3.2 years ago by
Homo_sapiens_nuHg19_mtrCRS is a composite reference genome we created that contains all the same data as hg19 except that the mitochondrial genome was swapped out with the updated Cambridge release. hg19 uses the mito release present in earlier human genome releases (hg17, hg18). hg_g1k_v37 uses the updated mito release. All three are different with respect to either chromosome identifiers or sequence content and should not be intermixed in an analysis.
If you have an example of a BWA-MEM job that was run with a built-in index (like hg19) at http://usegalaxy,org and the database metadata attribute was not assigned, please submit a bug report so that we can review the root cause. Please leave all inputs and outputs undeleted and include a link to this post in the comments.
If the job was run elsewhere, there could be other issues. Checking to see if this is reproducible at http://usegalaxy.org is one way to test if what job configuration issues could be present alternate server. Or if this is your own local/cloud, double check that you are running the latest version of the tool wrapper (with managed installed dependencies) and have indexed the genome(s) using Data Manager tools.
Hopefully this leads to a solution, but we will watch for the bug report is one is sent in. Jen, Galaxy team