Scripture collapsed when assemling read alignments

[Hunny]

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

--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.

[AlbertOuTw]

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!

[Hunny]

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

No, I gave it up.

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,

[AlbertOuTw]

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