SNPs annotation using SnpEff
Hi, I was following the instructions on https://pcingola.github.io/SnpEff/se_running/ t for SNPs annotation using the code the website provided :
Download using wget
$ wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip
# If you prefer to use 'curl' instead of 'wget', you can type:
# curl -L https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip > snpEff_latest_core.zip
# Install
$ unzip snpEff_latest_core.zip
$ java -Xmx8g -jar snpEff.jar GRCh37.75 examples/test.chr22.vcf > test.chr22.ann.vcf
Unfortunately, i keep on getting this error :Error: Unable to access jarfile snpEff.jar
After running cd snpEff and fixing the previous error got new one :( -> :
00:00:00 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh37.75.zip
tried to go to this link and got :
<Error>
<Code>BlobNotFound</Code>
<Message>The specified blob does not exist. RequestId:9617d414-401e-0029-5470-2e2c3b000000 Time:2023-01-22T14:44:59.4545522Z</Message>
</Error>
I can't seem to understand what is the problem and how to fix it and how to succefully preform SNP annotation using snpEff when getting those errors . Thank you:)
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the jar file is inside the snpEff folder created after "unzip". You should run
cd snpEffbeforejava -Xmx8g -jar ...@Pierre Lindenbaum after using what you suggested got :00:00:00 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_GRCh37.75.zip, what is the source of this problem ?
working behind a proxy ?
tried this on my PC nad on university cluster , didnt work on them . what do you mean by proxy?
https://www.fortinet.com/resources/cyberglossary/http-proxy
@Pierre Lindenbaum how does it affect the command ? It doesnt look that i musing proxy , is there any way to make it work ?