SRAToolKit-Sapelo2 - Revision history

Shtsai at 01:35, 5 April 2026

2026-04-05T01:35:16Z

← Older revision		Revision as of 21:35, 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 ==
	3.0.1, 3.0.3, 3.0.10		3.0.1, 3.0.3, 3.0.10
	===Author / Distributor===		==Author / Distributor==
	Please see https://github.com/ncbi/sra-tools		Please see https://github.com/ncbi/sra-tools
	===Description===		==Description==
	The SRA Toolkit from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. The Sequence Read Archives (SRA) store raw sequence data from "next-generation" sequencing technologies including Illumina, 454, IonTorrent, Complete Genomics, PacBio and OxfordNanopores. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. The SRA-Toolkit includes the following tools:		The SRA Toolkit from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives. The Sequence Read Archives (SRA) store raw sequence data from "next-generation" sequencing technologies including Illumina, 454, IonTorrent, Complete Genomics, PacBio and OxfordNanopores. In addition to raw sequence data, SRA now stores alignment information in the form of read placements on a reference sequence. The SRA-Toolkit includes the following tools:
	{\| class="wikitable"		{\| class="wikitable"
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	\|}		\|}

	=== Downloading SRA Data ===		== Downloading SRA Data ==

	The latest installed version of this application is at SRA-Toolkit/3.0.10-gompi-2023a		The latest installed version of this application is at SRA-Toolkit/3.0.10-gompi-2023a
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	For more information about the prefetch command refer to the [https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=prefetch documentation]		For more information about the prefetch command refer to the [https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=prefetch documentation]

	=== Running Program ===		== Running Program ==
	You can now run other SRA-Tools on the SRA data you've downloaded.		You can now run other SRA-Tools on the SRA data you've downloaded.
	Also refer to [[Running Jobs on Sapelo2]]		Also refer to [[Running Jobs on Sapelo2]]
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	Note that if you're downloading paired-end (Illumina) sequencing data and want the paired ends in separate .fastq files, use the '-S' option when extracting the files using fasterq-dump.		Note that if you're downloading paired-end (Illumina) sequencing data and want the paired ends in separate .fastq files, use the '-S' option when extracting the files using fasterq-dump.

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

	Please see https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc for the documentation of each tool.		Please see https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc for the documentation of each tool.

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

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

Jordan: /* Downloading SRA Data */

2025-05-27T20:40:22Z

Downloading SRA Data

← Older revision		Revision as of 16:40, 27 May 2025
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	=== Downloading SRA Data ===		=== Downloading SRA Data ===

	The ~~last~~ version of this application is at ~~/apps/eb/~~SRA-Toolkit/3.0.3-gompi-~~2022a~~		The latest installed version of this application is at SRA-Toolkit/3.0.10-gompi-2023a

	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 SRA-Toolkit/3.0.3-gompi-~~2022a~~		ml SRA-Toolkit/3.0.10-gompi-2023a
	</pre>		</pre>

Jordan: /* Running Program */

2025-05-27T20:39:37Z

Running Program

← Older revision		Revision as of 16:39, 27 May 2025
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	<nowiki>#</nowiki>SBATCH --ntasks=1<br>		<nowiki>#</nowiki>SBATCH --ntasks=1<br>
	<nowiki>#</nowiki>SBATCH --cpus-per-task=6 #fasterq-dump defaults to using 6 threads<br>		<nowiki>#</nowiki>SBATCH --cpus-per-task=6 #fasterq-dump defaults to using 6 threads<br>
	<nowiki>#</nowiki>SBATCH --mem=<u>~~10gb~~</u><br>		<nowiki>#</nowiki>SBATCH --mem=<u>24gb</u><br>
	<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>		<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>
	<nowiki>#</nowiki>SBATCH --output=~~fastq-dump~~.%j.out<br>		<nowiki>#</nowiki>SBATCH --output=%x.%j.out<br>
	<nowiki>#</nowiki>SBATCH --error=~~fastq-dump~~.%j.err<br>		<nowiki>#</nowiki>SBATCH --error=%x.%j.err<br>

