Got an error when running virusbreakend. I have tracked the error command and input. It happened in the VirusBreakendFilter step. Could you please help to find where did the error come from?
Thanks,
Qiang
$java -cp gridss-2.13.2-gridss-jar-with-dependencies.jar gridss.VirusBreakendFilter I=test_1.vcf O=test.vcf REFERENCE_SEQUENCE=GRCh38_full_analysis_set_plus_decoy_hla.fa
Exception in thread "main" java.lang.IllegalArgumentException: Malformed CIGAR string: -
at htsjdk.samtools.TextCigarCodec.decode(TextCigarCodec.java:69)
at au.edu.wehi.idsv.sam.ChimericAlignment.(ChimericAlignment.java:64)
at gridss.VirusBreakendFilter.lambda$infoToChimeric$4(VirusBreakendFilter.java:212)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at gridss.VirusBreakendFilter.infoToChimeric(VirusBreakendFilter.java:213)
at gridss.VirusBreakendFilter.shouldKeep(VirusBreakendFilter.java:194)
at gridss.VirusBreakendFilter.lambda$doWork$1(VirusBreakendFilter.java:82)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:174)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at gridss.VirusBreakendFilter.doWork(VirusBreakendFilter.java:85)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at gridss.VirusBreakendFilter.main(VirusBreakendFilter.java:57)
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sampleID
adjusted_kraken_taxid_333760_NC_001526.4 2963 gridss0f_284b G GAAGAAAGTGTTGTTTTCAGACCTGGCTCCACTAACAGTTTATTTTGCCCTCTTTCAAAGACTCAGATGAGAGCACTGCAGGAAGAAGAAAAACAAGTTCTGAAGTCTCCATGAGTCAATACTCCTGCAGAGCACAGGCCTTTTCTAAGTGGAGAGGAGGAGTTTTGGTGTAAATTGCCTGATCAGAAATTTGGATCCAATGTCTTTGCTGTTACTTCTGTCTCATGCCTTATCACCTCTACCATCATTCTAGGGAAAGGAAATCTCTCTCTTTCTTTTCTTTCTTTCTTTCCTTCTTTCCTTCCTTCCGTCCTTCCTTCCTTCCCTCCCTCCCTCCGTCCCTTTCTTTCTTTTTTTTTTTGAGACGGAGTCTCATTCTGTTGCCTAGGCTGGAGTGCAGTGGTGCAATCTCGGCTCACTGCAACCTCTGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGTCCCCGCCACCACGCCCGGCTAATTTGTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCT. 2183.10 PASS ANRP=0;ANRPQ=0.00;ANSR=0;ANSRQ=0.00;AS=0;ASC=1X;ASQ=0.00;ASRP=0;ASSR=0;BA=1;BAQ=1080.02;BASRP=32;BASSR=37;BEALN=HLA-DRB109:21:15226|-|14S35M1I512M|60,HLA-DRB107:01:01:01:15188|-|14S35M1I160M6D24M23D57M4I267M|,chr6_GL000253v2_alt:3989296|+|262M4I53M23D30M6D163M1I35M14S|,chr6_GL000252v2_alt:3814888|+|262M4I53M31D30M6D163M1I35M14S|,HLA-DRB1*07:01:01:02:15190|-|14S35M1I160M6D24M31D57M4I267M|;BEID=asm0-424;BEIDH=-1;BEIDL=0;BMQ=59.73;BMQN=40.00;BMQX=60.00;BQ=2183.10;BSC=41;BSCQ=551.23;BUM=31;BUMQ=551.86;BVF=58;CAS=0;CASQ=0.00;CQ=3521.86;EVENT=gridss0f_284;IC=0;INSRM=AluSx1#SINE/Alu|82|-|341S221M|1821|16,(TTCC)n#Simple_repeat|1|+|288S36M|28|2,(TCTT)n#Simple_repeat|1|+|264S24M|13|2;INSRMP=0.393;INSRMRC=SINE/Alu;INSRMRO=-;INSRMRT=AluSx1;INSTAXID=9606;IQ=0.00;RAS=0;RASQ=0.00;REF=9801;REFPAIR=4065;RP=0;RPQ=0.00;SB=0.42307693;SC=1X;SR=0;SRQ=0.00;SVTYPE=BND;VF=0 GT:AF:ANRP:ANRPQ:ANSR:ANSRQ:ASQ:ASRP:ASSR:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:4.165e-03:0:0.00:0:0.00:0.00:0:0:1080.02:32:37:2183.10:41:551.23:31:551.86:58:0.00:0:0.00:0.00:0.00:9801:4065:0:0.00:0:0.00:0
Hi,
Got an error when running
virusbreakend. I have tracked the error command and input. It happened in theVirusBreakendFilterstep. Could you please help to find where did the error come from?Thanks, Qiang
