Applications/Bowtie2 - Revision history

Pysdlb: /* Batch Job */

2022-11-16T16:46:00Z

‎Batch Job

2022-11-16T16:45:33Z

‎Batch Job

2022-11-16T16:44:42Z

‎Batch Job

2022-11-16T16:44:21Z

‎Batch Job

2022-11-16T16:43:38Z

‎Batch Job

2022-11-16T16:43:06Z

‎Batch Job

2022-11-16T16:42:30Z

2022-11-16T10:38:36Z

‎Navigation

2019-05-24T11:15:14Z

2018-06-07T14:07:41Z

@@ Line 51: / Line 51: @@
 #SBATCH -n 4
 #SBATCH --mem=8G
-#SBATCH -o output.%j.%N.txt
+#SBATCH -o output.%j.%N.out
-#SBATCH -e error.%j.%N.txt
+#SBATCH -e error.%j.%N.err
 # Unload all modules, then load the bowtie2 module:

@@ Line 44: / Line 44: @@
 ===Batch Job===
 <pre>
 #!/bin/bash

@@ Line 46: / Line 46: @@
 <pre>
 #!/bin/bash
-#SBATCH -J=test_bowtie2
+#SBATCH -J test_bowtie2
 #SBATCH --time=04:00:00
 #SBATCH -n 4

@@ Line 47: / Line 47: @@
 #!/bin/bash
 #SBATCH -J=test_bowtie2
-#SBATCH -time=04:00:00
+#SBATCH --time=04:00:00
 #SBATCH -n 4
 #SBATCH --mem=8G

@@ Line 46: / Line 46: @@
 <pre>
 #!/bin/bash
-#SBATCH --job-name=test_bowtie2
+#SBATCH -J=test_bowtie2
-#SBATCH --time=04:00:00
+#SBATCH -time=04:00:00
 #SBATCH -n 4
 #SBATCH --mem=8G

@@ Line 55: / Line 55: @@
 # Unload all modules, then load the bowtie2 module:
 module purge
-module load apps/bowtie/2.3.4.1
+module load bowtie2/gcc/2.2.9

← Older revision		Revision as of 16:42, 16 November 2022
Line 40:		Line 40:

	[username@login01 ~]$ module add bowtie2/gcc/2.2.9		[username@login01 ~]$ module add bowtie2/gcc/2.2.9
		+
		+	</pre>
		+
		+	===Batch Job===
		+	<pre>
		+	#!/bin/bash
		+	#SBATCH --job-name=test_bowtie2
		+	#SBATCH --time=04:00:00
		+	#SBATCH -n 4
		+	#SBATCH --mem=8G
		+	#SBATCH -o output.%j.%N.txt
		+	#SBATCH -e error.%j.%N.txt
		+
		+	# Unload all modules, then load the bowtie2 module:
		+	module purge
		+	module load apps/bowtie/2.3.4.1
		+
		+
		+	#always run in WORK when running batch jobs
		+	mkdir $WORK/bowtie
		+	cp $HOME/featureCounts_ex/*fa $WORK/bowtie
		+	cp $HOME/featureCounts_ex/fa $WORK/bowtie
		+	cp $HOME/trim_ex/SRR6202537_1.fastq $WORK/bowtie
		+	cp $HOME/trim_ex/SRR6202537_2.fastq $WORK/bowtie
		+	cd $WORK/bowtie
		+
		+
		+	#computation steps
		+
		+	bowtie2-build --threads 4 hg38.fa hg38
		+	bowtie2 -p 4 -x hg38 -1 SRR6202537_1.fastq -2 SRR6202537_2.fastq -S SRR6202537.sam --no-unal
		+
		+
		+	cp *.sam $HOME/bowtie_ex

	</pre>		</pre>

← Older revision		Revision as of 10:38, 16 November 2022
Line 48:		Line 48:
	* [http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml]		* [http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml]

−	~~==Navigation==~~	+	{{Modulepagenav}}
−
−	* [[Main_Page\|Home]]
−	~~* [[Applications\|Application support]] *~~
−	* [[General\|General]]
−	* [[Programming\|Programming support]]

@@ Line 48: / Line 48: @@
 * [http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml http://bowtie-bio.sourceforge.net/bowtie2/manual.shtml]
 * [[Main_Page|Home]]
-* [[Applications|Application support]]
+* [[Applications|Application support]] *
 * [[General|General]]
 * [[Programming|Programming support]]

@@ Line 39: / Line 39: @@
 <pre style="background-color: black; color: white; border: 2px solid black; font-family: monospace, sans-serif;">
-[username@login01 ~]$ module load bowtie2/gcc/2.2.9
+[username@login01 ~]$ module add bowtie2/gcc/2.2.9
 </pre>