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PharmGKB / PharmCAT

The Pharmacogenomic Clinical Annotation Tool
Mozilla Public License 2.0
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Problem running pharmcat-0.6.0-all.jar (BUG?) #20

Closed CarlosGAH closed 5 years ago

CarlosGAH commented 5 years ago

Hi, i have tried to use the release version 0.6.0 of pharmcat with the sample vcf that you can download, but i've got this error: First i downloaded the .jar from the release page. When i use the command alone i get this java -jar /home/usuario/tools_java/Pharmacat/pharmcat-0.6.0-all.jar Missing required options: vcf, o

usage: PharmCAT -a,--astrolabe-file path to astrolabe result file (TSV) -f,--output-file the base name used for ouput file names (will add file extensions), will default to same value as call-file if not specified -g,--guidelines-dir directory of guideline annotations (JSON files) -h,--help print this message -j,--write-report-json flag to write a JSON file of the data used to populate the final report -k,--keep-matcher-files flag to keep the intermediary matcher output files -na,--alleles-dir directory of named allele definitions (JSON files) -o,--output-dir directory to output to -v,--verbose enable verbose output -vcf,--sample-file input call file (VCF)

The normal output, but when i try to use it with a vcf:

java -jar /home/usuario/tools_java/Pharmacat/pharmcat-0.6.0-all.jar -vcf pharmcat.v0.6.0.vcf -o prueba_pharma com.google.gson.JsonSyntaxException: Apr 12, 2016 12:00:00 AM at com.google.gson.internal.bind.DateTypeAdapter.deserializeToDate(DateTypeAdapter.java:74) at com.google.gson.internal.bind.DateTypeAdapter.read(DateTypeAdapter.java:59) at com.google.gson.internal.bind.DateTypeAdapter.read(DateTypeAdapter.java:41) at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$1.read(ReflectiveTypeAdapterFactory.java:129) at com.google.gson.internal.bind.ReflectiveTypeAdapterFactory$Adapter.read(ReflectiveTypeAdapterFactory.java:220) at com.google.gson.Gson.fromJson(Gson.java:887) at com.google.gson.Gson.fromJson(Gson.java:825) at org.pharmgkb.pharmcat.util.DataSerializer.deserializeDefinitionsFromJson(DataSerializer.java:59) at org.pharmgkb.pharmcat.haplotype.DefinitionReader.readFile(DefinitionReader.java:103) at org.pharmgkb.pharmcat.haplotype.DefinitionReader.read(DefinitionReader.java:90) at org.pharmgkb.pharmcat.PharmCAT.(PharmCAT.java:123) at org.pharmgkb.pharmcat.PharmCAT.main(PharmCAT.java:79) Caused by: java.text.ParseException: Failed to parse date ["Apr 12, 2016 12:00:00 AM']: Invalid number: Apr at com.google.gson.internal.bind.util.ISO8601Utils.parse(ISO8601Utils.java:274) at com.google.gson.internal.bind.DateTypeAdapter.deserializeToDate(DateTypeAdapter.java:72) ... 11 more Caused by: java.lang.NumberFormatException: Invalid number: Apr at com.google.gson.internal.bind.util.ISO8601Utils.parseInt(ISO8601Utils.java:311) at com.google.gson.internal.bind.util.ISO8601Utils.parse(ISO8601Utils.java:129) ... 12 more The vcf is the one in the release page and this is my setting

  • PharmCAT Version: 0.6.0 release
  • JDK Version: openjdk version "10.0.2" 2018-07-17 OpenJDK Runtime Environment (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.4) OpenJDK 64-Bit Server VM (build 10.0.2+13-Ubuntu-1ubuntu0.18.04.4, mixed mode)
  • Environment: Linux Ubuntu 18.04

Thanks for your time and work!

CarlosGAH commented 5 years ago

I have tried to use the same jar in other computer and worked perfectly, so it must be a problem within my own computer. Thanks for your time and sorry for the incovenience.