snpEFF not able to download GRCH38 ?
2
0
Entering edit mode
3.6 years ago
pinn ▴ 130

HI Why snpEff not able to download GRCH38 ?

Always its showing error, But its work well with GRCH37 reference. Thanks for your comments.

likithreddy@Curium:~/Downloads/snpEff_latest_core/snpEff$ java -jar snpEff.jar download GRCh38.76
java.lang.RuntimeException: Property: 'GRCh38.76.genome' not found
    at org.snpeff.interval.Genome.<init>(Genome.java:106)
    at org.snpeff.snpEffect.Config.readGenomeConfig(Config.java:681)
    at org.snpeff.snpEffect.Config.readConfig(Config.java:649)
    at org.snpeff.snpEffect.Config.init(Config.java:480)
    at org.snpeff.snpEffect.Config.<init>(Config.java:117)
    at org.snpeff.SnpEff.loadConfig(SnpEff.java:451)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.runDownloadGenome(SnpEffCmdDownload.java:80)
    at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.run(SnpEffCmdDownload.java:72)
    at org.snpeff.SnpEff.run(SnpEff.java:1183)
    at org.snpeff.SnpEff.main(SnpEff.java:162)

T

Annotation genome • 3.9k views
ADD COMMENT
1
Entering edit mode

Hello pinninti1991reddy!

Please follow up on your questions. See C: Readgroups for a bam file ?

For this reason we have closed your question.

If you disagree please tell us why in a reply below, we'll be happy to talk about it.

Cheers!

ADD REPLY
0
Entering edit mode

Reopening question as user has provided feedback.

ADD REPLY
0
Entering edit mode

What is your command? can you post it here?

ADD REPLY
0
Entering edit mode

Sorry, its working with 38.86

ADD REPLY
0
Entering edit mode

The same thing happened to me. The command is: java -jar snpEff.jar download GRCh38.76

-> http://snpeff.sourceforge.net/download.html

ADD REPLY
0
Entering edit mode

Did you try the solution posted below by genomax?

ADD REPLY
4
Entering edit mode
3.6 years ago
GenoMax 106k

Try 38.86. That seems to be the latest GRCh38 as of now.

ADD COMMENT
0
Entering edit mode

I tried with 38.86 showing same error ?

ADD REPLY
0
Entering edit mode

Sorry for late reply, I'm able to download it.

ADD REPLY
2
Entering edit mode

Please accept genomax's answer if it worked for you.

ADD REPLY
1
Entering edit mode
6 days ago
geocarvalho ▴ 190

I had the same issue, just search for the version available and download it:

$ java -Xmx4g -jar snpEff.jar databases | grep GRCh38
OpenJDK 64-Bit Server VM warning: Insufficient space for shared memory file:
   526
Try using the -Djava.io.tmpdir= option to select an alternate temp location.

GRCh38.99                                                       Homo_sapiens                                                                                                          https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.99.zip
GRCh38.p13.RefSeq                                               Human genome GRCh38 using RefSeq transcripts                                                                          https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p13.RefSeq.zip

$ java -Xmx4g -jar snpEff.jar download -c snpEff.config -v GRCh38.99
ADD COMMENT

Login before adding your answer.

Traffic: 2487 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6