arguments incorrectly parsed

[thkuo]

My command was correctly stated in the log file, but the parameters exactly used weren't in line with that (e.g., coverage 50 -> 5). Could you kindly suggest solutions?

# File "/net/personal-backup/thkuo/WhichTree_Sim.v10/data/reads_sim/fastq/1_100_180.read.info.gz": generated at Wed Jan 20 12:04:02 2021 by the command:
#     pirs simulate -t 20 -l 100 -x 50 -m 250 -v 80 -z -o /net/personal-backup/thkuo/WhichTree_Sim.v10/data/reads_sim/fastq/1 /net/personal-backup/thkuo/WhichTree_Sim.v10/data/genome_evol_sim/335/DB/SE002_genome
.fa
# 
# This file is a log of every read that was simulated.  It shows
# exactly where each read came from and the substitution errors,
# insertions, and deletions (if any) that were made to it.
#
# The following lists the parameters of the simulation:
#
# Input reference sequence files:   /net/personal-backup/thkuo/WhichTree_Sim.v10/data/genome_evol_sim/335/DB/SE002_genome.fa
# Read length:                      100
# Insert length mean:               180
# Insert length standard deviation: 18
# Coverage:                         5
# Diploid:                          no
# Cyclized (jumping library):       no
# Simulate substitution errors:     yes
# Substitution error rate:          default of base-calling profile
# Base-calling profile:             /home/thkuo/miniconda3/envs/whichtree_env/share/pirs/Base-Calling_Profiles/humNew.PE100.matrix.gz
# Substitution error algorithm:     quality transition mode algorithm
# Simulate InDel errors:            yes
# InDel error profile:              /home/thkuo/miniconda3/envs/whichtree_env/share/pirs/InDel_Profiles/phixv2.InDel.matrix
# Simulate GC content bias:         yes
# GC bias profile:                  /home/thkuo/miniconda3/envs/whichtree_env/share/pirs/GC-depth_Profiles/humNew.gcdep_200.dat
# Output type:                      gzip
# Output prefix:                    /net/personal-backup/thkuo/WhichTree_Sim.v10/data/reads_sim/fastq/1
# Simulate quality values:          yes
# ASCII shift of quality value      33
# Mode of mask quality:             None
# Random seed:                      53141862935728
# Number of simulator threads:      20