Closed ialbert closed 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.
Quick fix for building that database (or any NCBI genbank), use SnpEff's script buildDbNcbi.sh
:
./scripts/buildDbNcbi.sh KJ660346.1
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.
@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.
thank you for the quick resolution
Database seems to be missing the server,
snpEff version 4.3 works as expected.
the issue originally reported as:
https://github.com/biostars/biostar-handbook-issues/issues/129