SNPs annotation using SnpEff
0
0
Entering edit mode
8 weeks ago
Eliza ▴ 20

Hi, I was following the instructions on https://pcingola.github.io/SnpEff/se_running/ t for SNPs annotation using the code the website provided :

$wget https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip # If you prefer to use 'curl' instead of 'wget', you can type: # curl -L https://snpeff.blob.core.windows.net/versions/snpEff_latest_core.zip > snpEff_latest_core.zip # Install$ 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:)

SNPEff snp annotation VCF. • 498 views
0
Entering edit mode

Unfortunately i keep on getting this erorr :Error: Unable to access jarfile snpEff.jar

the jar file is inside the snpEff folder created after "unzip". You should run cd snpEff before java -Xmx8g -jar ...

0
Entering edit mode

@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 ?

0
Entering edit mode

working behind a proxy ?

0
Entering edit mode

tried this on my PC nad on university cluster , didnt work on them . what do you mean by proxy?

0
Entering edit mode
0
Entering edit mode

@Pierre Lindenbaum how does it affect the command ? It doesnt look that i musing proxy , is there any way to make it work ?