# Difficulty indexing reference database for metaphlan4

**URL:** <https://forum.biobakery.org/t/difficulty-indexing-reference-database-for-metaphlan4/4460>\
**Category:** MetaPhlAn\
**Created:** [December 1, 2022, 1:58am UTC](https://forum.biobakery.org/t/difficulty-indexing-reference-database-for-metaphlan4/4460 "2022-12-01T01:58:18Z")\
**Posts on this page:** 4\
**Page:** 1

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**Author:** ![lorcan1601](https://avatars.discourse-cdn.com/v4/letter/l/43a26b/32.png) [@lorcan1601](https://forum.biobakery.org/u/lorcan1601)\
**Post date:** [December 1, 2022, 1:58am UTC](https://forum.biobakery.org/t/difficulty-indexing-reference-database-for-metaphlan4/4460/1 "2022-12-01T01:58:18Z")

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Hi,

I am having trouble with building the index for metaphlan4. The download seems to work ok but the build step stalls after creating the bt2l .3 and .4 files. I initially tried within the miniconda environment but then I tried outside the environment and also just by using bowtie2 (on the fna file that the metaphlan -index command created) but it was same either way.

 ![Bowtie metaphlan files](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/7/741de6a5cd407098b74636562889df64e52287b5.jpeg)

I have Bowtie version 2.3.5.1. The command for bowtie was:

bowtie2-build ~/reference\_databases/mpa\_vJan21\_CHOCOPhlAnSGB\_202103.fna mpa\_vJan21\_CHOCOPhlAnSGB\_202103 -f -threads 4

It stalls (or seems to) at the same point and the traceback call is the message displayed after I abandon the process

 ![Bowtie output](https://canada1.discourse-cdn.com/flex027/uploads/biobakery/original/2X/6/6cff01b1e6ff30c45ecb2a125206a09fa50e5032.jpeg)

Lorcan

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**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [December 1, 2022, 8:55am UTC](https://forum.biobakery.org/t/difficulty-indexing-reference-database-for-metaphlan4/4460/2 "2022-12-01T08:55:00Z")

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Hi @lorcan1601  
It seems your machine does not have enough memory to build the indexes. You can find here: [Index of /biobakery4/metaphlan\_databases/bowtie2\_indexes](http://cmprod1.cibio.unitn.it/biobakery4/metaphlan_databases/bowtie2_indexes/) the already pre-built indexes

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<div class="post-metadata">

**Author:** ![lorcan1601](https://avatars.discourse-cdn.com/v4/letter/l/43a26b/32.png) [@lorcan1601](https://forum.biobakery.org/u/lorcan1601)\
**Post date:** [December 1, 2022, 10:56am UTC](https://forum.biobakery.org/t/difficulty-indexing-reference-database-for-metaphlan4/4460/3 "2022-12-01T10:56:43Z")

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Thank you for your reply, Aitor and thank you for the link to the prebuilt indexes!

My computer has decided to try this time and it seems bowtie2 is working!! That said, it’s 7 hours and counting…

My computer has 16GB of RAM (which was fine for the previous version of metaphlan). Will this be enough for running Metaphlan?

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**Author:** ![aitor.blancomiguez](https://yyz1.discourse-cdn.com/flex027/user_avatar/forum.biobakery.org/aitor.blancomiguez/32/86_2.png) [@aitor.blancomiguez](https://forum.biobakery.org/u/aitor.blancomiguez)\
**Post date:** [December 6, 2022, 8:16am UTC](https://forum.biobakery.org/t/difficulty-indexing-reference-database-for-metaphlan4/4460/4 "2022-12-06T08:16:21Z")

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Hi @lorcan1601 depending on the overall load of your machine it might be not enough