[45690 INFO] 2024-06-09 09:14:32 NextDenovo start...
[45690 INFO] 2024-06-09 09:14:32 version:2.5.2 logfile:pid45690.log.info
[45690 WARNING] 2024-06-09 09:14:32 Re-write workdir
[45690 INFO] 2024-06-09 09:14:32 skip mkdir: /gws/nopw/j04/rotcotm/rominab/projects/NextDeNovo_Assembly
[45690 INFO] 2024-06-09 09:14:32 mkdir: /gws/nopw/j04/rotcotm/rominab/projects/NextDeNovo_Assembly/01.raw_align
[45690 INFO] 2024-06-09 09:14:32 mkdir: /gws/nopw/j04/rotcotm/rominab/projects/NextDeNovo_Assembly/02.cns_align
[45690 INFO] 2024-06-09 09:14:32 mkdir: /gws/nopw/j04/rotcotm/rominab/projects/NextDeNovo_Assembly/03.ctg_graph
[45690 INFO] 2024-06-09 09:14:32 options: 
rerun:                        3
task:                         all
deltmp:                       1
rewrite:                      1
blocksize:                    3g
seed_depth:                   45
read_type:                    ont
job_type:                     slurm
input_type:                   raw
read_cutoff:                  10k
random_round:                 50
parallel_jobs:                12
pa_correction:                12
seed_cutfiles:                12
genome_size:                  2.7g
seed_cutoff:                  20000
job_prefix:                   nextDenovo
ctg_cns_options:              -p 12
nextgraph_options:            -a 1
sort_options:                 -m 20g -t 30 -k 40
minimap2_options_raw:         -x ava-pb -t 80
minimap2_options_map:         -t 12 -x map-pb
correction_options:           -p 12 -min_len_seed 10000 -max_lq_length 1000 -r ont
minimap2_options_cns:         -t 12 -k 31 -w 17 --minlen 2000 --maxhan1 5000 -x ava-pb
workdir:                      /gws/nopw/j04/rotcotm/rominab/projects/NextDeNovo_Assembly
input_fofn:                   /gws/nopw/j04/rotcotm/rominab/projects/NextDeNovo_Assembly/input.fofn
raw_aligndir:                 /gws/nopw/j04/rotcotm/rominab/projects/NextDeNovo_Assembly/01.raw_align
cns_aligndir:                 /gws/nopw/j04/rotcotm/rominab/projects/NextDeNovo_Assembly/02.cns_align
ctg_graphdir:                 /gws/nopw/j04/rotcotm/rominab/projects/NextDeNovo_Assembly/03.ctg_graph
submit:                       sbatch -p long-serial --cpus-per-task=24 --mem-per-cpu=5g -o /gws/nopw/j04/rotcotm/rominab/projects/6_Pgrovesi_Nanopore/error/nextdenovo.out -e /gws/nopw/j04/rotcotm/rominab/projects/6_Pgrovesi_Nanopore/error/nextdenovo.out /gws/nopw/j04/rotcotm/rominab/projects/6_Pgrovesi_Nanopore/scripts/assembly_NextDeNovo_test.sh
[45690 INFO] 2024-06-09 09:14:37 Total jobs: 1
[45690 INFO] 2024-06-09 09:14:37 Submitted jobID:[33288665] jobCmd:[/gws/nopw/j04/rotcotm/rominab/projects/NextDeNovo_Assembly/01.raw_align/01.db_split.sh.work/db_split1/nextDenovo.sh] in the slurm_cycle.