SnpEff database compatibility

1

I’m getting a warning from snpeff while configuring the analysis. First, I made a custom snpeff database which is in my history. Then, I configure the snpeff tool and select the database. When I click run, I get a warning:
Parameter snpeff_db: This version of SnpEff will only work with 5.2 genome databases

But the database IS a 5.2 genome database. Note that the error appears in the tool config page and it never actually runs.

2

Hi @Michael_Thon

Yes, the tool is filtering for a specific version of a snpeffdb dataset (otherwise it would just fail anyway).

Which server are you working at? Maybe something server side is going on. And if you post the history share link, I’ll take a closer look at your specific issue too. Thanks! :slight_smile:

3

Hi @jennaj
Here’s a link to my history on usegalaxy.eu: Galaxy
I didn’t think about trying a different server. I’ll try it on usegalaxy.org and let you know.

4

I just tried it on usegalaxy.org and I get the same warning…

1 Like
5

Thanks @Michael_Thon I’m reviewing

6

Update: Resolved! Thanks @Michael_Thon for reported and thanks @wm75 for the quick fix :star_struck:

Hi @Michael_Thon

Yes, the behavior is very odd and I can reproduce it with your data and some other data I had around. I’ve reported the issue here with more details: Bug: snpEff 5.2+galaxy0 will not execute with a snpEff_build_gb 5.2+galaxy0 database · Issue #6571 · galaxyproject/tools-iuc · GitHub

For now, using the 4.3 database and effect tool is how I was able to get this to run. You might need to click on the submit button a few times. Not sure why yet. All servers appear to be impacted. There was a change a few weeks ago that seems to have introduced the problem. The developers will see the ticket and fix this up. :hammer_and_wrench:

Thanks for the example and follow up!

1 Like
7

Hi @jennaj et al,
The ticket was updated and I tried to run it again. This time when I click Run Tool the job is submitted but I get the following error. I tried it a few times in case its due to a misbehaving server node, but I keep getting the same error.
Here’s a link to my history.

java.lang.RuntimeException: Property: 'cgra01v4.genome' not found
	at org.snpeff.interval.Genome.<init>(Genome.java:103)
	at org.snpeff.snpEffect.Config.readConfig(Config.java:757)
	at org.snpeff.snpEffect.Config.init(Config.java:532)
	at org.snpeff.snpEffect.Config.<init>(Config.java:119)
	at org.snpeff.SnpEff.loadConfig(SnpEff.java:449)
	at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:889)
	at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:875)
	at org.snpeff.SnpEff.run(SnpEff.java:1173)
	at org.snpeff.SnpEff.main(SnpEff.java:163)
8

@Michael_Thon I think that’s the difference between a downloaded DB and a custom one. If you created the DB yourself, you need to choose custom.

1 Like
9

Yep… thanks for that!

Michael Thon
Professor (Catedrático de Universidad)
Institute for Agrobiotechnology Research (CIALE)
University of Salamanca