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_sub‐
       mit_workers(1) or uge_submit_workers(1) to start hundreds of workers in your local batch system.

COPYRIGHT

       The  Cooperative  Computing  Tools are Copyright (C) 2022 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_com‐
           press_reads(1)  sand_uncompress_reads(1)  work_queue_worker(1)

CCTools 7.14.5 FINAL                                                                        sand_align_master(1)