Biom add-metadata

Liam Shaw

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Apr 6, 2016, 9:05:46 AM4/6/16

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Hi,

I'm not able to replicate the biom add-metadata tutorial here (http://biom-format.org/documentation/adding_metadata.html).

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.

Thanks,

Liam

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:

https://github.com/biocore/qiime-default-reference/releases/tag/0.1.2

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:

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

min_sparse_otu_table.biom

obs_md.txt

jonsan

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Apr 6, 2016, 11:10:17 AM4/6/16

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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.

Cheers,

-jon

obs_md_tab.txt

Liam Shaw

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Apr 6, 2016, 11:19:18 AM4/6/16

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Hi Jon,

Works perfectly, thanks very much!

Cheers,

Liam

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