.6/site-packages/biom/cli/table_converter.py", line 129, in convert
    table_type, process_obs_metadata, tsv_metadata_formatter)
  File "/Users/bris469/miniconda3/envs/hundo-dev/lib/python3.6/site-packages/biom/cli/table_converter.py", line 207, in _convert
    write_biom_table(result, fmt, output_filepath)
  File "/Users/bris469/miniconda3/envs/hundo-dev/lib/python3.6/site-packages/biom/cli/util.py", line 26, in write_biom_table
    f.write(table.to_json(biom.parse.generatedby()))
  File "/Users/bris469/miniconda3/envs/hundo-dev/lib/python3.6/site-packages/biom/table.py", line 4278, in to_json
    raise TableException("Unsupported matrix data type.")
biom.exception.TableException: Unsupported matrix data type.

And here’s my .txt feature table.
featured_converted.txt (11.9 KB)

Colin

missing --to-json modifier?

biom convert -i ~/featured_converted.txt -o ~/featured_converted.biom --process-obs-metadata sc_separated --table-type “OTU table” --to-json

featured_converted.biom (20.0 KB)

Thanks Ben.

It’s still not working for me… I wonder if it’s due to OSX or something else in my conda environment.

Github issue: https://github.com/biocore/biom-format/issues/816

Here’s my conda list

# packages in environment at /Users/bris469/miniconda3/envs/hundo-dev:
#
# Name                    Version                   Build  Channel
aioeasywebdav             2.4.0                 py36_1000    conda-forge
aiohttp                   3.5.4            py36h1de35cc_0    conda-forge
appdirs                   1.4.3                      py_1    conda-forge
asn1crypto                0.24.0                py36_1003    conda-forge
async-timeout             3.0.1                   py_1000    conda-forge
attrs                     19.1.0                     py_0    conda-forge
bbmap                     37.17                         1    bioconda
bcrypt                    3.1.4            py36h470a237_0    conda-forge
biom-format               2.1.6            py36h7eb728f_0    conda-forge
biopython                 1.73             py36h1de35cc_0    conda-forge
blast                     2.6.0               boost1.64_2    bioconda
boto3                     1.9.137                    py_0    conda-forge
botocore                  1.12.137                   py_0    conda-forge
bzip2                     1.0.6             h1de35cc_1002    conda-forge
ca-certificates           2019.3.9             hecc5488_0    conda-forge
cachetools                2.1.0                      py_0    conda-forge
certifi                   2019.3.9                 py36_0    conda-forge
cffi                      1.12.3           py36hccf1714_0    conda-forge
chardet                   3.0.4                 py36_1003    conda-forge
click                     7.0                        py_0    conda-forge
configargparse            0.13.0                     py_1    conda-forge
cryptography              2.6.1            py36h212c5bf_0    conda-forge
datrie                    0.7.1            py36h1de35cc_0    conda-forge
decorator                 4.4.0                      py_0    conda-forge
docutils                  0.14                  py36_1001    conda-forge
dropbox                   9.2.0                      py_0    conda-forge
fasttree                  2.1.10               h1de35cc_3    bioconda
filechunkio               1.8                        py_2    conda-forge
freetype                  2.10.0               h24853df_0    conda-forge
ftputil                   3.4                        py_0    conda-forge
future                    0.17.1                py36_1000    conda-forge
gitdb2                    2.0.5                      py_0    conda-forge
gitpython                 2.1.11                     py_0    conda-forge
google-api-core           1.11.0                   py36_0    conda-forge
google-auth               1.6.3                      py_0    conda-forge
google-cloud-core         0.29.1                     py_0    conda-forge
google-cloud-storage      1.15.0                     py_0    conda-forge
google-resumable-media    0.3.2                      py_0    conda-forge
googleapis-common-protos  1.5.9                         1    conda-forge
graphviz                  2.38.0            hc6cc99f_1011    conda-forge
hundo                     1.3.0                    pypi_0    pypi
idna                      2.8                   py36_1000    conda-forge
idna_ssl                  1.1.0                 py36_1000    conda-forge
jinja2                    2.10.1                     py_0    conda-forge
jmespath                  0.9.4                      py_0    conda-forge
jpeg                      9c                h1de35cc_1001    conda-forge
jsonschema                3.0.1                    py36_0    conda-forge
libblas                   3.8.0                7_openblas    conda-forge
libcblas                  3.8.0                7_openblas    conda-forge
libcxx                    8.0.0                         2    conda-forge
libcxxabi                 8.0.0                         2    conda-forge
libffi                    3.2.1             h6de7cb9_1006    conda-forge
libgfortran               3.0.1                         0    conda-forge
liblapack                 3.8.0                7_openblas    conda-forge
libpng                    1.6.37               h2573ce8_0    conda-forge
libprotobuf               3.7.1                hfbae3c0_0    conda-forge
libtiff                   4.0.10            h79f4b77_1001    conda-forge
mafft                     7.313                         1    bioconda
markupsafe                1.1.1            py36h1de35cc_0    conda-forge
multidict                 4.5.2           py36h1de35cc_1000    conda-forge
ncurses                   6.1               h0a44026_1002    conda-forge
networkx                  2.3                        py_0    conda-forge
numpy                     1.16.4           py36h6b0580a_0    conda-forge
openblas                  0.3.5             h436c29b_1001    conda-forge
openjdk                   11.0.1            h01d97ff_1016    conda-forge
openssl                   1.1.1b               h01d97ff_2    conda-forge
pandas                    0.24.2           py36h86efe34_0    conda-forge
paramiko                  2.4.2                 py36_1000    conda-forge
pip                       19.1                     py36_0    conda-forge
prettytable               0.7.2                      py_2    conda-forge
protobuf                  3.7.1            py36h6de7cb9_0    conda-forge
psutil                    5.6.2            py36h01d97ff_0    conda-forge
pyasn1                    0.4.4                      py_1    conda-forge
pyasn1-modules            0.2.4                      py_0    conda-forge
pycparser                 2.19                     py36_1    conda-forge
pygraphviz                1.5             py36h1de35cc_1000    conda-forge
pynacl                    1.3.0           py36h1de35cc_1000    conda-forge
pyopenssl                 19.0.0                   py36_0    conda-forge
pyrsistent                0.15.2           py36h01d97ff_0    conda-forge
pysftp                    0.2.9                      py_1    conda-forge
pysocks                   1.7.0                    py36_0    conda-forge
python                    3.6.7             h8dc6b48_1004    conda-forge
python-dateutil           2.8.0                      py_0    conda-forge
python-irodsclient        0.7.0                      py_0    conda-forge
pytz                      2019.1                     py_0    conda-forge
pyyaml                    5.1              py36h1de35cc_0    conda-forge
ratelimiter               1.2.0                 py36_1000    conda-forge
readline                  7.0               hcfe32e1_1001    conda-forge
requests                  2.22.0                   py36_0    conda-forge
rsa                       3.4.2                      py_1    conda-forge
s3transfer                0.2.0                    py36_0    conda-forge
scipy                     1.3.0            py36hab3da7d_0    conda-forge
setuptools                41.0.1                   py36_0    conda-forge
six                       1.12.0                py36_1000    conda-forge
smmap2                    2.0.5                      py_0    conda-forge
snakemake                 5.4.5                         0    bioconda
snakemake-minimal         5.4.5                      py_0    bioconda
sqlite                    3.26.0            h1765d9f_1001    conda-forge
tk                        8.6.9             ha441bb4_1001    conda-forge
typing_extensions         3.7.2                 py36_1001    conda-forge
urllib3                   1.24.3                   py36_0    conda-forge
vsearch                   2.13.4               hacce2fa_4    bioconda
wheel                     0.33.4                   py36_0    conda-forge
wrapt                     1.11.1           py36h01d97ff_0    conda-forge
xmlrunner                 1.7.7                      py_0    conda-forge
xz                        5.2.4             h1de35cc_1001    conda-forge
yaml                      0.1.7             h1de35cc_1001    conda-forge
yarl                      1.3.0           py36h1de35cc_1000    conda-forge
zlib                      1.2.11            h1de35cc_1004    conda-forge

