# Error in running braker3

**URL:** https://help.galaxyproject.org/t/error-in-running-braker3/15845
**Category:** usegalaxy.eu support
**Tags:** troubleshooting, braker3
**Created:** [June 28, 2025, 9:04am UTC](https://help.galaxyproject.org/t/error-in-running-braker3/15845 "2025-06-28T09:04:33Z")
**Posts on this page:** 2
**Page:** 1

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### Author: ![amit\_babu](https://sea2.discourse-cdn.com/flex020/user_avatar/help.galaxyproject.org/amit_babu/32/7404_2.png) [@amit\_babu](https://help.galaxyproject.org/u/amit_babu)
#### Post date: [June 28, 2025, 9:04am UTC](https://help.galaxyproject.org/t/error-in-running-braker3/15845/1 "2025-06-28T09:04:33Z")

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This is the link of my history - [Galaxy](https://usegalaxy.eu/u/godamit69/h/unnamed-history).

The link of one of the jobs containing the same error is [https://usegalaxy.eu/api/datasets/26c75dcccb616ac8b2606328ac90df6b/display?to\_ext=gff3](https://usegalaxy.eu/api/datasets/26c75dcccb616ac8b2606328ac90df6b/display?to_ext=gff3)

I am running braker3 ( toolid - toolshed.g2.bx.psu.edu/repos/genouest/braker3/braker3/3.0.8+galaxy0) for annotation of Etroplus caranesis genome in galaxy EU server. The input files which I am using are -

1. Reference genome file with simplified headers (.fasta format),
2. .bam file (rna-seq data was aligned to the reference genome file) ,
3. Protein sequences in .fasta format(simplified headers) from another closely related species

**Running the tool is resulting in the following error - ERROR in file /opt/BRAKER/scripts/braker.pl at line 5939**  
**failed to execute: /opt/BRAKER/scripts/get\_gc\_content.py --sequences /data/dnb11/galaxy\_db/files/7/b/7/dataset\_7b75866e-a463-4df8-a08f-d0c26bd5fa54.dat --print\_sequence\_length 1\> /data/jwd07/main/085/300/85300852/working/braker/gc\_content.out 2\> /data/jwd07/main/085/300/85300852/working/braker/errors/gc\_content.stderr!.**

As i dont have access to the scripts of braker3 and the log files containing the errors. I request the help of the admin or the developers of braker3 to help me to proceed. Thank you.

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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: [July 1, 2025, 8:06pm UTC](https://help.galaxyproject.org/t/error-in-running-braker3/15845/2 "2025-07-01T20:06:15Z")

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Welcome @amit_babu

Thanks for sharing the history and the error, very helpful!

So, both of the fasta files appear to have been Uploaded in an odd format – both are reporting as “binary” which usually means a problem with the datatype detection, or that possibly the wrong datatype was selected/assigned.

 ![Screen Shot 2025-07-01 at 12.59.26 PM](https://us1.discourse-cdn.com/flex020/uploads/galaxy/original/2X/c/c1f5bcfd22e4b80b447e3eab9311cb19ba513d47.png)

**What to do**

1. Upload those two files again using all default settings, to allow Galaxy to “guess” the datatype. This can avoid mistyping. [Getting Data into Galaxy](https://help.galaxyproject.org/t/getting-data-into-galaxy/10868)

2. Confirm that the datatype is **fasta**. If you get something else, you might want to uncompress the data and load it again. While **fasta.gz** _might_ work with some tools, I’m not sure about this one (you could try, then fallback to fasta), and binary will definitely not work.

3. Once all of the inputs are ready, try running **Breaker3** again.

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Please let us know if this works or if you need more help! 🙂