	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml SRA-Toolkit/3.0.10-gompi-2023a<br>		ml SRA-Toolkit/3.0.10-gompi-2023a<br>
	prefetch SRR390728		prefetch SRR390728 <br>
	fasterq-dump /scratch/~~keekov~~/SRR390728.sra #You should use the directory you selected in the vdb-config step above<br>		fasterq-dump /scratch/MyID/SRR390728.sra #You should use the directory you selected in the vdb-config step above<br>
	</div>		</div>

			Note that if you're downloading paired-end (Illumina) sequencing data and want the paired ends in separate .fastq files, use the '-S' option when extracting the files using fasterq-dump.

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

Jordan: /* Running Program */

2025-05-27T20:35:01Z

Running Program

← Older revision		Revision as of 16:35, 27 May 2025
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	<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>		<nowiki>#</nowiki>SBATCH --mail-type=ALL<br>
	<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br>		<nowiki>#</nowiki>SBATCH --mail-user=<u>username@uga.edu</u><br>
	<nowiki>#</nowiki>SBATCH --ntasks=<u>1</u><br>		<nowiki>#</nowiki>SBATCH --ntasks=1<br>
			<nowiki>#</nowiki>SBATCH --cpus-per-task=6 #fasterq-dump defaults to using 6 threads<br>
	<nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br>		<nowiki>#</nowiki>SBATCH --mem=<u>10gb</u><br>
	<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>		<nowiki>#</nowiki>SBATCH --time=<u>08:00:00</u><br>
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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml SRA-Toolkit/3.0.3-gompi-~~2022a~~<br>		ml SRA-Toolkit/3.0.10-gompi-2023a<br>
	~~fastq~~-dump ~~-X 5 -Z~~ /scratch/keekov/SRR390728.sra #You should use the directory you selected in the vdb-config step above<br>		prefetch SRR390728
			fasterq-dump /scratch/keekov/SRR390728.sra #You should use the directory you selected in the vdb-config step above<br>
	</div>		</div>

Jordan: Edited to include v3.0.10 to the list of available versions.

2025-05-27T19:35:37Z

Edited to include v3.0.10 to the list of available versions.

← Older revision		Revision as of 15:35, 27 May 2025
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	Sapelo2		Sapelo2
	=== Version ===		=== Version ===
	3.0.1, 3.0.3		3.0.1, 3.0.3, 3.0.10
	===Author / Distributor===		===Author / Distributor===
	Please see https://github.com/ncbi/sra-tools		Please see https://github.com/ncbi/sra-tools

Jordan: /* Downloading SRA Data */

2024-06-25T18:53:09Z

Downloading SRA Data

← Older revision		Revision as of 14:53, 25 June 2024
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	Then press "s" or navigate to the save button and press enter to save. Then press "x" or navigate to the exit button and press enter to exit. Now you can start the data download by running the command prefetch followed by the run number. For example the following downloads the dataset SRR390728.		Then press "s" or navigate to the save button and press enter to save. Then press "x" or navigate to the exit button and press enter to exit. Now you can start the data download by running the command prefetch followed by the run number. For example the following downloads the dataset SRR390728.
	<pre>~~fetch~~ SRR390728</pre>		<pre>prefetch SRR390728</pre>

	For more information about the prefetch command refer to the [https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=prefetch documentation]		For more information about the prefetch command refer to the [https://trace.ncbi.nlm.nih.gov/Traces/sra/sra.cgi?view=toolkit_doc&f=prefetch documentation]


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

Jordan: Clarified a couple of points regarding file locations.

2024-05-28T14:40:21Z

Clarified a couple of points regarding file locations.

