Difference between revisions of "HPC:bowtie"
From HPC wiki
| Line 1: | Line 1: | ||
| − | === bowtie === | + | === bowtie * bowtie2 === |
| − | bowtie version 0.12.7 | + | 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 : | bowtie v0.12.7 is the system default : | ||
| Line 17: | Line 19: | ||
</pre> | </pre> | ||
| − | While bowtie2 | + | 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> | <pre> | ||
| Line 32: | Line 34: | ||
Options: -O3 -m64 -msse2 -funroll-loops -g3 | Options: -O3 -m64 -msse2 -funroll-loops -g3 | ||
Sizeof {int, long, long long, void*, size_t, off_t}: {4, 8, 8, 8, 8, 8} | 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 | ||
| + | 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} | ||
| + | |||
</pre> | </pre> | ||
Revision as of 17:18, 14 March 2018
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}
