# Error message for Biom Convert
**URL:** https://forum.qiime2.org/t/error-message-for-biom-convert/23753
**Category:** Other Bioinformatics Tools
**Tags:** biom
**Created:** [August 1, 2022, 1:20am UTC](https://forum.qiime2.org/t/error-message-for-biom-convert/23753 "2022-08-01T01:20:28Z")
**Posts on this page:** 10
**Page:** 1
### Author:  [@csung7](https://forum.qiime2.org/u/csung7)
#### Post date: [August 1, 2022, 1:20am UTC](https://forum.qiime2.org/t/error-message-for-biom-convert/23753/1 "2022-08-01T01:20:28Z")
Hi,
I am having an issue with using conda environment. I am trying to make biom files.
Below are the command lines that I am running.
conda activate qiime2-2022.2
cd projects
cd pilot
cd 0729
biom convert -i taxa\_L3.txt -o taxa\_L3.biom --table-type="OTU table" --to-json
biom add-metadata -i taxa\_L3.biom -o taxa\_L3\_meta.biom -m metadata.txt --observation-metadata-fp taxonomy\_L3.txt
However, I am getting the same error message as shown below. I have found a similar problem from previous post in the forum, but I was not able to solve the problem on my end.
From the previous post, I ran R -e ".libPaths()" and got below result. Can you help me how to solve the problem?
Thank you.
---
### Author:  [@jwdebelius](https://forum.qiime2.org/u/jwdebelius)
#### Post date: [August 1, 2022, 2:16pm UTC](https://forum.qiime2.org/t/error-message-for-biom-convert/23753/2 "2022-08-01T14:16:57Z")
Hi @csung7,
Just letting you know that I re-classified as "Other bioinformatic tools" and re-named it to make the title more clear!
Best,
Justine
---
### Author:  [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)
#### Post date: [August 1, 2022, 5:14pm UTC](https://forum.qiime2.org/t/error-message-for-biom-convert/23753/3 "2022-08-01T17:14:41Z")
Hi @csung7, You most likely need to pass the `--observation-header` parameter as it looks like your taxonomy file does not include column headers. This is documented in the biom-format documentation [here](http://biom-format.org/documentation/adding_metadata.html#renaming-or-naming-metadata-columns-while-adding). I suspect that you may need to adapt your command as follows:
```auto
biom add-metadata -i taxa_L3.biom -o taxa_L3_meta.biom -m metadata.txt --observation-metadata-fp taxonomy_L3.txt --observation-header OTUID,taxonomy,confidence
```
However the specifics will depend on what columns are in the `taxonomy_L3.txt` file, which in turn depends on how that file was created. If that command doesn't work, take a look at the `taxonomy_L3.txt` file by running the following command:
```auto
head -n 5 taxonomy_L3.txt
```
You should see the first few lines of that file, and that will allow you to determine which columns are present. You can adapt the value you provide for `--observation-header ` accordingly.
I hope this helps!
---
### Author:  [@csung7](https://forum.qiime2.org/u/csung7)
#### Post date: [August 1, 2022, 10:25pm UTC](https://forum.qiime2.org/t/error-message-for-biom-convert/23753/4 "2022-08-01T22:25:50Z")
Thank you for your response.
Based on your response, I ran commands but still having an issue. Please see below. I also added text files that I am using.
- taxa\_L3.txt
- taxonomy\_L3.txt
---
### Author:  [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)
#### Post date: [August 2, 2022, 1:48pm UTC](https://forum.qiime2.org/t/error-message-for-biom-convert/23753/5 "2022-08-02T13:48:00Z")
Hi @csung7, It looks like you have only two columns of metadata in your `taxonomy_L3.txt` file. Try running the following:
```auto
biom add-metadata -i taxa_L3.biom -o taxa_L3_meta.biom -m metadata.txt --observation-metadata-fp taxonomy_L3.txt --observation-header OTUID,taxonomy
```
---
### Author:  [@csung7](https://forum.qiime2.org/u/csung7)
#### Post date: [August 5, 2022, 3:18am UTC](https://forum.qiime2.org/t/error-message-for-biom-convert/23753/6 "2022-08-05T03:18:19Z")
Thank you for your reply. I have three files: taxa (as "taxa\_L3.txt), taxonomic information column data (as "taxonomy\_L3.txt" that includes only taxonomic information with two columns), and metadata (e.g., patients' age, race/ethnicity, and clinical information).
I ran the command line that you provided. But, I am still getting the same error message.
---
### Author:  [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)
#### Post date: [August 7, 2022, 11:13pm UTC](https://forum.qiime2.org/t/error-message-for-biom-convert/23753/7 "2022-08-07T23:13:03Z")
Hi @csung7, Can you provide the first few lines of the `metadata.txt` file? You can do this by pasting the output of running:
```auto
head -n 5 metadata.txt
```
Thanks!
---
### Author:  [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)
#### Post date: [August 7, 2022, 11:13pm UTC](https://forum.qiime2.org/t/error-message-for-biom-convert/23753/8 "2022-08-07T23:13:18Z")
---
### Author:  [@system](https://forum.qiime2.org/u/system)
#### Post date: [September 8, 2022, 5:13am UTC](https://forum.qiime2.org/t/error-message-for-biom-convert/23753/9 "2022-09-08T05:13:25Z")
This topic was automatically closed 31 days after the last reply. New replies are no longer allowed.
---
### Author:  [@gregcaporaso](https://forum.qiime2.org/u/gregcaporaso)
#### Post date: [September 29, 2022, 12:06am UTC](https://forum.qiime2.org/t/error-message-for-biom-convert/23753/10 "2022-09-29T00:06:11Z")