Weird, I’m simply running a biom convert built into a QIIME1.9.1 conda environment.

Name Version Build Channel

appnope 0.1.0 py27_0
backports 1.0 py27_0
biom-format 2.1.5 py27_3 bioconda
burrito 0.9.1 py27_0 bioconda
burrito-fillings 0.1.1 py27_0 bioconda
click 6.6 py27_0 bioconda
cogent 1.5.3 py27_0 bioconda
decorator 4.0.10 py27_1
emperor 0.9.51 py27_0 bioconda
enum34 1.1.6 py27_0
freetype 2.5.5 1
funcsigs 1.0.2 py27_0
future 0.16.0 py27_0
gdata 2.0.18 py27_0
get_terminal_size 1.0.0 py27_0
h5py 2.6.0 np110py27_1
hdf5 1.8.16 0
ipython 5.1.0 py27_1
ipython_genutils 0.1.0 py27_0
libpng 1.6.17 0
matplotlib 1.4.3 np110py27_3
mkl 11.3.3 0
mock 2.0.0 py27_0
natsort 3.5.0 py27_0
nose 1.3.7 py27_1
numpy 1.10.4 py27_2
openssl 1.0.2j 0
pandas 0.18.1 np110py27_0
path.py 9.0.1 py27_0
pathlib2 2.1.0 py27_0
pbr 1.10.0 py27_0
pexpect 4.0.1 py27_0
pickleshare 0.7.4 py27_0
pip 9.0.1 py27_1
prompt_toolkit 1.0.9 py27_0
ptyprocess 0.5.1 py27_0
pygments 2.1.3 py27_0
pynast 1.2.2 py27_0 bioconda
pyparsing 2.0.3 py27_0
pyqi 0.3.2 py27_0 bioconda
pyqt 4.11.4 py27_4
python 2.7.13 0
python-dateutil 2.3 py27_0 bioconda
pytz 2016.10 py27_0
qcli 0.1.1 py27_0 bioconda
qiime 1.9.1 np110py27_0 bioconda
qiime-default-reference 0.1.3 py27_0 bioconda
qt 4.8.7 4
readline 6.2 2
scikit-bio 0.2.3 np110py27_0 bioconda
scipy 0.17.1 np110py27_1
setuptools 27.2.0 py27_0
simplegeneric 0.8.1 py27_1
sip 4.18 py27_0
six 1.10.0 py27_0
sqlite 3.13.0 0
tk 8.5.18 0
traitlets 4.3.1 py27_0
wcwidth 0.1.7 py27_0
wheel 0.29.0 py27_0
zlib 1.2.8 3

Thanks for working through this with me.

Strange! We have a mystery :face_with_monocle:

I’ve just updated my biom-format but it didn’t seem to help…
biom-format 2.1.6-py36h7eb728f_0 --> 2.1.7-py36h917ab60_1002

:woman_shrugging:
Colin

1 Like

I just forgot, but when I ran it with your code, it asked for a biom format, that’s why I put in the -json modifier. So, it ran, I did not get the same error. Maybe just update your environment all together and see if ti gets ride of the error? Ben