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Error with BWA bam file but not Isaac BAM file

General Discussion
btrost
2017-07-26
2017-08-14

  • btrost

    btrost - 2017-07-26

    When I try to run qmotif on a BAM file generated by BWA, I get the following output. When I run qmotif on a BAM file from the same sample generated by Isaac, it works fine. Any idea what might be wrong? Thanks in advance for any help!

    $ java -Xmx20g -jar qmotif-1.2.jar --bam PGPC-0002B.bwa.bam --bai PGPC-0002B.bwa.bam.bai --ini qmotif_telomere_config.ini --log PGPC-0002B.bwa.bam.qmotif.log -o PGPC-0002B.bwa.bam.qmotif.xml -o PGPC-0002B.bwa.bam.qmotif.bam
    16:28:01.633 [main] EXEC org.qcmg.motif.Motif - Uuid 1fd16ebd-22b3-44b8-b9a2-dfe82e37159f
    16:28:01.633 [main] EXEC org.qcmg.motif.Motif - StartTime 2017-07-26 16:28:01
    16:28:01.634 [main] EXEC org.qcmg.motif.Motif - OsName Linux
    16:28:01.634 [main] EXEC org.qcmg.motif.Motif - OsArch amd64
    16:28:01.634 [main] EXEC org.qcmg.motif.Motif - OsVersion 2.6.32-642.6.2.el6.x86_64
    16:28:01.635 [main] EXEC org.qcmg.motif.Motif - RunBy btrost
    16:28:01.635 [main] EXEC org.qcmg.motif.Motif - ToolName qmotif
    16:28:01.635 [main] EXEC org.qcmg.motif.Motif - ToolVersion 1.2 (1407) (0.3)
    16:28:01.636 [main] EXEC org.qcmg.motif.Motif - CommandLine qmotif --bam PGPC-0002B.bwa.bam --bai PGPC-0002B.bwa.bam.bai --ini qmotif_telomere_config.ini --log PGPC-0002B.bwa.bam.qmotif.log -o PGPC-0002B.bwa.bam.qmotif.xml -o PGPC-0002B.bwa.bam.qmotif.bam
    16:28:01.636 [main] EXEC org.qcmg.motif.Motif - JavaHome /hpf/tools/centos6/java/1.8.0_91/jre
    16:28:01.636 [main] EXEC org.qcmg.motif.Motif - JavaVendor Oracle Corporation
    16:28:01.636 [main] EXEC org.qcmg.motif.Motif - JavaVersion 1.8.0_91
    16:28:01.637 [main] EXEC org.qcmg.motif.Motif - host qlogin1.hpf.new
    16:28:01.706 [main] INFO org.qcmg.motif.JobQueue - running with invariants.isIncludesOnlyMode: true
    16:28:01.707 [main] INFO org.qcmg.motif.JobQueue - Queueing jobs
    16:28:01.974 [main] INFO org.qcmg.motif.JobQueue - Number of queued coverage jobs: 51
    16:28:01.975 [main] INFO org.qcmg.motif.JobQueue - Queued jobs are: [chr1:10001-12464 coverage, chr1:249237907-249240620 coverage, chr2:10001-12592 coverage, chr2:243150480-243154648 coverage, chr2:243187373-243189372 coverage, chr3:60001-62000 coverage, chr3:197897576-197903397 coverage, chr3:197960430-197962429 coverage, chr4:10001-12193 coverage, chr4:191041613-191044275 coverage, chr5:10001-13806 coverage, chr5:180903260-180905259 coverage, chr6:60001-62000 coverage, chr6:171053067-171055066 coverage, chr7:10001-12238 coverage, chr7:159126558-159128662 coverage, chr8:10001-12000 coverage, chr8:146302022-146304021 coverage, chr9:10001-12359 coverage, chr9:141151431-141153430 coverage, chr10:60001-62000 coverage, chr10:135522469-135524746 coverage, chr11:60001-62000 coverage, chr11:134944458-134946515 coverage, chr12:60001-62000 coverage, chr12:93158-97735 coverage, chr12:133839458-133841894 coverage, chr13:19020001-19022000 coverage, chr13:115107878-115109877 coverage, chr14:19020001-19022000 coverage, chr14:107287540-107289539 coverage, chr15:20000001-20002000 coverage, chr15:102518969-102521391 coverage, chr16:60001-62033 coverage, chr16:90292753-90294752 coverage, chr17:1-2000 coverage, chr17:81193211-81195210 coverage, chr18:10001-12621 coverage, chr18:78014226-78017247 coverage, chr19:60001-62000 coverage, chr19:59116822-59118982 coverage, chr20:60001-62000 coverage, chr20:62963520-62965519 coverage, chr21:9411194-9413193 coverage, chr21:48117788-48119894 coverage, chr22:16050001-16052000 coverage, chr22:51242566-51244565 coverage, chrX:60001-62033 coverage, chrX:155257733-155260559 coverage, chrY:10001-12033 coverage, chrY:59360739-59363565 coverage]
    16:28:01.976 [main] INFO org.qcmg.motif.JobQueue - Commencing processing of jobs...
    16:28:01.977 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr1:10001-12464 coverage]
    16:28:01.977 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr1:10001-12464 coverage]
    16:28:01.977 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr1:10001-12464
    16:28:01.980 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr1:10001-12464 with 1 includes and 0 excludes
    16:28:01.981 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr1:10001-12464
    16:28:01.981 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    qmotif: java.lang.InterruptedException
    16:28:01.982 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr1:249237907-249240620 coverage]
    java.lang.InterruptedException
    at java.lang.Object.wait(Native Method)
    at java.lang.Thread.join(Thread.java:1245)
    at java.lang.Thread.join(Thread.java:1319)
    at org.qcmg.motif.JobQueue.processJobs(JobQueue.java:372)
    at org.qcmg.motif.JobQueue.execute(JobQueue.java:158)
    at org.qcmg.motif.JobQueue.<init>(JobQueue.java:151)
    at org.qcmg.motif.Motif.<init>(Motif.java:57)
    at org.qcmg.motif.Motif.main(Motif.java:351)
    16:28:01.985 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr1:249237907-249240620 coverage]
    16:28:01.986 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr1:249237907-249240620
    16:28:01.986 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr1:249237907-249240620 with 1 includes and 0 excludes
