Generate hic file error at finalize stage

[YaoZhou89]

Hello,

I run the run-asm-pipeline.sh pipeline successfully at the first try without --build-gapped-map parameter. As I need the .hic file, so I only re-run the pipeline with -s finalize and --build-gapped-map, but I got an error for writing .hic file like below:

Any problems with my script or data?

[dudcha]

Hello YaoZhou89,

I wasn't able to reproduce. Are you sure you are using original files as input?

Best, Olga

[YaoZhou89]

Thanks! I am sure about that. Here is my first try: run-asm-pipeline.sh -m diploid -r 5 ~/juicer/references/mygenome.fasta ~/HiC/mygenome/aligned/merged_nodups.txt

And then I tried the following in the same folder: run-asm-pipeline.sh -m diploid -s finalize -g 100 -e -f --build-gapped-map ~/juicer/references/mygenome.fasta ~/HiC/mygenome/aligned/merged_nodups.txt

As the juicer.sh could also generate the .hic file. I am trying using it to generate the .hic file (not finished yet) and the .assembly file generated here for manually checking. Is this fine?

[dudcha]

Ah, yes, diploid is different. You’ll have to realign al the data to the new reference and run visualize assembly after that.

I’ll add a check for diploid in the next release, thanks for the note on this.

Best, Olga

On May 16, 2019, at 10:10 PM, Yao Zhou [email protected] wrote:

I am sure about that. Here is my first try: run-asm-pipeline.sh -m diploid -r 5 ~/juicer/references/mygenome.fasta ~/HiC/mygenome/aligned/merged_nodups.txt

And then I tried the following in the same folder: run-asm-pipeline.sh -m diploid -s finalize -g 100 -e -f --build-gapped-map ~/juicer/references/mygenome.fasta ~/HiC/mygenome/aligned/merged_nodups.txt

As the juicer.sh could also generate the .hic file. I am trying using it to generate the .hic file (not finished yet) and the .assembly file generated here for manually checking. Is this fine?

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[YaoZhou89]

Good to know this. Thanks!

[gapalm]

Ah, yes, diploid is different. You’ll have to realign al the data to the new reference and run visualize assembly after that. I’ll add a check for diploid in the next release, thanks for the note on this. Best, Olga

I am getting the same error in diploid. Could you please specify what particular steps are have to be reran, is it -s merge step with the run-asm-pipeline.sh? and what is considered as new reference, is it final.fasta? Thank you and great software!

[dudcha]

Hello gapalm,

Sorry for the delay, was traveling.

If you want to build the final map in diploid mode you will have to 1) index the new genome & prep the restriction site file 2) run juicer to create the new merged_nodups.txt file and 3) run 3d-dna/utils/make-assembly-from-fasta.awk and 3d-dna/visualize/run-assembly-visualizer.sh to guild the new map.

The point of doing this is that unlike anchoring ordering and orienting figuring out liftover coordinates for merge is much more difficult. So while for other steps (all of them in haploid mode) one can just lift the coordinates of Hi-C contacts, for merge it is not (yet) possible.

Hope this helps, Olga