From: Sonja A. <son...@go...> - 2010-11-16 15:36:24
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Hello! I am a new user and I am not very familiar with Java... However I would like to use Useq on Chip-Seq data... My command fails and I dont know why. Can s.o. help? I paste my command and error message below! thanks! dani java -Xmx2G -jar /home/daniela/USeq_7.2/Apps/ChIPSeq -y eland -v H_sapiens_May_2004 -r /soft/bin/R -t /home/daniela/otherDatasets/NRSF/ChIP-Seq/allChip/ -c /home/daniela/otherDatasets/NRSF/ChIP-Seq/allMock/ -s /home/daniela/test_useq Checking parameters... Results directory = /home/daniela/test_useq Window filter file = null Alignment type = eland Maximum alignment score = 60.0 Minimum mapping quality score = 13.0 Genome version = H_sapiens_May_2004 Treatment replica directories: /home/daniela/otherDatasets/NRSF/ChIP-Seq/allChip Control replica directories: /home/daniela/otherDatasets/NRSF/ChIP-Seq/allMock Convert bar graph files to useq format = false Notes: Your save results directory exits, may overwrite the files within. ******************************************************************************* Parsing PointData from raw alignments... PointData directory exists, skipping parsing and using files within. Delete it to reprocess. ******************************************************************************* Filtering PointData for duplicate reads (same strand and start position)... DupFiltPointData directory exists, skipping filtering. Delete it to reprocess. Exception in thread "main" java.lang.NullPointerException at edu.utah.seq.analysis.ChIPSeq.filterDuplicates(ChIPSeq.java:223) at edu.utah.seq.analysis.ChIPSeq.<init>(ChIPSeq.java:74) at edu.utah.seq.analysis.ChIPSeq.main(ChIPSeq.java:408) |