Custom genome help and troubleshooting plus where to find HISAT2 alignment statistics

,
2

Welcome @zhwdong9

Are you sourcing the papAnu2 or papAnu4 genome from UCSC?

http://hgdownload.soe.ucsc.edu/downloads.html#baboon

Make certain that you get the fasta version of the genome. For papAnu4, this would be: Index of /goldenPath/papAnu4/bigZips >> papAnu4.fa.gz (soft-masked version, but the hard-masked is also available).

This particular data does not need to be reformatted through NormalizeFasta as in the first FAQ listed below states (will already be formatted correctly from this source). But you should load it in the Upload tool without setting a “datatype”. Allow Galaxy to uncompress the data and assign the final datatype (will be “fasta”).

FAQs: Galaxy Support - Galaxy Community Hub

Also, click on the tags I added for more help/prior Q&A for various related issues end users have had when first learning how to work with Custom Genomes/Builds. Some of these may inform you about how to resolve your problem.

However, if none of that helps, please share more information:

  1. Try at least one rerun to eliminate transient server/cluster issues. Let us know if the job fails again (and how/why) – and if you confirmed that the genome fasta is intact (fully loaded) and has the correct datatype assigned.
  2. Where are you working? Public Galaxy (URL)? Your own Galaxy?
  3. How does the job fail?
    • Review the contents of the “bug” icon report (it does not need to be submitted, but if you do, include a link to this post for context).
    • Click into the “i” icon for job details and review the stderr and stdout reports. These often explain exactly what the problem is.

For reference, many Galaxy Tutorials from the GTN include the tool HISAT2. Start with those in the group “Transcriptomics”:

Thanks!