Difference between revisions of "HPC:bowtie"

Latest revision as of 15:23, 13 August 2019

bowtie & bowtie2

bowtie version 0.12.7 is installed on all HPC nodes.

bowtie2 versions 2.1.0 and 2.3.4.1 are installed on all HPC nodes.

bowtie v0.12.7 is the system default :

$ which bowtie
/usr/bin/bowtie

$ bowtie --version
bowtie version 0.12.7
64-bit
Built on x86-13.phx2.fedoraproject.org
Tue Jun 28 13:08:38 UTC 2011
Compiler: gcc version 4.4.5 20110214 (Red Hat 4.4.5-6) (GCC) 
Options: -O3  -O2 -g -pipe -Wall -Wp,-D_FORTIFY_SOURCE=2 -fexceptions -fstack-protector --param=ssp-buffer-size=4 -m64 -mtune=generic  
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

While bowtie2 versions 2.1.0 and 2.3.4.1 can be used after loading the correct module in an interactive/non-interactive node:

[asrini@consign ~]$ bsub -Is bash 
[asrini@node061 ~]$ module load bowtie2-2.1.0 
[asrini@node061 ~]$ which bowtie2
/opt/software/bowtie2/bowtie2-2.1.0/bowtie2
[asrini@node061 ~]$ bowtie2 --version
/opt/software/bowtie2/bowtie2-2.1.0/bowtie2-align version 2.1.0
64-bit
Built on node061.hpc.local
Tue Aug 20 06:46:02 EDT 2013
Compiler: gcc version 4.4.7 20120313 (Red Hat 4.4.7-3) (GCC) 
Options: -O3 -m64 -msse2 -funroll-loops -g3 
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

Note the difference in module usage:

[asrini@consign ~]$ bsub -Is bash 

[asrini@node062 ~]$ module load bowtie2/2.3.4.1 

[asrini@node062 ~]$ which bowtie2
/opt/software/bowtie2/2.3.4.1/bin/bowtie2

[asrini@node062 ~]$ bowtie2 --version
/opt/software/bowtie2/2.3.4.1/bin/bowtie2-align-s version 2.3.4.1
64-bit
Built on node001.hpc.local
Wed Mar 14 12:47:02 EDT 2018
Compiler: gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC) 
Options: -O3 -m64 -msse2 -funroll-loops -g3 -std=c++98 -DPOPCNT_CAPABILITY
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}

@@ Line 1: / Line 1: @@
-=== bowtie ===
+=== bowtie & bowtie2 ===
-bowtie version 0.12.7 and bowtie2-2.1.0 are installed on all HPC nodes.
+bowtie version 0.12.7 is installed on all HPC nodes.
+bowtie2 versions 2.1.0 and 2.3.4.1 are installed on all HPC nodes.
 bowtie v0.12.7 is the system default :
@@ Line 17: / Line 19: @@
 </pre>
-While bowtie2-2.1.0 needs can be used via a module in an interactive/non-interactive node:
+While bowtie2 versions 2.1.0 and 2.3.4.1 can be used after loading the correct module in an interactive/non-interactive node:
 <pre>
@@ Line 32: / Line 34: @@
 Options: -O3 -m64 -msse2 -funroll-loops -g3
 Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
+</pre>
+'''Note the difference in module usage:'''
+<pre>
+[asrini@consign ~]$ bsub -Is bash
+[asrini@node062 ~]$ module load bowtie2/2.3.4.1
+[asrini@node062 ~]$ which bowtie2
+/opt/software/bowtie2/2.3.4.1/bin/bowtie2
+[asrini@node062 ~]$ bowtie2 --version
+/opt/software/bowtie2/2.3.4.1/bin/bowtie2-align-s version 2.3.4.1
+-bit
+Built on node001.hpc.local
+Wed Mar 14 12:47:02 EDT 2018
+Compiler: gcc version 4.4.7 20120313 (Red Hat 4.4.7-11) (GCC)
+Options: -O3 -m64 -msse2 -funroll-loops -g3 -std=c++98 -DPOPCNT_CAPABILITY
+Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8}
 </pre>
 === Other Pages ===
+----
+<div class="mw-collapsible mw-collapsed">
+*[[HPC:FAQ|HPC FAQ ]]
+*[[HPC:Login|Connecting to the PMACS cluster]]
+*[[HPC:User_Guide|User Guide]]
 *[[HPC:Software|Available Software]]
-*[[HPC:User_Guide|User Guide]]
+*[[HPC:Archive System|PMACS Archive System]]
-*[[HPC:Main_Page|HPC Main Page]]
+</div>
-*[[HPC:Login|Connecting to the PMACS cluster]]