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hartwigmedical / hmftools

Various algorithms for analysing genomics data
GNU General Public License v3.0
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Exception in thread "main" java.lang.IllegalArgumentException: No enum constant com.hartwig.hmftools.common.amber.BaseDepthData.Base.GA #448

Closed gagank4911 closed 1 year ago

gagank4911 commented 1 year ago

:~/gagan/ECLIPSE_Final$ java -Xmx16G -cp amber-3.9.jar com.hartwig.hmftools.amber.AmberApplication -reference VSI_15_S24 -reference_bam VSI_15_S24_sentieon_match_4.1_deduped.bam -tumor TCS176_S33 -tumor_bam TCS176___S33_sentieon_match_4.1_deduped.bam -output_dir /amber_out -ref_genomeversion 38 -threads 8 -loci TCS176S33_TNscope_NEW.vcf 10:07:20.610 INFO [main] - AMBER version: 3.9 10:07:20.613 INFO [main] - Loading vcf file TCS176___S33_TNscope_NEW.vcf 10:07:21.186 INFO [main] - loaded 5439 baf loci 10:07:21.262 INFO [main] - Processing 5439 potential sites in reference bam VSI_15_S24_sentieon_match_4.1_deduped.bam Exception in thread "main" java.lang.IllegalArgumentException: No enum constant com.hartwig.hmftools.common.amber.BaseDepthData.Base.GA at java.base/java.lang.Enum.valueOf(Enum.java:240) at com.hartwig.hmftools.common.amber.BaseDepthData$Base.valueOf(BaseDepthData.java:11) at com.hartwig.hmftools.common.amber.BaseDepthFactory.fromAmberSite(BaseDepthFactory.java:46) at java.base/java.util.stream.ReferencePipeline$3$1.accept(ReferencePipeline.java:195) at java.base/java.util.ArrayList$ArrayListSpliterator.forEachRemaining(ArrayList.java:1655) at com.google.common.collect.CollectSpliterators$FlatMapSpliterator.lambda$forEachRemaining$1(CollectSpliterators.java:377) at java.base/java.util.HashMap$ValueSpliterator.forEachRemaining(HashMap.java:1693) at com.google.common.collect.CollectSpliterators$FlatMapSpliterator.forEachRemaining(CollectSpliterators.java:373) at java.base/java.util.stream.AbstractPipeline.copyInto(AbstractPipeline.java:484) at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(AbstractPipeline.java:474) at java.base/java.util.stream.ReduceOps$ReduceOp.evaluateSequential(ReduceOps.java:913) at java.base/java.util.stream.AbstractPipeline.evaluate(AbstractPipeline.java:234) at java.base/java.util.stream.ReferencePipeline.collect(ReferencePipeline.java:578) at com.hartwig.hmftools.amber.AmberGermline.germlineDepth(AmberGermline.java:101) at com.hartwig.hmftools.amber.AmberGermline.(AmberGermline.java:65) at com.hartwig.hmftools.amber.AmberApplication.runNormalMode(AmberApplication.java:102) at com.hartwig.hmftools.amber.AmberApplication.run(AmberApplication.java:79) at com.hartwig.hmftools.amber.AmberApplication.main(AmberApplication.java:238)

charlesshale commented 1 year ago

The Amber sites VCF must only contain SNVs. In this case it has been passed an MNV (with value 'GA').

