Hi,
I am trying to make a local database with bacterial genomes assembled ourself ( about 200 genomes) with the NCBI Blast+makeblasedb tool, However, I am keeping get error message, any suggestion?
Thanks,
Guangzhi
1 Like
Welcome @Guangzhi_Zhang
Guide for troubleshooting problems: Troubleshooting resources for errors or unexpected results
If your error is not covered there, the job may be still be actually too large to execute or there is an input problem. Error messages can vary.
This recent Q&A (and many others) explain how to review errors: DexSeq Count issue -- Job failing for exceeding memory resources: input problem or actually too large to execute at public server
I would suggest starting by checking that your input fasta is formatted correctly. Run the tool NormalizeFasta with the options wrap at 80 bases and trim the title line at the first white-space. The rules for formatting a Custom genome will apply for this case as well and has an FAQ:
- Support hub: https://galaxyproject.org/support/
- Preparing and using a Custom Reference Genome or Build
My guess is that the data is actually too large given what you state. But it is worth checking the format first before exploring other Galaxy choices.
- My job ended with an error. What can I do? – even if your error message does not match up exactly, the help can still aid in resolving problems.
- Galaxy choices summarized (if the job is truly too large to run at whatever public server you are using): https://galaxyproject.org/choices/
- Ways to use Galaxy, including setting up your own server with sufficient resources to work with such large data: https://galaxyproject.org/use/
Thanks!