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