gagank4911 commented 1 year ago

/gagan/ECLIPSE_Final$ java -Xmx16G -cp amber-3.9.jar com.hartwig.hmftools.amber.AmberApplication -reference VSI_15_S24 -reference_bam VSI_15_S24_sentieon_match_4.1_deduped.bam -tumor TCS176_S33 -tumor_bam TCS176___S33_sentieon_match_4.1_deduped.bam -output_dir /amber_out -ref_genomeversion 38 -threads 8 -loci TCS176S33_TNscope_N1_filter.vcf 06:01:14.583 INFO [main] - AMBER version: 3.9 06:01:14.585 INFO [main] - Loading vcf file TCS176_S33_TNscope_N1_filter.vcf 06:01:14.922 INFO [main] - loaded 4083 baf loci 06:01:14.952 INFO [main] - Processing 4083 potential sites in reference bam VSI_15_S24_sentieon_match_4.1_deduped.bam 06:01:14.972 INFO [main] - 4083 loci, 2366 genome regions, min gap = 2000 Exception in thread "worker-0" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400) at com.hartwig.hmftools.amber.AsyncBamLociReader$BamReaderThread.run(AsyncBamLociReader.java:69) Exception in thread "worker-1" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400) at com.hartwig.hmftools.amber.AsyncBamLociReader$BamReaderThread.run(AsyncBamLociReader.java:69) Exception in thread "worker-2" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400) at com.hartwig.hmftools.amber.AsyncBamLociReader$BamReaderThread.run(AsyncBamLociReader.java:69) Exception in thread "worker-3" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400) at com.hartwig.hmftools.amber.AsyncBamLociReader$BamReaderThread.run(AsyncBamLociReader.java:69) Exception in thread "worker-4" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400) at com.hartwig.hmftools.amber.AsyncBamLociReader$BamReaderThread.run(AsyncBamLociReader.java:69) Exception in thread "worker-5" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400) at com.hartwig.hmftools.amber.AsyncBamLociReader$BamReaderThread.run(AsyncBamLociReader.java:69) Exception in thread "worker-6" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400) at com.hartwig.hmftools.amber.AsyncBamLociReader$BamReaderThread.run(AsyncBamLociReader.java:69) 06:01:15.332 INFO [main] - 8 bam reader threads started Exception in thread "worker-7" java.lang.IllegalArgumentException: Invalid reference index -1 at htsjdk.samtools.QueryInterval.(QueryInterval.java:24) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:538) at htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.queryOverlapping(SamReader.java:400) at com.hartwig.hmftools.amber.AsyncBamLociReader$BamReaderThread.run(AsyncBamLociReader.java:69) 06:01:15.334 INFO [main] - 8 bam reader threads finished 06:01:15.341 INFO [main] - Median normal depth is 0 reads: filtering reads outside of 0 and 0 06:01:15.351 INFO [main] - 0 heterozygous, 0 homozygous in reference bams 06:01:15.383 INFO [main] - Median normal depth is 0 reads: filtering reads outside of 0 and 0 06:01:15.388 INFO [main] - Processing 0 germline heterozygous loci in tumor bam TCS176___S33_sentieon_match_4.1deduped.bam 06:01:15.388 INFO [main] - Processing 0 germline homozygous loci in tumor bam TCS176S33_sentieon_match_4.1_deduped.bam for contamination 06:01:15.390 INFO [main] - 0 loci, 0 genome regions, min gap = 2000 WARNING: BAM index file /home/moubeen.fauzul/gagan/ECLIPSE_Final/TCS176_S33_sentieon_match_4.1_deduped.bam.bai is older than BAM /home/moubeen.fauzul/gagan/ECLIPSEFinal/TCS176S33_sentieon_match_4.1_deduped.bam WARNING: BAM index file /home/moubeen.fauzul/gagan/ECLIPSE_Final/TCS176_S33_sentieon_match_4.1_deduped.bam.bai is older than BAM /home/moubeen.fauzul/gagan/ECLIPSEFinal/TCS176S33_sentieon_match_4.1_deduped.bam WARNING: BAM index file /home/moubeen.fauzul/gagan/ECLIPSE_Final/TCS176_S33_sentieon_match_4.1_deduped.bam.bai is older than BAM /home/moubeen.fauzul/gagan/ECLIPSEFinal/TCS176S33_sentieon_match_4.1_deduped.bam WARNING: BAM index file /home/moubeen.fauzul/gagan/ECLIPSE_Final/TCS176_S33_sentieon_match_4.1_deduped.bam.bai is older than BAM /home/moubeen.fauzul/gagan/ECLIPSEFinal/TCS176S33_sentieon_match_4.1_deduped.bam WARNING: BAM index file /home/moubeen.fauzul/gagan/ECLIPSE_Final/TCS176_S33_sentieon_match_4.1_deduped.bam.bai is older than BAM /home/moubeen.fauzul/gagan/ECLIPSEFinal/TCS176S33_sentieon_match_4.1_deduped.bam WARNING: BAM index file /home/moubeen.fauzul/gagan/ECLIPSE_Final/TCS176_S33_sentieon_match_4.1_deduped.bam.bai is older than BAM /home/moubeen.fauzul/gagan/ECLIPSEFinal/TCS176S33_sentieon_match_4.1_deduped.bam WARNING: BAM index file /home/moubeen.fauzul/gagan/ECLIPSE_Final/TCS176_S33_sentieon_match_4.1_deduped.bam.bai is older than BAM /home/moubeen.fauzul/gagan/ECLIPSEFinal/TCS176S33_sentieon_match_4.1_deduped.bam WARNING: BAM index file /home/moubeen.fauzul/gagan/ECLIPSE_Final/TCS176_S33_sentieon_match_4.1_deduped.bam.bai is older than BAM /home/moubeen.fauzul/gagan/ECLIPSEFinal/TCS176S33_sentieon_match_4.1_deduped.bam 06:01:15.540 INFO [main] - 8 bam reader threads started 06:01:15.541 INFO [main] - 8 bam reader threads finished 06:01:15.547 INFO [main] - Median tumor depth at potential contamination sites is 0 reads 06:01:15.557 INFO [main] - No evidence of contamination. Exception in thread "main" java.nio.file.NoSuchFileException: /amber_out/TCS176___S33.amber.qc at java.base/sun.nio.fs.UnixException.translateToIOException(UnixException.java:92) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:111) at java.base/sun.nio.fs.UnixException.rethrowAsIOException(UnixException.java:116) at java.base/sun.nio.fs.UnixFileSystemProvider.newByteChannel(UnixFileSystemProvider.java:219) at java.base/java.nio.file.spi.FileSystemProvider.newOutputStream(FileSystemProvider.java:478) at java.base/java.nio.file.Files.newOutputStream(Files.java:220) at java.base/java.nio.file.Files.write(Files.java:3565) at java.base/java.nio.file.Files.write(Files.java:3616) at com.hartwig.hmftools.common.amber.qc.AmberQCFile.write(AmberQCFile.java:36) at com.hartwig.hmftools.amber.AmberPersistence.persistQC(AmberPersistence.java:57) at com.hartwig.hmftools.amber.AmberApplication.runNormalMode(AmberApplication.java:112) at com.hartwig.hmftools.amber.AmberApplication.run(AmberApplication.java:79) at com.hartwig.hmftools.amber.AmberApplication.main(AmberApplication.java:238)