sand_filter_master(1)

💖 sand_filter_master — bestie's guide to filtering sequences in parallel 💖

okay so this is sand_filter_master(1), from the Cooperative Computing Tools manual, and it's literally the glow-up step of the SAND assembler. let's get into it 🫶

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✨ NAME ✨

sand_filter_master — filter sequences for alignment in parallel. that's the whole vibe. 💅

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🌸 SYNOPSIS 🌸

sand_filter_master [options] sequences.cfa candidates.cand

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🦋 DESCRIPTION 🦋

so. sand_filter_master is the first step in the SAND assembler, no cap. it reads in a whole body of sequences and then uses a linear-time algorithm to produce a list of candidate sequences that sand_align_master(1) is gonna align in detail later. it's giving ✨preprocessing era✨.

this program uses the Work Queue system to distribute tasks among processors. so after you start sand_filter_master, you must start a bunch 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 filtering is performed by sand_filter_kernel(1) on each machine. teamwork makes the dream work fr fr 🧚

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👑 OPTIONS 👑

• -p <port> — port number for the 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

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💀 EXIT STATUS 💀

on success, returns zero. on failure, returns non-zero. that's it, that's the whole thing. 🙈

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🌈 EXAMPLES 🌈

if you begin with a FASTA formatted file of reads, use sand_compress_reads(1) to produce a compressed FASTA (cfa) file. to run filtering sequentially, start a single work_queue_worker(1) 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) 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. imagine the main character energy 🔥

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🎀 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.

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⭐ 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)

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and that's the tea, bestie 🍓 this whole page is CCTools 8.0.0 DEVELOPMENT era, and yeah the header said sand_filter_master(1) at the top and the footer said the same thing at the bottom, which is honestly so consistent of it 💜 go forth and filter, you absolute icon 💖✨