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_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_filter_master(1)