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) 2005-2019 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)