About Spades output dir error

Question

[ranakmal2]

Hello When i run spades command == Error == the output_dir is not set this error appears, Please guide how to set out put directory? this directory is needed to set in spades or other folder?

Answer 1

[Mensur Dlakic]

Have you tried running spades.py without any other parameters? It will print out something like this (shown only partially):

SPAdes genome assembler v3.14.0

Usage: spades.py [options] -o <output_dir>

Basic options:
  -o <output_dir>             directory to store all the resulting files (required)
  --isolate                   this flag is highly recommended for high-coverage isolate and multi-cell data
  --sc                        this flag is required for MDA (single-cell) data
  --meta                      this flag is required for metagenomic sample data
  --bio                       this flag is required for biosyntheticSPAdes mode
  --rna                       this flag is required for RNA-Seq data
  --plasmid                   runs plasmidSPAdes pipeline for plasmid detection
  --iontorrent                this flag is required for IonTorrent data
  --test                      runs SPAdes on toy dataset
  -h, --help                  prints this usage message
  -v, --version               prints version

It tells you on the second text line from top that a command ends with an output directory, and two lines later it tells you that this parameter is required.

So whatever your command is, it must include -o some_directory_name which specifies where SPAdes output will be saved. If the directory doesn't exist, it will be created.