Question: snpEff Apis_mellifera genome
0
gravatar for a.hasankhani74
5 months ago by
a.hasankhani740 wrote:

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?

snp rna-seq software error • 191 views
ADD COMMENTlink modified 5 months ago by colindaven2.1k • written 5 months ago by a.hasankhani740

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.

ADD REPLYlink written 5 months ago by genomax80k
0
gravatar for colindaven
5 months ago by
colindaven2.1k
Hannover Medical School
colindaven2.1k wrote:

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
ADD COMMENTlink modified 5 months ago • written 5 months ago by colindaven2.1k
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