Hi ,
When I am using Scripture(scripture-beta2.jar) to assemble read alignmets, the program collapsed with following output
What I did previously include
Any solutions or suggestions? Thank you in advance.
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)
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)
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
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