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pcingola / SnpEff

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database missing on the remote server #261

Closed ialbert closed 3 years ago

ialbert commented 3 years ago

Database seems to be missing the server, 

$ snpEff download ebola_zaire
00:00:00        ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_ebola_zaire.zip
java.lang.RuntimeException: java.lang.RuntimeException: File not found on the server. Make sure the database name is correct.

snpEff version 4.3 works as expected.

the issue originally reported as:

https://github.com/biostars/biostar-handbook-issues/issues/129

j-es-craig commented 3 years ago

I am experiencing a similar issue, when I search for the database, it provides me with a link (http://downloads.sourceforge.net/project/snpeff/databases/v4_3/snpEff_v4_3_daucus_carota.zip), yet I cannot download it as it is missing from the server.

pcingola commented 3 years ago

Quick fix for building that database (or any NCBI genbank), use SnpEff's script buildDbNcbi.sh:

./scripts/buildDbNcbi.sh KJ660346.1
pcingola commented 3 years ago

Fixed:

$ java -jar snpEff.jar download -v ebola_zaire
00:00:00    SnpEff version SnpEff 5.0b (build 2020-10-16 14:33), by Pablo Cingolani
00:00:00    Command: 'download'
00:00:00    Reading configuration file 'snpEff.config'. Genome: 'ebola_zaire'
00:00:00    Reading config file: /Users/kqrw311/workspace/SnpEff/config/snpEff.config
00:00:00    done
00:00:00    Downloading database for 'ebola_zaire'
00:00:00    Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_ebola_zaire.zip
00:00:01    Local file name: '/var/folders/s9/y0bgs3l55rj_jkkkxr2drz4157r1dz/T//snpEff_v5_0_ebola_zaire.zip'

00:00:01    Donwload finished. Total 6124 bytes.
00:00:01    Extracting file 'data/ebola_zaire/snpEffectPredictor.bin'
00:00:01    Unzip: OK
00:00:01    Deleted local file '/var/folders/s9/y0bgs3l55rj_jkkkxr2drz4157r1dz/T//snpEff_v5_0_ebola_zaire.zip'
00:00:01    Done
00:00:01    Logging
00:00:02    Done.
pcingola commented 3 years ago

@j-es-craig : Daucus_carota is also there (SnpEff version 5.0)

$ java -jar snpEff.jar download -v Daucus_carota
00:00:00    SnpEff version SnpEff 5.0b (build 2020-10-16 14:33), by Pablo Cingolani
00:00:00    Command: 'download'
00:00:00    Reading configuration file 'snpEff.config'. Genome: 'Daucus_carota'
00:00:00    Reading config file: /Users/kqrw311/workspace/SnpEff/config/snpEff.config
00:00:00    done
00:00:00    Downloading database for 'Daucus_carota'
00:00:00    Connecting to https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_Daucus_carota.zip
00:00:01    Local file name: '/var/folders/s9/y0bgs3l55rj_jkkkxr2drz4157r1dz/T//snpEff_v5_0_Daucus_carota.zip'
...................
00:00:06    Donwload finished. Total 20906703 bytes.
00:00:06    Extracting file 'data/Daucus_carota/snpEffectPredictor.bin'
00:00:06    Creating local directory: '/Users/kqrw311/workspace/SnpEff/config/./data/Daucus_carota'
00:00:06    Unzip: OK
00:00:06    Deleted local file '/var/folders/s9/y0bgs3l55rj_jkkkxr2drz4157r1dz/T//snpEff_v5_0_Daucus_carota.zip'
00:00:06    Done
00:00:06    Logging
00:00:07    Done.
ialbert commented 3 years ago

thank you for the quick resolution