/usr/local/bin/markdups: line 6: warning: setlocale: LC_ALL: cannot change locale (en_US.UTF-8): No such file or directory
09:26:34.407 [main] [INFO ] MarkDups version 1.1.7
09:26:34.535 [main] [INFO ] output(./)
09:26:34.751 [main] [INFO ] loaded 80309 unmapping regions from unmap_regions.38.tsv
09:26:34.751 [main] [INFO ] duplicate logic: UMIs
09:26:34.752 [main] [INFO ] sample(1d64792d-1e59-40b4-be28-79916df34e9c) starting mark duplicates
09:26:35.186 [Thread-1] [ERROR] read(id(B0479ABXX110308:5:1201:11107:16966) coords(chr1:1009343-1009418) cigar(76M) mate(chr1:1009443) flags(99)) exception: java.lang.StringIndexOutOfBoundsException: Range [0, -1) out of bounds for length 5
java.lang.StringIndexOutOfBoundsException: Range [0, -1) out of bounds for length 5
	at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:55)
	at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:52)
	at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:213)
	at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:210)
	at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:98)
	at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckFromToIndex(Preconditions.java:112)
	at java.base/jdk.internal.util.Preconditions.checkFromToIndex(Preconditions.java:349)
	at java.base/java.lang.String.checkBoundsBeginEnd(String.java:4914)
	at java.base/java.lang.String.substring(String.java:2876)
	at com.hartwig.hmftools.markdups.umi.UmiGroupBuilder.splitUmi(UmiGroupBuilder.java:505)
	at com.hartwig.hmftools.markdups.umi.UmiGroupBuilder.hasDuplexUmiMatch(UmiGroupBuilder.java:493)
	at com.hartwig.hmftools.markdups.umi.UmiGroupBuilder.collapseCoordinateGroup(UmiGroupBuilder.java:444)
	at com.hartwig.hmftools.markdups.umi.UmiGroupBuilder.processUmiGroups(UmiGroupBuilder.java:289)
	at com.hartwig.hmftools.markdups.common.DuplicateGroupBuilder.processDuplicateGroups(DuplicateGroupBuilder.java:248)
	at com.hartwig.hmftools.markdups.PartitionReader.accept(PartitionReader.java:357)
	at com.hartwig.hmftools.markdups.PartitionReader.accept(PartitionReader.java:43)
	at com.hartwig.hmftools.markdups.ReadPositionsCache.checkFlush(ReadPositionsCache.java:276)
	at com.hartwig.hmftools.markdups.ReadPositionsCache.storeInitialRead(ReadPositionsCache.java:166)
	at com.hartwig.hmftools.markdups.ReadPositionsCache.processRead(ReadPositionsCache.java:141)
	at com.hartwig.hmftools.markdups.PartitionReader.processSamRecord(PartitionReader.java:216)
	at com.hartwig.hmftools.markdups.BamReader.sliceRegion(BamReader.java:58)
	at com.hartwig.hmftools.markdups.PartitionReader.processRegion(PartitionReader.java:125)
	at com.hartwig.hmftools.markdups.PartitionThread.run(PartitionThread.java:61)
09:26:35.187 [Thread-0] [ERROR] read(id(B04A0ABXX110309:2:1103:17160:23465) coords(chr1:31462-31537) cigar(76M) mate(chr1:31594) flags(163)) exception: java.lang.StringIndexOutOfBoundsException: Range [0, -1) out of bounds for length 5
java.lang.StringIndexOutOfBoundsException: Range [0, -1) out of bounds for length 5
	at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:55)
	at java.base/jdk.internal.util.Preconditions$1.apply(Preconditions.java:52)
	at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:213)
	at java.base/jdk.internal.util.Preconditions$4.apply(Preconditions.java:210)
	at java.base/jdk.internal.util.Preconditions.outOfBounds(Preconditions.java:98)
	at java.base/jdk.internal.util.Preconditions.outOfBoundsCheckFromToIndex(Preconditions.java:112)
	at java.base/jdk.internal.util.Preconditions.checkFromToIndex(Preconditions.java:349)
	at java.base/java.lang.String.checkBoundsBeginEnd(String.java:4914)
	at java.base/java.lang.String.substring(String.java:2876)
	at com.hartwig.hmftools.markdups.umi.UmiGroupBuilder.splitUmi(UmiGroupBuilder.java:505)
	at com.hartwig.hmftools.markdups.umi.UmiGroupBuilder.hasDuplexUmiMatch(UmiGroupBuilder.java:493)
	at com.hartwig.hmftools.markdups.umi.UmiGroupBuilder.collapseCoordinateGroup(UmiGroupBuilder.java:444)
	at com.hartwig.hmftools.markdups.umi.UmiGroupBuilder.processUmiGroups(UmiGroupBuilder.java:289)
	at com.hartwig.hmftools.markdups.common.DuplicateGroupBuilder.processDuplicateGroups(DuplicateGroupBuilder.java:248)
	at com.hartwig.hmftools.markdups.PartitionReader.accept(PartitionReader.java:357)
	at com.hartwig.hmftools.markdups.PartitionReader.accept(PartitionReader.java:43)
	at com.hartwig.hmftools.markdups.ReadPositionsCache.checkFlush(ReadPositionsCache.java:276)
	at com.hartwig.hmftools.markdups.ReadPositionsCache.storeInitialRead(ReadPositionsCache.java:166)
	at com.hartwig.hmftools.markdups.ReadPositionsCache.processRead(ReadPositionsCache.java:141)
	at com.hartwig.hmftools.markdups.PartitionReader.processSamRecord(PartitionReader.java:216)
	at com.hartwig.hmftools.markdups.BamReader.sliceRegion(BamReader.java:58)
	at com.hartwig.hmftools.markdups.PartitionReader.processRegion(PartitionReader.java:125)
	at com.hartwig.hmftools.markdups.PartitionThread.run(PartitionThread.java:61)