Cannot get json formatted biom file to load in phinch at all.

[Emily Cole]

I cannot get my biom file to load in Phinch.

Here is the biom file info:

{"id": "None","format": "Biological Observation Matrix 1.0.0","format_url": "http://biom-format.org","matrix_type": "sparse","generated_by": "BIOM-Format 2.1.4","date": "2015-08-15T17:17:34.616747","type": "OTU table","matrix_element_type": "float","shape": [1160, 25],"data":

When I load into phinch, it never even progresses past the spinning taxa wheel....

Anyone have a suggestion, I have converted back and forth form txt to json biom several time with no luck.

I'm relatively new to QIIME so it may be in the script, all help is welcome.

[Emily Cole]

To add more specific data, i'm working with macqiime, 1.9.1

16s rRNA otu tables, with metadata and taxonomy....

[Holly Bik]

Hi Emily,

You're not the only one who has been having problems with QIIME 1.9 files - I will look into this further, but in the meantime you can follow the troubleshooting advice listed here:

For users having trouble with QIIME 1.9 file conversion, please troubleshoot according to this thread:https://github.com/PitchInteractiveInc/Phinch/issues/46

If your BIOM 1.0 file is correctly formatted and still not working, then can you try the suggestions in this thread (converting back to classic OTU table and then back to BIOM with metadata re-added):https://groups.google.com/forum/#!topic/phinch/rsIk8DCQ0VM

Let me know if you get it to work in the meantime.

-Holly 

[Jay T]

Holly I have used your commands before but I am having the same issue. Did the commands change? 

I've attached my biom file created in qiime 1.91.

I added my metadata and then converted it to JSON and PHINCH just did the spinning wheel thing.

Please help!!

Thanks,

JT

[Chloe Stenkamp-strahm]

Hi Holly,

I'm having the same issue with the QIIME 1.9 hdf5 files. I've been going through all of the trouble shooting notes on these forums (converting to json, converting to classic OTU table, etc) but not having any luck. I'm wondering if someone has come across a fix for this issue?

I can give many more specifics on what I'm doing/files, but figured if the issue had been resolved you could just point me in the right direction?

Thanks for your help,

Chloe

[Holly Bik]

Jay and Chloe,

I'm not sure what the problem is, but here are some further things you can try:

1. Use "incognito" mode in Chrome to access Phinch - sometimes removing the browser cache via anonymous browsing will fix the spinning wheel

2. Check the line breaks on the converted file using a text editor such as TextWrangler or BBedit - they should be Unix line feeds (LF), NOT carraige returns (CRs - this sometimes gets changed if you open a tab-delimited file in Excel)

3. Try making a new BIOM file using the OTU map that gets outputted from the pick_otus.py worflow. An example command would be as follows:

make_otu_table.py -i final_otu_map_mc2.txt -o otu_table_mc2_w_tax.biom -t rep_set_tax_assignments.txt

(Your BIOM file may be outputted in HDF5 format if you're using QIIME 1.9 - so use the "head" command to look at the text file output)

4. Get access to QIIME 1.8 somehow, and execute the above make_otu_table.py command - this will avoid the HDF5 BIOM 2.0 file issue entirely. I use MacQIIME on my local laptop, and it is super easy to switch back and forth between QIIME versions (basically you just rename folders and refresh the terminal windows). Amazon EC2 and many University HPC systems also support several QIIME versions with different modules.

On QIIME 1.8, after you make the OTU table you will then have to add the metadata before loading the JSON-formatted BIOM file into Phinch: 

biom add-metadata -i otu_table_mc2_w_tax.biom -o otu_table_mc2_w_tax_and_metadata.biom -m sample_metadata_mapping_file.txt

Let me know if any of these suggestions does the trick! And if you find out what was the issue with QIIME 1.9 files, please let me know too - many people seem to be encountering the same error.

Thanks,

Holly

[Jay T]

I decided to just create a qiime 1.8 virtual box installation and run the make_otu_table.py command followed by the add_metadata.py command and it works without a hitch. Also I made sure to make my categories numerical, as phinch doesn't seem to play nice with actual names.

Thanks Holly,

JT