visualizer format issue "Unexpected column count"

[Sara Oppenheim]

I ran juicer and now am trying to run 3d-dna but I can't get past an error at the visualize step. I see that other threads have referenced the error I'm getting, but those situations all involved non-juicer outputs that needed to be reformatted. My mnd file is standard 8 column juicer output. 

Thanks,

Sara

The scaffold step works fine.

My scaffold command
run-liger-scaffolder.sh -s 15000 \
cs_hifi_hic.cprops cs_hifi_hic.juicer.merged_nodups.txt

My visualize command
run-asm-visualizer.sh cs_hifi_hic_juicer_mnd_to_3D.final.cprops cs_hifi_hic_juicer_mnd_to_3D.final.asm cs_hifi_hic.juicer.merged_nodups.txt

head cs_hifi_hic_juicer_mnd_to_3D.final.cprops
ptg000017l:::fragment_2 1 34114879
ptg000015l 2 25316186
ptg000018l 3 23830072

head cs_hifi_hic_juicer_mnd_to_3D.final.asm
1
2
3

head cs_hifi_hic.juicer.merged_nodups.txt

0 ptg000001l 638 1 16 ptg000001l 649 2
0 ptg000001l 748 1 16 ptg000001l 657 2
0 ptg000001l 592 1 16 ptg000001l 753 3

My error report
...Remapping contact data from the original contig set to assembly
...Building track files
...Building the hic file
WARNING: sun.reflect.Reflection.getCallerClass is not supported. This will impact performance.
WARN [2024-03-24T15:48:31,491]  [Globals.java:138] [main]  Development mode is enabled
Using 1 CPU thread(s)
Not including fragment map
Start preprocess
Writing header
Writing body
java.io.IOException: Unexpected column count.  Check file format
at juicebox.tools.utils.original.AsciiPairIterator.advance(AsciiPairIterator.java:167)
at juicebox.tools.utils.original.AsciiPairIterator.<init>(AsciiPairIterator.java:74)
at juicebox.tools.utils.original.Preprocessor.computeWholeGenomeMatrix(Preprocessor.java:565)
at juicebox.tools.utils.original.Preprocessor.writeBody(Preprocessor.java:658)
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)
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)

[Olga Dudchenko]

Hello,

It seems you are trying to run subpieces of 3d-dna? Or you are just reporting parts of the workflow? 

What you are shoing for mnd file is not the long format that is used by 3d-dna.

Best,

Olga

[Sara Oppenheim]

🤯 Hi Olga, my mnd is the "merged30.txt" output that juicer produced and stored in the juicer/aligned directory.

What am I supposed to be using? 

I initially tried running the run-asm-pipeline.sh wrapper and providing my hic file, but that failed. So then I tried running the tools individually, which is what my query was about.

I feel like maybe I have misunderstood something very fundamental.

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[Olga Dudchenko]

I suggest you take a look at the DNA Zoo Genome Assembly Cookbook for basics (dnazoo.org/methods). Looks like you are running Juicer2 w/o providing the --assembly flag. If you do it will generate a standard Juicer-1-style merged_nodups.txt file that you can use as input to 3d-dna. Best, -Olga