yibo dong

lua5.3 ../../bin/update_references.lua lua5.3: ../../bin/update_references.lua:20: attempt to index a nil value (global 'gt') stack traceback: ../../bin/update_references.lua:20: in main chunk [C]: in ?

when I run "../../bin/update_references.lua", error outputted: " gt: error: could not execute script ../../bin/update_references.lua:268: bad argument #1 to 'pairs' (table expected, got nil) "

The database (Candida_auris) can not be downloaded [dongyibo@login8 variants]$ singularity exec -B ./:/data docker://staphb/snpeff:5.1 snpeff download Candida_auris INFO: Using cached SIF image 00:00:00 ERROR while connecting to https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_Candida_auris.zip 00:00:00 ERROR...

[dongyibo@login8 variants]$ singularity exec docker://staphb/snpeff:5.2a snpEff Candida_auris /blue/bphl-florida/dongyibo/Dev_Candida_PB/output-202402231521 23/variants/bc2085bc2085.vcf > /blue/bphl-florida/dongyibo/Dev_Candida_PB/output-20240223152123/variants/test.ann.vcf INFO: Using cached SIF image FATAL ERROR: Failed to download database from [https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_Candida_auris.zip, https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_Candida_auris.zip, https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_Candida_auris.zip] [dongyibo@login8 variants]$

[dongyibo@login8 variants]$ singularity exec docker://staphb/snpeff:5.2a snpeff Candida_auris /blue/bphl-florida/dongyibo/Dev_Candida_PB/output-202402231521 23/variants/bc2085bc2085.vcf > /blue/bphl-florida/dongyibo/Dev_Candida_PB/output-20240223152123/variants/test.ann.vcf INFO: Using cached SIF image FATAL ERROR: Failed to download database from [https://snpeff.blob.core.windows.net/databases/v5_2/snpEff_v5_2_Candida_auris.zip, https://snpeff.blob.core.windows.net/databases/v5_0/snpEff_v5_0_Candida_auris.zip, https://snpeff.blob.core.windows.net/databases/v5_1/snpEff_v5_1_Candida_auris.zip]

how to use my own databases in this docker image?

I mean that I need build a database by myself. but may I use it in the docker container?

How can I check/list all snpeff db or genome?

Why only chr21 is analyzed by freebayes? When I checked the vcf generated by freebayes, I found only chr21 was analyzed, and the line "##commandline="freebayes -f genome.fa --target chr21_1-46709983.bed --min-alternate-fraction...

> I'd check the https://pcingola.github.io/SnpEff/ and https://www.ensembl.org/info/docs/tools/vep/index.html website for it, they have tons of genomes and lots of different versions. We also mirror some of them in https://annotation-cache.github.io/ Would you...