Biom add-metadata

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Liam Shaw

Apr 6, 2016, 9:05:46 AM4/6/16
to Qiime 1 Forum

I'm not able to replicate the biom add-metadata tutorial here ( 

The command 

biom add-metadata -i min_sparse_otu_table.biom -o table.w_omd.biom --observation-metadata-fp obs_md.txt

doesn't return an error. However, the table generated apparently contains no metadata. The output of biom summarize-table -i table.w_omd.biom is

Num samples: 6

Num observations: 5

Total count: 27

Table density (fraction of non-zero values): 0.500

Counts/sample summary:

 Min: 3.0

 Max: 7.0

 Median: 4.000

 Mean: 4.500

 Std. dev.: 1.500

 Sample Metadata Categories: None provided

 Observation Metadata Categories: None provided

Counts/sample detail:

Sample5: 3.0

Sample2: 3.0

Sample6: 4.0

Sample3: 4.0

Sample4: 6.0

Sample1: 7.0

i.e. no metadata seems to have been added. I've tried a number of combinations of converting between json/hdf5/tsv and nothing seems to work.  

What's gone wrong?

System information below.


System information


         Platform: darwin

   Python version: 2.7.10 |Anaconda 2.2.0 (x86_64)| (default, May 28 2015, 17:04:42)  [GCC 4.2.1 (Apple Inc. build 5577)]

Python executable: /macqiime/anaconda/bin/python

QIIME default reference information


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

Dependency versions


          QIIME library version: 1.9.1

           QIIME script version: 1.9.1

qiime-default-reference version: 0.1.2

                  NumPy version: 1.11.0

                  SciPy version: 0.17.0

                 pandas version: 0.16.1

             matplotlib version: 1.4.3

            biom-format version: 2.1.5

                   h5py version: 2.4.0 (HDF5 version: 1.8.14)

                   qcli version: 0.1.1

                   pyqi version: 0.3.2

             scikit-bio version: 0.2.3

                 PyNAST version: 1.2.2

                Emperor version: 0.9.51

                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 [Jun  2 2015 14:40:16]

                          gdata: Installed.

QIIME config values


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

                     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


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



Apr 6, 2016, 11:10:17 AM4/6/16
to Qiime 1 Forum
Hi Liam, 

The problem lies in the field separation in the metadata file. It's got spaces between fields, but it needs to be tab separated. Try it with the attached. 


Liam Shaw

Apr 6, 2016, 11:19:18 AM4/6/16
to Qiime 1 Forum
Hi Jon,

Works perfectly, thanks very much!

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