Hello,
I am having trouble annotating my vcf file using a database that I built. It seems as though snpEff wants to go to sourceforge.net to retieve a built database. Can someone help me identify what my problem is?
Here is my code
java -Xmx4g -jar /pkgs/snpeff-4.3.1p-1/share/snpeff-4.3.1p-1/snpEff.jar eff -c /pkgs/snpeff-4.3.1p-1/share/snpeff-4.3.1p-1/snpEff.config Sorghum EMSmutboth.vcf > var.ann.vcf
Here is the error I continue to receive:
ERROR while connecting to http://downloads.sourceforge.net/pro..._3_Sorghum.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:998)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
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:998)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
I built a database that seemed to work, so I am not sure what information I am missing. When I built the database I used the following command:
java -jar location/to/snpEff.jar build -gffs -v Sorghum
Thank you for any help
I am having trouble annotating my vcf file using a database that I built. It seems as though snpEff wants to go to sourceforge.net to retieve a built database. Can someone help me identify what my problem is?
Here is my code
java -Xmx4g -jar /pkgs/snpeff-4.3.1p-1/share/snpeff-4.3.1p-1/snpEff.jar eff -c /pkgs/snpeff-4.3.1p-1/share/snpeff-4.3.1p-1/snpEff.config Sorghum EMSmutboth.vcf > var.ann.vcf
Here is the error I continue to receive:
ERROR while connecting to http://downloads.sourceforge.net/pro..._3_Sorghum.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:998)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
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:998)
at org.snpeff.snpEffect.commandLine.SnpEffCmdEff.run(SnpEffCmdEff.java:981)
at org.snpeff.SnpEff.run(SnpEff.java:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
I built a database that seemed to work, so I am not sure what information I am missing. When I built the database I used the following command:
java -jar location/to/snpEff.jar build -gffs -v Sorghum
Thank you for any help
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