building database in snpEff

Question

[reza]

i created database for dromedary camel in snpEff as following:

• i downloded referense file (fasta) and gff3 file from NCBI

• converting gff3 to gtf using gffread

i followed database building Instructions (http://snpeff.sourceforge.net/SnpEff_manual.html#databases).

i ran "vi snpEff.config" and added following lines:

C.dromedary genome, version DD1.14

DD1.14.genome : C.dromedary

i renamed my fasta file to "DD1.14.fasta" and gtf file to "genes.gtf" then put them in snpEff/data/genomes and snpEff/data/DD1.14, respectively. finally i ran "java -jar snpEff.jar build gtf22 -v DD1.14". for cheking added database ran "java -jar snpEff.jar databases | grep -i DD1.14" command and i get following line:

DD1.14 C.dromedary http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_DD1.14.zip

Now when i want to annotate my vcf file using builded database i get error.

java -Xmx16G -jar snpEff.jar eff -v DD1.14 SNPs.vcf > snpeffout.vcf

00:00:00 Reading config file: /home/dr_hedayati/Downloads/snpEff/snpEff/snpEff.config

00:00:00 done

00:00:00 Reading database for genome version 'DD1.14' from file '/home/dr_hedayati/Downloads/snpEff/snpEff/./data/DD1.14/snpEffectPredictor.bin' (this might take a while)

00:00:00 Database not installed

Attempting to download and install database 'DD1.14'

00:00:00 Reading configuration file 'snpEff.config'. Genome: 'DD1.14'

00:00:00 Reading config file: /home/dr_hedayati/Downloads/snpEff/snpEff/snpEff.config

00:00:00 done

00:00:00 Downloading database for 'DD1.14'

00:00:00 Connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_DD1.14.zip

00:00:01 ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_DD1.14.zip

java.lang.RuntimeException: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct.

at org.snpeff.util.Download.download(Download.java:178)

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00:00:01 Logging

00:00:03 Checking for updates...

anybody know what is my wrong? why database not installed?

[HannahT]

Hello,

Did you determine what the problem was? I have received the same error when trying to use my own database.

Thank you

[reza]

Have you built your own database? check it using below command.

"java -jar snpEff.jar databases | grep -i your_database_name

[HannahT]

It appears that I have not! But now I am at the point that I get the following script to run: java -jar snpEff.jar build -gff3 -v Sorghum

And it appears to work, without major error messages, but I never get an output snpEffectPredictor.bin to work with downstream. The problems I was having earlier were related to directory names and the config file entry, but now I can see that the 'build' command in finding the directory and the genes.gff file.

But I am missing something about why this is not running. Am I not completing the build?

Thank you for replying

[reza]

it is not clear to me what you did exactly. convert your gff file to gtf and then try it again. check your reference and annotation files directories as mentioned in snpeff manual.