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  • Scripture collapsed when assemling read alignments

    Hi ,

    When I am using Scripture(scripture-beta2.jar) to assemble read alignmets, the program collapsed with following output

    .....
    Computing alignment global stats for chromosome chr4
    Computing alignment global stats for chromosome chr5
    Computing alignment global stats for chromosome chr6
    Computing alignment global stats for chromosome chr7
    Computing alignment global stats for chromosome chr8
    Computing alignment global stats for chromosome chr9
    Computing alignment global stats for chromosome chrM
    model stats loaded, initializing model
    Built the model: 0.0 free memory: 288473920
    Segmenting accross graph
    Going to get read iterator to make graph with counts
    Exception in thread "main" java.lang.NullPointerException
    at java.util.TreeMap.getEntry(TreeMap.java:341)
    at java.util.TreeMap.get(TreeMap.java:272)
    at broad.pda.seq.segmentation.ContinuousDataAlignmentModel.makeGraphWithCounts(ContinuousDataAlignmentModel.java:1271)
    at broad.pda.seq.segmentation.ContinuousDataAlignmentModel.contiguousAcrossGraph(ContinuousDataAlignmentModel.java:1212)
    at broad.pda.seq.segmentation.ContinuousDataAlignmentModel.main(ContinuousDataAlignmentModel.java:2306)
    What I did previously include

    HTML Code:
    --Generated accepted_hits.bam by running Tophat-1.3.2 on paired-end RNA-seq reads. 
    
    --Extract the first 100000 reads of the accepted_hits.bam and named it with test.sam for testing
    
    --Built index (test.sam.sai)
    $ igvtools index test.sam
    
    --Run Scripture
    $ java -jar scripture-beta2.jar -alignment test.sorted.sam -sizeFile Zv9.chrom.sizes
    Any solutions or suggestions? Thank you in advance.

  • #2
    Hi Hunny,

    I am not sure if you already solved the problem or still wait someone's help.

    I just run the scripture and I think you have to give -chr (the chromosome you interested in) and -chrSequence (the chromosome sequence in fasta format). They are mandatory parameters (http://www.broadinstitute.org/softwa...mentation_task) although they are not checked by the program itself.

    I tried your input parameters with the test set and get exactly the same error message but it is OK when I also gave -chr and -chrSequence parameters. So I think it is just this problem.

    Another thing I have to say is: make sure all your chromosome ID in any SAM/BAM file ,chromosomeSequence file (*.fa) and sizeFile are with "chr" prefix. If not, there might be some other errors when you run this program. Good Luck!

    Comment


    • #3
      Originally posted by AlbertOuTw View Post
      Hi Hunny,
      I am not sure if you already solved the problem or still wait someone's help.
      No, I gave it up.

      Originally posted by AlbertOuTw View Post
      I just run the scripture and I think you have to give -chr (the chromosome you interested in) and -chrSequence (the chromosome sequence in fasta format). They are mandatory parameters (http://www.broadinstitute.org/softwa...mentation_task) although they are not checked by the program itself.

      I tried your input parameters with the test set and get exactly the same error message but it is OK when I also gave -chr and -chrSequence parameters. So I think it is just this problem.
      Thank you for your trying. However, I intended to run Scripture for all chromosomes. It seems a little bit trivial to run with -chr and -chrSequence parameters for all chromosomes.

      Best wishes,

      Comment


      • #4
        Originally posted by Hunny View Post
        No, I gave it up.
        Thank you for your trying. However, I intended to run Scripture for all chromosomes. It seems a little bit trivial to run with -chr and -chrSequence parameters for all chromosomes.

        Best wishes,
        Although it is a little bit inconvenient, but you can run Scripture segmentation chromosome by chromosome and cat all the results into one bed file. Then use the bed file to score all results by using "-task score".

        It is a good tool to use but need some time to get used to how it represents its results.

        Best wishes

        Comment

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