Error building database in snpEff

Question

[Bioinfonext]

I am getting some error while building database in SnpEff:

java -jar /home/yog/software/snpEff/snpEff.jar  build -gtf22 -v genome

00:00:00 SnpEff version SnpEff 4.3k (build 2017-03-29 17:16), by Pablo Cingolani

00:00:00 Command: 'build'

00:00:00 Building database for 'genome'

00:00:00 Reading configuration file 'snpEff.config'. Genome: 'genome'

00:00:00 Reading config file: /home/yog/software/snpEff/snpEff.config

java.lang.RuntimeException: Property: 'genome.genome' not found

Please suggest how to build database exactly. I have gtf and genome fasta file.

Please also suggest how to add information in snp.Eff.config?

Answer 1

[Santosh Anand]

The path to genome might be wrong. See

http://snpeff.sourceforge.net/SnpEff_manual.html#buildGtf

Note: The FASTA file can be either in 
/path/to/snpEff/data/genomes/mm37.61.fa 
or in 
/path/to/snpEff/data/mm37.61/sequences.fa

[Bioinfonext]

Sorry, I am not able to understand in which folder I should store gtf and fasta file.... and which path and name should I mention in snp.Eff.config.

My fasta file name is Radish.fasta

gtf file name is genes.gtf

[Bioinfonext]

Thanks. It is resolved.

[HannahT]

I too am having the same problem. Can you advise me on how you solved your problem? I have a fasta file renamed with extension .genome and a gff3 file in a dir. I am not sure I entered the information correctly in the snpEFF.config file or if I am not pointing the build command to match that in the config file.

I added the following to my config file:

Sorghum_bicolor genome, version 3.0.1

Sbicolor_454_v3.0.1.genome : Sorghum

And my genome file is located here: /pkgs/snpeff-4.3.1p-1/share/snpeff-4.3.1p-1/Sbicolor_454_v3.0.1/genome

I am running the following command: java -jar snpEff.jar build -gff3 -v Sbicolor_454_v3.0.1

[Bioinfonext]

Please make a folder like (mm37.61) in this path:

/home/path/snpEff/data/mm37.61

put fasta and gtf file there

and then in config file mention these file like this:

data_dir = /home/path/snpEff/data/mm37.61

I hope this may help you.