CD-HIT-2D-PARA.PL(1)

✨ cd-hit-2d-para.pl — the bestie era of clustering ✨

okay so picture this: you've got a BIG clustering job, it's giving main character energy, and it's just... too much for one little computer?? bestie, same. that's literally what cd-hit-2d-para.pl is for. it chops your giant job into lil pieces and yeets them at remote computers over the network so they all run at once, in parallel. 🦋

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🌸 NAME 🌸

cd-hit-2d-para.pl — divide a big clustering job into pieces so you can run cd-hit-2d or cd-hit-est-2d jobs 💅

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🎀 SYNOPSIS 🎀

cd-hit-2d-para.pl options

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💖 DESCRIPTION 💖

This script divides a big clustering job into pieces and submits the jobs to remote computers over a network so everything runs parallel. no cap. once all the jobs finish, the script merges the clustering results back together, as if you had just run a single cd-hit-2d or cd-hit-est-2d the whole time. it's giving effortless. ✨

You can also use it to divide big jobs on a single computer, if your computer does not have enough RAM — that's what the -L option is for. lowkey a lifesaver. 🫶

🌈 Requirements 🌈

1. When you run this script over a network, the directory where you run the scripts and the input files must be available on all the remote hosts with identical path. like, the same path everywhere. fr fr.
2. If you choose "ssh" to submit jobs, you have to have passwordless ssh to any remote host — see the ssh manual to know how to set up passwordless ssh. 🔑
3. I suggest to use a queuing system instead of ssh. I currently support PBS and SGE. 👑
4. cd-hit-2d, cd-hit-est-2d, cd-hit-div and cd-hit-div.pl must be in the same directory where this script is in. they're a package deal, iykyk. 💀

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💅 Options 💅

• -i — input filename for 1st db in fasta format, required 🍓
• -i2 — input filename for 2nd db in fasta format, required 🍓
• -o — output filename, required 🍓
• --P — program, "cd-hit-2d" or "cd-hit-est-2d", default "cd-hit-2d" ✨
• --B — filename of list of hosts, required unless -Q or -L option is supplied
• --L — number of cpus on local computer, default 0 when you are not running it over a cluster. you can use this option to divide a big clustering job into small pieces. I suggest you just use "--L 1" unless you have enough RAM for each cpu. 😭
• --S — Number of segments to split 1st db into, default 2
• --S2 — Number of segments to split 2nd db into, default 8
• --Q — number of jobs to submit to queue queuing system, default 0. by default, the program uses ssh mode to submit remote jobs.
• --T — type of queuing system, "PBS" and "SGE" are supported, default PBS
• --R — restart file, used after a crash of run. 🩹 (we've all been there)
• -h — print this help 🙈

More cd-hit-2d/cd-hit-est-2d options can be speicified in command line. 🌟

Questions, bugs, contact Weizhong Li at liwz@sdsc.edu 📧

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okay that's the whole vibe check 💜 this was cd-hit-2d-para.pl, version 4.8.1, from August 2021 — go forth and cluster, bestie, you've got this 👑🌸