Medusa-Sapelo2 - Revision history

Shtsai at 01:06, 5 April 2026

2026-04-05T01:06:01Z

← Older revision		Revision as of 21:06, 4 April 2026
Line 1:		Line 1:
	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==
	Bioinformatics		Bioinformatics
	=== Program On ===		== Program On ==
	Sapelo2		Sapelo2
	=== Version ===		== Version ==
	1.6		1.6
	===Author / Distributor===		==Author / Distributor==
	Please see https://github.com/combogenomics/medusa		Please see https://github.com/combogenomics/medusa
	===Description===		==Description==
	Medusa is a draft genome scaffolder that uses multiple reference genomes in a graph-based approach. For more information, please see https://github.com/combogenomics/medusa		Medusa is a draft genome scaffolder that uses multiple reference genomes in a graph-based approach. For more information, please see https://github.com/combogenomics/medusa
	=== Running Program ===		== Running Program ==

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
Line 60:		Line 60:
	</pre>		</pre>

	=== Documentation ===		== Documentation ==

	<pre class="gcommand">		<pre class="gcommand">
Line 130:		Line 130:
	</pre>		</pre>

	=== Installation ===		== Installation ==
	*Version 1.6, source code downloaded from https://github.com/combogenomics/medusa and compiled with ant		*Version 1.6, source code downloaded from https://github.com/combogenomics/medusa and compiled with ant

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

Chelsea: /* Version 1.6-foss-2021b */

2023-09-06T18:04:38Z

Version 1.6-foss-2021b

← Older revision		Revision as of 14:04, 6 September 2023
Line 16:		Line 16:
	For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.		For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

	*Version 1.6, installed in /apps/eb/Medusa/1.6-foss-~~2019b~~-Python-3.7.4-Java-1.8.~~0_144~~		*Version 1.6, installed in /apps/eb/Medusa/1.6-foss-2021b-Python-3.9.6-Java-1.8.0_241

	To use this version of Medusa, please first load the module with		To use this version of Medusa, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	ml Medusa/1.6-foss-~~2019b~~-Python-3.7.4-Java-1.8.~~0_144~~		ml Medusa/1.6-foss-2021b-Python-3.9.6-Java-1.8.0_241
	</pre>		</pre>
	This module automatically loads Python/3.7.4-GCCcore-8.3.0, Biopython/1.75-foss-~~2019b-Python-3.7.4~~, networkx/2.4-foss-~~2019b-Python-3.7.4~~, MUMmer/4.0.0beta2-~~foss~~-~~2019b~~, Java/1.8.~~0_144~~, and other dependencies.		This module automatically loads Python/3.9.6-GCCcore-11.2.0, Biopython/1.79-foss-2021b, networkx/2.6.3-foss-2021b, MUMmer/4.0.0beta2-GCCcore-11.2.0, Java/1.8.0_241, and other dependencies.

	Sample job submission script (sub.sh) to run medusa.jar:		Sample job submission script (sub.sh) to run medusa.jar:
Line 40:		Line 40:
	cd $SLURM_SUBMIT_DIR		cd $SLURM_SUBMIT_DIR

	ml Medusa/1.6-foss-~~2019b~~-Python-3.7.4-Java-1.8.~~0_144~~		ml Medusa/1.6-foss-2021b-Python-3.9.6-Java-1.8.0_241

	java -jar ${EBROOTMEDUSA}/medusa.jar --threads 6 [options]		java -jar ${EBROOTMEDUSA}/medusa.jar --threads 6 [options]
Line 63:		Line 63:

	<pre class="gcommand">		<pre class="gcommand">
	ml Medusa/1.6-foss-~~2019b~~-Python-3.7.4-Java-1.8.~~0_144~~		ml Medusa/1.6-foss-2021b-Python-3.9.6-Java-1.8.0_241

	java -jar ${EBROOTMEDUSA}/medusa.jar -h		[cft07037@d2-13 ~]$ java -jar ${EBROOTMEDUSA}/medusa.jar -h
	Medusa version 1.6		Medusa version 1.6
	usage: java -jar medusa.jar -i inputfile -v		usage: java -jar medusa.jar -i inputfile -v
Line 127:		Line 127:
	scheme. Using a different weighting		scheme. Using a different weighting
	scheme may lead to better results.		scheme may lead to better results.


	</pre>		</pre>

Shtsai: /* Documentation */

2021-05-05T00:18:09Z

Documentation

← Older revision		Revision as of 20:18, 4 May 2021
Line 63:		Line 63:

	<pre class="gcommand">		<pre class="gcommand">
	~~mlMedusa~~/1.6-foss-2019b-Python-3.7.4-Java-1.8.0_144		ml Medusa/1.6-foss-2019b-Python-3.7.4-Java-1.8.0_144

	java -jar ${EBROOTMEDUSA}/medusa.jar -h		java -jar ${EBROOTMEDUSA}/medusa.jar -h
Line 130:		Line 130:

	</pre>		</pre>

	=== Installation ===		=== Installation ===
	*Version 1.6, source code downloaded from https://github.com/combogenomics/medusa and compiled with ant		*Version 1.6, source code downloaded from https://github.com/combogenomics/medusa and compiled with ant

Shtsai: Created page with "Category:Sapelo2Category:SoftwareCategory:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.6 ===Author / Distributor==..."

