Nothing doneДЄt first it says it finds one transcript and then it says 0 are marked.Д¬ode: :~/snpEff$ java -Xmx4g -jar snpEff.jar dengue_DR59_2 /data/ebel_lab/Weger/Experiment_27/36_Exp/test/323.vcf > 323_ann.vcf -noGenomeД®rror: Error while processing VCF entry (line 93) :ДЄB122022 3152. Protein check: dengue_DR59_2 OK: 1 Not found: 0 Errors: 0 Error percentage: 0.0%Д 0:00:00 Reading regulation elements: GFFД 0:00:00 Warning: Cannot read optional regulation file '/home/weger/snpEff/./data/dengue_DR59_2/regulation.gff', nothing done.Д 0:00:00 Reading regulation elements: BEDД 0:00:00 Cannot find optional regulation dir '/home/weger/snpEff/./data/dengue_DR59_2/regulation.bed/', nothing done.Д 0:00:00 Warning: Cannot open PWMs file /home/weger/snpEff/./data/dengue_DR59_2/pwms.bin. Marking as 'coding' from CDS information:Д 0:00:00 Caracterizing exons by splicing (stage 1) :Д 0:00:00 Caracterizing exons by splicing (stage 2) :Д 0:00:00 Rare amino acid annotationsД 0:00:00 Warning: Cannot read optional protein sequence file '/home/weger/snpEff/./data/dengue_DR59_2/protein.fa', nothing done.Д 0:00:00 Protein check file: '/home/weger/snpEff/./data/dengue_DR59_2/genes.gbk'Д 0:00:00 Checking database using protein sequencesД 0:00:00 Reading proteins from file '/home/weger/snpEff/./data/dengue_DR59_2/genes.gbk'. Genome: 'dengue_DR59_2'Д 0:00:00 Reading config file: /home/weger/snpEff/nfigД¬ollapsing zero length introns (if needed):ДЄdding genomic sequences to exons: Done (1 sequences added, 0 ignored). :~/snpEff$ java -jar snpEff.jar build -genbank -v dengue_DR59_2Д 0:00:00 SnpEff version SnpEff 4.3o (build 09:40), by Pablo CingolaniД 0:00:00 Building database for 'dengue_DR59_2'Д 0:00:00 Reading configuration file 'nfig'.

So I rebuilt the database, here is the output # WARNING! : No protein coding transcripts found.

# Chromosomes : Format 'chromo_name size codon_table' The program is not detecting the coding region which is clearly in the. I have tried using different variant callers (lofreq and callvariants.sh).

Annotate a vcf file with atext file