snpEff Apis_mellifera genome

Question

[a.hasankhani74]

Hi I have a problem with snpEff genome. I want to obtain snp annotation with snpEff. my organism is Apis_mellifera. I run snpEff with below command.

java  -jar snpEff/snpEff.jar  -c snpEff/snpEff.config   -v Apis_mellifera    New\ folder/Ligustica_snp.vcf > New\ folder/Ligustica_ann.vcf

but I got this error:

00:00:01        Downloading database for 'Apis_mellifera'
00:00:01        Connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_ENSEMBL_BFMPP_32_24.zip
00:00:36        ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_ENSEMBL_BFMPP_32_24.zip
java.lang.RuntimeException: java.lang.RuntimeException: Error code from server: 403
        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: Error code from server: 403
        at org.snpeff.util.Download.download(Download.java:128)
        ... 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)
00:00:36        Logging
00:00:37        Checking for updates...
00:00:40        Done.

how can I resolve this problem?

[GenoMax]

Are you able to directly download the file being refrenced using this link? If not the problem is likely with a local firewall/your geographic location restriction.

Answer 1

[colindaven]

Do you have a proxy ?

You might be able to get it to work by putting this in your .bashrc and logging out and back in.

Obviously edit MYPROXYIPADDRESS and port 8080 to your institutions's details.

_JAVA_OPTIONS=-Dhttp.proxyHost=MYPROXYIPADDRESS -Dhttp.proxyPort=8080 -Dhttps.proxyHost=MYPROXYIPADDRESS -Dhttps.proxyPort=8080

You can check it worked by checking

env | grep JAVA