---
name: "sand_align_master"
section: "1"
platform: "linux"
package: "coop-computing-tools"
version: "1:7.14.5-1+b2"
release: "Debian 13 (Trixie)"
platforms: ["linux"]
url: "https://new.carta.tech/sand_align_master"
---

# sand\_align\_master(1)

align candidate sequences in parallel

## NAME

**sand\_align\_master** - align candidate sequences in parallel

## SYNOPSIS

FCsand\_align\_master \[options\] sand\_align\_kernel candidates.cand sequences.cfa overlaps.ovlFT

## DESCRIPTION

**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)](/sand_filter_master/1.md)**. 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)](/work_queue_worker/1.md)** 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)](/sand_align_kernel/1.md)** on each machine.

## 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.

## EXAMPLES

Suppose that you begin with a compressed FASTA file (FCmydata.cfaFT) and a list of candidate reads (FCmydata.candFT) generated by **[sand\_filter\_master(1)](/sand_filter_master/1.md)**. First, start a single **[work\_queue\_worker(1)](/work_queue_worker/1.md)** 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)](/condor_submit_workers/1.md)** or **[uge\_submit\_workers(1)](/uge_submit_workers/1.md)** 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_master/1.md)**  **[sand\_filter\_kernel(1)](/sand_filter_kernel/1.md)**  **[sand\_align\_master(1)](/sand_align_master/1.md)**  **[sand\_align\_kernel(1)](/sand_align_kernel/1.md)**  **[sand\_compress\_reads(1)](/sand_compress_reads/1.md)**  **[sand\_uncompress\_reads(1)](/sand_uncompress_reads/1.md)**  **[work\_queue\_worker(1)](/work_queue_worker/1.md)**