Scripture Java Exception

[mhadidi2002]

Hello,

I have used scripture to do the segmentation task.

The command:

scripture$ java -jar scripture-beta2.jar -alignment lyco.sam -out lyc_scrip.txt -sizeFile spe.sizes.txt -chr SL2.40ch01 -chrSequences S_lycopersicum.fa



It gives me exceptions while running, I have copied the lines, it is repeated, but here I am showing it only for one position (below)
I also have some empty files, which are:

1. extendedpieces.bed
2. firstGraph.bed
3. igv.log
4. introns.bed

The exception is pasted below.
Your help is highly appreciated.

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java.lang.NullPointerException
at broad.pda.gene.GeneTools.orientationFromSpliceSites(GeneTools.java:62 8)
at broad.pda.gene.GeneTools.orientationFromSpliceSites(GeneTools.java:65 6)
at broad.pda.seq.segmentation.ContinuousDataAlignmentModel.makeGraphWith Counts(ContinuousDataAlignmentModel.java:1298)
at broad.pda.seq.segmentation.ContinuousDataAlignmentModel.contiguousAcr ossGraph(ContinuousDataAlignmentModel.java:1212)
at broad.pda.seq.segmentation.ContinuousDataAlignmentModel.main(Continuo usDataAlignmentModel.java:2306)
SL2.40ch01 90217921 90217933 SL2.40ch01:90217921-90217933 0

##################################################

[AlbertOuTw]

Hi mhadidi2002,

From your command line you use -chr SL2.40ch01 to name a chromosome but as far as my using experience of scripture, a "legal" chromosome name "MUST" start with "chr". So if you name your chromosome chrSL2.40ch01 it might work.

Just make sure the chromosome id in all *.sam/*.bam, sizeFile and chromosomeFile must start with chr. The easiest way is to modify all chromosome ids in the chromosomeFiles and re-built the bowtie index and remapping them again. Or you can use some scripting language to modify them. Good Luck!