Trying to convert txt. file to biom file

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Incog Nito

Oct 22, 2017, 2:21:45 PM10/22/17
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Can someone help?

Tried the following command:

biom convert -i OTU_original.txt -o OTU_original.biom --table-type "OTU table" --to-hdf5 --process-obs-metadata taxonomy

this is what I got:

biom convert: error: option -i: file does not exist: 'OTU.txt'

-bash-4.2$ biom convert -i OTU_original.txt -o OTU_original.biom --table-type "OTU table" --process-obs-metadata taxonomy

Traceback (most recent call last):

  File "/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/bin/pyqi", line 4, in <module>

    __import__('pkg_resources').run_script('pyqi==0.3.2', 'pyqi')

  File "build/bdist.linux-x86_64/egg/pkg_resources/", line 738, in run_script

  File "build/bdist.linux-x86_64/egg/pkg_resources/", line 1499, in run_script

  File "/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/lib/python2.7/site-packages/pyqi-0.3.2-py2.7.egg/EGG-INFO/scripts/pyqi", line 184, in <module>

    optparse_main(cmd_obj, argv[1:])

  File "/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/lib/python2.7/site-packages/pyqi-0.3.2-py2.7.egg/pyqi/core/interfaces/optparse/", line 275, in optparse_main

    result = optparse_cmd(local_argv[1:])

  File "/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/lib/python2.7/site-packages/pyqi-0.3.2-py2.7.egg/pyqi/core/", line 39, in __call__

    cmd_result = self.CmdInstance(**cmd_input)

  File "/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/lib/python2.7/site-packages/pyqi-0.3.2-py2.7.egg/pyqi/core/", line 137, in __call__

    result =**kwargs)

  File "/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/lib/python2.7/site-packages/biom/commands/", line 217, in run

    raise CommandError(convert_error_msg)

pyqi.core.exception.CommandError: Input does not look like a classic table. Did you forget to specify that a classic table file should be created from a BIOM table file?

Help would be very much appreciated - I am super lost!


Incog Nito

Oct 23, 2017, 3:19:48 PM10/23/17
to Qiime 1 Forum

zech xu

Oct 23, 2017, 5:01:25 PM10/23/17
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Hi Incog,

Are you using the table you attached in the email? It does not like a classic table file to convert to biom format. It should be something like what I attached here.
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