.TH "sand_align_master" 1 "" "CCTools 8.0.0 DEVELOPMENT" "Cooperative Computing Tools"

.SH NAME
.LP
\fBsand_align_master\fP - align candidate sequences in parallel

.SH SYNOPSIS
.LP
\FC\fBsand_align_master [options] sand_align_kernel candidates.cand sequences.cfa overlaps.ovl\fP\FT

.SH DESCRIPTION
.LP

\fBsand_align_master\fP 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 \fBsand_filter_master(1)\fP.
It then performs all of the comparisons and produces a list
of overlaps (in OVL format) that exceed a quality threshhold.
.PP
This program uses the Work Queue system to distributed tasks
among processors.  After starting \fBsand_align_master\fP,
you must start a number of \fBwork_queue_worker(1)\fP processes
on remote machines.  The workers will then connect back to the
master process and begin executing tasks.  The actual alignments
are performed by \fBsand_align_kernel(1)\fP on each machine.

.SH OPTIONS
.LP

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


.SH EXIT STATUS
.LP
On success, returns zero.  On failure, returns non-zero.

.SH EXAMPLES
.LP

Suppose that you begin with a compressed FASTA file (\FCmydata.cfa\FT)
and a list of candidate reads (\FCmydata.cand\FT) generated by \fBsand_filter_master(1)\fP.
First, start a single \fBwork_queue_worker(1)\fP process in the background.
Then, invoke \fBsand_align_master()\fP as follows:

.fam C
.nf
.nh
.IP "" 8
% work_queue_worker localhost 9123 &
% sand_align_master sand_align_kernel mydata.cand mydata.cfa mydata.ovl
.fi
.hy
.fam
.P

To speed up the process, run more \fBwork_queue_worker()\fP processes
on other machines, or use \fBcondor_submit_workers(1)\fP or \fBsge_submit_workers(1)\fP to start hundreds of workers in your local batch system.

.SH COPYRIGHT
.LP

The Cooperative Computing Tools are Copyright (C) 2005-2019 The University of Notre Dame.  This software is distributed under the GNU General Public License.  See the file COPYING for details.

.SH SEE ALSO
.LP


.IP \(bu 4
\fBCooperative Computing Tools Documentation\fP
.IP \(bu 4
\fBSAND User Manual\fP
.IP \(bu 4
\fBsand_filter_master(1)\fP  \fBsand_filter_kernel(1)\fP  \fBsand_align_master(1)\fP  \fBsand_align_kernel(1)\fP  \fBsand_compress_reads(1)\fP  \fBsand_uncompress_reads(1)\fP  \fBwork_queue_worker(1)\fP