search

ablab / spades

SPAdes Genome Assembler
http://ablab.github.io/spades/
Other
763 stars 138 forks source link

k-mer counting take too long #1111

Open muzi9841 opened 1 year ago

muzi9841 commented 1 year ago

Description of bug

Hi, I am assembling my sequencing data on a cluster but this step takes me more than 12 hours. Is there any problem with it?

spades.log

spades.log

params.txt

params.txt

SPAdes version

3.15.4

Operating System

Linux-3.10.0-1160.36.2.el7.x86_64-x86_64-with-glibc2.2.5

Python Version

3.8.6

Method of SPAdes installation

conda

No errors reported in spades.log

asl commented 1 year ago

Hello

First of all, it seems you're having lots of input reads. So this is going to take a while. However, the most important problem is as follows:

  0:00:00.001     1M / 17M   INFO    General                 (main.cpp                  :  78)   Maximum # of threads to use (adjusted due to OMP capabilities): 1

It seems that your cluster imposes some additional restrictions on jobs that use OpenMP. You'd likely need to check with your system administrator how to setup # of OpenMP threads during your job submission