Open arundurvasula opened 6 months ago
carsonbroeker
commented
6 months ago I had the same issue. I ended up having to redo part of my pipeline and realign to mm10, which I was able to download with snpEff. It looks like the latest sourceforge availability for databases is from 2018, before mm39 was released: https://sourceforge.net/projects/snpeff/files/databases/. Doesn't look like you can manually get mm39 from here and install it yourself.
arundurvasula
commented
6 months ago Thanks for the comment. It would be great to have the database for mm39 given how much newer the genome is. Hopefully this is just a matter of reuploading existing files.
maxmilianr
commented
4 months ago Hi, i still get the same error today. Did anyone find a good solution/workaround to this or was able to build the db manually?
arundurvasula
commented
4 months ago I haven’t found a solution or workaround yet. Hoping this is just a database update upstream that will fix the issue as soon as the developer can get to it.
On Tue, Jun 18, 2024 at 12:44 AM Maximilian Radtke @.***> wrote:
Hi, i still get the same error today. Did anyone find a good solution/workaround to this or was able to build the db manually?
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lukedow
commented
4 months ago I had the same issue with mm39, but was eventually able to build the db manually. I tried a few of the options in the snpEff documentation, but the one that ultimately worked was the .gtf approach.
Most of what you need to know is in the documentation, but not always super clear. Here were the key points for me:
Mus_musculus.GRCm39.dna.primary_assembly.fa.gz: sequences.fa Mus_musculus.GRCm39.cds.all.fa.gz: cds.fa Mus_musculus.GRCm39.pep.all.fa.gz: protein.fa Mus_musculus.GRCm39.112.gtf.gz: genes.gtf
Modify the snpEff.config file to include the line:
mm39.genome : Mouse
Build the database:
java -Xmx4g -jar snpEff.jar build -gtf22 -v mm39
This should create and save the .bin files required for annotation into /snpEff/data/mm39/
Should be good to go!
pgonzale60
commented
2 months ago Hi,
This worked for me:
mkdir tmp; snpEff -Djava.io.tmpdir=tmp download -v EquCab3.0.105
Originally I had the following issue
while connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_EquCab3.0.105.zip FATAL ERROR: Failed to download database from [https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_EquCab3.0.105.zip, https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_EquCab3.0.105.zip, https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_EquCab3.0.105.zip]
Describe the bug Unable to download mm39
To Reproduce
java -Xmx60g -jar ~/software/snpEff/snpEff.jar mm39 data/vcf/$ID.vcf.gzFATAL ERROR: Failed to download database from [https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_mm39.zip, https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_mm39.zip, https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_mm39.zip]Expected behavior SnpEff should download the database.
Data N/A (reproducible with
java -Xmx60g -jar ~/software/snpEff/snpEff.jar download mm39:Additional context Issue is potentially related to #374, but not sure there is an applicable solution.