Trouble running arrowhead on ENCODE portal .hic files

[Brian Roberts]

I am having trouble getting arrowhead to run on .hic files from the ENCODE portal.

Here is the code I am running:

wget https://www.encodeproject.org/files/ENCFF616PUW/@@download/ENCFF616PUW.hic

chr="chr21"

java -jar <path to>/juicer_tools_2.13.06.jar arrowhead -r 5000 -m 2000 -k VC-SQRT -c $chr ENCFF616PUW.hic ${chr}

While this executes without errors, it yields a file with 0 domains. This happens on every chromosome. I believe I am following the workflow on: https://www.encodeproject.org/experiments/ENCSR545YBD/ that yields ENCFF271SAF.  

I may be using the wrong flags; I used those suggested on the arrowhead wiki. I used the "VC-SQRT" normalization because ENCFF616PUW.hic does not appear to have KR normalization. I have checked ENCFF616PUW.hic with juicer_tools_2.13.06.jar validate and it passes. I can pull data from ENCFF616PUW.hic with straw. I have used this same arrowhead command successfully (yielding over 10k domains) on my own .hic file and this one: https://www.ncbi.nlm.nih.gov/geo/download/?acc=GSE201353&format=file&file=GSE201353%5FLIMA%5FTHP1%5FWT%5FLPIF%5FCMB%5FS%5F0%2E0%2E0%5FomegaMap%5Finter%5FwithNorms%2Ehic.

I have also tried this on ENCFF080DPJ.hic and get 0 domains.

Any help in figuring out what's going on here would be appreciated.

Brian

[Brian Roberts]

Nevermind. "VC-SQRT" should have been "VC_SQRT". Sorry for the mistake.