# Error with biom.info

**URL:** <https://forum.mothur.org/t/error-with-biom-info/20246>\
**Category:** Integrating mothur with other programs\
**Created:** [December 5, 2019, 3:18pm UTC](https://forum.mothur.org/t/error-with-biom-info/20246 "2019-12-05T15:18:48Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![xiangli](https://avatars.discourse-cdn.com/v4/letter/x/e56c9b/32.png) [@xiangli](https://forum.mothur.org/u/xiangli)\
**Post date:** [December 5, 2019, 3:18pm UTC](https://forum.mothur.org/t/error-with-biom-info/20246/1 "2019-12-05T15:18:49Z")

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Hi everyone,

I am trying to import a .biom file from metagenomeseq 1.16.0 to mothur (1.43.0), but it keeps giving me error message that  
[ERROR]: you file does not have a type provided.  
[ERROR]: you file does not have a matrix\_type provided.  
[ERROR]: you file does not have a matrix\_element\_type provided.  
[ERROR]: you file does not have a rows provided.  
[ERROR]: you file does not have a columns provided.  
[ERROR]: you file does not have a shape provided.  
[ERROR]: you file does not have a data provided.

The part of my biom file looks like this:  
{  
“id”: null,  
format: “Biological Observation Matrix 1.0.0-dev”,  
format\_url: “[http://biom-format.org/documentation/format\_versions/biom-1.0.html](http://biom-format.org/documentation/format_versions/biom-1.0.html)”,  
type: “OTU table”,  
generated\_by: “metagenomeSeq 1.16.0”,  
date: “2018-05-24 07:37:51”,  
matrix\_type: “dense”,  
matrix\_element\_type: “float”,  
shape: [5030, 237],  
rows: [  
{  
“id”: “OTU\_88”,  
metadata: {  
“taxonomy”: [“k\_\_Bacteria”, “p\_\_Proteobacteria”, “c\_\_Betaproteobacteria”, “o\_\_Burkholderiales”, “f\_\_Comamonadaceae”, “g\_\_Polaromonas”, “s\_\_”]  
}  
},  
{  
“id”: “OTU\_53”,  
metadata: {  
“taxonomy”: [“k\_\_Bacteria”, “p\_\_Bacteroidetes”, “c\_\_Sphingobacteriia”, “o\_\_Sphingobacteriales”, “f\_\_”, “g\_\_”, “s\_\_”]  
}  
},  
{  
“id”: “OTU\_1”,  
metadata: {  
“taxonomy”: [“k\_\_Bacteria”, “p\_\_Cyanobacteria”, “c\_\_Nostocophycideae”, “o\_\_Nostocales”, “f\_\_Nostocaceae”, “g\_\_Dolichospermum”, “s\_\_”]  
}  
},

Could anyone help with this? Thanks a lot!

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<div class="post-metadata">

**Author:** ![westcott](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/westcott/32/18_2.png) [@westcott](https://forum.mothur.org/u/westcott)\
**Post date:** [December 10, 2019, 3:51pm UTC](https://forum.mothur.org/t/error-with-biom-info/20246/2 "2019-12-10T15:51:40Z")

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Could you send your biom file and log file to [mothur.bugs@gmail.com](mailto:mothur.bugs@gmail.com) so I can take a closer look?

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**Author:** ![system](https://yyz2.discourse-cdn.com/flex036/user_avatar/forum.mothur.org/system/32/2_2.png) [@system](https://forum.mothur.org/u/system)\
**Post date:** [December 20, 2019, 3:51pm UTC](https://forum.mothur.org/t/error-with-biom-info/20246/3 "2019-12-20T15:51:47Z")

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