Trinity-Sapelo2 - Revision history

Shtsai at 19:56, 11 May 2026

2026-05-11T19:56:28Z

← Older revision		Revision as of 15:56, 11 May 2026
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	Trinity is now published online at [http://www.nature.com/nbt/journal/v29/n7/abs/nbt.1883.html Nature Biotechnology]. The Broad Institute’s [http://www.broadinstitute.org/blog/suite-tools-takes-flight blog] has a story on how the Trinity project came together.		Trinity is now published online at [http://www.nature.com/nbt/journal/v29/n7/abs/nbt.1883.html Nature Biotechnology]. The Broad Institute’s [http://www.broadinstitute.org/blog/suite-tools-takes-flight blog] has a story on how the Trinity project came together.

	More details at [~~http~~://~~trinityrnaseq.~~github.io/ Trinity]		More details at [https://github.com/trinityrnaseq/trinityrnaseq/ Trinity github page]

	== Description ==		== Description ==

	From ~~[http~~://~~trinityrnaseq.~~github.io/ ~~Trinity]~~:		From https://github.com/trinityrnaseq/trinityrnaseq/wiki:

	"Trinity, developed at the [http://www.broadinstitute.org/ Broad Institute], represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Briefly, the process works like so:		"Trinity, developed at the [http://www.broadinstitute.org/ Broad Institute], represents a novel method for the efficient and robust de novo reconstruction of transcriptomes from RNA-Seq data. Trinity combines three independent software modules: Inchworm, Chrysalis, and Butterfly, applied sequentially to process large volumes of RNA-Seq reads. Trinity partitions the sequence data into many individual de Bruijn graphs, each representing the transcriptional complexity at at a given gene or locus, and then processes each graph independently to extract full-length splicing isoforms and to tease apart transcripts derived from paralogous genes. Briefly, the process works like so:
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	* To run Trinity in conjunction with HpcGridRunner, please see [[Trinity-HpcGridRunner\|our wiki page on Trinity HpcGridRunner]].		* To run Trinity in conjunction with HpcGridRunner, please see [[Trinity-HpcGridRunner\|our wiki page on Trinity HpcGridRunner]].

	* ~~Here is a post for memory~~ estimates. For a 4 billion base mouse, it uses about 50 GB memory at peak. ~~[http://trinityrnaseq.github.io/performance/index.html performance]~~		* Memory estimates according to an old Trinity documentation: For a 4 billion base mouse, it uses about 50 GB memory at peak.

	* Do not ask for more than 24 CPU cores at the command and double the quantity of requesting CPU from queue. e.g. at the following, command ask for 8 CPU cores and at the header, it asks for --cpus-per-task=8.		* Do not ask for more than 24 CPU cores at the command and double the quantity of requesting CPU from queue. e.g. at the following, command ask for 8 CPU cores and at the header, it asks for --cpus-per-task=8.
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	==Documentation ==		==Documentation ==

	More details at [~~http~~://~~trinityrnaseq.~~github.io/ Trinity]		More details at [https://github.com/trinityrnaseq/trinityrnaseq/wiki/ Trinity wiki page]

	<pre class="gcommand">		<pre class="gcommand">
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	== Installation==		== Installation==

	Sources are downloaded from [https://~~trinityrnaseq.~~github.~~io Trinity]~~		Sources are downloaded from https://github.com/trinityrnaseq/trinityrnaseq

	==System==		==System==

Shtsai at 19:35, 11 May 2026

2026-05-11T19:35:14Z

← Older revision		Revision as of 15:35, 11 May 2026
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	* Mostly trinity needs to run at large memory queue, namely highmem_p, as in the sample script below.		* Mostly trinity needs to run at large memory queue, namely highmem_p, as in the sample script below.
	* '''<u>Trinity is best run utilizing /lscratch, please ~~click~~ [[Trinity-Sapelo2#Utilizing .2Flscratch in Trinity Job Submission Script\|~~here~~]] or scroll down to see how to configure your job submission script to use /lscratch</u>'''		* '''<u>Trinity is best run utilizing /lscratch, please see [[Trinity-Sapelo2#Utilizing .2Flscratch in Trinity Job Submission Script\|Utilizing /lscratch for Trinity Jobs]] or scroll down to see how to configure your job submission script to use /lscratch</u>'''
	* To run Trinity in conjunction with HpcGridRunner, please see [[Trinity-HpcGridRunner\|~~here~~]].		* To run Trinity in conjunction with HpcGridRunner, please see [[Trinity-HpcGridRunner\|our wiki page on Trinity HpcGridRunner]].

