Spades

Question

[saifulislam99121]

Hi,

I am using MacOS and using spades through conda. It is showing the following error.

Running: /opt/anaconda3/bin/spades-core /Users/mustafizurrahman/Downloads/Brac_WGS/assembly/K21/configs/config.info /Users/mustafizurrahman/Downloads/Brac_WGS/assembly/K21/configs/isolate_mode.info

  0:00:00.000     1M / 9M    INFO    General                 (main.cpp                  :  99)   Loaded config from /Users/mustafizurrahman/Downloads/Brac_WGS/assembly/K21/configs/config.info
  0:00:00.000     1M / 9M    INFO    General                 (main.cpp                  :  99)   Loaded config from /Users/mustafizurrahman/Downloads/Brac_WGS/assembly/K21/configs/isolate_mode.info
  0:00:00.000     1M / 9M    ERROR   General                 (memory_limit.cpp          :  47)   setrlimit(2) call failed, errno = 22


== Error ==  system call for: "['/opt/anaconda3/bin/spades-core', '/Users/mustafizurrahman/Downloads/Brac_WGS/assembly/K21/configs/config.info', '/Users/mustafizurrahman/Downloads/Brac_WGS/assembly/K21/configs/isolate_mode.info']" finished abnormally, OS return value: 22

What is this error about? How to solve?

I am using spades 3.15.2

The command line was-

spades.py -1 R1p.fastq -2 R2p.fastq --careful --cov-cutoff auto -o assembly

Thank you

Answer 1

[Mensur Dlakic]

The solution to your problem is easy to find by Googling:

https://github.com/ablab/spades/issues/943

It boils down to upgrading to SPAdes 3.15.4.

By the way, I suggest you start your assembly without the --careful switch. I have done my share of assemblies with and without it, and can't remember that I ever got a better assembly by using --careful. And the assembly will take much longer with that switch.

Answer 2

[Dave Carlson]

From a reply by one of the Spades Devs to a similar issue on Github:

This is known MacOS issue. Consider upgrading to SPAdes 3.15.4