@isaacovercast Thank you for your help!
The data type is single end RAD-seq data, and the consuming time in step 6 for two methods are as below. once before I run step 6 by reference method successfully (in a rational time) by using v. 0.5.**, but there was something wrong with vcf file output. The total_filtered_loci number for denovo-method is 272,942 (v. 0.6.24).