Error in snpeff tool for download databae

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#1

I have installed snpeff and want to download a databse via this menu item:
SnpEff download: download a pre-built database
I tried to download “GRCh38.86” but this error occurred for me:
00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani

  • 00:00:00 Command: ‘download’*
  • 00:00:00 Reading configuration file ‘snpEff.config’. Genome: ‘GRCz10.86’*
  • 00:00:00 Reading config file: /home/galaxy/galaxy/database/jobs_directory/000/134/working/snpEff.config*
  • 00:00:00 Reading config file: /home/galaxy/galaxy/database/dependencies/_conda/envs/__snpeff@4.3.1t/share/snpeff-4.3.1t-3/snpEff.config*
  • 00:00:00 done*
  • 00:00:00 Downloading database for ‘GRCz10.86’*
  • 00:00:00 Connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_GRCz10.86.zip*
  • 00:00:06 ERROR while connecting to http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_GRCz10.86.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: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)*

  •   ... 5 more*
  • 00:00:06 Logging*
  • 00:00:07 Done.*
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#2

Well, you have a typo in the genome name, don’t you?

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#3

Hi @esmaeil

There may still be a database mixup – but I just was able to download both human and zebrafish at both usegalaxy.org and usegalaxy.eu. There are different tool versions available at the servers, but that didn’t make a difference.

Please try again. And if you are working at some other public Galaxy server, maybe there is a server-specific problem. Try at least one rerun then write back with the server’s URL if you cannot find the direct contact information (usually on the home page of the server or at the server’s directory page here: https://galaxyproject.org/use).

Test1

  • Server - usegalaxy.org
  • Tool/version - SnpEff download: download a pre-built database (Galaxy Version 4.3+T.galaxy2)
  • human - GRCh38.86 (successful)
  • zebrafish - GRCz10.86 (successful)

Test2

  • Server - usegalaxy.eu
  • Tool/version - SnpEff Download Download a new database (Galaxy Version 4.3r.1)
  • human - GRCh38.86 (still running, but I would expect it to have failed by now if a similar connection problem was still going on)
  • zebrafish - GRCz10.86 (successful)

Note: The public server usegalaxy.org has some server issues related to a routine update this morning. A bit of that is still in progress but didn’t seem to impact this tool. The current status for usegalaxy.* servers can always be found here: https://galaxyproject.statuspage.io/

Thanks!

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#4

Oh … missed this part:

This is on your own Galaxy server.

A 403 connection error means that authentication failed. Is your server set up in some way that would block inbound connections/downloads? A firewall? Are you able to download other 3rd party data (“Get Data” tools would be good tests)?

Keep in mind the connection could be blocked by a firewall at a higher level if you are working at an institution. If that sounds possible, check with your local admins to eliminate this as a factor.

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#5

Yes there was problem in sever. I resolved it and now there is no 403 error but at the end this error occured:

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…
Extracting file ‘data/GRCh38.86/regulation_H3K36me3-neutro_myelocyte_(BM)_enriched_sites.bin’
java.lang.RuntimeException: java.io.EOFException: Unexpected end of ZLIB input stream
at org.snpeff.util.Download.unzip(Download.java:296)
at org.snpeff.snpEffect.commandLine.SnpEffCmdDownload.downloadAndInstall(SnpEffCmdDownload.java:33)
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:1183)
at org.snpeff.SnpEff.main(SnpEff.java:162)
Caused by: java.io.EOFException: Unexpected end of ZLIB input stream
at java.base/java.util.zip.InflaterInputStream.fill(InflaterInputStream.java:245)
at java.base/java.util.zip.InflaterInputStream.read(InflaterInputStream.java:159)
at java.base/java.util.zip.ZipInputStream.read(ZipInputStream.java:195)
at org.snpeff.util.Download.unzip(Download.java:275)
… 5 more
Logging
Done.

#6

This seems to indicate an interrupted/incomplete download. Just try again. If the problem persists, you may want to check your own connectivity.

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