# How database assignments are used to access a fasta index: custom genomes, custom builds, server indexes

**URL:** <https://help.galaxyproject.org/t/how-database-assignments-are-used-to-access-a-fasta-index-custom-genomes-custom-builds-server-indexes/12225>\
**Category:** Resources\
**Tags:** fasta-manipulation, reference-index, custom-genome, galaxy-local, troubleshooting, custom-build, resources\
**Created:** [April 16, 2024, 8:23pm UTC](https://help.galaxyproject.org/t/how-database-assignments-are-used-to-access-a-fasta-index-custom-genomes-custom-builds-server-indexes/12225 "2024-04-16T20:23:01Z")\
**Posts on this page:** 3\
**Page:** 1

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**Author:** ![Choute](https://avatars.discourse-cdn.com/v4/letter/c/65b543/32.png) [@Choute](https://help.galaxyproject.org/u/Choute)\
**Post date:** [April 16, 2024, 8:23pm UTC](https://help.galaxyproject.org/t/how-database-assignments-are-used-to-access-a-fasta-index-custom-genomes-custom-builds-server-indexes/12225/1 "2024-04-16T20:23:01Z")

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I’m currently encountering some issues while running a dataset through the Qualimap BamQC tool. Specifically, I’m receiving the following errors:

1. Fatal error: Exit code 1
2. Input mapping file not found

Has anyone experienced similar issues or knows why this might be happening? Why would the tool not have access to the mapping file? I’ve double-checked the file paths. Any insights or suggestions would be greatly appreciated. I also want to mention that we are hosting the site on AWS if that is important.

Thank you in advance for your help!

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [April 17, 2024, 6:35pm UTC](https://help.galaxyproject.org/t/how-database-assignments-are-used-to-access-a-fasta-index-custom-genomes-custom-builds-server-indexes/12225/2 "2024-04-17T18:35:32Z")

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Welcome, @Choute

Thanks for including the part about AWS! Knowing that the error is occurring on your own server is important 🙂

Some tool use the metadata assigned to input datasets to access server indexed reference files.

For this tool specifically, the metadata to pay attention to is the **database** assignment. The database key informs the tool about which fasta index (genome.fa.fai) to use during processing.

That fasta index can be a **global reference** accessible to all users of the instance or a **custom reference** specific to an account.

For a **global reference** , that could be an index that you created with Data Managers, or an indexed included in a mounted CVMFS resource.

- [GTN Materials Search](https://training.galaxyproject.org/training-material/search2?query=data+manager) (query=data+manager)
- [GTN Materials Search](https://training.galaxyproject.org/training-material/search2?query=cvmfs) (query=cvmfs)

For a **custom reference** , how to create one is described at

- [https://training.galaxyproject.org/training-material/faqs/galaxy/reference\_genomes\_custom\_genomes.html](https://training.galaxyproject.org/training-material/faqs/galaxy/reference_genomes_custom_genomes.html)
- Remember that a custom reference is account-specific. This means if one person creates it, the index will _only_ be available to them and not other users.
- For reference genomes that will be used by multiple people, as the administrator you will need to decide whether to index the genome locally, or to put the fasta into a common location like a Data Library and share how to create the database key. The first will be much simpler for users who are collaborating, and easier for you to support.

* * *

Since where this was broken might not be trapped perfectly by the tool, you’ll need to check the entire chain:

1. Confirm that the input BAM has a database assignment (required)
2. If a global reference, check to see if that index is mounted correctly (or possibly, indexed correctly?).
3. If a custom reference, check to see if that database is defined in the account the tool was run in.
4. And, I’m not sure exactly how this tool traps potential _mismatches_ between the assigned database reference, and the actual content of that reference’s index versus the reference the input data was based on. So I would look at that if the other steps do not resolve the problem. As an example, this guide explains about the technical variations in common human genome builds → [Reference genomes at public Galaxy servers: GRCh38/hg38 example](https://help.galaxyproject.org/docs?topic=11616)

Let’s start there! There are other items to check depending on the parameters used.

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**Author:** ![jennaj](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/jennaj/32/27_2.png) [@jennaj](https://help.galaxyproject.org/u/jennaj)\
**Post date:** [September 17, 2024, 7:49pm UTC](https://help.galaxyproject.org/t/how-database-assignments-are-used-to-access-a-fasta-index-custom-genomes-custom-builds-server-indexes/12225/3 "2024-09-17T19:49:13Z")

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