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biocore / qiime

Official QIIME 1 software repository. QIIME 2 (https://qiime2.org) has succeeded QIIME 1 as of January 2018.
GNU General Public License v2.0
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Trying to convert txt. file to biom file #2204

Closed Acetylcholine88 closed 6 years ago

Acetylcholine88 commented 6 years ago

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 

__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 

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

jairideout commented 6 years ago

Can you post this on the biom-format issue tracker? Thanks!