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) 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)