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) 2005-2015 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)