	* Here is a post for memory estimates. For a 4 billion base mouse, it uses about 50 GB memory at peak. [http://trinityrnaseq.github.io/performance/index.html performance]		* Here is a post for memory estimates. For a 4 billion base mouse, it uses about 50 GB memory at peak. [http://trinityrnaseq.github.io/performance/index.html performance]

Shtsai at 01:38, 5 April 2026

2026-04-05T01:38:34Z

← Older revision		Revision as of 21:38, 4 April 2026
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	[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]		[[Category:Sapelo2]][[Category:Software]][[Category:Bioinformatics]]
	=== Category ===		== Category ==

	Bioinformatics		Bioinformatics

	=== Program On ===		== Program On ==

	Sapelo2		Sapelo2

	=== Version ===		== Version ==

	2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2		2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2

	=== Author / Distributor ===		== Author / Distributor ==

	Trinity is now published online at [http://www.nature.com/nbt/journal/v29/n7/abs/nbt.1883.html Nature Biotechnology]. The Broad Institute’s [http://www.broadinstitute.org/blog/suite-tools-takes-flight blog] has a story on how the Trinity project came together.		Trinity is now published online at [http://www.nature.com/nbt/journal/v29/n7/abs/nbt.1883.html Nature Biotechnology]. The Broad Institute’s [http://www.broadinstitute.org/blog/suite-tools-takes-flight blog] has a story on how the Trinity project came together.
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	More details at [http://trinityrnaseq.github.io/ Trinity]		More details at [http://trinityrnaseq.github.io/ Trinity]

	=== Description ===		== Description ==

	From [http://trinityrnaseq.github.io/ Trinity]:		From [http://trinityrnaseq.github.io/ Trinity]:
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Running Program ===		== Running Program ==

	====General Instructions====		===General Instructions===

	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
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	* If previous jobs left dir trinity_out_dir, remove it before start another trinity job.		* If previous jobs left dir trinity_out_dir, remove it before start another trinity job.

	====Trinity versions 2.5.1, 2.8.4, and 2.8.5 Singularity Container on Sapelo2====		===Trinity versions 2.5.1, 2.8.4, and 2.8.5 Singularity Container on Sapelo2===

	On the Sapelo2 cluster, singularity containers have access to the users home directory ($HOME), scratch directory (/scratch), lscratch directory (/lscratch), /tmp directory (/tmp) inside the container.		On the Sapelo2 cluster, singularity containers have access to the users home directory ($HOME), scratch directory (/scratch), lscratch directory (/lscratch), /tmp directory (/tmp) inside the container.
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	====Trinity versions 2.15.1 and 2.15.2 Software Module on Sapelo2 ====		===Trinity versions 2.15.1 and 2.15.2 Software Module on Sapelo2 ===

	*version 2.15.1 running with Python3 is installed at /apps/eb/Trinity/2.15.1-foss-2022a		*version 2.15.1 running with Python3 is installed at /apps/eb/Trinity/2.15.1-foss-2022a
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	===Utilizing /lscratch in Trinity Job Submission Script===		==Utilizing /lscratch in Trinity Job Submission Script==
	* Utilizing /lscratch allows Trinity jobs to run much faster and smoother and also negates the effects of heavy IO traffic.		* Utilizing /lscratch allows Trinity jobs to run much faster and smoother and also negates the effects of heavy IO traffic.
	* This /lscratch directory resides on the local hard drive of the compute node that your job gets allocated to (which means you cannot access this directory outside the job submission script).		* This /lscratch directory resides on the local hard drive of the compute node that your job gets allocated to (which means you cannot access this directory outside the job submission script).
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	* Please feel free to submit a ticket to us if you would like further help, explanations of how /lscratch works, or to even look over your submission script to ensure it is correctly utilizing /lscratch!		* Please feel free to submit a ticket to us if you would like further help, explanations of how /lscratch works, or to even look over your submission script to ensure it is correctly utilizing /lscratch!

