Provided by: coop-computing-tools_7.0.22-1ubuntu1_amd64
sand_align_master - align candidate sequences in parallel
sand_align_master [options] sand_align_kernel candidates.cand sequences.cfa overlaps.ovl
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.
-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.
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 batch system.
The Cooperative Computing Tools are Copyright (C) 2003-2004 Douglas Thain and Copyright (C) 2005-2015 The University of Notre Dame. This software is distributed under the GNU General Public License. See the file COPYING for details.
· 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)