SnpEff build unable to read protein sequence

[arupgsh]

While building a SnpEff database using NCBI Genebank file the tool is unable to read the protein sequence details mentioned in the file.

Command line: bash ./scripts/buildDbNcbi.sh NC_012920.1

Output:

Downloading genome NC_012920.1 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 69919 0 69919 0 0 29390 0 --:--:-- 0:00:02 --:--:-- 29377 00:00:00 SnpEff version SnpEff 4.3t (build 2017-11-24 10:18), by Pablo Cingolani 00:00:00 Command: 'build' 00:00:00 Building database for 'NC_012920.1' 00:00:00 Reading configuration file 'snpEff.config'. Genome: 'NC_012920.1' 00:00:00 Reading config file: /Toolbox/snpEff/snpEff.config 00:00:00 done Chromosome: 'NC_012920' length: 16569

Create exons from CDS (if needed): ............. Exons created for 13 transcripts.

Deleting redundant exons (if needed): Total transcripts with deleted exons: 0

Collapsing zero length introns (if needed): Total collapsed transcripts: 0 Adding genomic sequences to exons: Done (13 sequences added, 0 ignored).

Adjusting transcripts: Adjusting genes: Adjusting chromosomes lengths: Ranking exons: Create UTRs from CDS (if needed): Remove empty chromosomes:

Marking as 'coding' from CDS information: Done: 0 transcripts marked 00:00:00 Caracterizing exons by splicing (stage 1) :

00:00:00 Caracterizing exons by splicing (stage 2) : 00:00:00 done. 00:00:00 [Optional] Rare amino acid annotations 00:00:00 Done. 00:00:00 Protein check file: '/Toolbox/snpEff/./data/NC_012920.1/genes.gbk'

00:00:00 Checking database using protein sequences 00:00:00 Comparing Proteins... Labels: '+' : OK '.' : Missing '*' : Error

---

Protein check: NC_012920.1 OK: 0 Not found: 0 Errors: 13 Error percentage: 100.0% 00:00:00 Saving database 00:00:00 [Optional] Reading regulation elements: GFF 00:00:00 Warning: Cannot read optional regulation file '/Toolbox/snpEff/./data/NC_012920.1/regulation.gff', nothing done. 00:00:00 [Optional] Reading regulation elements: BED 00:00:00 Cannot find optional regulation dir '/Toolbox/snpEff/./data/NC_012920.1/regulation.bed/', nothing done. 00:00:00 [Optional] Reading motifs: GFF 00:00:00 Warning: Cannot open PWMs file /Toolbox/snpEff/./data/NC_012920.1/pwms.bin. Nothing done 00:00:00 Done 00:00:00 Logging 00:00:01 Checking for updates... 00:00:02 Done.

[pcingola]

Closing old issues.

[yirenheihei]

I have the same question,how can i solve this ?

[pcingola]

Please open a new issue with specific details on what is not working for you.