SNPSift - Token Recognition Error
0
0
Entering edit mode
6.1 years ago
anon123 ▴ 10

I'm using Git Bash and SnpSift. The following command line extracts the columns of interest from my VCF file.

java -jar SnpSift.jar extractfields filename.vcf CHROM POS ID REF AL "SampleID@1232" > sample2.vcf

The command line works perfectly until the addition of the "SampleID@1232". I get the following error message:
 

line 1:7 token recognition error at: '@'
Exception in thread "main" java.lang.RuntimeException: Error parsing expression 
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdExtractFields.parseFields(SnpSiftCmdExtractFields.java:105)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdExtractFields.run(SnpSiftCmdExtractFields.java:124)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdExtractFields.run(SnpSiftCmdExtractFields.java:117)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSift.run(SnpSift.java:364)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSift.main(SnpSift.java:69)
Caused by: java.lang.RuntimeException: java.lang.RuntimeException: LexerNoViableAltException('@')
        at ca.mcgill.mcb.pcingola.snpSift.lang.LangFactory.compile(LangFactory.java:129)
        at ca.mcgill.mcb.pcingola.snpSift.SnpSiftCmdExtractFields.parseFields(SnpSiftCmdExtractFields.java:103)
        ... 4 more
Caused by: java.lang.RuntimeException: LexerNoViableAltException('@')
        at ca.mcgill.mcb.pcingola.snpSift.lang.LangFactory$1.recover(LangFactory.java:118)
        at org.antlr.v4.runtime.Lexer.nextToken(Lexer.java:169)
        at org.antlr.v4.runtime.BufferedTokenStream.fetch(BufferedTokenStream.java:187)
        at org.antlr.v4.runtime.BufferedTokenStream.sync(BufferedTokenStream.java:170)
        at org.antlr.v4.runtime.BufferedTokenStream.consume(BufferedTokenStream.java:154)
        at org.antlr.v4.runtime.atn.ParserATNSimulator.execATN(ParserATNSimulator.java:566)
        at org.antlr.v4.runtime.atn.ParserATNSimulator.adaptivePredict(ParserATNSimulator.java:423)
        
at ca.mcgill.mcb.pcingola.snpSift.antlr.SnpSiftParser.expression(SnpSiftParser.java:498)
 
      at ca.mcgill.mcb.pcingola.snpSift.antlr.SnpSiftParser.compilationUnit(SnpSiftParser.java:90)
        at ca.mcgill.mcb.pcingola.snpSift.lang.LangFactory.compile(LangFactory.java:126)
        ... 5 more
Caused by: LexerNoViableAltException('@')
        at org.antlr.v4.runtime.atn.LexerATNSimulator.failOrAccept(LexerATNSimulator.java:329)
        at org.antlr.v4.runtime.atn.LexerATNSimulator.execATN(LexerATNSimulator.java:250)
        at org.antlr.v4.runtime.atn.LexerATNSimulator.match(LexerATNSimulator.java:143)
        at org.antlr.v4.runtime.Lexer.nextToken(Lexer.java:165)
        ... 13 more

I've tried the following based on the suggest of an alternate thread:


"SampleID@1232!=='synonymous_variant'"

However, I'm still getting the same error. 

I'd appreciate any suggestions. Thanks.

snpsift tokenrecognitionerror • 1.8k views
ADD COMMENT

Login before adding your answer.

Traffic: 2435 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6