Error Reading gencode.v38.genes.json.gz File in SvAnna CLI Tool
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7 weeks ago
pragnapcu • 0

Hello,

I am experiencing an issue while running the SvAnna CLI tool. I receive the following error message when executing the command:

ERROR o.m.svanna.cli.cmd.PrioritizeCommand - Error: Error reading genes from /path/to/svanna-data/gencode.v38.genes.json.gz

Here is the exact command I used:

java -jar svanna-cli-1.0.4.jar prioritize \
  -d svanna-data \
  --vcf example.vcf \
  --phenotype-term HP:0011890 \
  --phenotype-term HP:0000978\
  --phenotype-term HP:0012147 \
  --out-dir results \
  --prefix example

I have verified the integrity of the gencode.v38.genes.json.gz file using checksum, and it says Ok. Additionally, the head of the file appears to be correctly formatted (JSON structure), showing gene information as expected.

[ {
"id" : {
"acc" : "ENSG00000160856.21",
"symbol" : "FCRL3",
"hgncId" : "HGNC:18506"
},
"loc" : {
"gbAccession" : "CM000663.2",
"strand" : "-",
"start" : 91255653,

SVAnna version: svanna-cli v1.0.4

java -jar --version
openjdk 11.0.13 2021-10-19
OpenJDK Runtime Environment JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21)
OpenJDK 64-Bit Server VM JBR-11.0.13.7-1751.21-jcef (build 11.0.13+7-b1751.21, mixed mode)

I have checked file permissions and ensured that the file is readable. Despite these checks, the error persists.

Has anyone encountered this issue before, or does anyone have suggestions on how to resolve it? Any help would be greatly appreciated.

Thank you.

Structural-Variant SVAnna • 284 views
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Does your json file need to be uncompressed?

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Uncompressed file is also throwing the error

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