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nservant / HiC-Pro

HiC-Pro: An optimized and flexible pipeline for Hi-C data processing
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hicpro2juicebox.sh NullPointerException at zoom FRAG_20 #463

Closed esebesty closed 3 years ago

esebesty commented 3 years ago

I'm trying to convert the result files with hicpro2juicebox.sh but getting the following error.

Error message ``` HiC-Pro format > 2.7.5 detected ... Generating Juicebox input files ... Running Juicebox ... WARN [2021-07-27T19:02:37,145] [Globals.java:138] [main] Development mode is enabled Using 1 CPU thread(s) Start preprocess Writing header Writing body ...................................................................................................................................................................................................................................................................................................................................... Writing footer nBytesV5: 1893810 masterIndexPosition: 706792378 Finished preprocess Calculating norms for zoom BP_2500000 Calculating norms for zoom BP_1000000 Calculating norms for zoom BP_500000 Calculating norms for zoom BP_250000 Calculating norms for zoom BP_100000 Calculating norms for zoom BP_50000 Calculating norms for zoom BP_25000 Calculating norms for zoom BP_10000 Calculating norms for zoom BP_5000 Calculating norms for zoom BP_1000 Calculating norms for zoom FRAG_500 Calculating norms for zoom FRAG_200 Calculating norms for zoom FRAG_100 Calculating norms for zoom FRAG_50 Calculating norms for zoom FRAG_20java.lang.NullPointerException at juicebox.data.iterator.ListOfListIterator.hasNext(ListOfListIterator.java:45) at juicebox.data.iterator.IteratorContainer.getNumberOfContactRecords(IteratorContainer.java:51) at juicebox.data.iterator.ListOfListIteratorContainer.getIsThereEnoughMemoryForNormCalculation(ListOfListIteratorContainer.java:52) at juicebox.tools.utils.norm.NormalizationCalculations.(NormalizationCalculations.java:59) at juicebox.tools.utils.norm.NormalizationVectorUpdater.updateHicFile(NormalizationVectorUpdater.java:178) at juicebox.tools.clt.old.AddNorm.launch(AddNorm.java:87) at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:170) at juicebox.tools.HiCTools.main(HiCTools.java:94) done ! ```

Not sure if this is a memory issue, the node I'm using has ~32Gb memory. Have you seen this error?

Update: probably not memory related, as sampling 1M or 500k reads does not help, and the error happens trying to process different files/samples.

esebesty commented 3 years ago

Conversion works without the restriction fragment site file.