Trying to convert txt. file to biom file

30 views
Skip to first unread message

Incog Nito

unread,
Oct 22, 2017, 2:21:45 PM10/22/17
to Qiime 1 Forum
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/__init__.py", line 738, in run_script

  File "build/bdist.linux-x86_64/egg/pkg_resources/__init__.py", 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/__init__.py", 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/interface.py", 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/command.py", line 137, in __call__

    result = self.run(**kwargs)

  File "/ycga-gpfs/apps/hpc/software/Python/2.7.13-foss-2016b/lib/python2.7/site-packages/biom/commands/table_converter.py", 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!


test.xlsx

Incog Nito

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

zech xu

unread,
Oct 23, 2017, 5:01:25 PM10/23/17
to Qiime 1 Forum
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.
x.tsv
Reply all
Reply to author
Forward
0 new messages