Canu-Sapelo2 - Revision history

Chelsea at 15:46, 8 July 2025

2025-07-08T15:46:31Z

← Older revision		Revision as of 11:46, 8 July 2025
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	=== Version ===		=== Version ===
	~~2.2,~~ 2.3		2.3

	=== Author / Distributor ===		=== Author / Distributor ===
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	=== Running Program ===		=== Running Program ===

	'''Version 2.2'''		'''Version 2.3'''

	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml canu/2.2-GCCcore-11.2.0		ml canu/2.3-GCCcore-13.3.0-Java-11
	</pre>		</pre>
	~~or with~~
	~~<pre class="gscript">~~
	~~ml canu/2.2-GCCcore-11.3.0~~
	~~</pre>~~

	~~'''Version 2.3'''~~

	~~To use this version, please load the module with~~
	~~<pre class="gscript">~~
	~~ml canu/2.3-GCC-12.3.0~~
	~~</pre>~~
	~~or with~~
	~~<pre class="gscript">~~
	~~ml canu/2.3-GCCcore-12.3.0~~
	~~</pre>~~


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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml canu/2.2-GCCcore-11.2.0		ml canu/2.3-GCCcore-13.3.0-Java-11

	canu gridOptions=" --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 " [options]		canu gridOptions=" --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 " [options]
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	=== Documentation ===		=== Documentation ===
	<pre class="gcommand">		<pre class="gcommand">
	~~[cft07037@d2-13 canu]$~~ ml canu/2.2-GCCcore-11.2.0		ml canu/2.3-GCCcore-13.3.0-Java-11
	~~[cft07037@d2-13 canu]$~~ canu --help		canu --help

	usage: canu [-version] [-citation] \		usage: canu [-version] [-citation] \

Jordan at 16:50, 17 April 2025

2025-04-17T16:50:07Z

← Older revision		Revision as of 12:50, 17 April 2025
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	=== Version ===		=== Version ===
	2.2		2.2, 2.3

	=== Author / Distributor ===		=== Author / Distributor ===
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	ml canu/2.2-GCCcore-11.3.0		ml canu/2.2-GCCcore-11.3.0
	</pre>		</pre>

			'''Version 2.3'''

			To use this version, please load the module with
			<pre class="gscript">
			ml canu/2.3-GCC-12.3.0
			</pre>
			or with
			<pre class="gscript">
			ml canu/2.3-GCCcore-12.3.0
			</pre>


	When you invoke canu, please use the gridOptions to pass queueing system options for the jobs the canu pipeline submits. At a minimum, please specify a partition, the number of tasks and the walltime. For example, use '''gridOptions = --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 '''. The --mem-per-cpu option will be added automatically by the pipeline scripts, but you can also add it if the pipeline is not able to estimate the memory needed correctly.		When you invoke canu, please use the gridOptions to pass queueing system options for the jobs the canu pipeline submits. At a minimum, please specify a partition, the number of tasks and the walltime. For example, use '''gridOptions = --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 '''. The --mem-per-cpu option will be added automatically by the pipeline scripts, but you can also add it if the pipeline is not able to estimate the memory needed correctly.

Chelsea: /* Running Program */

2024-05-09T14:30:51Z

Running Program

← Older revision		Revision as of 10:30, 9 May 2024
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	To use this version, please load the module with		To use this version, please load the module with
	<pre class="gscript">		<pre class="gscript">
	ml canu/2.2-GCCcore-11.2.0.~~lua~~		ml canu/2.2-GCCcore-11.2.0
			</pre>
			or with
			<pre class="gscript">
			ml canu/2.2-GCCcore-11.3.0
	</pre>		</pre>
	When you invoke canu, please use the gridOptions to pass queueing system options for the jobs the canu pipeline submits. At a minimum, please specify a partition, the number of tasks and the walltime. For example, use '''gridOptions = --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 '''. The --mem-per-cpu option will be added automatically by the pipeline scripts, but you can also add it if the pipeline is not able to estimate the memory needed correctly.		When you invoke canu, please use the gridOptions to pass queueing system options for the jobs the canu pipeline submits. At a minimum, please specify a partition, the number of tasks and the walltime. For example, use '''gridOptions = --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 '''. The --mem-per-cpu option will be added automatically by the pipeline scripts, but you can also add it if the pipeline is not able to estimate the memory needed correctly.



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	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml canu/2.2-GCCcore-11.2.0~~.lua~~		ml canu/2.2-GCCcore-11.2.0

	canu gridOptions=" --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 " [options]		canu gridOptions=" --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 " [options]

Chelsea: Updated Sapelo2 Rocky 8 system only has canu version 2.2. Updated page accordingly.

2023-09-06T15:16:37Z

Updated Sapelo2 Rocky 8 system only has canu version 2.2. Updated page accordingly.

