jgi_summarize_bam_contig_depths threads setting

[Former user]

Hi, I have one questions. How many cores will jgi_summarize_bam_contig_depths using for abundance table generation and could we set the cores numbers?

[Rob Egan]

By default it uses all the cores of the node. You can adjust it down by setting the -t argument, or the OMP_NUM_THREADS environmental variable. The jgi_summarize_bam_contig_depths program will generally only use only as many threads as you have samples. metabat1 & metabat2 will use all the cores for most of the stages of the program