$java -cp gridss-2.13.2-gridss-jar-with-dependencies.jar gridss.VirusBreakendFilter I=test_1.vcf O=test.vcf REFERENCE_SEQUENCE=GRCh38_full_analysis_set_plus_decoy_hla.fa Exception in thread "main" java.lang.IllegalArgumentException: Malformed CIGAR string: - at htsjdk.samtools.TextCigarCodec.decode(TextCigarCodec.java:69) at au.edu.wehi.idsv.sam.ChimericAlignment.(ChimericAlignment.java:64)
at gridss.VirusBreakendFilter.lambda$infoToChimeric$4(VirusBreakendFilter.java:212)
at java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:193)
at java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1382)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at gridss.VirusBreakendFilter.infoToChimeric(VirusBreakendFilter.java:213)
at gridss.VirusBreakendFilter.shouldKeep(VirusBreakendFilter.java:194)
at gridss.VirusBreakendFilter.lambda$doWork$1(VirusBreakendFilter.java:82)
at java.util.stream.ReferencePipeline$2$1.accept(ReferencePipeline.java:174)
at java.util.Iterator.forEachRemaining(Iterator.java:116)
at java.util.Spliterators$IteratorSpliterator.forEachRemaining(Spliterators.java:1801)
at java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:481)
at java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:471)
at java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:708)
at java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234)
at java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:499)
at gridss.VirusBreakendFilter.doWork(VirusBreakendFilter.java:85)
at picard.cmdline.CommandLineProgram.instanceMain(CommandLineProgram.java:305)
at gridss.VirusBreakendFilter.main(VirusBreakendFilter.java:57)
CHROM POS ID REF ALT QUAL FILTER INFO FORMAT sampleID
adjusted_kraken_taxid_333760_NC_001526.4 2963 gridss0f_284b G GAAGAAAGTGTTGTTTTCAGACCTGGCTCCACTAACAGTTTATTTTGCCCTCTTTCAAAGACTCAGATGAGAGCACTGCAGGAAGAAGAAAAACAAGTTCTGAAGTCTCCATGAGTCAATACTCCTGCAGAGCACAGGCCTTTTCTAAGTGGAGAGGAGGAGTTTTGGTGTAAATTGCCTGATCAGAAATTTGGATCCAATGTCTTTGCTGTTACTTCTGTCTCATGCCTTATCACCTCTACCATCATTCTAGGGAAAGGAAATCTCTCTCTTTCTTTTCTTTCTTTCTTTCCTTCTTTCCTTCCTTCCGTCCTTCCTTCCTTCCCTCCCTCCCTCCGTCCCTTTCTTTCTTTTTTTTTTTGAGACGGAGTCTCATTCTGTTGCCTAGGCTGGAGTGCAGTGGTGCAATCTCGGCTCACTGCAACCTCTGCCTCCCGGGTTCAAGCGATTCTCCTGCCTCAGCCTCCTGAGTAGCTGGGATTACAGGTCCCCGCCACCACGCCCGGCTAATTTGTTGTATTTTTAGTAGAGACAGGGTTTCACCATGTTAGCCAGGATGGTCT. 2183.10 PASS ANRP=0;ANRPQ=0.00;ANSR=0;ANSRQ=0.00;AS=0;ASC=1X;ASQ=0.00;ASRP=0;ASSR=0;BA=1;BAQ=1080.02;BASRP=32;BASSR=37;BEALN=HLA-DRB109:21:15226|-|14S35M1I512M|60,HLA-DRB107:01:01:01:15188|-|14S35M1I160M6D24M23D57M4I267M|,chr6_GL000253v2_alt:3989296|+|262M4I53M23D30M6D163M1I35M14S|,chr6_GL000252v2_alt:3814888|+|262M4I53M31D30M6D163M1I35M14S|,HLA-DRB1*07:01:01:02:15190|-|14S35M1I160M6D24M31D57M4I267M|;BEID=asm0-424;BEIDH=-1;BEIDL=0;BMQ=59.73;BMQN=40.00;BMQX=60.00;BQ=2183.10;BSC=41;BSCQ=551.23;BUM=31;BUMQ=551.86;BVF=58;CAS=0;CASQ=0.00;CQ=3521.86;EVENT=gridss0f_284;IC=0;INSRM=AluSx1#SINE/Alu|82|-|341S221M|1821|16,(TTCC)n#Simple_repeat|1|+|288S36M|28|2,(TCTT)n#Simple_repeat|1|+|264S24M|13|2;INSRMP=0.393;INSRMRC=SINE/Alu;INSRMRO=-;INSRMRT=AluSx1;INSTAXID=9606;IQ=0.00;RAS=0;RASQ=0.00;REF=9801;REFPAIR=4065;RP=0;RPQ=0.00;SB=0.42307693;SC=1X;SR=0;SRQ=0.00;SVTYPE=BND;VF=0 GT:AF:ANRP:ANRPQ:ANSR:ANSRQ:ASQ:ASRP:ASSR:BAQ:BASRP:BASSR:BQ:BSC:BSCQ:BUM:BUMQ:BVF:CASQ:IC:IQ:QUAL:RASQ:REF:REFPAIR:RP:RPQ:SR:SRQ:VF .:4.165e-03:0:0.00:0:0.00:0.00:0:0:1080.02:32:37:2183.10:41:551.23:31:551.86:58:0.00:0:0.00:0.00:0.00:9801:4065:0:0.00:0:0.00:0