Error Reading gencode.v38.genes.json.gz File in SvAnna CLI Tool #242
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Hi @pragnapcu , literally one of the lines that you see in the Terminal? |
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Yes, in the output. Except /path/to/ where actual path was mentioned |
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So, I assume that you are providing a proper path via the First, I would like to ask you to provide an absolute path, in case you already did not do that. If absolute path does not help, I would like to ask you to increase the CLI verbosity using |
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absolute path did not help. Here is the terminal output using -vv java -jar svanna-cli-1.0.4.jar prioritize -d /path/to/svanna-data --vcf example.vcf --phenotype-term HP:0011890 --phenotype-term HP:0000978 --phenotype-term HP:0012147 --out-dir results --prefix example -vv / / _/ | ____ ____ ____ _ Structural Variant Annotation and Analysis 10:08:31.675 [main] INFO o.m.svanna.cli.cmd.PrioritizeCommand - Using 3 phenotype features supplied via CLI |
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Hi @pragnapcu I did a fresh download of SvAnna 1.0.4 distribution from GitHub releases and I downloaded and unpacked the 2304 database files from Downloads. Then I downloaded the example.vcf (I believe it is the same one that you used) and ran the app with your CLI input: java -jar svanna-cli-1.0.4.jar prioritize -d $(pwd)/data --vcf example.vcf --phenotype-term HP:0011890 --phenotype-term HP:0000978 --phenotype-term HP:0012147 --out-dir results --prefix example -vvThis is the output I got: So, crucially, there was no issue during deserialization of the gencode JSON file. This is the SHA256 checksum of the JSON file: sha256sum gencode.v38.genes.json.gz
9d326c5fe6be97602633a1aca68275a61a0bf48b0d62c4b62c843733442eb4ed gencode.v38.genes.json.gzThe checksum matches the content of the Can you please check if you get the same checksum? |
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I was having this issue but it was fixed by using 2304 version of the data zip. I was previously using the 2204 version because I was given an error ( |
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I got the same error when using 2204 version, so I tried to download the 2304 one. |
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.gzHere 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 exampleI 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.
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