Long running Juicer

[mushroom astar]

Hello, when I use juicer, I stopped at Gwak for a long time. Now I have a diploid genome of about 2G. I think my server can fully meet it. It has 64 cores and 256g memory. I'm still iterating. What should I do?

I found that there is no - C parameter in jucier 1.6, which means I can't split it to get faster speed. Now how can I use it?

[Neva Durand]

Hello,

What version are you using? Slurm cpu etc? There is a -C option is juicer 1.6. I am also not sure what step it’s stopped at from your explanation. Note that if your goal is assembly you should use the -e flag. 

On Fri, Jul 23, 2021 at 9:57 PM mushroom astar <tanxingd...@gmail.com> wrote:

Hello, when I use juicer, I stopped at Gwak for a long time. Now I have a diploid genome of about 2G. I think my server can fully meet it. It has 64 cores and 256g memory. I'm still iterating. What should I do?

I found that there is no - C parameter in jucier 1.6, which means I can't split it to get faster speed. Now how can I use it?

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Neva Cherniavsky Durand, Ph.D. | she, her, hers

Assistant Professor |  Molecular and Human Genetics

Aiden Lab | Baylor College of Medicine

www.aidenlab.org

[mushroom astar]

Hello! I am using the CPU version of juicer1.6. When I enter juicer.sh - h, the - C option does not appear. I want to ask how I can get corresponding changes in this version to speed up the speed?

Usage: juicer.sh [-g genomeID] [-d topDir] [-s site] [-a about] 

                 [-S stage] [-p chrom.sizes path] [-y restriction site file]

                 [-z reference genome file] [-D Juicer scripts directory]

                 [-b ligation] [-t threads] [-h] [-f] [-j]