    16:28:01.986 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr1:249237907-249240620
    16:28:01.987 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:01.987 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr2:10001-12592 coverage]
    16:28:01.988 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr2:10001-12592 coverage]
    16:28:01.988 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr2:10001-12592
    16:28:01.988 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr2:10001-12592 with 1 includes and 0 excludes
    16:28:01.988 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr2:10001-12592
    16:28:01.989 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:01.989 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr2:243150480-243154648 coverage]
    16:28:01.989 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr2:243150480-243154648 coverage]
    16:28:01.990 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr2:243150480-243154648
    16:28:01.990 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr2:243150480-243154648 with 1 includes and 0 excludes
    16:28:01.990 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr2:243150480-243154648
    16:28:01.990 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:01.991 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr2:243187373-243189372 coverage]
    16:28:02.007 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr2:243187373-243189372 coverage]
    16:28:02.007 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr2:243187373-243189372
    16:28:02.007 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr2:243187373-243189372 with 1 includes and 0 excludes
    16:28:02.007 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr2:243187373-243189372
    16:28:02.008 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:02.008 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr3:60001-62000 coverage]
    16:28:02.008 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr3:60001-62000 coverage]
    16:28:02.008 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr3:60001-62000
    16:28:02.008 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr3:60001-62000 with 1 includes and 0 excludes
    16:28:02.009 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr3:60001-62000
    16:28:02.009 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:02.009 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr3:197897576-197903397 coverage]
    16:28:02.009 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr3:197897576-197903397 coverage]
    16:28:02.009 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr3:197897576-197903397
    16:28:02.010 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr3:197897576-197903397 with 1 includes and 0 excludes
    16:28:02.010 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr3:197897576-197903397
    16:28:02.010 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:02.010 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr3:197960430-197962429 coverage]
    16:28:02.011 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr3:197960430-197962429 coverage]
    16:28:02.011 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr3:197960430-197962429
    16:28:02.011 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr3:197960430-197962429 with 1 includes and 0 excludes
    16:28:02.012 [main] SEVERE org.qcmg.motif.Motif - java.lang.InterruptedException
    java.lang.InterruptedException
    java.lang.Object.wait(Native Method)
    java.lang.Thread.join(Thread.java:1245)
    java.lang.Thread.join(Thread.java:1319)
    org.qcmg.motif.JobQueue.processJobs(JobQueue.java:372)
    org.qcmg.motif.JobQueue.execute(JobQueue.java:158)
    org.qcmg.motif.JobQueue.<init>(JobQueue.java:151)
    org.qcmg.motif.Motif.<init>(Motif.java:57)
    org.qcmg.motif.Motif.main(Motif.java:351)
    16:28:02.012 [main] SEVERE org.qcmg.motif.Motif - java.lang.Object.wait(Native Method)
    16:28:02.012 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr3:197960430-197962429
    16:28:02.013 [main] SEVERE org.qcmg.motif.Motif - java.lang.Thread.join(Thread.java:1245)
    16:28:02.013 [main] SEVERE org.qcmg.motif.Motif - java.lang.Thread.join(Thread.java:1319)
    16:28:02.013 [main] SEVERE org.qcmg.motif.Motif - org.qcmg.motif.JobQueue.processJobs(JobQueue.java:372)
    16:28:02.013 [main] SEVERE org.qcmg.motif.Motif - org.qcmg.motif.JobQueue.execute(JobQueue.java:158)
    16:28:02.014 [main] SEVERE org.qcmg.motif.Motif - org.qcmg.motif.JobQueue.<init>(JobQueue.java:151)
    16:28:02.014 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:02.014 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr4:10001-12193 coverage]
    16:28:02.014 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr4:10001-12193 coverage]
    16:28:02.014 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr4:10001-12193
    16:28:02.015 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr4:10001-12193 with 1 includes and 0 excludes
    16:28:02.015 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr4:10001-12193
    16:28:02.015 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:02.015 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr4:191041613-191044275 coverage]
    16:28:02.016 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr4:191041613-191044275 coverage]
