There was a problem importing redsea.biom: redsea.biom is not a(n) BIOMV210Format file

[bck243]

Hello!

I'm am running through the red sea tutorial and was not able to import the redsea.biom table.

I've just installed the latest conda (4.9.2) and qiime 2020.6.

Then I installed songbird within qiime. When I run qiime songbird --help, songbird seems to be installed properly, but I get a warning when refreshing cache.

Install songbird:

• source activate qiime2-2020.6
• pip install songbird
• qiime dev refresh-cache

  qiime dev refresh-cache QIIME is caching your current deployment for improved performance. This may take a few moments and should only happen once per deployment. /usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/ijson/backends/init.py:22: UserWarning: Cannot determine yajl version, assuming <1.0.12 warnings.warn('Cannot determine yajl version, assuming <1.0.12')

• check installation: qiime songbird --help

  
  Usage: qiime songbird [OPTIONS] COMMAND [ARGS]...
  
  Description: This is a QIIME 2 plugin supporting statistical models on
  feature tables and metadata.
  
  Plugin website: https://github.com/mortonjt/songbird
  
  Getting user support: Please post to the QIIME 2 forum for help with this
  plugin: https://forum.qiime2.org

Options: --version Show the version and exit. --citations Show citations and exit. --help Show this message and exit.

Commands: multinomial Multinomial regression summarize-paired Paired regression summary statistics summarize-single Regression summary statistics

I got the tutorial data like so: 
* `wget https://github.com/biocore/songbird/blob/master/data/redsea/feature_metadata.txt`
* `wget https://github.com/biocore/songbird/blob/master/data/redsea/redsea.biom`
* `wget https://github.com/biocore/songbird/blob/master/data/redsea/redsea_metadata.txt`

Then tried to run the tutorial:
* `source activate qiime2-2020.6`
* import biom table to qiime:
`qiime tools import \
    --input-path redsea.biom \
    --output-path redsea.biom.qza \
    --type FeatureTable[Frequency]`

And I get this error: 

/usr/local/path/installations/miniconda3/envs/qiime2-2020.6/lib/python3.6/site-packages/ijson/backends/init.py:22: UserWarning: Cannot determine yajl version, assuming <1.0.12 warnings.warn('Cannot determine yajl version, assuming <1.0.12') There was a problem importing redsea.biom:

redsea.biom is not a(n) BIOMV210Format file

So, I'm not sure if the problem is with the installation of songbird (yajl verison warning), or with the redsea.biom file. Any help would be appreciated. Thank you!

[gibsramen]

Hi, @bck243 .

I think the problem is that you cannot wget the biom file as you've done. When I did so and opened the file manually it was just an HTML page. You can download the files manually and it should work.

[bck243]

Thanks @gibsramen! I am still getting the "UserWarning: Cannot determine yajl version, assuming <1.0.12", with every command, but it is working now. Should I be concerned about the warning?

[mortonjt]

Glad to hear its working @bck243 !

Not only sure where that warning is happening - but this does appear to be happening in the qiime2 envrionment https://forum.qiime2.org/t/when-used-other-alpha-diversity-indices-showing-error-in-qiime2-2019-10/12816

[bck243]

Ok, thanks!