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lindenb / jvarkit

Java utilities for Bioinformatics
https://jvarkit.readthedocs.io/
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msa2vcf #105

Closed vinay104 closed 6 years ago

vinay104 commented 6 years ago

Hello,

i am vinay lkumar reddy nannuru, i want to convert a fasta alignment file into vcf. I installed jvarkit and when i follow the next steps like make msa3vcf, it gives following error.

" vinay410@server230:jvarkit > make msa2vcf mkdir -p /storage2/active/nvinay/mthesis/jvarkit/dist/ rm -rf "/storage2/active/nvinay/mthesis/jvarkit/_tmp-2.15.0" mkdir -p /storage2/active/nvinay/mthesis/jvarkit/_tmp-2.15.0/META-INF/services echo "com.github.lindenb.jvarkit.annotproc.JVarkitAnnotationProcessor" > /storage2/active/nvinay/mthesis/jvarkit/_tmp-2.15.0/META-INF/services/javax.annotation.processing.Processor echo '### Printing javac version : it should be Oracle 1.8 (NOT OpenJDK). if Not, check your $${PATH}.'

Printing javac version : it should be Oracle 1.8 (NOT OpenJDK). if Not, check your $${PATH}.

javac -version javac 1.6.0_41

compile

javac -d /storage2/active/nvinay/mthesis/jvarkit/_tmp-2.15.0 -sourcepath /storage2/active/nvinay/mthesis/jvarkit/src/main/java:/storage2/active/nvinay/mthesis/jvarkit/src/main/generated-sources/java /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:84: illegal start of expression map(C->C.getName()). ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:169: illegal start of expression filter(E->E.getKind()==ElementKind.CLASS). ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:170: illegal start of expression filter(E-> E.getAnnotation(IncludeSourceInJar.class) !=null). ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:171: illegal start of expression forEach(E->{
^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:171: illegal start of expression forEach(E->{
^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:171: ';' expected forEach(E->{
^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:172: not a statement if( thisDir==null || thisDir.isEmpty()) return; ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:172: ';' expected if( thisDir==null || thisDir.isEmpty()) return; ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:174: illegal start of type }); ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:180: expected roundEnv.getElementsAnnotatedWith(Program.class).stream(). ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:180: expected roundEnv.getElementsAnnotatedWith(Program.class).stream(). ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:180: ';' expected roundEnv.getElementsAnnotatedWith(Program.class).stream(). ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:182: illegal start of type filter(E->{final Program prog=E.getAnnotation(Program.class); return prog!=null && prog.generate_doc();}). ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:182: ';' expected filter(E->{final Program prog=E.getAnnotation(Program.class); return prog!=null && prog.generate_doc();}). ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:183: invalid method declaration; return type required forEach(E->{ ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:183: expected forEach(E->{ ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:183: ';' expected forEach(E->{ ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:233: illegal start of expression map(T->"["+T.getAccession()+"]"+T.getLabel()). ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:294: illegal start of type }); ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:295: illegal start of type return true; ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:295: ';' expected return true; ^ /storage2/active/nvinay/mthesis/jvarkit/src/main/java/com/github/lindenb/jvarkit/annotproc/JVarkitAnnotationProcessor.java:300: class, interface, or enum expected } ^ 22 errors make: *** [/storage2/active/nvinay/mthesis/jvarkit/dist/annotproc.jar] Error 1 vinay410@server230:jvarkit > "

Can someone help me out of this issue and also what is the usage for msa2vcf to convert a fasta to vcf format.

Thanks, Vinay

lindenb commented 6 years ago

The problem is clearly displayed, in the first lines:

Printing javac version : it should be Oracle 1.8 (NOT OpenJDK). if Not, check your $${PATH}.

javac -version
javac 1.6.0_41

use the correct version of javac

closing.