MSblender TACC: Difference between revisions

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<pre> $ module load jdk64
<pre> $ module load jdk64
$ java -Xmx4000M -cp /home1/00992/linusben/git/MSblender/extern/MSGFPlus.jar edu.ucsd.msjava.msdbsearch.BuildSA -d XenopusHybrid_xlJGIv16_xtJGIv83.combined.fa -tda 0  
$ java -Xmx4000M -cp /home1/00992/linusben/git/MSblender/extern/MSGFPlus.jar edu.ucsd.msjava.msdbsearch.BuildSA -d XenopusHybrid_xlJGIv16_xtJGIv83.combined.fa -tda 0</pre>


== Prepare mzXML files ==
== Prepare mzXML files ==
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Copy your mzXML files on this diretory ($SCRATCH/myProject/mzXML).
Copy your mzXML files on this diretory ($SCRATCH/myProject/mzXML).


== Prepare search ==
== Run comet ==
<pre>$ python ~/git/MS-toolbox/bin/prepare-tandemK.py
Create /scratch/00992/linusben/xenopus.prot/TXGP_XENLA_Prot_Kwon201109/tandemK.
Write /scratch/00992/linusben/xenopus.prot/TXGP_XENLA_Prot_Kwon201109/tandemK/tandem-taxonomy.xml.
Write /scratch/00992/linusben/xenopus.prot/TXGP_XENLA_Prot_Kwon201109/tandemK/20110713_XENLA_Egg1_1.tandemK.xml
...


TandemK is ready. Run /scratch/00992/linusben/xenopus.prot/TXGP_XENLA_Prot_Kwon201109/scripts/run-tandemK.sh.</pre>
== Run MSGF+ ==


<pre>$ python ~/git/MS-toolbox/bin/prepare-inspect.py
== Run X!Tandem ==
Create /scratch/00992/linusben/xenopus.prot/TXGP_XENLA_Prot_Kwon201109/inspect.
Write /scratch/00992/linusben/xenopus.prot/TXGP_XENLA_Prot_Kwon201109/inspect/20110713_XENLA_Egg1_1.inspect_in.
Write /scratch/00992/linusben/xenopus.prot/TXGP_XENLA_Prot_Kwon201109/inspect/20110713_XENLA_Egg1_2.inspect_in.
...
 
InsPecT is ready. Run /scratch/00992/linusben/xenopus.prot/TXGP_XENLA_Prot_Kwon201109/scripts/run-inspect.sh.</pre>
 
<pre>$ python ~/git/MS-toolbox/bin/prepare-MSGFDB.py
Create /scratch/00992/linusben/xenopus.prot/TXGP_XENLA_Prot_Kwon201109/MSGFDB.
20110713_XENLA_Egg1_1.mzXML
20110713_XENLA_Egg1_2.mzXML
....
 
MSGFDB is ready. Run /scratch/00992/linusben/xenopus.prot/TXGP_XENLA_Prot_Kwon201109/scripts/run-MSGFDB.sh.</pre>
 
== Run search ==
In a standalone workstation, you can run ./script/run-(search_engine).sh directly to start. But you shouldn't do this in TACC login terminal. Put the following parameters on each run-*.sh script, then submit a job by qsub.
 
* If you use lonestar, replace '4way 8' to '8way to 24'. See [http://www.tacc.utexas.edu/user-services/user-guides/lonestar-user-guide Lonestar user guide] and [http://www.tacc.utexas.edu/user-services/user-guides/longhorn-user-guide Longhorn user guide] for detail.
* Don't forget to put your email address at -M.
* Put short job name to check the status easily.
 
<pre>#!/bin/bash
#$ -V                  # Inherit the submission environment
#$ -cwd                # Start job in submission directory
#$ -j y                # Combine stderr and stdout
#$ -o $JOB_NAME.o$JOB_ID
#$ -pe 4way 8
#$ -q long
#$ -l h_rt=24:00:00    # Run time (hh:mm:ss)
#$ -M (your email)
#$ -m be                # Email at Begin and End of job
#$ -P hpc
set -x
 
#$ -N (job name)
(put the remaining part of run-* script after #!/bin/bash line) </pre>

Revision as of 18:02, 2 March 2015

Before you start

  • To use this setting, your TACC account needs to be allocated to our lab project('A-cm10'). If you don't have an account, create it at https://portal.tacc.utexas.edu/. Then, ask Edward to assign your account as a member of lab project.
  • This document is for 'stampede'.
  • Always work at $SCRATCH directory, not at /corral or your $HOME.

Install MSblender (and comet, MSGFDB, X!Tandem)

$ cd ~
$ mkdir git
$ cd git
$ git clone https://github.com/marcottelab/MSblender.git

Prepare a working space

$ module load python
$ cd $SCRATCH
$ mkdir myProject
$ cd myProject
$ mkdir mzXML
$ mkdir DB

Prepare database

  • You can run this process on any computer. If it takes longer than a minute, it would be better to process it on other than TACC login node (your account may be locked).
$ python $HOME/git/MSblender/pre/fasta-reverse.py my_seq.fa
$ cat my_seq.fa.* > my_seq.combined.fa

DB setup for X!tandem

 $ $HOME/git/MSblender/extern/fasta_pro.exe my_seq.conbind.fa

You may see the message like below: 

$ ~/git/MSblender/extern/fasta_pro.exe my_seq.combined.fa 
fasta_pro file conversion utility, v. 2006.09.15
 input path = my_seq.combined.fa
output path = my_seq.combined.fa.pro
db type = plain

DB setup for comet

You don't need to do anything for this.

DB setup for MSGF+

It uses significant amount of computing resources (i.e. memory), so it may not be suitable to run on login node. 

 $ module load jdk64
$ java -Xmx4000M -cp /home1/00992/linusben/git/MSblender/extern/MSGFPlus.jar edu.ucsd.msjava.msdbsearch.BuildSA -d XenopusHybrid_xlJGIv16_xtJGIv83.combined.fa -tda 0

Prepare mzXML files

Copy your mzXML files on this diretory ($SCRATCH/myProject/mzXML).

Run comet

Run MSGF+

Run X!Tandem

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