2021-05-05T00:15:14Z

Created page with "Category:Sapelo2 Category:Software Category:Bioinformatics === Category === Bioinformatics === Program On === Sapelo2 === Version === 1.6 ===Author / Distributor==..."

New page

[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
=== Category ===
Bioinformatics
=== Program On ===
Sapelo2
=== Version ===
1.6
===Author / Distributor===
Please see https://github.com/combogenomics/medusa
===Description===
Medusa is a draft genome scaffolder that uses multiple reference genomes in a graph-based approach. For more information, please see https://github.com/combogenomics/medusa
=== Running Program ===

Also refer to [[Running Jobs on Sapelo2]]

For more information on Environment Modules on Sapelo2 please see the [[Lmod]] page.

*Version 1.6, installed in /apps/eb/Medusa/1.6-foss-2019b-Python-3.7.4-Java-1.8.0_144

To use this version of Medusa, please first load the module with
<pre class="gscript">
ml Medusa/1.6-foss-2019b-Python-3.7.4-Java-1.8.0_144
</pre>
This module automatically loads Python/3.7.4-GCCcore-8.3.0, Biopython/1.75-foss-2019b-Python-3.7.4, networkx/2.4-foss-2019b-Python-3.7.4, MUMmer/4.0.0beta2-foss-2019b, Java/1.8.0_144, and other dependencies.

Sample job submission script (sub.sh) to run medusa.jar:

<pre class="gscript">
#!/bin/bash
#SBATCH --job-name=medusajob
#SBATCH --partition=batch
#SBATCH --ntasks=1
#SBATCH --nodes=1
#SBATCH --cpus-per-task=6
#SBATCH --mem=10gb
#SBATCH --time=36:00:00
#SBATCH --output=%x.%j.out
#SBATCH --error=%x.%j.err

cd $SLURM_SUBMIT_DIR

ml Medusa/1.6-foss-2019b-Python-3.7.4-Java-1.8.0_144

java -jar ${EBROOTMEDUSA}/medusa.jar --threads 6 [options]

</pre>

where [options] need to be replaced by the options (command and arguments) you want to use. Note that, Medusa scripts are installed in its medusa_scripts/ folder; if you want to use them, you need to specify its path by using its option of -scriptPath, i.e.,

<pre class="gscript">
-scriptPath ${EBROOTMEDUSA}/medusa_scripts
</pre>

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. In this example, the number of threads for the medusa.jar program is set to 6 and the number of cores requested for the job is also 6 (--cpus-per-task=6).

Submit the job to the queue with
<pre class="gcommand">
sbatch sub.sh
</pre>

=== Documentation ===

<pre class="gcommand">
mlMedusa/1.6-foss-2019b-Python-3.7.4-Java-1.8.0_144

java -jar ${EBROOTMEDUSA}/medusa.jar -h
Medusa version 1.6
usage: java -jar medusa.jar -i inputfile -v
available options:
-d OPTIONAL PARAMETER;The option *-d*
allows for the estimation of the
distance between pairs of contigs
based on the reference genome(s):
in this case the scaffolded contigs
will be separated by a number of N
characters equal to this estimate.
The estimated distances are also
saved in the
<targetGenome>_distanceTable file.
By default the scaffolded contigs
are separated by 100 Ns
-f <<draftsFolder>> OPTIONAL PARAMETER; The option *-f*
is optional and indicates the path
to the comparison drafts folder
-gexf OPTIONAL PARAMETER;Conting network
and path cover are given in gexf
format.
-h Print this help and exist.
-i <<targetGenome>> REQUIRED PARAMETER;The option *-i*
indicates the name of the target
genome file.
-n50 <<fastaFile>> OPTIONAL PARAMETER; The option
*-n50* allows the calculation of
the N50 statistic on a FASTA file.
In this case the usage is the
following: java -jar medusa.jar
-n50 <name_of_the_fasta>. All the
other options will be ignored.
-o <<outputName>> OPTIONAL PARAMETER; The option *-o*
indicates the name of output fasta
file.
-random <<numberOfRounds>> OPTIONAL PARAMETER;The option
*-random* is available (not
required). This option allows the
user to run a given number of
cleaning rounds and keep the best
solution. Since the variability is
small 5 rounds are usually
sufficient to find the best score.
-scriptPath <<medusaScriptsFolder>> OPTIONAL PARAMETER; The folder
containing the medusa scripts.
Default value: medusa_scripts
-threads <<numberOfThreads>> OPTIONAL PARAMETER; The option
*-threads* indicates the number of
threads to be used with mummer
(requires version >= 4.0)
-v RECOMMENDED PARAMETER; The option
*-v* (recommended) print on console
the information given by the
package MUMmer. This option is
strongly suggested to understand if
MUMmer is not running properly.
-w2 OPTIONAL PARAMETER;The option *-w2*
is optional and allows for a
sequence similarity based weighting
scheme. Using a different weighting
scheme may lead to better results.

</pre>
=== Installation ===
*Version 1.6, source code downloaded from https://github.com/combogenomics/medusa and compiled with ant

=== System ===
64-bit Linux