CD-HIT-PARA.PL(1)

📦
version 4.8.1 · 2 versions
, in debian bookworm, debian trixie, ubuntu jammy, ubuntu noble

💖 CD-HIT-PARA.PL 💖

okay bestie, so this is the manual for cd-hit-para.pl — it's a lil script that takes one BIG clustering job and slices it into pieces so you can run cd-hit or cd-hit-est jobs all over the place. yes queen, parallelism. 👑

✨ NAME ✨

cd-hit-para.pl — divide a big clustering job into pieces to run cd-hit or cd-hit-est jobs 🧚

🌸 SYNOPSIS 🌸

cd-hit-para.pl options

🦋 DESCRIPTION 🦋

so basically this script takes a big clustering job, divides it into pieces, and submits those pieces to remote computers over a network to make the whole thing parallel. it's giving divide and conquer, fr fr. after all the jobs finish, the script merges the clustering results back together as if you just ran a single cd-hit or cd-hit-est. iconic behavior, no cap. 💅

you can also use it to divide big jobs on a single computer if your computer does not have enough RAM (with the -L option). lowkey a lifesaver when your RAM is fighting for its life. 😭

🎀 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. same path everywhere, bestie, no exceptions. 💖
  2. if you choose "ssh" to submit jobs, you have to have passwordless ssh to any remote host, see ssh manual to know how to set up passwordless ssh. 🫶
  3. I suggest to use queuing system instead of ssh, I currently support PBS and SGE. slay. ✨
  4. cd-hit cd-hit-2d cd-hit-est cd-hit-est-2d cd-hit-div cd-hit-div.pl must be in same directory where this script is in. they're a package deal, they come as a set. 👑

👑 Options 👑

  • -i — input filename in fasta format, required. like you literally cannot skip this one. 🌸
  • -o — output filename, required. also mandatory, bestie. 💜
  • --P — program, "cd-hit" or "cd-hit-est", default "cd-hit". pick your fighter. 🔥
  • --B — filename of list of hosts, required unless -Q or -L option is supplied. give it the host list or give it -Q/-L, one or the other. ⭐
  • --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 jobs into small pieces, I suggest you just use "--L 1" unless you have enough RAM for each cpu. one cpu at a time unless your RAM is truly thriving. 💀
  • --S — Number of segments to split input DB into, default 64. sixty-four lil pieces, cute. 🎀
  • --Q — number of jobs to submit to queue queuing system, default 0. by default, the program use ssh mode to submit remote jobs. 🌈
  • --T — type of queuing system, "PBS", "SGE" are supported, default PBS. 🦋
  • --R — restart file, used after a crash of run. for when things went 💀 and you need to pick up where you left off. 🙈
  • -h — print this help. the classic. 💖

More cd-hit/cd-hit-est options can be speicified in command line. yes you read that right, extra options just vibe along for the ride. 🧚

Questions, bugs, contact Weizhong Li at liwz@sdsc.edu — he's the main character here, show him some respect. 🫶

and that's the whole thing, bestie!! this manual is from cd-hit-para.pl 4.8.1, dated August 2021. go forth and cluster, you absolute legend. 💅✨👑

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