HpcGridRunner-Sapelo2 - Revision history

Chelsea: /* HpcGridRunner submission script parameters: */

2026-04-29T18:43:58Z

HpcGridRunner submission script parameters:

← Older revision		Revision as of 14:43, 29 April 2026
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	* --out_dir: The blast results for the each of the split group will be in a separate file under the specified output directory. The file name will end in fa.OUT.		* --out_dir: The blast results for the each of the split group will be in a separate file under the specified output directory. The file name will end in fa.OUT.

	'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.		'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.

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

Chelsea: /* HpcGridRunner submission script parameters: */

2026-04-29T18:43:45Z

HpcGridRunner submission script parameters:

← Older revision		Revision as of 14:43, 29 April 2026
Line 48:		Line 48:
	* --out_dir: The blast results for the each of the split group will be in a separate file under the specified output directory. The file name will end in fa.OUT.		* --out_dir: The blast results for the each of the split group will be in a separate file under the specified output directory. The file name will end in fa.OUT.

	'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.		'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.

	<pre class="gscript">		<pre class="gscript">
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	find OUTPUT_DIR -name '*.fa.OUT' \| xargs cat > combined_blast_results.out		find OUTPUT_DIR -name '*.fa.OUT' \| xargs cat > combined_blast_results.out
	</pre>		</pre>


	====<u>Configuration file contents:</u>====		====<u>Configuration file contents:</u>====

Chelsea: /* HpcGridRunner submission script parameters: */

2026-04-29T18:36:53Z

HpcGridRunner submission script parameters:

← Older revision		Revision as of 14:36, 29 April 2026
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	===Running a blast job in parallel by splitting the fasta file===		===Running a blast job in parallel by splitting the fasta file===

	====HpcGridRunner submission script parameters:====		====<u>HpcGridRunner submission script parameters:</u>====

	* --grid_conf: The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters below.		* --grid_conf: The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters below.
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	====Configuration file contents:====		====<u>Configuration file contents:</u>====

	* cmd: This is the actual command that will be used to submit the HpcGridRunner command from the submission script specified in "--cmd_template". You will want to request enough resources for a single blastp command here.		* cmd: This is the actual command that will be used to submit the HpcGridRunner command from the submission script specified in "--cmd_template". You will want to request enough resources for a single blastp command here.

Chelsea: /* Running a blast job in parallel by splitting the fasta file: */

2026-04-29T18:36:32Z

Running a blast job in parallel by splitting the fasta file:

← Older revision		Revision as of 14:36, 29 April 2026
Line 37:		Line 37:


	===Running a blast job in parallel by splitting the fasta file:===		===Running a blast job in parallel by splitting the fasta file===

	====HpcGridRunner submission script parameters:====		====HpcGridRunner submission script parameters:====

Chelsea: /* Running a blast job in parallel by splitting the fasta file: */

2026-04-29T18:36:20Z

Running a blast job in parallel by splitting the fasta file:

← Older revision		Revision as of 14:36, 29 April 2026
Line 37:		Line 37:


	=Running a blast job in parallel by splitting the fasta file:=		===Running a blast job in parallel by splitting the fasta file:===

	HpcGridRunner submission script parameters:		====HpcGridRunner submission script parameters:====

	* --grid_conf: The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters below.		* --grid_conf: The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters below.
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	Configuration file contents:		====Configuration file contents:====

	* cmd: This is the actual command that will be used to submit the HpcGridRunner command from the submission script specified in "--cmd_template". You will want to request enough resources for a single blastp command here.		* cmd: This is the actual command that will be used to submit the HpcGridRunner command from the submission script specified in "--cmd_template". You will want to request enough resources for a single blastp command here.

Chelsea: /* Running Program */

2026-04-29T18:35:17Z

Running Program

← Older revision		Revision as of 14:35, 29 April 2026
Line 37:		Line 37:


	Running a blast job in parallel by splitting the fasta file:		=Running a blast job in parallel by splitting the fasta file:=

	HpcGridRunner submission script parameters:		HpcGridRunner submission script parameters:
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	cmds_per_node=1		cmds_per_node=1
	</pre>		</pre>


	== Documentation ==		== Documentation ==

Chelsea: /* Running Program */

2026-04-29T18:34:41Z

Running Program

@@ Line 35: / Line 35: @@
 ml HpcGridRunner/1.0.2-GCCcore-14.2.0
 </pre>
 Running a blast job in parallel by splitting the fasta file:
@@ Line 40: / Line 41: @@
 HpcGridRunner submission script parameters:
-* --grid_conf:   The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters here.
+* --grid_conf:   The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters below.
 * --cmd_template:  The cmd_template can be change to reflect your blast command. Leave the -query parameter set to __QUERY_FILE__ value and hpc_FASTA_Gridrunner will fill it dynamically. You can also change the values for outfmt, evalue, max_target_seqs and db.
 * --seqs_per_bin:
 * --query_fasta: You will need to change the YOUR_QUERY_FASTA.fasta to the name of your fasta file.
@@ Line 60: / Line 62: @@
 hpc_FASTA_GridRunner.pl \
 --grid_conf=$HPCGR_CONF_DIR/sapelo_1c_3g.conf \
---cmd_template "blastp -query __QUERY_FILE__ -db /db/uniprot/latest/uniprot_sprot  -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_threads 1" \
+--cmd_template "blastp -query __QUERY_FILE__ -db /db/uniprot/latest/uniprot_sprot  -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_threads 4" \
 --seqs_per_bin 250 \
 --query_fasta YOUR_QUERY_FASTA.fasta \
@@ Line 72: / Line 74: @@
 find OUTPUT_DIR -name '*.fa.OUT' | xargs cat > combined_blast_results.out
 </pre>
 == Documentation ==

Chelsea: /* Running Program */

2026-04-29T14:51:29Z

Running Program

← Older revision		Revision as of 10:51, 29 April 2026
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	== Running Program ==		== Running Program ==


			For instruction on running HpcGridRunner in conjunction with Trinity, please see [[Trinity-HpcGridRunner\|here]].

