# PhyloPhlAn database

**URL:** <https://forum.biobakery.org/t/phylophlan-database/725>\
**Category:** PhyloPhlAn\
**Created:** [July 15, 2020, 3:08pm UTC](https://forum.biobakery.org/t/phylophlan-database/725 "2020-07-15T15:08:39Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![barbara\_shih](https://avatars.discourse-cdn.com/v4/letter/b/258eb7/32.png) [@barbara\_shih](https://forum.biobakery.org/u/barbara_shih)\
**Post date:** [July 15, 2020, 3:08pm UTC](https://forum.biobakery.org/t/phylophlan-database/725/1 "2020-07-15T15:08:39Z")

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I tried to run phylophlan, but I couldn’t understand the error it is giving me.

I noticed that phylophlan.dmnd seems to be a very small file (104 byte). I tried to run diamond using the phylophlan.dmnd, but it wouldn’t work. I am wondering if there is a link that I can download this file from?

Thank you

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**Author:** ![f.asnicar](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/f.asnicar/32/196_2.png) [@f.asnicar](https://forum.biobakery.org/u/f.asnicar)\
**Post date:** [July 15, 2020, 7:28pm UTC](https://forum.biobakery.org/t/phylophlan-database/725/2 "2020-07-15T19:28:14Z")

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Hi,

the `phylophlan.dmnd` should be 178M, so I guess something went wrong with diamond during the database creation.  
PhyloPhlAn automatically downloads the database file and the build the index at runtime. So, you can check that the in database folder you should have a folder named `phylophlan` that contains: `phylophlan.faa` (175M) and `phylophlan.faa.bz2` (65M). If this is the case, please remove the `phylophlan.dmnd` and re-run PhyloPhlAn. If the above 2 files have different dimensions it might be that they were not properly downloaded, so you can remove the whole database folder `phylophlan` and re-run PhyloPhlAn.

In re-runnning PhyloPhlAn please use the `--verbose` param and store the output to a file, so that you should have any problem you can also provide the output file that can help understand what’s not working.

Many thanks,  
Francesco

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**Author:** ![barbara\_shih](https://avatars.discourse-cdn.com/v4/letter/b/258eb7/32.png) [@barbara\_shih](https://forum.biobakery.org/u/barbara_shih)\
**Post date:** [July 22, 2020, 10:34am UTC](https://forum.biobakery.org/t/phylophlan-database/725/3 "2020-07-22T10:34:32Z")

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Thank you. Removing the folder and re-running helped.