batch-blast-bias

Convenient scripts for batch blast search on NIBB bias

Compatible with updated bias4 (April 1, 2014).

Requrement

• ruby
• rake
• NCBI blast+ (not classical blastall)

Quick Start

1) Download software

Download batch-blast-bias package from https://github.com/shujishigenobu/batch-blast-bias/archive/1.0.tar.gz and then extract it.

Or you can clone the latest version of batch-blast-bias from github using git command.

$ git clone git://github.com/shujishigenobu/batch-blast-bias.git

You can also download example.fasta for practice from https://github.com/shujishigenobu/batch-blast-bias/downloads .

2) Prepare coniguration file, conf.yml

batch-blast-bias requires conf.yml, a configuration file. An example file is included in the package. It would be good idea to create your own conf.yml from conf.yml.example.

$ cp conf.yml.example conf.yml

Edit conf.yml using your favorite editor. An example is as follows:

query: example.fasta
db:    /bio/db/blast/db/swissprot
num_fasta_per_subfile: 100

batch_script_template:     templates/run_blastx.sh.template
batch_script_template_sge: templates/sge.bias.small

3) 4 steps for starting batch jobs

$  rake build_batch_template

edit build_batch_template if needed.

$  rake split_query
$  rake generate_batch_jobs
$  rake sge_submit_jobs

Now your jobs are queued. Monitor your jobs by SGE command like qstat.

4) 3 steps for combine BLAST results

$ rake postchk_sge
$ rake combine_blast_results
$ rake finalize

Tips

Monitor progress

Use scripts/monitor_progress.rb

(example)

$ ruby scripts/monitor_progress.rb

ORF_Dpul_131012.pep_1.fasta     job1    100
ORF_Dpul_131012.pep_2.fasta     job112  100
...
ORF_Dpul_131012.pep_658.fasta	job621	100
ORF_Dpul_131012.pep_659.fasta	job622	60
# 64300 / 65860 (97.63%)

Columns are 1) query name, 2) job ID and 3) number of completed queries.

Find/Rescue failed jobs

Useful scripts:

• scripts/rescue_killed_jobs.rb
• ``scripts/detect_failed_batch_scripts.rb`

License

Copyright 2012 Shuji Shigenobu.

Licensed under the MIT License