juicer result - .hic files are empty

[Benedikt]

I am trying to run juicer and everything seems to run to completion without error, however the .hic files contain no information. The file size of the inter.hic file is ~15kb (attached). When I try to load it into juicebox, I receive an error "Error loading [object File]: RangeError: Offset is outside the bounds of the DataView".

Here is the content of inter.txt:

Experiment description: Juicer version 1.6; BWA 0.7.16a-r1181; 8 threads; splitsize 90000000; openjdk version "1.8.0_91"; Juicer Tools Version 1.22.01; /work/project/ladsie_002/juicer/scripts/juicer.sh -d ./6-juicer -p ./5-phase/output/phased.0.fasta.fai -y ./6-juicer_old/P10_assembly_MboI.txt -z ./5-phase/output/phased.0.fasta                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                                 

Sequenced Read Pairs:  198.719.564

 Normal Paired: 155.223.372 (78.11%)

 Chimeric Paired: 26.033.901 (13.10%)

 Chimeric Ambiguous: 8.872.717 (4.46%)

 Unmapped: 8.589.574 (4.32%)

 Ligation Motif Present: 103.013.744 (51.84%)

Alignable (Normal+Chimeric Paired): 181.257.273 (91.21%)

Unique Reads: 149,494,961 (75,502,505.56%)

PCR Duplicates: 31,732,449 (16,026,489.39%)

Optical Duplicates: 29,863 (15,082.32%)

Library Complexity Estimate: 455,145,782

Intra-fragment Reads: 1,981,486 (997129.62% / 1.33%)

Below MAPQ Threshold: 60,192,008 (30290011.52% / 40.26%)

Hi-C Contacts: 87,321,467 (43942183.18% / 58.41%)

 Ligation Motif Present: 42,374,626  (21323892.53% / 28.35%)

 3' Bias (Long Range): 81% - 19%

 Pair Type %(L-I-O-R): 25% - 25% - 25% - 25%

Inter-chromosomal: 43,902,142  (22092573.94% / 29.37%)

Intra-chromosomal: 43,419,325  (21849609.25% / 29.04%)

Short Range (<20Kb): 18,595,620  (9357746.37% / 12.44%)

Long Range (>20Kb): 24,823,618  (12491819.10% / 16.60%)

The intermediate files are reasonably sized, for example merged_nodups.txt is about 45GB. I have no idea where to look for the problem, any help is appreciated.

[Neva Durand]

Is there no output in the debug folder around hic file creation? I am unsure "fai" would work for chrom.sizes though it might be fine.

It's clear that the file isn't correct, it's too small.

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Neva Cherniavsky Durand, Ph.D.

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Assistant Professor, Aiden Lab

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[Benedikt]

I missed the error in the debug folder, my bad. It says during hic creation:

Picked up _JAVA_OPTIONS: -Xmx49152m -Xms49152m

java.lang.RuntimeException: No reads in Hi-C contact matrices. This could be because the MAPQ filter is set too high (-q) or because all reads map to the same fragment.

at juicebox.tools.utils.original.MatrixZoomDataPP.mergeAndWriteBlocks(MatrixZoomDataPP.java:276)

at juicebox.tools.utils.original.Preprocessor.writeMatrix(Preprocessor.java:970)

at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:659)

at juicebox.tools.utils.original.Preprocessor.preprocess(Preprocessor.java:425)

at juicebox.tools.clt.old.PreProcessing.run(PreProcessing.java:139)

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

I am unsure what causes this error, the stats look okay and the merged_nodups.txt contains 45GB. Could this be because of the fai file?

I can chop off the unneeded columns from the fai file to create a true chrom.sizes and run it again, no problem. But fai used to work fine in the past (if I remember correctly). Is there anything else you would recommend checking before I give it another try?

Thank you for your help!

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[Neva Durand]

I would check that the sequence names in the fai file match exactly the sequence names in the merged_nodups file (fields 2 and 6).

If you download a new jar, you will see that Pre no longer throws out intrafragment reads by default, which might be the other source of the problem.

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