search

tseemann / snippy

:scissors: :zap: Rapid haploid variant calling and core genome alignment
GNU General Public License v2.0
462 stars 113 forks source link

snpEff stack overflow build command #75

Closed conmeehan closed 7 years ago

conmeehan commented 8 years ago

Hi Torsten,

I am getting the following error when I run snippy 3.0:

snpEff build -c reference/snpeff.config -dataDir . -gff3 ref

java.lang.StackOverflowError at java.lang.Character.toLowerCase(Character.java:6338) at java.lang.Character.toLowerCase(Character.java:6309) at java.lang.String.toLowerCase(String.java:2581) at java.lang.String.toLowerCase(String.java:2670) at ca.mcgill.mcb.pcingola.interval.GffMarker.hasAttr(GffMarker.java:207) at ca.mcgill.mcb.pcingola.interval.GffMarker.getGffParentId(GffMarker.java:135) at ca.mcgill.mcb.pcingola.interval.GffMarker.getGeneId(GffMarker.java:119) at ca.mcgill.mcb.pcingola.interval.GffMarker.getGffParentId(GffMarker.java:140)

And the last 2 lines repeat over and over. Any idea what is going on here?

Thanks in advance for the help.

Conor

andersgs commented 8 years ago

I have had the same issue. It is an snpEff version 3 issue. If you downgrade to version 2.x it should work fine. Otherwise, supply your reference as a FASTA file, which will skip the SNP effect step.

Downgrading snpEff is easy if using brew.

conmeehan commented 8 years ago

That worked! Thanks so much. Hopefully snpEff will fix this issue soon.

Thanks again,

Con

tseemann commented 8 years ago

@otogishu The error seems to happen randomly. Sometimes snpEff 4.2 works but then it doesn't. I have found snpEff 4.1l to be stable.

tseemann commented 7 years ago

snpEff 4.3p seems to be working in a stable manner.

Nheyer commented 6 years ago

getting the error on 4.3t, any sugestions

rturba commented 3 years ago

I am also getting the same error with version 4.3t. Tried downgrading to v4.3p and I still see the same issue.

Edit: I think there was an issue with the latest version I downloaded. v5 worked fine!