	===Job Submission===		==Job Submission==

	Submit a job submission script (sub.sh) to Sapelo2:		Submit a job submission script (sub.sh) to Sapelo2:
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

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

	More details at [http://trinityrnaseq.github.io/ Trinity]		More details at [http://trinityrnaseq.github.io/ Trinity]
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	=== Installation===		== Installation==

	Sources are downloaded from [https://trinityrnaseq.github.io Trinity]		Sources are downloaded from [https://trinityrnaseq.github.io Trinity]

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

	[[#top\|Back to Top]]		[[#top\|Back to Top]]

Shtsai: /* Trinity v2.15.1 and 2.15.2 Software Module on Sapelo2 */

2025-02-21T15:29:53Z

Trinity v2.15.1 and 2.15.2 Software Module on Sapelo2

← Older revision		Revision as of 11:29, 21 February 2025
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	====Trinity v2.15.1 and 2.15.2 Software Module on Sapelo2 ====		====Trinity versions 2.15.1 and 2.15.2 Software Module on Sapelo2 ====

	*version 2.15.1 running with Python3 is installed at /apps/eb/Trinity/2.15.1-foss-2022a		*version 2.15.1 running with Python3 is installed at /apps/eb/Trinity/2.15.1-foss-2022a

Shtsai: /* Trinity v2.5.1, v2.8.4 and v2.8.5 Singularity Container on Sapelo2 */

2025-02-21T15:29:35Z

Trinity v2.5.1, v2.8.4 and v2.8.5 Singularity Container on Sapelo2

← Older revision		Revision as of 11:29, 21 February 2025
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	* If previous jobs left dir trinity_out_dir, remove it before start another trinity job.		* If previous jobs left dir trinity_out_dir, remove it before start another trinity job.

	====Trinity v2.5.1, v2.8.4 and v2.8.5 Singularity Container on Sapelo2====		====Trinity versions 2.5.1, 2.8.4, and 2.8.5 Singularity Container on Sapelo2====

	On the Sapelo2 cluster, singularity containers have access to the users home directory ($HOME), scratch directory (/scratch), lscratch directory (/lscratch), /tmp directory (/tmp) inside the container.		On the Sapelo2 cluster, singularity containers have access to the users home directory ($HOME), scratch directory (/scratch), lscratch directory (/lscratch), /tmp directory (/tmp) inside the container.

Shtsai at 15:28, 21 February 2025

2025-02-21T15:28:55Z

← Older revision		Revision as of 11:28, 21 February 2025
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	=== Version ===		=== Version ===

	2.5.1, 2.8.4, 2.8.5, 2.15.1		2.5.1, 2.8.4, 2.8.5, 2.15.1, 2.15.2

	=== Author / Distributor ===		=== Author / Distributor ===
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	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]

	Trinity v2.5.1, v2.8.4, v2.8.5, and v2.15.1 are installed at Sapelo2.		Trinity versions 2.5.1, 2.8.4, 2.8.5, 2.15.1, and 2.15.2 are installed on Sapelo2.

	* Mostly trinity needs to run at large memory queue, namely highmem_p, as in the sample script below.		* Mostly trinity needs to run at large memory queue, namely highmem_p, as in the sample script below.
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	[[#top\|Back to Top]]		[[#top\|Back to Top]]

	====Trinity v2.15.1 Software Module on Sapelo2 ====		====Trinity v2.15.1 and 2.15.2 Software Module on Sapelo2 ====

	*version 2.15.1 running with Python3 is installed at /apps/eb/Trinity/2.15.1-foss-2022a		*version 2.15.1 running with Python3 is installed at /apps/eb/Trinity/2.15.1-foss-2022a
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	<pre class="gcommand">		<pre class="gcommand">
	module load Trinity/2.15.1-foss-2022a		module load Trinity/2.15.1-foss-2022a
			</pre>

			*version 2.15.2 running with Python3 is installed at /apps/eb/Trinity/2.15.2-foss-2023a

			To run Trinity v2.15.2, please load the module:

