Error converting out_JBAT.txt to out_JBAT.hic

[Alex van Rensburg]

Dear Aiden lab, 

I'm trying to create a .hic file from an initial .bin file (created in yahs). 

I'm using two commands: 

1: juicer pre -a -o out_JBAT hic-to-contigs.bin scaffolds_final.agp contigs.fa.fai >out_JBAT.log 2>&1

This works and generates 5 output files: 

out_JBAT.txt - BED format file for hic links out_JBAT.liftover.agp - coordinate file between new and old contigs out_JBAT.assembly - assembly annotation file for Juicebox out_JBAT.assembly.agp - AGP file contains same information as the assembly annotation file. Not a real AGP file as there are no gaps. out_JBAT.log - the output log file

2. The second command fails with the error below: 

java -Xmx16g -jar ~/software/juicer_tools_2.17.00.jar pre out_JBAT.txt out_JBAT.hic genomesize 

genomesize is a file containing the size of the de novo assembly: 

assembly 450920569

Output from the command: 

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

WARN [2022-10-26T13:44:02,788]  [Globals.java:138] [main]  Development mode is enabled

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

..

Writing footer

nBytesV5: 2484682

masterIndexPosition: 99651623

Finished preprocess

Calculating norms for zoom BP_2500000java.lang.NullPointerException: Cannot invoke "java.util.Iterator.hasNext()" because "this.currentIterator" is null

   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.PreProcessing.run(PreProcessing.java:185)

    at juicebox.tools.HiCTools.main(HiCTools.java:97)

Do you know how I can troubleshoot this? This is theoretically the last step before I have a .hic file that I can import into Juicer for manual curation.. 

Thank you 

Alex

[Olga Dudchenko]

Hello,

Jahs is not our tool, so I cannot comment on the workflow: I do not know what's a .bin file. Happy to commend on the 3d-dna workflow (dnazoo.org/methods).

Thanks,

Olga