You signed in with another tab or window. Reload to refresh your session.You signed out in another tab or window. Reload to refresh your session.You switched accounts on another tab or window. Reload to refresh your session.Dismiss alert
I tried to remove the -f=V option but then complains that it needs the format specified.
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:43)
at lib.util.AbstractMethod.getWorkerDispatcherInstance(AbstractMethod.java:63)
at lib.util.AbstractTool.run(AbstractTool.java:59)
at jacusa.JACUSA.main(JACUSA.java:96)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
The text was updated successfully, but these errors were encountered:
JACUSA2 Version: 2.0.1 call-2 -p 72 -filterNH 99 -filterNM 99 -c 3 -f=V -a E:file=dbsnp_138.b37.vcf:type=VCF -r DoxvsADAR3.out BAM_files/H2171_1_Dox_S1/H2171_1_Dox_S1_sorted.bam,BAM_files/H2171_1_Dox_S2/H2171_1_Dox_S2_sorted.bam,BAM_files/H2171_1_Dox_S3/H2171_1_Dox_S3_sorted.bam BAM_files/H2171_4_Dox_S1/H2171_4_Dox_S1_sorted.bam,BAM_files/H2171_4_Dox_S2/H2171_4_Dox_S2_sorted.bam,BAM_files/H2171_4_Dox_S3/H2171_4_Dox_S3_sorted.bam
I tried to remove the -f=V option but then complains that it needs the format specified.
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:43)
at lib.util.AbstractMethod.getWorkerDispatcherInstance(AbstractMethod.java:63)
at lib.util.AbstractTool.run(AbstractTool.java:59)
at jacusa.JACUSA.main(JACUSA.java:96)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
at java.base/jdk.internal.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:77)
at java.base/jdk.internal.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
The text was updated successfully, but these errors were encountered: