RuntimeError: h5py is not installed - it is installed

[Vini Salazar]

Hello guys, first of all thanks for the open source software and all the great support.

I'm still struggling to start using qiime. I have managed to do a successful native base install on OS X after having a few problems.

While doing the 454 Overview Tutorial, when I input the command:

$ biom summarize_table -i otus/otu_table.biom

I get the following output:

Traceback (most recent call last):

  File "/Library/Frameworks/Python.framework/Versions/2.7/bin/biom", line 9, in <module>

    load_entry_point('biom-format==2.1.5', 'console_scripts', 'biom')()

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click/core.py", line 700, in __call__

    return self.main(*args, **kwargs)

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click/core.py", line 680, in main

    rv = self.invoke(ctx)

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click/core.py", line 1027, in invoke

    return _process_result(sub_ctx.command.invoke(sub_ctx))

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click/core.py", line 873, in invoke

    return ctx.invoke(self.callback, **ctx.params)

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/click/core.py", line 508, in invoke

    return callback(*args, **kwargs)

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/biom/cli/table_summarizer.py", line 47, in summarize_table

    table = load_table(input_fp)

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/biom/parse.py", line 652, in load_table

    with biom_open(f) as fp:

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/contextlib.py", line 17, in __enter__

    return self.gen.next()

  File "/Library/Frameworks/Python.framework/Versions/2.7/lib/python2.7/site-packages/biom/util.py", line 444, in biom_open

    raise RuntimeError("h5py is not installed, cannot parse HDF5 "

RuntimeError: h5py is not installed, cannot parse HDF5 BIOM file

However, I have h5py and HDF5 installed. I can check it when I run the config script:

$ print_qiime_config.py -t

System information

==================

         Platform:      darwin

   Python version:      2.7.11 |Anaconda 2.3.0 (x86_64)| (default, Dec  6 2015, 18:57:58)  [GCC 4.2.1 (Apple Inc. build 5577)]

Python executable:      //anaconda/bin/python

QIIME default reference information

===================================

For details on what files are used as QIIME's default references, see here:

 https://github.com/biocore/qiime-default-reference/releases/tag/0.1.3

Dependency versions

===================

          QIIME library version:        1.9.0-rc2

           QIIME script version:        1.9.0-rc2

qiime-default-reference version:        0.1.3

                  NumPy version:        1.10.4

                  SciPy version:        0.17.0

                 pandas version:        0.16.2

             matplotlib version:        1.4.3

            biom-format version:        2.1.2

                   h5py version:        2.5.0 (HDF5 version: 1.8.15)

                   qcli version:        0.1.1

                   pyqi version:        0.3.2

             scikit-bio version:        0.2.3

                 PyNAST version:        1.2.2

                Emperor version:        0.9.5

                burrito version:        0.9.1

       burrito-fillings version:        Installed.

              sortmerna version:        SortMeRNA version 2.0, 29/11/2014

              sumaclust version:        Not installed.

                  swarm version:        Swarm 1.2.19 [Jan 29 2015 09:06:53]

                          gdata:        Installed.

QIIME config values

===================

For definitions of these settings and to learn how to configure QIIME, see here:

 http://qiime.org/install/qiime_config.html

 http://qiime.org/tutorials/parallel_qiime.html

                     blastmat_dir:      None

      pick_otus_reference_seqs_fp:      //anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

                         sc_queue:      all.q

      topiaryexplorer_project_dir:      None

     pynast_template_alignment_fp:      //anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set_aligned/85_otus.pynast.fasta

                  cluster_jobs_fp:      start_parallel_jobs.py

pynast_template_alignment_blastdb:      None

assign_taxonomy_reference_seqs_fp:      //anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/rep_set/97_otus.fasta

                     torque_queue:      friendlyq

                    jobs_to_start:      1

            denoiser_min_per_core:      50

assign_taxonomy_id_to_taxonomy_fp:      //anaconda/lib/python2.7/site-packages/qiime_default_reference/gg_13_8_otus/taxonomy/97_otu_taxonomy.txt

                         temp_dir:      /tmp/

                     slurm_memory:      None

                      slurm_queue:      None

                      blastall_fp:      blastall

                 seconds_to_sleep:      1

QIIME base install test results

===============================

.........

----------------------------------------------------------------------

Ran 9 tests in 0.033s

OK

I have tried reinstalling both packages to no avail. I've searched the forum for solutions but couldn't find any. Sorry if this is a silly question but I'm a beginner user and new to this type of tool, so any other advice is appreciated.

Thanks a lot

[zech xu]

Hello,

I noticed you were using anaconda from your qiime config, but the biom error message shows that your global biom library is used. Probably you have installed two bioms, one globally and the other in your anaconda virtual env. First, could you double check you print_qiime_config.py and your biom command were run in the same virtual environment? And if so and you still get the error, could you check your anaconda env dir to see if you have another biom installed in that virtual env?

[Vini Salazar]

I run both of them on the command line without making any intentional changes to which virtual environment was used, like explained in the linked tutorial. My biom apparently is installed in the anaconda env dir.

[zech xu]

You error message clearly shows the biom you were using is not from anaconda virtual env: /Library/Frameworks/Python.framework/Versions/2.7/bin/biom

[Vini Salazar]

Thanks for pointing that out. Do you have any suggestions on how to fix it? I get the error message for the h5py package, and not the biom package

[Colin Brislawn]

Try loading the conda virtual environment first, then running the scripts from inside the environment. 

Colin

[Vini Salazar]

Thanks for the reply Colin.

I have, and I get the same error message.

[Colin Brislawn]

Hum... I think there is some small step I'm missing when trying to activate the environment. 

Try this,

Open a new terminal or ssh connection. Then run

which python

source activate YourQiimeEnvironmentName

which python

conda list

which print_qiime_config.py

print_qiime_config,py -t

I feel like I'm missing something, but I'm not sure what. Thank you for helping me find it.

Colin