---
name: "sand_filter_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_filter_master"
---

# sand\_filter\_master(1)

filter sequences for alignment in parallel

## NAME

**sand\_filter\_master** - filter sequences for alignment in parallel

## SYNOPSIS

FCsand\_filter\_master \[options\] sequences.cfa candidates.candFT

## 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)](/sand_align_master/1.md)**.

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)](/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 filtering is performed by **[sand\_filter\_kernel(1)](/sand_filter_kernel/1.md)** 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)](/sand_compress_reads/1.md)** to produce a compressed FASTA (cfa) file.  To run filtering sequentially, start a single **[work\_queue\_worker(1)](/work_queue_worker/1.md)** 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)](/work_queue_worker/1.md)** 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)**