Question: snpEff database error
1
gravatar for sorrymouse
2.5 years ago by
sorrymouse70
sorrymouse70 wrote:

I do not have a problem generally downloading databases from snpEff. I downloaded the mus musculus database just fine using the following command:

java -jar snpEff.jar download GRCm38.75

and it is in my 'data' folder:

cd data/

ls

GRCm38.75

However I need the Drosophila database and when I attempt to download this I get the following error:

java -jar snpEff.jar download dm6.03

00:00:00 ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_dm6.03.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) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:32) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:86) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72) at org.snpeff.SnpEff.run(SnpEff.java:1040) at org.snpeff.SnpEff.main(SnpEff.java:158) Caused by: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at org.snpeff.util.Download.download(Download.java:127) ... 5 more

And the same for other versions of Drosophila:

java -jar snpEff.jar download dm5.48

00:00:00 ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_dm5.48.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) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:32) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:86) at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72) at org.snpeff.SnpEff.run(SnpEff.java:1040) at org.snpeff.SnpEff.main(SnpEff.java:158) Caused by: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct. at org.snpeff.util.Download.download(Download.java:127)

As databases are working in general I have no idea what the problem could be here. These databases are listed as a part of snpEFF as follows:

Drosophila_melanogaster http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_dm5.48.zip Drosophila_melanogaster http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_dm6.03.zip

If anybody has any idea what is wrong, it would be most appreciated.

Thank you!

java snpeff database • 1.5k views
ADD COMMENTlink written 2.5 years ago by sorrymouse70

When I try to directly download (wget) the database files I get a 404, so something is wrong with hosting the databases by snpeff. You can find the email address of the maintainer here, I think that's your best bet.

ADD REPLYlink written 2.5 years ago by WouterDeCoster39k

I was trying to download the same drosophila database but got the same error. Did you figure it out already, sasignor?

ADD REPLYlink written 2.4 years ago by mufernando10
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