Difference between revisions of "Dorado"
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In order to run the software, you may need to load the modules "cuda" and "pytorch". You may need to also "pip install pre-commit", as per the author's recommendation. | In order to run the software, you may need to load the modules "cuda" and "pytorch". You may need to also "pip install pre-commit", as per the author's recommendation. | ||
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| + | Note that for fast5 to pod5 conversions with Dorado if you have too many reads the program may exit before completing the conversions without an error. If you are not counting the reads you may miss this and lose data. Since the program doesn't exit with an error SLURM doesn't fail the job, so the failure is silent. Make sure to request sufficient memory for the conversion. | ||
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Latest revision as of 16:04, 22 February 2024
Description
Dorado is a high-performance, easy-to-use, open source basecaller for Oxford Nanopore reads
Environment Modules
Run module spider dorado to find out what environment modules are available for this application.
System Variables
- HPC_DORADO_DIR - installation directory
- HPC_DORADO_BIN - executable directory
Additional Information
In order to run the software, you may need to load the modules "cuda" and "pytorch". You may need to also "pip install pre-commit", as per the author's recommendation.
Note that for fast5 to pod5 conversions with Dorado if you have too many reads the program may exit before completing the conversions without an error. If you are not counting the reads you may miss this and lose data. Since the program doesn't exit with an error SLURM doesn't fail the job, so the failure is silent. Make sure to request sufficient memory for the conversion.