I am getting a red exclamation symbol next to multiple genes - it is stopping retrieving the number of variants found in those genes. When I click on the individual genes, it attempts the annotation again and works.
This is the error message in the front-end received when I searched on Gene GLB1 (as part of a phenolyzer call for ALS amyotrophic...) - is it due to a missing tbi for v4.0.0.calypso.vcf.gz or the extra / in front of /gru_data?:
Could not annotate variants due to server error. Error: ============================================= vcfanno version 0.3.5 [built with go1.19.3] see: https://github.com/brentp/vcfanno ============================================= vcfanno.go:113: [Flatten] unable to open file: //gru_data/annotations/GRCh38/gnomad/gnomad.genomes.v4.0.0.calypso.vcf.gz normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency true [q] quiet false [d] debug false [r] reference FASTA file /gru_data/data/references/homo_sapiens/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.18.fa decompose v0.5 options: input VCF file - [s] smart decomposition true (experimental) [o] output VCF file - subset v0.5 Options: input VCF File - [s] sample file list 1 samples Unknown option: no_plugins Ignoring unsupported option 'no_plugins' found via ENV variable or INI file Unknown option: no_htslib Ignoring unsupported option 'no_htslib' found via ENV variable or INI file Unknown option: pluginsdir Ignoring unsupported option 'pluginsdir' found via ENV variable or INI file Unknown option: no_update Ignoring unsupported option 'no_update' found via ENV variable or INI file stats: samples : 1/1 variants : 68/154 Time elapsed: 0.01s stats: no. variants : 68 no. biallelic variants : 67 no. multiallelic variants : 1 no. additional biallelics : 1 total no. of biallelics : 69 Time elapsed: 0.01s stats: biallelic no. left trimmed : 0 no. right trimmed : 6 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 6 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 6 total no. variants observed : 69 total no. reference observed : 0 Time elapsed: 0.01s
Best regards
Oliver
I am getting a red exclamation symbol next to multiple genes - it is stopping retrieving the number of variants found in those genes. When I click on the individual genes, it attempts the annotation again and works.
This is the error message in the front-end received when I searched on Gene GLB1 (as part of a phenolyzer call for ALS amyotrophic...) - is it due to a missing tbi for v4.0.0.calypso.vcf.gz or the extra / in front of /gru_data?:
Could not annotate variants due to server error. Error: ============================================= vcfanno version 0.3.5 [built with go1.19.3] see: https://github.com/brentp/vcfanno ============================================= vcfanno.go:113: [Flatten] unable to open file: //gru_data/annotations/GRCh38/gnomad/gnomad.genomes.v4.0.0.calypso.vcf.gz normalize v0.5 options: input VCF file - [o] output VCF file - [w] sorting window size 10000 [m] no fail on masked reference inconsistency false [n] no fail on reference inconsistency true [q] quiet false [d] debug false [r] reference FASTA file /gru_data/data/references/homo_sapiens/GRCh38/Homo_sapiens.GRCh38.dna.chromosome.18.fa decompose v0.5 options: input VCF file - [s] smart decomposition true (experimental) [o] output VCF file - subset v0.5 Options: input VCF File - [s] sample file list 1 samples Unknown option: no_plugins Ignoring unsupported option 'no_plugins' found via ENV variable or INI file Unknown option: no_htslib Ignoring unsupported option 'no_htslib' found via ENV variable or INI file Unknown option: pluginsdir Ignoring unsupported option 'pluginsdir' found via ENV variable or INI file Unknown option: no_update Ignoring unsupported option 'no_update' found via ENV variable or INI file stats: samples : 1/1 variants : 68/154 Time elapsed: 0.01s stats: no. variants : 68 no. biallelic variants : 67 no. multiallelic variants : 1 no. additional biallelics : 1 total no. of biallelics : 69 Time elapsed: 0.01s stats: biallelic no. left trimmed : 0 no. right trimmed : 6 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. biallelic normalized : 6 multiallelic no. left trimmed : 0 no. right trimmed : 0 no. left and right trimmed : 0 no. right trimmed and left aligned : 0 no. left aligned : 0 total no. multiallelic normalized : 0 total no. variants normalized : 6 total no. variants observed : 69 total no. reference observed : 0 Time elapsed: 0.01s
Best regards
Oliver