			<pre class="gcommand">
			module load Trinity/2.15.2-foss-2023a
	</pre>		</pre>

Chelsea: /* Trinity v2.15.1 Software Module on Sapelo2 */

2024-07-31T18:10:00Z

Trinity v2.15.1 Software Module on Sapelo2

← Older revision		Revision as of 14:10, 31 July 2024
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	* Mostly trinity needs to run at large memory queue, namely highmem_p, as in the sample script below.		* Mostly trinity needs to run at large memory queue, namely highmem_p, as in the sample script below.
	* '''<u>Trinity is best run utilizing /lscratch, please click [[Trinity-Sapelo2#Utilizing .2Flscratch in Trinity Job Submission Script\|here]] or scroll down to see how to configure your job submission script to use /lscratch</u>'''		* '''<u>Trinity is best run utilizing /lscratch, please click [[Trinity-Sapelo2#Utilizing .2Flscratch in Trinity Job Submission Script\|here]] or scroll down to see how to configure your job submission script to use /lscratch</u>'''
			* To run Trinity in conjunction with HpcGridRunner, please see [[Trinity-HpcGridRunner\|here]].

	* Here is a post for memory estimates. For a 4 billion base mouse, it uses about 50 GB memory at peak. [http://trinityrnaseq.github.io/performance/index.html performance]		* Here is a post for memory estimates. For a 4 billion base mouse, it uses about 50 GB memory at peak. [http://trinityrnaseq.github.io/performance/index.html performance]

Chelsea: /* Utilizing /lscratch in Trinity Job Submission Script */

2024-01-10T18:23:37Z

Utilizing /lscratch in Trinity Job Submission Script

← Older revision		Revision as of 14:23, 10 January 2024
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	* This /lscratch directory resides on the local hard drive of the compute node that your job gets allocated to (which means you cannot access this directory outside the job submission script).		* This /lscratch directory resides on the local hard drive of the compute node that your job gets allocated to (which means you cannot access this directory outside the job submission script).
	* Below is a sample job submission script including steps so you can see what you need to add to your job submission script in order to make your Trinity job utilize /lscratch.		* Below is a sample job submission script including steps so you can see what you need to add to your job submission script in order to make your Trinity job utilize /lscratch.
	** As well as adding the 6 steps below, please also add the Slurm header --gres=lscratch:___ which requests space in /lscratch. The default units for this is GB and in the example submission script below, we are requesting 200GB of space with the line '''''#SBATCH --gres=lscratch:200''''' (it is the last Slurm header)~~'''~~.~~'''~~		** As well as adding the 6 steps below, please also add the Slurm header --gres=lscratch:___ which requests space in /lscratch. The default units for this is GB and in the example submission script below, we are requesting 200GB of space with the line '''''#SBATCH --gres=lscratch:200''''' (it is the last Slurm header). Please only request as much space in /lscratch as is needed for your job.

	<pre class="gscript">		<pre class="gscript">

Chelsea: /* Utilizing /lscratch in Trinity Job Submission Script */

2024-01-10T18:22:54Z

Utilizing /lscratch in Trinity Job Submission Script

← Older revision		Revision as of 14:22, 10 January 2024
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	* This /lscratch directory resides on the local hard drive of the compute node that your job gets allocated to (which means you cannot access this directory outside the job submission script).		* This /lscratch directory resides on the local hard drive of the compute node that your job gets allocated to (which means you cannot access this directory outside the job submission script).
	* Below is a sample job submission script including steps so you can see what you need to add to your job submission script in order to make your Trinity job utilize /lscratch.		* Below is a sample job submission script including steps so you can see what you need to add to your job submission script in order to make your Trinity job utilize /lscratch.
	** As well as adding the 6 steps below, please also add the Slurm header --gres=lscratch:___. ~~You can see~~ this ~~Slurm header~~ below, it is the last ~~one under --mail-type~~.		** As well as adding the 6 steps below, please also add the Slurm header --gres=lscratch:___ which requests space in /lscratch. The default units for this is GB and in the example submission script below, we are requesting 200GB of space with the line '''''#SBATCH --gres=lscratch:200''''' (it is the last Slurm header)'''.'''

	<pre class="gscript">		<pre class="gscript">

Chelsea: /* Utilizing /lscratch in Trinity Job Submission Script */

2024-01-10T14:04:21Z

Utilizing /lscratch in Trinity Job Submission Script

← Older revision		Revision as of 10:04, 10 January 2024
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	cp file3.bam /lscratch/${USER}/${SLURM_JOB_ID}/trinity_outputs		cp file3.bam /lscratch/${USER}/${SLURM_JOB_ID}/trinity_outputs


	# Step 3: change directories into /lscratch		# Step 3: change directories into /lscratch