Running juicer.sh

Amina Hussein

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Aug 9, 2021, 5:09:22 PM8/9/21

to 3D Genomics

Hello,

I completed steps 1 - 10 on the page 'Running Juicer on a cluster' and now I am trying to run the juicer.sh script (slurm).

The command I used is

python juicer.sh -g Xentr10 -d /dfs6/pub/aminaoh/juicedir/restriction_sites -s DpnII -y /dfs6/pub/aminaoh/juicedir/restriction_sites/Xentr10_DpnII.txt -z /dfs6/pub/aminaoh/juicedir/references/Xtrop_V10.fasta

and I get the error

File "juicer.sh", line 66

shopt -s extglob

^

SyntaxError: invalid syntax

What could be causing this? Also, is there anything I need to edit in the juicer.sh script before proceeding?

Thank you,

Amina

Muhammad Saad Shamim

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Aug 9, 2021, 5:50:47 PM8/9/21

to Amina Hussein, 3D Genomics

Hey Amina,

There shouldn't be a call to python; should just be

juicer.sh ...

(May need to do chmod +x juicer.sh)

You should not need to edit the script, but see the answer here regarding specifying flags specific to your cluster:

https://groups.google.com/g/3d-genomics/c/z8UZcBKCx5I/m/F8_neaJOAwAJ

Best,

- Muhammad Saad Shamim

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Amina Hussein

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Aug 9, 2021, 6:37:31 PM8/9/21

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Hello Muhammad,

Thank you so much, that solved the issue. I have another question about the flags that I don't think is addressed in the link you provided. When I run juicer.sh with the command above (without python), I get this error message:

***! You must define a chrom.sizes file or a standard genome ID via the "-p" flag that delineates the lengths of the chromosomes in the genome at /dfs6/pub/aminaoh/juicedir/references/Xtrop_V10.fasta; you may use "-p hg19" or other standard genomes

I don't think the xenopus tropicalis genome is standard, so how could I make a chrom.sizes file for it?

Best,

Amina

Olga Dudchenko

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Aug 26, 2021, 3:56:59 PM8/26/21

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Hello Amina,

All you need to do is to create a tab-separeted file that looks like

chr1_seq_name chr_length

chr_seq_name chr_length

...

For sequences that are labeled as chromosomes on your respective genome. For X. tropicalis there should be 10 lines in this file.

Best,

Olga

Shilpi Singh

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May 4, 2022, 7:35:09 PM5/4/22

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Hello,

I have a similar issue. My draft assembly is at contig level, 2024 Mb draft genome from Illumina reads. My species has 9 chromosome. Please suggest how to prepare chrom.sizes to run juicer.

Regards

Shilpi

Olga Dudchenko

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May 11, 2022, 10:14:18 AM5/11/22

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Hello Shilpi,

If your goal is downstream assembly you should not run Juicer with chrom.sizes at all. Please consult the Genome Assembly Cookbook (dnazoo.org/methods) on how to run Juicer and 3D-DNA for assembly purposes.