Entering edit mode
3 months ago
doggie • 0
I am trying to built a database, called Tre1. I used the sequences.fa and genes.gtf stored in
snpEff/data/Tre1. I assume the database was built properly as I followed the instructions in snpEff website.
And when I try to annotate SNPs in snpEff/vcfs with the following command:
java -Xmx8g -jar snpEff.jar Tre1 vcfs/21.filtered_snps_final.vcf > 21.anno.vcf
the error comes out like this:
00:00:00 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_Tre1.zip 00:00:00 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_Tre1.zip FATAL ERROR: Failed to download database from [https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_Tre1.zip, https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_Tre1.zip]
What might be the problem? Did I not build the database successfully?
It would be best to check the log files rather than assuming it was done correctly. Looks like snpEff is trying to connect to a remote location for the files yet you said you built a custom database locally.
I am very sorry, I wasnt aware of that. Just new to bioinformatics and this page.
Nothing to be sorry about. All part of learning. Did you follow the steps here: https://pcingola.github.io/SnpEff/se_buildingdb/#building-a-database Were there any log files produced when you built the database? Have you checked those to see if there were any errors.
Yes i followed all the steps there. And ya u are right, the database were not built, cus i didn't see any log files produced. I think I am missing CDS and protein sequences so I got errors like Error in CDS and protein check... I thought gtf and fa files were the only ones required at first....
Do i need to extract CDS and protein sequences from the genome annotation file in GTF format?
Step 2 should need just GTF. You will need to provide CDS in step 3 where it checks your database against that information. Are you using a custom genome or one that is available some place like NCBI.
I am using a custom genome
doggie Why did you delete this post?