Open jjssuuhh opened 7 months ago
It seems that the thread parameter (80) you set is too large, which consumes too much memory and crashed. So please reduce this value.
[General] job_type = local job_prefix = nextDenovo task = all # 'all', 'correct', 'assemble' rewrite = yes # yes/no deltmp = yes rerun = 3 parallel_jobs = 10 input_type = raw read_type = ont input_fofn = ./input.fofn workdir = ./NextDenovorunned
[correct_option] read_cutoff = 1k genome_size = 1.44g seed_cutoff = 13966 blocksize = 10g pa_correction = 15 seed_cutfiles = 5 sort_options = -m 40g -t 80 -k 60 minimap2_options_raw = -x ava-ont -t 80 correction_options = -p 80 -b
[assemble_option] minimap2_options_cns = -x ava-ont -t 80 -k17 -w17 minimap2_options_map = -x map-ont -t 80 nextgraph_options = -a 1
this is my run.cfg file, should i have to remove sort_options -t 80? or every -t 80?
try minimap2_options_map = -x map-ont -t 20
thankyou!! l will try that!
Describe the bug i got some error
Error message [17613 ERROR] 2024-02-14 06:28:37 ctg_align failed: please check the following logs: [17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align01/nextDenovo.sh.e [17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align02/nextDenovo.sh.e [17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align07/nextDenovo.sh.e [17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align08/nextDenovo.sh.e [17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align09/nextDenovo.sh.e [17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align11/nextDenovo.sh.e [17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align12/nextDenovo.sh.e [17613 ERROR] 2024-02-14 06:28:37 /var2/NGS_RAW_DATA/Magnoliaceae/nanopore/NextDenovorunned/03.ctg_graph/02.ctg_align.sh.work/ctg_align13/nextDenovo.sh.e
and i check the file
hostname
Genome characteristics genome size option was 1.44G