    16:28:02.016 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr4:191041613-191044275
    16:28:02.017 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr4:191041613-191044275 with 1 includes and 0 excludes
    16:28:02.017 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr4:191041613-191044275
    16:28:02.017 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:02.018 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr5:10001-13806 coverage]
    16:28:02.018 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr5:10001-13806 coverage]
    16:28:02.018 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr5:10001-13806
    16:28:02.018 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr5:10001-13806 with 1 includes and 0 excludes
    16:28:02.018 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr5:10001-13806
    16:28:02.019 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:02.019 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr5:180903260-180905259 coverage]
    16:28:02.019 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr5:180903260-180905259 coverage]
    16:28:02.020 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr5:180903260-180905259
    16:28:02.020 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr5:180903260-180905259 with 1 includes and 0 excludes
    16:28:02.020 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr5:180903260-180905259
    16:28:02.020 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:02.021 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr6:60001-62000 coverage]
    16:28:02.021 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr6:60001-62000 coverage]
    16:28:02.021 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr6:60001-62000
    16:28:02.021 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr6:60001-62000 with 1 includes and 0 excludes
    16:28:02.021 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr6:60001-62000
    16:28:02.023 [main] SEVERE org.qcmg.motif.Motif - org.qcmg.motif.Motif.<init>(Motif.java:57)
    16:28:02.024 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:02.025 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr6:171053067-171055066 coverage]
    16:28:02.025 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr6:171053067-171055066 coverage]
    16:28:02.025 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr6:171053067-171055066
    16:28:02.025 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr6:171053067-171055066 with 1 includes and 0 excludes
    16:28:02.025 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr6:171053067-171055066
    16:28:02.026 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:02.026 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr7:10001-12238 coverage]
    16:28:02.026 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr7:10001-12238 coverage]
    16:28:02.026 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr7:10001-12238
    16:28:02.026 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr7:10001-12238 with 1 includes and 0 excludes
    16:28:02.027 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr7:10001-12238
    16:28:02.027 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)
    16:28:02.027 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 obtained job [chr7:159126558-159128662 coverage]
    16:28:02.027 [Thread-1] INFO org.qcmg.motif.WorkerThread - Thread-1 running job [chr7:159126558-159128662 coverage]
    16:28:02.027 [Thread-1] INFO org.qcmg.motif.CoverageJob - Starting job for: chr7:159126558-159128662
    16:28:02.028 [main] SEVERE org.qcmg.motif.Motif - org.qcmg.motif.Motif.main(Motif.java:351)
    16:28:02.028 [main] EXEC org.qcmg.motif.Motif - StopTime 2017-07-26 16:28:02
    16:28:02.028 [main] EXEC org.qcmg.motif.Motif - TimeTaken 00:00:00
    16:28:02.028 [main] EXEC org.qcmg.motif.Motif - ExitStatus 1
    16:28:02.029 [Thread-1] INFO org.qcmg.motif.CoverageJob - created 1 regions for chr7:159126558-159128662 with 1 includes and 0 excludes
    16:28:02.029 [Thread-1] INFO org.qcmg.motif.CoverageJob - Performing coverage for: chr7:159126558-159128662
    16:28:02.029 [Thread-1] SEVERE org.qcmg.motif.CoverageJob - Exception caught in run method of CoverageJob
    java.lang.IllegalArgumentException: Invalid reference index -1
    htsjdk.samtools.QueryInterval.<init>(QueryInterval.java:24)
    htsjdk.samtools.SamReader$PrimitiveSamReaderToSamReaderAdapter.query(SamReader.java:503)
    org.qcmg.motif.CoverageJob.performCoverage(CoverageJob.java:121)
    org.qcmg.motif.CoverageJob.run(CoverageJob.java:101)
    org.qcmg.motif.WorkerThread.run(WorkerThread.java:50)

     

    • Ollie Holmes

      Ollie Holmes - 2017-08-08

      Hi,
      This looks like it could be to do with "chr" not appearing in your BWA mapped bam, but appearing in your ISAAC mapped bam.
      The contig names in your bam must match those in the qmotif ini file. If they don't, update the ini file to reflect the names that appear in your bam file (or vice versa if you have lots of time on your hands).
      If this doesn't fix it, please let me know and I'll dig further.
      Thanks,
      Ollie Holmes

       

  • btrost

    btrost - 2017-08-14

    That did the trick. Thanks for your help!

     

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