inter.hic and inter_30.hic issues & inter_30_loops could not be parsed

[Nolan Ruffenach]

Hi,

I sent several emails before this one but this time I can't correct my mistakes.

All the pipeline run perfectly except at the end.

- The feature annotation successfully completed but, when files are checked, i have these errors : 

Either inter.hic or inter_30.hic were not created.

But, these files are used for with HICCUPS for example so, i don't know why o had this issue.

Moreover, i have also this one :

inter_30_loops could not be parsed.

Loop list is empty or incorrect path provided.

I send the output here :

Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. 

Using 1 CPU thread(s) for primary task 

Picked up _JAVA_OPTIONS: -Xmx1024m -Xms1024m 

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. 

Using 1 CPU thread(s) for primary task 

Picked up _JAVA_OPTIONS: -Xmx1024m -Xms512m 

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. 

Using 1 CPU thread(s) for primary task 

Using 10 CPU thread(s) for secondary task 

Not including fragment map 

Start preprocess Writing header

Writing body .Exception in thread "main" java.lang.OutOfMemoryError: Java heap space          at java.base/java.lang.AbstractStringBuilder.<init>(AbstractStringBuilder.java:86) 

          at java.base/java.lang.StringBuilder.<init>(StringBuilder.java:103) 

          at juicebox.tools.utils.original.MatrixZoomDataPP.incrementCount(MatrixZoomDataPP.java:212) 

  at juicebox.tools.utils.original.MatrixPP.incrementCount(MatrixPP.java:148) 

  at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:743)

   at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:436)

   at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:165) 

          at juicebox.tools.HiCTools.main(HiCTools.java:94) 

real 34m51.025s

user 20m46.235s

sys 0m18.578s

Picked up _JAVA_OPTIONS: -Xmx1024m -Xms512m 

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. 

Using 10 CPU thread(s) for primary task 

  

Calculating norms for zoom BP_2500000java.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.<init>(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.AddNorm.run(AddNorm.java:137) 

         at juicebox.tools.HiCTools.main(HiCTools.java:94) 

  real 0m0.484s 

user 0m0.983s 

sys 0m0.061s 

Tue Mar 29 09:03:14 CET 2022

 Picked up _JAVA_OPTIONS: -Xmx1024m -Xms512m 

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. 

Using 1 CPU thread(s) for primary task 

Using 10 CPU thread(s) for secondary task 

Not including fragment map 

Start preprocess Writing header Writing body .

Exception in thread "main" java.lang.OutOfMemoryError: Java heap space 

  at juicebox.tools.utils.original.MatrixZoomDataPP.incrementCount(MatrixZoomDataPP.java:212) 

  at juicebox.tools.utils.original.MatrixPP.incrementCount(MatrixPP.java:148) 

  at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:743) 

  at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:436) 

  at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:165) 

  at juicebox.tools.HiCTools.main(HiCTools.java:94) 

  real 18m58.703 

user 15m57.144s

 sys 0m13.904s 

Picked up _JAVA_OPTIONS: -Xmx1024m -Xms512m 

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. 

Using 10 CPU thread(s) for primary task 

  Calculating norms for zoom BP_2500000java.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.<init>(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.AddNorm.run(AddNorm.java:137) 

  at juicebox.tools.HiCTools.main(HiCTools.java:94) 

  real 0m0.468s 

user 0m1.001s 

sys 0m0.105s 

/media/nolan.ruffenach/DATA/juicer/scripts/common/juicer_tools is post-processing Hi-C for mm10 

Data read from /media/nolan.ruffenach/DATA/Documents/MLL3_project_serveur/HiC/aligned/inter_30.hic. Motifs read from /media/nolan.ruffenach/DATA/juicer/references/motif 

  ARROWHEAD: 

  Picked up _JAVA_OPTIONS: -Xmx1024m -Xms512m WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. 

Reading file: /media/nolan.ruffenach/DATA/Documents/MLL3_project_serveur/HiC/aligned/inter_30.hic Using 1 CPU thread(s) for primary task Unable to assess map sparsity; continuing with Arrowhead Default settings for 10kb being used No valid chromosome matrices at given resolution HiCCUPS: Picked up _JAVA_OPTIONS: -Xmx1024m -Xms512m WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. 

Reading file: /media/nolan.ruffenach/DATA/Documents/MLL3_project_serveur/HiC/aligned/inter_30.hic No valid configurations specified, using default settings Using 1 CPU thread(s) for primary task Unable to assess map sparsity; continuing with HiCCUPS Default settings for 5kb, 10kb, and 25kb being used Running HiCCUPS for resolution 5000 Running HiCCUPS for resolution 10000 Running HiCCUPS for resolution 25000 HiCCUPS complete APA: 

  Picked up _JAVA_OPTIONS: -Xmx1024m -Xms512m 

WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance. 

Reading file: /media/nolan.ruffenach/DATA/Documents/MLL3_project_serveur/HiC/aligned/inter_30.hic Using 1 CPU thread(s) for primary task Processing APA for resolution 25000 File /media/nolan.ruffenach/DATA/Documents/MLL3_project_serveur/HiC/aligned/inter_30_loops could not be parsed Loop list is empty or incorrect path provided. 

***! Can't find folder /media/nolan.ruffenach/DATA/juicer/references/motif 

***! Not running motif finder 

  (-: Feature annotation successfully completed (-:

***! Error! Either inter.hic or inter_30.hic were not created 

Either inter.hic or inter_30.hic were not created. Check for results

- So, i have hic files and feature annotation successfully completed but i don't know why these files seems to be "not created" and i don't know why inter_30_loops could not be parsed as well ....

By the way, inter_30_loops is, for me, a directory with 3 files :

- fdr_thresholds_10000

- fdr_thresholds_25000

- fdr_thresholds_5000

these files were not empty ...

If someone can help please to fix these issues, it would help me a lot.

Thanks,

RUFFENACH Nolan.

[Nolan Ruffenach]

Hi everyone,

When i checked it well, i thought issues came from "java.lang" issues :

-  Exception in thread "main" java.lang.OutOfMemoryError: Java heap space 

-  Calculating norms for zoom BP_2500000java.lang.NullPointerException

When i checked it on the web or on this group, i don't find something to help me to solve it ...

Can someone help me to fix these java issues please ? 

For me, the " java.lang.NullPointerException" error was because the " java.lang.OutOfMemoryError" error occurs (but i'm not sure about this).

Really hope someone will can help me.

Thanks,

Nolan.