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:
The exception is pasted below.
Your help is highly appreciated.
##################################################
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
##################################################
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:
- extendedpieces.bed
- firstGraph.bed
- igv.log
- introns.bed
The exception is pasted below.
Your help is highly appreciated.
##################################################
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
##################################################
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