Unable to run simulated human HiFi reads

[Oieswarya]

Hello, I have been trying to run goldrush with simulated HiFi reads of Human. The coverage of the reads is 10x. I have used goldrush for several other simulated inputs and it ran. I also checked if there is any non actg characters on my fq file and found none.

I have used this command: goldrush run reads=Human_nonACTG_fq G=3120e6 track_time=1 m=10000 --debug

This is the .out file:

GNU Make 4.3 Built for x86_64-conda-linux-gnu Copyright (C) 1988-2020 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Reading makefiles... Updating makefiles.... Updating goal targets.... File 'run' does not exist. Must remake target 'run'. mkdir -p goldrush_intermediate_files cd goldrush_intermediate_files && ln -sf ../Human_nonACTG_fq.fq && goldrush run-in-dir reads=Human_nonACTG_fq G=3120e6 t=48 z=1000 track_time=1 k=22 w=16 tile=1000 b=10 u=5 a=1 o=0.1 x=10 h=3 s=1011011110110111101101 m=10000 M=5 r=0.9 P=15 d=5 span=2 dist=500 k_ntLink=40 w_ntLink=250 rounds=5 polisher=goldpolish polisher_mapper=minimap2 shared_mem=/dev/shm GNU Make 4.3 Built for x86_64-conda-linux-gnu Copyright (C) 1988-2020 Free Software Foundation, Inc. License GPLv3+: GNU GPL version 3 or later http://gnu.org/licenses/gpl.html This is free software: you are free to change and redistribute it. There is NO WARRANTY, to the extent permitted by law. Reading makefiles... make[1]: Entering directory '/home/goldrush_intermediate_files' Updating makefiles.... Updating goal targets.... File 'run-in-dir' does not exist. File 'check-G' does not exist. Must remake target 'check-G'. Successfully remade target file 'check-G'. File 'check-reads' does not exist. Must remake target 'check-reads'. Successfully remade target file 'check-reads'. File 'clean' does not exist. File 'goldrush_asm_golden_path.fa' does not exist. File 'goldrush_asm_silver_path_all.fq' does not exist. File 'goldrush_asm_silver_path_5.fq' does not exist. Must remake target 'goldrush_asm_silver_path_5.fq'. command time -v -o goldrush_asm_silver_path_5.fq.time goldrush-path -k 22 -w 16 -t 1000 -u 5 -a 1 -o 0.1 -p goldrush_asm_silver_path -i Human_nonACTG_fq.fq -h 3 -j 48 -x10 -P 15 -d 5 -s 1011011110110111101101 -g 3120e6 -b 10 -r 0.9 --silver_path -M 5 -m 10000 --verbose make[1]: Leaving directory '/home/goldrush_intermediate_files'

This is the .err file: make[1]: *** [/home/.conda/envs/goldrush_env/bin/goldrush.make:251: goldrush_asm_silver_path_5.fq] Error 127 make: *** [/home/.conda/envs/goldrush_env/bin/goldrush.make:203: run] Error 2

Can you kindly guide me as to where I am going wrong.