I receive the following error:
00:00:00 ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_Walnut.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:1221)
at org.snpeff.SnpEff.loadDb(SnpEff.java:515)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1001)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
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)
... 9 more
java.lang.RuntimeException: Genome download failed!
at org.snpeff.SnpEff.loadDb(SnpEff.java:516)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1001)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
pcingola
commented
4 years ago
Hello,
I built a database from my own genome, and checked that it was present on the snpEff server with:
java -jar snpEff.jar databases | grep -i Walnut
Walnut Walnut http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_Walnut.zip
However, when I try to run the command:
java -jar /home/cary/bin/snpEff/snpEff.jar eff -c /home/cary/bin/snpEff/snpEff.config -i vcf -o vcf Walnut /mnt/gn3/gnome3/DropBox/Cary/walnut/mpileup-1.8/output_mpileup_1.8.vcf
I receive the following error: 00:00:00 ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_Walnut.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:1221) at org.snpeff.SnpEff.loadDb(SnpEff.java:515) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1001) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984) at org.snpeff.SnpEff.run(SnpEff.java:1183) at org.snpeff.SnpEff.main(SnpEff.java:162) 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) ... 9 more java.lang.RuntimeException: Genome download failed! at org.snpeff.SnpEff.loadDb(SnpEff.java:516) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:1001) at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:984) at org.snpeff.SnpEff.run(SnpEff.java:1183) at org.snpeff.SnpEff.main(SnpEff.java:162)
I do not see my file when I browse the database server at http://downloads.sourceforge.net/project/snpeff/databases/v4_3/, even though the database command indicates the file is there.
Any thoughts?
Thanks