dudcha

Hi WTara, Note that while you certainly can, you don't have to do things manually. You can use JBAT to visualize contact maps and associated tracks (split.*.wig and split.*.bed) to...

Hi Tianyu, The messages you show suggest that the .hic files didn't build. Look for messages upstream from what you share from Java that might give you a clue why....

Hi Tianyu, The aligned folder and hic files generated by Juicer are irrelevant here. The file that is not being found by 3D-DNA is the one after assembly. Has a...

The folder in which you are running 3d-dna. -Olga > On Jan 4, 2021, at 10:25 PM, Huangtianyu-caas wrote: > > > Hi Olga, > > Thanks for your explanation,...

Make sure you make run-asm-pipeline executable or execute directly with bash. I highly recommend installing GNU parallel. In theory we support the non-parallel version, but it is much less tested...

See this: https://github.com/aidenlab/3d-dna/issues/25. Also check the awk version. -Olga > On Jan 4, 2021, at 11:36 PM, Huangtianyu-caas wrote: > > > GNU parallel was installed, and has been detected...

Hi Tianyu, Check your coreutils: "sort: unrecognized option '--parallel=24’". See in readme: GNU coreutils sort >=8.11 Best, Olga > On Jan 7, 2021, at 9:22 PM, Huangtianyu-caas wrote: > >...

Here’s your error juicebox_tools.sh: line 3: 14278 Killed java -Xms49152m -Xmx49152m -jar `dirname $0`/juicebox_tools.jar $* Make sure you have enough memory Olga > On Jan 8, 2021, at 11:08 PM,...

Hello Tianyu, The warning is not of concern, this is just a note in an off chance that your contig names contain sequences like this (which would be a problem)....

Hello YaoZhou89, I wasn't able to reproduce. Are you sure you are using original files as input? Best, Olga