sand_align_master(1)

NAME

sand_align_master - align candidate sequences in parallel

SYNOPSIS

sand_align_master [options] sand_align_kernel candidates.cand sequences.cfa overlaps.ovl

DESCRIPTION

sand_align_master is the second step in the SAND assembler. It reads in a list of sequences and a list of candidate pairs to consider, generated by sand_filter_master(1). It then performs all of the comparisons and produces a list of overlaps (in OVL format) that exceed a quality threshhold.

This program uses the Work Queue system to distributed tasks among processors. After starting sand_align_master, you must start a number of work_queue_worker(1) processes on remote machines. The workers will then connect back to the master process and begin executing tasks. The actual alignments are performed by sand_align_kernel(1) on each machine.

OPTIONS

-p <port>
Port number for work queue master to listen on. (default: 9123)
-n <number>
Maximum number of candidates per task. (default is 10000)
-e <args>
Extra arguments to pass to the alignment program.
-d <subsystem>
Enable debugging for this subsystem. (Try -d all to start.)
-F <mult>
Work Queue fast abort multiplier.(default is 10.)
-Z <file>
Select port at random and write it out to this file.
-o <file>
Send debugging to this file.
-v Show version string.
-h Show help text.

EXIT STATUS

On success, returns zero. On failure, returns non-zero.

EXAMPLES

Suppose that you begin with a compressed FASTA file (mydata.cfa) and a list of candidate reads (mydata.cand) generated by sand_filter_master(1). First, start a single work_queue_worker(1) process in the background. Then, invoke sand_align_master() as follows:
% work_queue_worker localhost 9123 &
% sand_align_master sand_align_kernel mydata.cand mydata.cfa mydata.ovl
To speed up the process, run more work_queue_worker() processes on other machines, or use condor_submit_workers(1) or sge_submit_workers(1) to start hundreds of workers in your local batch system.

COPYRIGHT

The Cooperative Computing Tools are Copyright (C) 2003-2004 Douglas Thain and Copyright (C) 2005-2011 The University of Notre Dame. This software is distributed under the GNU General Public License. See the file COPYING for details.

SEE ALSO

  • Cooperative Computing Tools Documentation
  • SAND User Manual
  • sand_filter_master(1)
  • sand_filter_kernel(1)
  • sand_align_master(1)
  • sand_align_kernel(1)
  • sand_compress_reads(1)
  • sand_uncompress_reads(1)
  • work_queue_worker(1)

  • CCTools 4.1.4rc5 released on 04/10/2014