	Also refer to [[Running Jobs on Sapelo2]].		Also refer to [[Running Jobs on Sapelo2]].

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	Running a blast job in parallel by splitting the fasta file:		Running a blast job in parallel by splitting the fasta file:
	You ~~will need to~~ change the ~~YOUR_QUERY_FASTA~~.~~fasta~~ to ~~the name of~~ your ~~fasta~~ file. The cmd_template can be change to reflect your blast command. Leave the -query parameter set to __QUERY_FILE__ value and hpc_FASTA_Gridrunner will fill it dynamically.
	You can also change the values for outfmt, evalue, max_target_seqs and db.		HpcGridRunner submission script parameters:
	The ~~grid_conf~~ file specified ~~below~~ will ~~request one CPU core and 3GB of RAM~~.
			* --grid_conf: The grid_conf file specified below will request one CPU core and 3GB of RAM. You can change this by copying the .conf file to your own directory and editing it. More instructions on .conf file parameters here.
			* --cmd_template: The cmd_template can be change to reflect your blast command. Leave the -query parameter set to __QUERY_FILE__ value and hpc_FASTA_Gridrunner will fill it dynamically. You can also change the values for outfmt, evalue, max_target_seqs and db.
			* --seqs_per_bin:
			* --query_fasta: You will need to change the YOUR_QUERY_FASTA.fasta to the name of your fasta file.
			* --out_dir: The blast results for the each of the split group will be in a separate file under the specified output directory. The file name will end in fa.OUT.

	'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.		'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.
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	ml BLAST+/2.13.0-gompi-2022a		ml BLAST+/2.13.0-gompi-2022a

	hpc_FASTA_GridRunner.pl --grid_conf=$HPCGR_CONF_DIR/sapelo_1c_3g.conf --cmd_template "blastp -query __QUERY_FILE__ -db /db/uniprot/latest/uniprot_sprot -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_threads 1" --seqs_per_bin 250 --query_fasta YOUR_QUERY_FASTA.fasta --out_dir blast_result		hpc_FASTA_GridRunner.pl \
			--grid_conf=$HPCGR_CONF_DIR/sapelo_1c_3g.conf \
			--cmd_template "blastp -query __QUERY_FILE__ -db /db/uniprot/latest/uniprot_sprot -max_target_seqs 1 -outfmt 6 -evalue 1e-5 -num_threads 1" \
			--seqs_per_bin 250 \
			--query_fasta YOUR_QUERY_FASTA.fasta \
			--out_dir blast_result

	</pre>		</pre>

	~~The blast results for the each of the split group will be in a separate file under the specified output directory. The file name will end in fa.OUT.~~ To gather the blast output you can generally concatenate all the individual outputs. You can use the following command to find and concatenate all the output files.		To gather the blast output you can generally concatenate all the individual outputs. You can use the following command to find and concatenate all the output files.

	<pre class="gcommand">		<pre class="gcommand">
	find OUTPUT_DIR -name '*.fa.OUT' \| xargs cat > combined_blast_results.out		find OUTPUT_DIR -name '*.fa.OUT' \| xargs cat > combined_blast_results.out
	</pre>		</pre>


	~~For instruction on running HpcGridRunner in conjunction with Trinity, please see [[Trinity-HpcGridRunner\|here]].~~

	== Documentation ==		== Documentation ==

Chelsea: /* Running Program */

2026-04-29T13:49:54Z

Running Program

← Older revision		Revision as of 09:49, 29 April 2026
Line 25:		Line 25:
	Also refer to [[Running Jobs on Sapelo2]].		Also refer to [[Running Jobs on Sapelo2]].

	*~~Version~~ 1.0.2~~, installed in /apps/eb/~~HpcGridRunner/1.0.2		*HpcGridRunner/1.0.2-GCCcore-12.3.0
			*HpcGridRunner/1.0.2-GCCcore-14.2.0

	To use ~~this version of~~ HpcGridRunner, please first load the module with		To use HpcGridRunner, please first load the module with
	<pre class="gscript">		<pre class="gscript">
	ml HpcGridRunner/1.0.2		ml HpcGridRunner/1.0.2-GCCcore-14.2.0
	</pre>		</pre>

Chelsea: /* Running Program */

2026-04-23T16:29:07Z

Running Program

← Older revision		Revision as of 12:29, 23 April 2026
Line 37:		Line 37:
	The grid_conf file specified below will request one CPU core and 3GB of RAM.		The grid_conf file specified below will request one CPU core and 3GB of RAM.

	Please request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.		'''Please''' request the same number of threads with "-num_threads" as cpu cores with "--cpus-per-task" in the .conf file (not in the submission script Slurm headers) specified with "--grid_conf". You only need to request a single cpu core in the actual submission script Slurm headers.

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