BinPro / CONCOCT

Clustering cONtigs with COverage and ComposiTion
Other
119 stars 48 forks source link

Why is concoct using all available threads instead of the mentioned number? #330

Open anw-sh opened 9 months ago

anw-sh commented 9 months ago

Hi all,

I installed concoct with conda and faced the OpenBLAS problem. Reinstalled it using these instructions. Then there was TypeError: Feature names are... error. Rectified it by installing scikit-learn 1.1.0 as per this post. It worked. I am able to use multiple threads. However, even though I gave -t 24 it started using all the available threads. Where am I doing wrong...?

Command used...

concoct --composition_file MN108/contigs_10K.fa --coverage_file MN108/coverage_table.tsv -b MN108/sub_contigs/ -t 24

Initial output in the terminal...

Up and running. Check /data/cmi_admin/anwesh/SG_Meta/CInd_Gut/concoct_out/MN108/sub_contigs/log.txt for progress
/apps/codes/mambaforge/envs/concoct/lib/python3.8/site-packages/sklearn/utils/validation.py:1854: FutureWarning: Feature names only support names that are all strings. Got feature names with dtypes: ['int', 'str']. An error will be raised in 1.2.
  warnings.warn(
/apps/codes/mambaforge/envs/concoct/lib/python3.8/site-packages/sklearn/utils/validation.py:1854: FutureWarning: Feature names only support names that are all strings. Got feature names with dtypes: ['int', 'str']. An error will be raised in 1.2.
  warnings.warn(
83062 2596 24
Setting 24 OMP threads
Generate input data
0,-3355428.135938,64970.038361

Actual CPU usage... Screenshot from 2023-10-05 18-22-27