unexpected command line complaint with -r

[AMChalkie]

java -Xmx6g -jar JACUSA_v2.0.0-RC5.jar call-1 -b Sppl2a.bed -f V -r Sppl2a.jacusa2.vcf myfile.bam
INFO 00:00:00 Computing overlap between sequence records.

JACUSA2 Version: 2.0.0-RC5 call-1 -b Sppl2a.bed -f V -r Sppl2a.jacusa2.vcf myfile.bam

java.lang.IllegalArgumentException: Cannot set a file type if the output is not to a file.
at htsjdk.variant.variantcontext.writer.VariantContextWriterBuilder.setOutputFileType(VariantContextWriterBuilder.java:185)
at jacusa.io.format.call.VCFcallWriter.(VCFcallWriter.java:59)
at jacusa.io.format.call.VCFcallFormat.createWriter(VCFcallFormat.java:41)
at lib.worker.WorkerDispatcher.(WorkerDispatcher.java:53)
at lib.util.AbstractMethod.getWorkerDispatcherInstance(AbstractMethod.java:60)
at lib.util.AbstractTool.run(AbstractTool.java:64)
at jacusa.JACUSA.main(JACUSA.java:99)
at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
at java.lang.reflect.Method.invoke(Method.java:498)
at org.eclipse.jdt.internal.jarinjarloader.JarRsrcLoader.main(JarRsrcLoader.java:61)

[AMChalkie]

Note that without the -f V, an output file is produced.

[ellalalalalalala]

Hi AMChalkie, how did you solve the error? If I remove the -f V option, will my output then still be VCF, given the file ending of the output file name? In the manual it says, that the default output is BED. I did not have any comparable problems with the combination of the "-f V" and "-r file.out" option, when I used Jacusa1...

[ellalalalalalala]

I tried by removing -f V and labeling the output file as FILE.vcf... no error anymore but results in an empty output file :(

[piechottam]

I have found the problem and I will publish a new release with the fix today.

Please post issues in:
https://github.com/dieterich-lab/JACUSA2

This repository is for JACUSA1

[ellalalalalalala]

Hi piechottam, great, thanks a lot for your fast reply and help 🥇 Sorry for posting in the wrong repository, ich just found this thread and it was exactly my problem. :)

[piechottam]

Follow dieterich-lab/JACUSA2#39