Show changes

Shtsai: /* Installation */

2021-09-20T19:40:17Z

Installation

← Older revision		Revision as of 15:40, 20 September 2021
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	=== Installation ===		=== Installation ===

	Source code obtained from https://github.com/marbl/canu/releases/download/v2.1.1/		Source code obtained from https://github.com/marbl/canu/releases/download/v2.1.1/ and https://github.com/marbl/canu/releases/download/v2.2

	=== System ===		=== System ===
	64-bit Linux		64-bit Linux

Shtsai at 19:39, 20 September 2021

2021-09-20T19:39:18Z

← Older revision		Revision as of 15:39, 20 September 2021
Line 9:		Line 9:

	=== Version ===		=== Version ===
	2.1.1		2.1.1, 2.2

	=== Author / Distributor ===		=== Author / Distributor ===
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	ml canu/2.1.1-GCCcore-8.3.0-Java-11		ml canu/2.1.1-GCCcore-8.3.0-Java-11
	</pre>		</pre>
	When you invoke canu, please use the gridOptions to pass queueing system options for the jobs the canu pipeline submits. At a minimum, please specify a partition, the number of tasks and the walltime. For example, use '''gridOptions = --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 '''. The --mem option will be added automatically by the pipeline scripts.		When you invoke canu, please use the gridOptions to pass queueing system options for the jobs the canu pipeline submits. At a minimum, please specify a partition, the number of tasks and the walltime. For example, use '''gridOptions = --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 '''. The --mem-per-cpu option will be added automatically by the pipeline scripts, but you can also add it if the pipeline is not able to estimate the memory needed correctly.

			'''Version 2.2'''

			To use this version, please load the module with
			<pre class="gscript">
			ml canu/2.2-GCCcore-8.3.0-Java-11
			</pre>
			When you invoke canu, please use the gridOptions to pass queueing system options for the jobs the canu pipeline submits. At a minimum, please specify a partition, the number of tasks and the walltime. For example, use '''gridOptions = --partition=batch --ntasks=1 --cpus-per-task=4 --time=168:00:00 '''. The --mem-per-cpu option will be added automatically by the pipeline scripts, but you can also add it if the pipeline is not able to estimate the memory needed correctly.

Ben: updated external documentation link, added clarifying note about Slurm headers, updated Slurm header values

2021-07-15T16:03:05Z

updated external documentation link, added clarifying note about Slurm headers, updated Slurm header values

← Older revision		Revision as of 12:03, 15 July 2021
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	=== Description ===		=== Description ===
	"Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). "		"Canu is a fork of the Celera Assembler, designed for high-noise single-molecule sequencing (such as the PacBio RS II/Sequel or Oxford Nanopore MinION). "
	More details are at [~~http~~://~~www~~.~~repeatmasker~~.~~org Canu~~]		More details are at Canu's [https://canu.readthedocs.io/en/latest/index.html documentation].

	=== Running Program ===		=== Running Program ===
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	Here is an example of a shell script, sub.sh, to run on the batch queue:		Here is an example of a shell script, sub.sh, to run Canu on the batch queue:
	<pre class="gscript">		<pre class="gscript">
	#!/bin/bash		#!/bin/bash
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	#SBATCH --job-name=canujobname		#SBATCH --job-name=canujobname
	#SBATCH --ntasks=1		#SBATCH --ntasks=1
	~~#SBATCH --cpus-per-task=2~~		#SBATCH --time=1:00:00
	#SBATCH --time=~~120~~:00:00		#SBATCH --mem=10G
	#SBATCH --mem=~~40G~~

	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR
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	</pre>		</pre>
	where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.		where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well. Please note that the Slurm headers (#SBATCH lines) are only for Canu's initial job. The resource limits of all of the jobs that Canu spawns will be determined by what is defined in the gridOptions.

Shtsai: /* Documentation */

2021-03-25T16:32:42Z

Documentation

← Older revision		Revision as of 12:32, 25 March 2021
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	Complete documentation at http://canu.readthedocs.org/en/latest/		Complete documentation at http://canu.readthedocs.org/en/latest/


	</pre>		</pre>


	<pre class="gcommand">		<pre class="gcommand">
	[shtsai@b1-24 ~]$ ml canu/2.1.1-GCCcore-8.3.0-Java-11		[shtsai@b1-24 ~]$ ml canu/2.1.1-GCCcore-8.3.0-Java-11

Shtsai: /* Running Program */

2021-03-25T16:31:55Z

Running Program

← Older revision		Revision as of 12:31, 25 March 2021
Line 47:		Line 47:

	</pre>		</pre>
			where [options] need to be replaced by the options (command and arguments) you want to use. Other parameters of the job, such as the maximum wall clock time, maximum memory, the number of cores per node, and the job name need to be modified appropriately as well.

Shtsai: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.1.1 === Author / Distrib..."

2021-03-25T16:27:39Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 2.1.1 === Author / Distrib..."

Show changes