TypeError: Object dtype dtype('O') has no native HDF5 equivalent

[Yukinobu Kutsuwada]

Hi.All

I'm a QIIME beginner, thank you.

I upgraded version from 1.8.0 to 1.9.1. and errors occur.

I understand biom-format change, from json to hdf5, but I don't know how to solve them.

Traceback (most recent call last):

  File "/macqiime/anaconda/bin/single_rarefaction.py", line 87, in <module>

    main()

  File "/macqiime/anaconda/bin/single_rarefaction.py", line 84, in main

    empty_otus_removed=(not opts.keep_empty_otus), subsample_f=subsample_f)

  File "/macqiime/anaconda/lib/python2.7/site-packages/qiime/rarefaction.py", line 68, in rarefy_to_file

    self._write_rarefaction(output_fname, sub_otu_table)

  File "/macqiime/anaconda/lib/python2.7/site-packages/qiime/rarefaction.py", line 75, in _write_rarefaction

    write_biom_table(sub_otu_table, fname)

  File "/macqiime/anaconda/lib/python2.7/site-packages/qiime/util.py", line 577, in write_biom_table

    biom_table.to_hdf5(biom_file, generated_by, compress)

  File "/macqiime/anaconda/lib/python2.7/site-packages/biom/table.py", line 3605, in to_hdf5

    self.group_metadata(axis='observation'), 'csr', compression)

  File "/macqiime/anaconda/lib/python2.7/site-packages/biom/table.py", line 3577, in axis_dump

    formatter[category](grp, category, md, compression)

  File "/macqiime/anaconda/lib/python2.7/site-packages/biom/table.py", line 246, in general_formatter

    compression=compression)

  File "/macqiime/anaconda/lib/python2.7/site-packages/h5py/_hl/group.py", line 105, in create_dataset

    dsid = dataset.make_new_dset(self, shape, dtype, data, **kwds)

  File "/macqiime/anaconda/lib/python2.7/site-packages/h5py/_hl/dataset.py", line 93, in make_new_dset

    tid = h5t.py_create(dtype, logical=1)

  File "h5py/h5t.pyx", line 1450, in h5py.h5t.py_create (/Users/ilan/minonda/conda-bld/work/h5py/h5t.c:16090)

  File "h5py/h5t.pyx", line 1470, in h5py.h5t.py_create (/Users/ilan/minonda/conda-bld/work/h5py/h5t.c:15924)

  File "h5py/h5t.pyx", line 1525, in h5py.h5t.py_create (/Users/ilan/minonda/conda-bld/work/h5py/h5t.c:15825)

TypeError: Object dtype dtype('O') has no native HDF5 equivalent

QIIME config is: 

System information

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

         Platform: darwin

   Python version: 2.7.13 |Anaconda 2.2.0 (x86_64)| (default, Dec 20 2016, 23:05:08)  [GCC 4.2.1 Compatible Apple LLVM 6.0 (clang-600.0.57)]

Python executable: /macqiime/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: 1.9.1

           QIIME script version: 1.9.1

qiime-default-reference version: 0.1.3

                  NumPy version: 1.12.1

                  SciPy version: 0.19.0

                 pandas version: 0.19.2

             matplotlib version: 2.0.0

            biom-format version: 2.1.5

                   h5py version: 2.6.0 (HDF5 version: 1.8.17)

                   qcli version: 0.1.1

                   pyqi version: 0.3.2

             scikit-bio version: 0.2.3

                 PyNAST version: 1.2.2

                Emperor version: 0.9.60

                burrito version: 0.9.1

       burrito-fillings version: 0.1.1

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

              sumaclust version: SUMACLUST Version 1.0.00

                  swarm version: Swarm 1.2.19 [Mar 17 2017 17:53:06]

                          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: /macqiime/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: /macqiime/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: /macqiime/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

                       slurm_time: None

            denoiser_min_per_core: 50

assign_taxonomy_id_to_taxonomy_fp: /macqiime/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: 60

QIIME base install test results

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

.........

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

Ran 9 tests in 0.052s

What can I do??

Thank you for your help!!

yukinobu

[Yukinobu Kutsuwada]

Hi.All

Sorry, I may notice my mistake.

I will challenge continuously.

Thank you for all.

Yukinobu

[Daniel McDonald]

Hi Yukinobu,

Okay, thanks. My guess is that the BIOM table has an unexpected format...

Best,

Daniel

[Yukinobu Kutsuwada]

Hi Daniel,

Yes, I think so too.

So, I'm checking my biom file again.

Thanks for you reaction!

Best,

Yukinobu