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Hi!, I'm having some issues running the pipeline f...
# oncoanalyser
s
Hi!, I'm having some issues running the pipeline for paired normal/tumor data in targeted mode. I get the following error in the MarkDups (1.1.7) step just at the start:
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Aug-28 11:26:35.470 [TaskFinalizer-1] DEBUG nextflow.processor.TaskProcessor - Handling unexpected condition for
  task: name=NFCORE_ONCOANALYSER:TARGETED:READ_PROCESSING:MARKDUPS (TCGA-DJ-A13O_1d64792d-1e59-40b4-be28-79916df34e9c); work-dir=work/a7/a7ba79fcada67adeaaebf1954b1ed5
  error [nextflow.exception.ProcessFailedException]: Process `NFCORE_ONCOANALYSER:TARGETED:READ_PROCESSING:MARKDUPS (TCGA-DJ-A13O_1d64792d-1e59-40b4-be28-79916df34e9c)` terminated with an error exit status (1)
Aug-28 11:26:35.482 [TaskFinalizer-1] ERROR nextflow.processor.TaskProcessor - Error executing process > 'NFCORE_ONCOANALYSER:TARGETED:READ_PROCESSING:MARKDUPS (TCGA-DJ-A13O_1d64792d-1e59-40b4-be28-79916df34e9c)'

Caused by:
  Process `NFCORE_ONCOANALYSER:TARGETED:READ_PROCESSING:MARKDUPS (TCGA-DJ-A13O_1d64792d-1e59-40b4-be28-79916df34e9c)` terminated with an error exit status (1)


Command executed:

  markdups \
      -Xmx36721970381 \
       \
      \
      -samtools $(which samtools) \
      -sambamba $(which sambamba) \
      \
      -sample 1d64792d-1e59-40b4-be28-79916df34e9c \
      -input_bam a21bf2df-ffb9-416b-a024-1d2c2dcd8dc5_wxs_gdc_realn.bam \
      \
      -umi_enabled -umi_duplex -umi_duplex_delim + \
      \
      -unmap_regions unmap_regions.38.tsv \
      -ref_genome GCA_000001405.15_GRCh38_no_alt_analysis_set.fna \
      -ref_genome_version 38 \
      \
      -write_stats \
      -threads 6 \
      \
      -output_bam 1d64792d-1e59-40b4-be28-79916df34e9c.markdups.bam
  
  cat <<-END_VERSIONS > versions.yml
  "NFCORE_ONCOANALYSER:TARGETED:READ_PROCESSING:MARKDUPS":
      markdups: $(markdups -version | awk '{ print $NF }')
      sambamba: $(sambamba --version 2>&1 | egrep '^sambamba' | head -n 1 | awk '{ print $NF }')
      samtools: $(samtools --version 2>&1 | egrep '^samtools\s' | head -n 1 | sed 's/^.* //')
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  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)

Work dir:
  work/a7/a7ba79fcada67adeaaebf1954b1ed5
Invocation command:
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nextflow run ${HOME}/oncoanalyser \
  -profile singularity \
  -c $CONFIG_FILE \
  -params-file $PARAMS_FILE \
  --input samplesheet.csv \
  --panel tso500 \
  --outdir $OUTPUT_DIR \
  --ref_data_panel_data_path $PANEL_DIR
I saw a similar error posted in an issue at the GitHub Is there any file needed to better diagnose the error? Running manually the command leads to a similar error:
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12:49:40.850 [main] [INFO ] MarkDups version 1.1.7
12:49:40.884 [main] [INFO ] output(./)
12:49:41.058 [main] [INFO ] loaded 80309 unmapping regions from unmap_regions.38.tsv
12:49:41.058 [main] [INFO ] duplicate logic: UMIs
12:49:41.059 [main] [INFO ] sample(1d64792d-1e59-40b4-be28-79916df34e9c) starting mark duplicates
12:49:41.362 [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: begin 0, end -1, length 5
java.lang.StringIndexOutOfBoundsException: begin 0, end -1, length 5
        at java.base/java.lang.String.checkBoundsBeginEnd(String.java:4606)
        at java.base/java.lang.String.substring(String.java:2709)
        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)
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