How to report time of a single line

[wym199633 (王雨民)]

Hi everyone,

I am running deblur step and it takes a long time. I want to test if I change --p-min-reads 1 --p-min-size 1 to --p-min-reads 2 --p-min-size 1, how much time I will save. Is there a command to record the time spent on this line, or I need to record time with my mobile?

Best,
Oliver

[Nicholas_Bokulich]

@wym199633

Is there a command to record the time spent on this line, or I need to record time with my mobile?

Just precede any command you want to use with time and the runtime will be displayed at the end of the command (once it is done running of course). For example:

$ time qiime --help
Usage: qiime [OPTIONS] COMMAND [ARGS]...

  QIIME 2 command-line interface (q2cli)
  --------------------------------------

  To get help with QIIME 2, visit https://qiime2.org.

  To enable tab completion in Bash, run the following command or add it to
  your .bashrc/.bash_profile:

      source tab-qiime

  To enable tab completion in ZSH, run the following commands or add them to
  your .zshrc:

      autoload bashcompinit && bashcompinit && source tab-qiime

Options:
  --version  Show the version and exit.
  --help     Show this message and exit.

Commands:
  info                Display information about current deployment.
  tools               Tools for working with QIIME 2 files.
  dev                 Utilities for developers and advanced users.
  alignment           Plugin for generating and manipulating alignments.
  composition         Plugin for compositional data analysis.
  cutadapt            Plugin for removing adapter sequences, primers, and
                      other unwanted sequence from sequence data.
  dada2               Plugin for sequence quality control with DADA2.
  deblur              Plugin for sequence quality control with Deblur.
  demux               Plugin for demultiplexing & viewing sequence quality.
  diversity           Plugin for exploring community diversity.
  emperor             Plugin for ordination plotting with Emperor.
  feature-classifier  Plugin for taxonomic classification.
  feature-table       Plugin for working with sample by feature tables.
  gneiss              Plugin for building compositional models.
  longitudinal        Plugin for paired sample and time series analyses.
  metadata            Plugin for working with Metadata.
  phylogeny           Plugin for generating and manipulating phylogenies.
  quality-control     Plugin for quality control of feature and sequence data.
  quality-filter      Plugin for PHRED-based filtering and trimming.
  sample-classifier   Plugin for machine learning prediction of sample
                      metadata.
  taxa                Plugin for working with feature taxonomy annotations.
  vsearch             Plugin for clustering and dereplicating with vsearch.

real	0m0.684s
user	0m0.325s
sys	0m0.101s

[wym199633 (王雨民)]

Hi Nicholas,
Thanks! That’s cool!

Oliver