I am trying to generate the final scaffolds (hopefully pseudo-chromosomes) of a de novo assembly of a forest species by integrating Hi-C data to my contigs. I have followed the methodology described in Yahs:
I mapped the readings with the arima methodology;
And I followed the whole process without problems. However, in the last step, when generating the file to load it in JBAT (and do manual curation) with this command:
the out_JBAT.hic file starts to generate, and then fails with this error.
java.lang.NullPointerException
at juicebox.data.iterator.ListOfListIterator.hasNext(ListOfListIterator.java:44)
at juicebox.data.iterator.IteratorContainer.getNumberOfContactRecords(IteratorContainer.java:54)
at juicebox.data.iterator.ListOfListIteratorContainer.getIsThereEnoughMemoryForNormCalculation(ListOfListIteratorContainer.java:56)
at juicebox.tools.utils.norm.NormalizationCalculations.(NormalizationCalculations.java:59)
at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.getWGVectors(GenomeWideNormalizationVectorUpdater.java:167)
at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.updateHicFileForGWfromPreAddNormOnly(GenomeWideNormalizationVectorUpdater.java:132)
at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:159)
at juicebox.tools.clt.old.AddNorm.launch(AddNorm.java:83)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:185)
at juicebox.tools.HiCTools.main(HiCTools.java:97)
I have searched other forums for the same error, but have not been able to find any solid references. Any comments would be appreciated and thanks in advance.
Hi everyone,
I am trying to generate the final scaffolds (hopefully pseudo-chromosomes) of a de novo assembly of a forest species by integrating Hi-C data to my contigs. I have followed the methodology described in Yahs:
https://github.com/c-zhou/yahs#yahs-yet-another-hi-c-scaffolding-tool-
I mapped the readings with the arima methodology; And I followed the whole process without problems. However, in the last step, when generating the file to load it in JBAT (and do manual curation) with this command:
(java -jar -Xmx32G juicer_tools.1.9.9_jcuda.0.8.jar pre out_JBAT.txt out_JBAT.hic.part <(cat out_JBAT.log | grep PRE_C_SIZE | awk '{print $2" "$3}')') && (mv out_JBAT.hic.part out_JBAT.hic)
the out_JBAT.hic file starts to generate, and then fails with this error.
java.lang.NullPointerException at juicebox.data.iterator.ListOfListIterator.hasNext(ListOfListIterator.java:44) at juicebox.data.iterator.IteratorContainer.getNumberOfContactRecords(IteratorContainer.java:54) at juicebox.data.iterator.ListOfListIteratorContainer.getIsThereEnoughMemoryForNormCalculation(ListOfListIteratorContainer.java:56) at juicebox.tools.utils.norm.NormalizationCalculations.(NormalizationCalculations.java:59)
at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.getWGVectors(GenomeWideNormalizationVectorUpdater.java:167)
at juicebox.tools.utils.norm.GenomeWideNormalizationVectorUpdater.updateHicFileForGWfromPreAddNormOnly(GenomeWideNormalizationVectorUpdater.java:132)
at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:159)
at juicebox.tools.clt.old.AddNorm.launch(AddNorm.java:83)
at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:185)
at juicebox.tools.HiCTools.main(HiCTools.java:97)
My out_JBAT.txt | head
0 assembly 2042957211 0 1 assembly 1240680856 1 0 assembly 2042957211 0 1 assembly 1240680857 1 0 assembly 2042957212 0 1 assembly 1240680857 1 0 assembly 2042957262 0 1 assembly 2042957399 1 0 assembly 2042957337 0 1 assembly 905071720 1 0 assembly 2042957429 0 1 assembly 2042957523 1 0 assembly 2042957536 0 1 assembly 2042957530 1 0 assembly 2042957782 0 1 assembly 2042957961 1 0 assembly 2042957850 0 1 assembly 2042958033 1 0 assembly 2042957851 0 1 assembly 2042958038 1
I have searched other forums for the same error, but have not been able to find any solid references. Any comments would be appreciated and thanks in advance.