SNpEff build Java error

Dear Galaxy community,
I am trying to build database for Mycobacterium tuberculosis H37Rv using GFF annotation. I tried to use .fna and .gff files from ncbi but am getting following error:Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m
Exception in thread “main” java.lang.ArrayIndexOutOfBoundsException: 1
at org.snpeff.SnpEff.parseArgs(
Is this something related to my computer or am I doing something wrong?
I also tried .fasta and .gff3 files but came back with the same result.
Alternatively, I tried to snpEff download and received following error message: Picked up _JAVA_OPTIONS: -Xmx7g -Xms256m
00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani
00:00:00 Command: ‘download’
00:00:00 Reading configuration fil

I wonder if anyone can help me get through this.

Thank you

1 Like

Hi Sanjay

Nice to meet you. It sounds like there might be a problem with the data that you are trying to analyse.

Firstly when it comes to M. tuberculosis, the snpEff database to use is Mycobacterium_tuberculosis_h37rv. This corresponds to the NCBI NC000962.3 genome (i.e. H37Rv). You can either download this (using the snpEff download tool) and use it from your history or just use the text string in your snpEff.

I don’t know what you are using for variant calling, but if you use snippy with Genbank reference input (i.e. the one from here it will run snpEff on your VCF for you automatically. This works for me with the 4.3.6+galaxy2 snippy tool.


Thanks Peter. It worked.