MSblender TACC

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

• Copy your FASTA file to 'myProject/DB' directory.

$ python ~/git/MS-toolbox/bin/fasta-reverse.py XENLA_prot_v4.fasta 
$ mv XENLA_prot_v4.fasta.target XENLA_prot_v4_combined.fasta
$ cat XENLA_prot_v4.fasta.reverse >> XENLA_prot_v4_combined.fasta
$ head -n 1 XENLA_prot_v4.fasta
>10a1.1|XB-GENE-6077477|AAH55957|33416620
$ head -n 1 XENLA_prot_v4.fasta.reverse 
>rv_nadkd1|XB-GENE-991229|AAI46629|148921623 

DB setup for X!tandem

 $~/src.MS/local/bin/fasta_pro.exe (my combined fasta file) 

It makes an index file with '.pro' suffix after your FASTA filename.

 $~/src.MS/local/bin/fasta_pro.exe XENLA_prot_v4_combined.fasta 
fasta_pro file conversion utility, v. 2006.09.15
 input path = XENLA_prot_v4_combined.fasta
output path = XENLA_prot_v4_combined.fasta.pro
db type = plain

DB setup for Crux

 $~/src.MS/local/bin/crux create-index --enzyme trypsin --missed-cleavages 2 --peptide-list T --decoys none (my combined fasta file) (my index name)

• If you want to use Crux function separately (or other embeded post-processing tool, i.e. percolator or q-ranker), you should use FASTA file with target sequence only, with certain decoy option (default option is protein-shuffle, but peptide-shuffle would be better.)
• 'peptide-list' is optional.
• Trypsin digestion pattern in Crux is '[KR]|{P}', so it does not cut K/R if the next AA is P. If you want to ignore this 'Proline' constraint, you can use '--custom-enzyme "[KR]|[X]"' instead of '--enzyme trypsin'.

DB setup for InsPecT

 $~/src.MS/inspect/current/PrepDB.py FASTA (my fasta file)

• It makes an index file with '.trie' suffix after your FASTA filename.

DB setup for MSGFDB

$ java -cp ~/src.MS/MSGFDB/current/MSGFDB.jar msdbsearch.BuildSA -d (my FASTA file) -tda 0

• It generates .canno, .cnlcp, .csarr & .cseq files.
• If you want to use native MS-GFDB function, use -tda 2 (generate target & combined database) with target-only FASTA file.

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

Prepare search

$ 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.

$ python ~/git/MS-toolbox/bin/prepare-inspect.py 
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.

$ 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.

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 Lonestar user guide and Longhorn user guide for detail.
• Don't forget to put your email address at -M.
• Put short job name to check the status easily.

#!/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)