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  • Error with RNA-SeQC

    Hi,

    I used following 4 steps to get sequencing statistics from RNASeqC but I get error, could anyone help me understand and get rid of this error?

    Thanks.

    RNA-SeQC v1.1.7 05/14/12
    Creating rRNA Interval List based on given GTF annotations
    java.lang.ArrayIndexOutOfBoundsException: 1
    at org.broadinstitute.cga.rnaseq.RNASeqMetrics$MetricSample.readInSamples(RNASeqMetrics.java:1369)
    at org.broadinstitute.cga.rnaseq.RNASeqMetrics.prepareFiles(RNASeqMetrics.java:182)
    at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:165)
    at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:135)
    RNA-SeQC Total Runtime: 0 min
    -----------------

    java -jar picard-tools/v1.87/AddOrReplaceReadGroups.jar I=MCF7/accepted_hits.bam O=MCF7/accepted_hits_readgrps.bam VALIDATION_STRINGENCY=LENIENT SORT_ORDER=coordinate RGID=MCF7 RGCN=MCF7 RGLB=lane6 RGPL=illumina RGPU=lane6 RGSM=accepted_hits.bam

    java -jar picard-tools/v1.87/SortSam.jar I=MCF7/accepted_hits_readgrps.bam O=MCF7/accepted_hits_readgrps_sorted.bam SO=coordinate

    java -jar picard-tools/v1.87/ReorderSam.jar I=MCF7/accepted_hits_readgrps_sorted.bam O=MCF7/accepted_hits_readgrps_sorted.reordered.bam R=refGenome/hg19.fa CREATE_INDEX=true

    java -jar softwares/RNA-SeQC_v1.1.7.jar -n 1000 -s MCF7/accepted_hits_readgrps_sorted.reordered.bam -t index/Homo_sapiens/UCSC/hg19/Annotation/Archives/archive-2012-03-09-03-24-41/Genes/genes.gtf -r refGenome/hg19.fa -o reportMCF7

  • #2
    I get exactly the same error

    RNA-SeQC v1.1.7 05/14/12
    Creating rRNA Interval List based on given GTF annotations
    java.lang.ArrayIndexOutOfBoundsException: 1
    at org.broadinstitute.cga.rnaseq.RNASeqMetrics$MetricSample.readInSamples(RNASeqMetrics.java:1369)
    at org.broadinstitute.cga.rnaseq.RNASeqMetrics.prepareFiles(RNASeqMetrics.java:182)
    at org.broadinstitute.cga.rnaseq.RNASeqMetrics.execute(RNASeqMetrics.java:165)
    at org.broadinstitute.cga.rnaseq.RNASeqMetrics.main(RNASeqMetrics.java:135)
    RNA-SeQC Total Runtime: 1 min

    I do not understand the reason for this error, I also noticed that the header of my original bam file had 3 columns and after i ran reordersam, the columns in bam file increased, could this be a problem. I am just pasting few lines:
    ORIGINAL FILE:
    @HD VN:1.0 SO:coordinate
    @SQ SN:chr1 LN:195471971
    @SQ SN:chr10 LN:130694993
    @SQ SN:chr11 LN:122082543
    @SQ SN:chr12 LN:120129022
    @SQ SN:chr13 LN:120421639
    @SQ SN:chr14 LN:124902244
    @SQ SN:chr15 LN:104043685
    @SQ SN:chr16 LN:98207768
    @SQ SN:chr17 LN:94987271
    @SQ SN:chr18 LN:90702639
    @SQ SN:chr19 LN:61431566
    @SQ SN:chr1_GL456210_random LN:169725
    @SQ SN:chr1_GL456211_random LN:241735
    @SQ SN:chr1_GL456212_random LN:153618
    @SQ SN:chr1_GL456213_random LN:39340

    AFTER REORDERING:
    @HD VN:1.0 SO:coordinate
    @SQ SN:chr1 LN:195471971 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:c4ec915e7348d42648eefc1534b71c99
    @SQ SN:chr10 LN:130694993 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:7831ecda5dd6bcf838e2452ea0139eac
    @SQ SN:chr11 LN:122082543 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:e168c7a3194813f597181f26bb1bd13f
    @SQ SN:chr12 LN:120129022 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:671f85bb54a6e097d631e2e2dd813ad4
    @SQ SN:chr13 LN:120421639 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:7f9b9fa3fbd9a38634107dfdc7fd8dc8
    @SQ SN:chr14 LN:124902244 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:bf4e1efa25a8fd23b41c91f9bcb86388
    @SQ SN:chr15 LN:104043685 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:106358dace00e5825ae337c1f1821b5e
    @SQ SN:chr16 LN:98207768 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:5482110a6cedd3558272325eee4c5a17
    @SQ SN:chr17 LN:94987271 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:0d21e8edbfcd8410523b2b94e6dae892
    @SQ SN:chr18 LN:90702639 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:46fda2f7e6dbf91bff91d6703e004afb
    @SQ SN:chr19 LN:61431566 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:7d363594531514ce41dfacfd97bc995d
    @SQ SN:chr1_GL456210_random LN:169725 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:0cc560d98f9f22f4385397db82e1c108
    @SQ SN:chr1_GL456211_random LN:241735 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:36e85680c669756c9a1554cf31c9de03
    @SQ SN:chr1_GL456212_random LN:153618 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:4c4dc3bfe987e3bc4ef4756bef269373
    @SQ SN:chr1_GL456213_random LN:39340 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:d4cb9051fe171205dd39980e110bf63e
    @SQ SN:chr1_GL456221_random LN:206961 UR:file:/work_Fid/sukmb277/references/mouse_mm10/mm10.fa M5:e21da65d7276b256b8edf92660a928b0

    But i did follow the same steps as mentioned on :


    and then ran RNA-SeQC v1.1.7 , My Java version on cluster is: java version "1.6.0_31"
    Java(TM) SE Runtime Environment (build 1.6.0_31-b04)
    Java HotSpot(TM) 64-Bit Server VM (build 20.6-b01, mixed mode)

    Could anyone help me to know the cause of this problem ?

    Thanks a lot,

    regards,

    Priya
    Last edited by pkachroo; 03-03-2014, 08:46 AM.

    Comment


    • #3
      I am also having the same problem, except with a bam file created with STAR output. Anyone have any ideas?

      Comment


      • #4
        The error message says there is a problem with "readInSamples"

        The correct use of the -s option is, according to http://www.broadinstitute.org/cancer/cga/rnaseqc_run:

        -s <arg>

        Sample File: tab-delimited description of samples and their bams. This file header is:
        Sample ID Bam File Notes
        When running on just one sample, this argument can be a string of the form
        "Sample ID|Bam File|Notes", where Bam File is the path to the input file.
        Rather than

        Originally posted by angerusso View Post
        -s MCF7/accepted_hits_readgrps_sorted.reordered.bam
        I got this error by accidentally having '\t' in my tab-delimited samples file rather than a literal tab. My mistake was to use:

        echo "Sample ID\tBam File\tNotes" > ${OUTDIR}/Samples.txt

        rather than including the -e option:

        echo -e "Sample ID\tBam File\tNotes" > ${OUTDIR}/Samples.txt

        Comment

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