sand_align_master(1)

💖 sand_align_master(1) 💖

okay bestie, welcome to the Cooperative Computing Tools manual, and specifically to the glow-up era of sand_align_master ✨

---

🌸 NAME 🌸

sand_align_master — align candidate sequences in parallel 🧬✨

---

🎀 SYNOPSIS 🎀

sand_align_master [options] sand_align_kernel candidates.cand
sequences.cfa overlaps.ovl

---

🦋 DESCRIPTION 🦋

so sand_align_master is literally the second step in the SAND assembler, and it's giving main character energy fr fr 💅

It reads in a list of sequences and a list of candidate pairs to consider — and those candidate pairs were made by sand_filter_master(1), so shoutout to the previous step 🫶 Then it goes and performs all of the comparisons and produces a list of overlaps (in OVL format) that exceed a quality threshhold. no cap. 🔥

This program uses the Work Queue system to distribute tasks among processors. So here's the vibe: after you start sand_align_master, you must start a bunch of work_queue_worker(1) processes on remote machines. Those workers then connect back to the master process and begin executing tasks. The actual alignments are performed by sand_align_kernel(1) on each machine. it's a whole collaborative moment, obsessed 😭💖

---

✨ 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. that's the whole vibe check 💀

---

⭐ 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_submit_workers(1) or sge_submit_workers(1) to start hundreds of workers in your local batch system. hundreds. like a whole army of workers, iconic 👑🔥

---

💜 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)

---

and that's the page bestie!! this whole thing lives in the <strong>CCTools 8.0.0 DEVELOPMENT</strong> era, and yeah it's the sand_align_master(1) manual page, periodt 💅✨ go align some sequences, you got this 🌸