Snpeff build galaxy6 failures at Jetstream2 ORG

[jennaj]

Xref galaxyproject/tools-iuc#5647

SNPeff build fails at jetstream2.

https://usegalaxy.org/u/jen/h/snpeff-build-testing-simple

Failed galaxy6

	Correcting exons based on frame information.
	
	Remove empty chromosomes: 
		Removing empty chromosome: 'AgamP3:2R:1:61545105:1'
		Removing empty chromosome: 'AgamP3:3L:1:41963435:1'
		Removing empty chromosome: 'AgamP3:Y_unplaced:1:237045:1'
		Removing empty chromosome: 'AgamP3:3R:1:53200684:1'
		Removing empty chromosome: 'AgamP3:2L:1:49364325:1'
		Removing empty chromosome: 'AgamP3:UNKN:1:42389979:1'
		Removing empty chromosome: 'AgamP3:X:1:24393108:1'
		Chromosome left: 2R X 3L 2L UNKN Y_unplaced 3R 

	Marking as 'coding' from CDS information: 
	Done: 0 transcripts marked

Success galaxy5

	Correcting exons based on frame information.
	
	Remove empty chromosomes: 

	Marking as 'coding' from CDS information: 
	Done: 14667 transcripts marked

[jennaj]

This happened with another user example today. Be good if we could fix this.

[mvdbeek]

Did you have any reason to link up galaxyproject/tools-iuc#5647 ?

[mvdbeek]

Fixed in galaxyproject/galaxy#18179