NAME

       sand_filter_master - filter sequences for alignment in parallel

SYNOPSIS

       sand_filter_master [options] sequences.cfa candidates.cand

DESCRIPTION

       sand_filter_master  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
       sand_align_master(1).

       This  program  uses  the  Work  Queue  system  to  distributed  tasks  among  processors.  After starting
       sand_filter_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 filtering is
       performed by sand_filter_kernel(1) on each machine.

OPTIONS

        -p <port>
              Port number for queue master to listen on. (default: 9123)

        -s <size>
              Number of sequences in each filtering task. (default: 1000)

        -r <file>
              A meryl file of repeat mers to be filtered out.

        -R <n>
              Automatically retry failed jobs up to n times. (default: 100)

        -k <size>
              The k-mer size to use in candidate selection (default is 22).

        -w <size>
              The minimizer window size. (default is 22).

        -u    If set, do not unlink temporary binary output files.

        -c <file>
              Checkpoint filename; will be created if necessary.

        -d <flag>
              Enable debugging for this subsystem.  (Try -d all to start.)

        -F <number>
              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 this help screen

EXIT STATUS

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

EXAMPLES

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

               % sand_compress_reads mydata.fasta mydata.cfa
               % work_queue_worker localhost 9123 &
               % sand_filter_master mydata.cfa mydata.cand

       To  speed  up  the  process,  run  more  work_queue_worker(1)  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) 2005-2015 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)