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Unable to download some databases with new SnpEff v5.0.0 #248

Closed gel001 closed 3 years ago

gel001 commented 4 years ago

Greetings,

We are excited to check out SnpEff v5.0.0 but it appears that some of the databases we are interested in are not able to be downloaded right now.

If we look at the output of the "databases" command we can see the three we are interested in as being listed.

java -jar snpEff.jar databases | grep GRCh38.p7.RefSeq
GRCh38.p7.RefSeq                                                Human genome GRCh38 using RefSeq transcripts                                                                https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p7.RefSeq.zip

java -jar snpEff.jar databases | grep GRCh37.p13.RefSeq
GRCh37.p13.RefSeq                                               Human genome GRCh37 using RefSeq transcripts                                                                https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh37.p13.RefSeq.zip

java -jar snpEff.jar databases | grep GRCh37.87
GRCh37.87                                                       Human genome GRCh37 using transcripts                                                                       https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh37.87.zip

However, trying to download them returns errors:

 java -jar snpEff.jar download -v GRCh38.p7.RefSeq
00:00:00    SnpEff version SnpEff 5.0 (build 2020-08-09 21:23), by Pablo Cingolani
00:00:00    Command: 'download'
00:00:00    Reading configuration file 'snpEff.config'. Genome: 'GRCh38.p7.RefSeq'
00:00:00    Reading config file: /Users/gel001/Desktop/snpEff_5.0/snpEff.config
00:00:00    done
00:00:00    Downloading database for 'GRCh38.p7.RefSeq'
00:00:00    Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p7.RefSeq.zip
00:00:01    ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh38.p7.RefSeq.zip
java.lang.RuntimeException: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct.
    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:1194)
    at org.snpeff.SnpEff.main(SnpEff.java:167)
Caused by: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct.
    at org.snpeff.util.Download.download(Download.java:127)
    ... 5 more
00:00:01    Logging
00:00:02    Done.
java -jar snpEff.jar download -v GRCh37.p13.RefSeq
00:00:00    SnpEff version SnpEff 5.0 (build 2020-08-09 21:23), by Pablo Cingolani
00:00:00    Command: 'download'
00:00:00    Reading configuration file 'snpEff.config'. Genome: 'GRCh37.p13.RefSeq'
00:00:00    Reading config file: /Users/gel001/Desktop/snpEff_5.0/snpEff.config
00:00:00    done
00:00:00    Downloading database for 'GRCh37.p13.RefSeq'
00:00:00    Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh37.p13.RefSeq.zip
00:00:00    ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh37.p13.RefSeq.zip
java.lang.RuntimeException: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct.
    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:1194)
    at org.snpeff.SnpEff.main(SnpEff.java:167)
Caused by: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct.
    at org.snpeff.util.Download.download(Download.java:127)
    ... 5 more
00:00:00    Logging
00:00:01    Done.
java -jar snpEff.jar download -v GRCh37.87
00:00:00    SnpEff version SnpEff 5.0 (build 2020-08-09 21:23), by Pablo Cingolani
00:00:00    Command: 'download'
00:00:00    Reading configuration file 'snpEff.config'. Genome: 'GRCh37.87'
00:00:00    Reading config file: /Users/gel001/Desktop/snpEff_5.0/snpEff.config
00:00:00    done
00:00:00    Downloading database for 'GRCh37.87'
00:00:00    Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh37.87.zip
00:00:00    ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_GRCh37.87.zip
java.lang.RuntimeException: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct.
    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:1194)
    at org.snpeff.SnpEff.main(SnpEff.java:167)
Caused by: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct.
    at org.snpeff.util.Download.download(Download.java:127)
    ... 5 more
00:00:00    Logging
00:00:01    Done.

I did some poking around the blob store (although I may have been doing it wrong, I am more of an AWS guy) and I didn't see them listed under any kind of alternate either.

curl https://snpeff.blob.core.windows.net/databases?restype=container&comp=list&prefix=v5_0 > databases.xml

Is it possible some automated deployment croaked when uploading them? Downloading other ones, like "hg19" works just fine.

Thanks!

pcingola commented 4 years ago

OK, looks like I need to rebuild and upload those. Thank you for the heads-up

aardes commented 3 years ago

Hi,

@pcingola Do you have an update for this, I have the same issue.

regards

Phillip-a-richmond commented 3 years ago

+1 on this issue as well. Perhaps worth staying with 4.3?

pcingola commented 3 years ago

GRCh37.p13.RefSeq ahs been uploaded.

pcingola commented 3 years ago

GRCh38.p13.RefSeq ahs been uploaded. GRCh37.75 is also available. GRCh37.87 is also available.