Minimap2 should be able to map from fastq or fasta files. Galaxy Minimap2 cannot see fastq files. When galaxy minimap2 is run on fasta files it fails where it previously ran effectively. This same data was processed through galaxy a few weeks ago, something is different.
Hi @nblewett
You might just need to change the datatype Changing the datatype. Next time you Upload data, allow Galaxy to “auto-detect” the datatype.
If the “auto-detect” guess is wrong and you are working with reads, there is very likely some problem with that data (format, content, compression that Galaxy cannot uncompress,…). For the compression issues, try uncompressing locally first. If that works, upload the uncompressed data to Galaxy. If that fails, some problem was introduced upstream and the data is corrupted and not usable anywhere, not just Galaxy. Maybe an upstream data transfer failed?
Once you have Uploaded intact data, run some QA before attempting to map.
More about how to learn what datatypes a tool is looking for, plus other general fastq help is in the topic below. The datatype restrictions are a very basic quality/format sanity check – not to be confused full QA. A tool can fail for odd reasons when given data in a format that it wasn’t designed to work with, or produce putatively successful results that have scientific problems. The latter isn’t always easy to detect.
Tutorials
- https://training.galaxyproject.org/training-material/search?query=minimap
- https://training.galaxyproject.org/training-material/search?query=quality
If you need more help, please share more details. This is the information people at this forum will usually need. Be sure to capture the server URL. Troubleshooting errors
That’s a very detailed and helpful reply, I appreciate the insight.
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