← Older revision		Revision as of 10:40, 28 May 2024
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	<pre>vdb-config --interactive</pre>		<pre>vdb-config --interactive</pre>

	This will open a screen where you operate the buttons by pressing the letter highlighted in red, or by pressing the tab-key until the wanted button is reached and then pressing the space- or the enter-key. Make sure there is an X by the "'''Enable Remote Access'''" option on the MAIN tab, and X by the "'''enable local file-caching'''" option in the CACHE tab. Then set the "location of user-repository" to the empty folder you created. In the following image the data will be downloaded to /scratch/~~keeko~~/prefetchData. These settings are stored in a file called '''user-settings.mkfg''' in a hidden directory called .ncbi in the top level of your home directory.		This will open a screen where you operate the buttons by pressing the letter highlighted in red, or by pressing the tab-key until the wanted button is reached and then pressing the space- or the enter-key. Make sure there is an X by the "'''Enable Remote Access'''" option on the MAIN tab, and X by the "'''enable local file-caching'''" option in the CACHE tab. Then set the "location of user-repository" to the empty folder you created. In the following image the data will be downloaded to /scratch/keekov/prefetchData. These settings are stored in a file called '''user-settings.mkfg''' in a hidden directory called .ncbi in the top level of your home directory.
	[[File:Sratools.png\|thumb]]		[[File:Sratools.png\|thumb]]

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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml SRA-Toolkit/3.0.3-gompi-2022a<br>		ml SRA-Toolkit/3.0.3-gompi-2022a<br>
	fastq-dump -X 5 -Z /scratch/keekov/SRR390728.sra<br>		fastq-dump -X 5 -Z /scratch/keekov/SRR390728.sra #You should use the directory you selected in the vdb-config step above<br>
	</div>		</div>

Jordan: /* Running Program */

2024-05-28T13:58:18Z

Running Program

← Older revision		Revision as of 09:58, 28 May 2024
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	cd $SLURM_SUBMIT_DIR<br>		cd $SLURM_SUBMIT_DIR<br>
	ml SRA-Toolkit/2.11.1-~~centos_linux64~~<br>		ml SRA-Toolkit/3.0.3-gompi-2022a<br>
	fastq-dump -X 5 -Z /scratch/keekov/SRR390728.sra<br>		fastq-dump -X 5 -Z /scratch/keekov/SRR390728.sra<br>
	</div>		</div>

Jordan: Updated the listed version from 3.0.1 to 3.0.3

2024-05-28T13:57:31Z

Updated the listed version from 3.0.1 to 3.0.3

← Older revision		Revision as of 09:57, 28 May 2024
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	=== Downloading SRA Data ===		=== Downloading SRA Data ===

	The last version of this application is at /apps/eb/SRA-Toolkit/3.0.1-~~centos_linux64~~		The last version of this application is at /apps/eb/SRA-Toolkit/3.0.3-gompi-2022a

	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 SRA-Toolkit/3.0.1-~~centos_linux64~~		ml SRA-Toolkit/3.0.3-gompi-2022a
	</pre>		</pre>

Chelsea: /* Version */

2024-05-14T13:36:03Z

Version

← Older revision		Revision as of 09:36, 14 May 2024
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	Sapelo2		Sapelo2
	=== Version ===		=== Version ===
	2.9.6-1,2.10.~~8,2.11.1~~		3.0.1, 3.0.3
	===Author / Distributor===		===Author / Distributor===
	Please see https://github.com/ncbi/sra-tools		Please see https://github.com/ncbi/sra-tools
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	=== Downloading SRA Data ===		=== Downloading SRA Data ===

	The last version of this application is at /apps/eb/SRA-Toolkit/2.11.1-centos_linux64/		The last version of this application is at /apps/eb/SRA-Toolkit/3.0.1-centos_linux64

	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 SRA-Toolkit/2.11.1-centos_linux64		ml SRA-Toolkit/3.0.1-centos_linux64
	</pre>		</pre>