3d-dna : unable to dump Matrix normalization missing for : assembly_assembly_BP_25000

[shivani...@berkeley.edu]

Hi, 

I am trying to use your 3d-dna pipeline to assemble a fly genome (D.miranda) . I am running into the following error at some point of the code where it says that it is unable to dump the data . Can you please suggest a way to fix this issue ? As I understand, the matrix resolutions are hard coded in at the moment. Here is the error that I get.

HiC file version: 8

Unable to dump

java.io.IOException: Normalization missing for: assembly_assembly_BP_25000

        at juicebox.data.DatasetReaderV2.readNormalizedBlock(DatasetReaderV2.java:719)

        at juicebox.data.MatrixZoomData.dump(MatrixZoomData.java:675)

        at juicebox.tools.clt.old.Dump.dumpMatrix(Dump.java:282)

        at juicebox.tools.clt.old.Dump.run(Dump.java:505)

        at juicebox.tools.HiCTools.main(HiCTools.java:86)

...Estimating necessary saturation level for requested misassembly sensitivity

...Analyzing near-diagonal mismatches

...Filtering mismatch calls without better alternative: Not functional yet, skipping

...Thinning mismatch region boundaries.

...Dumping 1000 resolution matrix

HiC file version: 8

...Estimating necessary saturation level for requested misassembly sensitivity

...Analyzing near-diagonal mismatches

:) -w flag was triggered, performing cursory search for repeat at 25000 resolution

:) -t flag was triggered, flagging regions with coverage higher than 4

...Dumping 25000 resolution coverage track

HiC file version: 8

...-p flag was triggered. Running with GNU Parallel support parameter set to true.

...-r flag was triggered, output will be labeled as *.1.*

...applying edits to cprops file

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

...applying edits to mnd file

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"

:| Warning: No input for label1 was provided. Default for label1 is ":::fragment_"

:| Warning: No input for label2 was provided. Default for label2 is ":::debris"'

Thanks, 

Shivani Mahajan

[Olga Dudchenko]

Dear Shivani,

From what you are describing it seems that Juicer was not able to normalize the matrix at the resolution used by default for misassembly detection. Assuming the earlier steps have worked and the hic matrix is not empty this probably suggests that the data is not dense enough to work with default parameters.

Please note that the uploaded code focuses on reproducing the assemblies reported in the paper. We are working to make additional code available as soon as possible.

Sincerely yours,

Olga