sand_align_master - align candidate sequences in parallel
sand_align_master [options] sand_align_kernel candidates.cand sequences.cfa
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
- -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.
- Show version string.
- Show help text.
On success, returns zero. On failure, returns non-zero.
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
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.