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

.SH NAME
.LP
\fBsand_filter_master\fP - filter sequences for alignment in parallel

.SH SYNOPSIS
.LP
\FC\fBsand_filter_master [options] sequences.cfa candidates.cand\fP\FT

.SH DESCRIPTION
.LP

\fBsand_filter_master\fP is the first step in the SAND assembler.
It reads in a body of sequences, and uses a linear-time algorithm
to produce a list of candidate sequences to be aligned in detail
by \fBsand_align_master(1)\fP.
.PP
This program uses the Work Queue system to distributed tasks
among processors.  After starting \fBsand_filter_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 filtering
is performed by \fBsand_filter_kernel(1)\fP on each machine.

.SH OPTIONS
.LP

.LP
.TP
.BI \ -p \ <port>
.
Port number for queue master to listen on. (default: 9123)
.TP
.BI \ -s \ <size>
.
Number of sequences in each filtering task. (default: 1000)
.TP
.BI \ -r \ <file>
.
A meryl file of repeat mers to be filtered out.
.TP
.BI \ -R \ <n>
.
Automatically retry failed jobs up to n times. (default: 100)
.TP
.BI \ -k \ <size>
.
The k-mer size to use in candidate selection (default is 22).
.TP
.BI \ -w \ <size>
.
The minimizer window size. (default is 22).
.TP
.B \ -u
.
If set, do not unlink temporary binary output files.
.TP
.BI \ -c \ <file>
.
Checkpoint filename; will be created if necessary.
.TP
.BI \ -d \ <flag>
.
Enable debugging for this subsystem.  (Try \fB-d all\fP to start.)
.TP
.BI \ -F \ <number>
.
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 this help screen


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

.SH EXAMPLES
.LP

If you begin with a FASTA formatted file of reads,
used \fBsand_compress_reads(1)\fP to produce a
compressed FASTA (cfa) file.  To run filtering sequentially,
start a single \fBwork_queue_worker(1)\fP process in the background.
Then, invoke \fBsand_filter_master\fP.

.fam C
.nf
.nh
.IP "" 8
% sand_compress_reads mydata.fasta mydata.cfa
% work_queue_worker localhost 9123 &
% sand_filter_master mydata.cfa mydata.cand
.fi
.hy
.fam
.P

To speed up the process, run more \fBwork_queue_worker(1)\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