Stop at ctg_graph, and no nd.asm.fasta.stat file

[rubbyai]

Describe the bug
There is no error message, but stop at ctg_graph, and the nd.asm.fasta.stat file is empty.

Error message
$cat pid397038.log.info
[397038 INFO] 2024-09-19 14:50:39 NextDenovo start...
[397038 INFO] 2024-09-19 14:50:39 version:2.5.2 logfile:pid397038.log.info
[397038 WARNING] 2024-09-19 14:50:39 Re-write workdir
[397038 INFO] 2024-09-19 14:50:39 mkdir: /DATA/User/wangyuru/nd_test/./01_rundir
[397038 INFO] 2024-09-19 14:50:39 mkdir: /DATA/User/wangyuru/nd_test/./01_rundir/01.raw_align
[397038 INFO] 2024-09-19 14:50:39 mkdir: /DATA/User/wangyuru/nd_test/./01_rundir/02.cns_align
[397038 INFO] 2024-09-19 14:50:39 mkdir: /DATA/User/wangyuru/nd_test/./01_rundir/03.ctg_graph
[397038 INFO] 2024-09-19 14:50:44 Total jobs: 1
[397038 INFO] 2024-09-19 14:50:44 Submitted jobID:[397101] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/01.db_stat.sh.work/db_stat1/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 14:53:35 db_stat done
[397038 INFO] 2024-09-19 14:53:35 updated options:
rerun: 3
task: all
deltmp: 1
rewrite: 1
read_type: clr
job_type: local
input_type: raw
read_cutoff: 1k
parallel_jobs: 2
seed_depth: 45.0
pa_correction: 2
seed_cutfiles: 3
seed_cutoff: 31467
genome_size: 308161
job_prefix: nextDenovo
blocksize: 21254056928
ctg_cns_options: -p 15
nextgraph_options: -a 1
sort_options: -m 1g -t 2 -k 40
minimap2_options_map: -x map-pb
minimap2_options_raw: -t 8 -x ava-pb
workdir: /DATA/User/wangyuru/nd_test/./01_rundir
input_fofn: /DATA/User/wangyuru/nd_test/./input.fofn
raw_aligndir: /DATA/User/wangyuru/nd_test/./01_rundir/01.raw_align
cns_aligndir: /DATA/User/wangyuru/nd_test/./01_rundir/02.cns_align
ctg_graphdir: /DATA/User/wangyuru/nd_test/./01_rundir/03.ctg_graph
correction_options: -p 15 -max_lq_length 1000 -r clr -min_len_seed 15733
minimap2_options_cns: -t 8 -x ava-pb -k 17 -w 17 --minlen 2000 --maxhan1 5000
[397038 INFO] 2024-09-19 14:53:35 summary of input data:
file: /DATA/User/wangyuru/nd_test/./01_rundir/01.raw_align/input.reads.stat
[Read length stat]
Types Count (#) Length (bp)
N10 92896 11914
N20 231831 8963
N30 409363 7193
N40 627599 5901
N50 892600 4873
N60 1213882 4001
N70 1608923 3228
N80 2104007 2531
N90 2760865 1818

Types Count (#) Bases (bp) Depth (X)
Raw 4715834 14758686284 47892.78
Filtered 934723 576114420 1869.52
Clean 3781111 14182571864 46023.25

Suggested seed_cutoff (genome size: 0.31Mb, expected seed depth: 45, real seed depth: 45.00): 31467 bp
[397038 INFO] 2024-09-19 14:53:40 Total jobs: 1
[397038 INFO] 2024-09-19 14:53:40 Submitted jobID:[399041] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/02.db_split.sh.work/db_split1/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 14:56:51 db_split done
[397038 INFO] 2024-09-19 14:56:51 Total jobs: 9
[397038 INFO] 2024-09-19 14:56:51 Submitted jobID:[401236] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align1/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 14:56:51 Submitted jobID:[401242] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align2/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 14:56:54 Submitted jobID:[401326] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align3/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 14:56:56 Submitted jobID:[401380] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align4/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 14:56:59 Submitted jobID:[401434] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align5/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:02:22 Submitted jobID:[405678] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align6/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:02:25 Submitted jobID:[405732] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align7/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:02:28 Submitted jobID:[405797] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align8/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:03:00 Submitted jobID:[406341] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align9/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:08:25 raw_align done
[397038 INFO] 2024-09-19 15:08:30 Total jobs: 3
[397038 INFO] 2024-09-19 15:08:30 Submitted jobID:[410287] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/04.sort_align.sh.work/sort_align1/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:08:30 Submitted jobID:[410307] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/04.sort_align.sh.work/sort_align2/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:09:02 Submitted jobID:[410666] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/04.sort_align.sh.work/sort_align3/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:09:33 sort_align done
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align4/input.seed.002.2bit.3.ovl
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align7/input.seed.002.2bit.6.ovl
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align8/input.seed.002.2bit.7.ovl
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align9/input.seed.002.2bit.8.ovl
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align1/input.seed.003.2bit.0.ovl
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align2/input.seed.003.2bit.1.ovl
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align3/input.seed.003.2bit.2.ovl
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align4/input.seed.003.2bit.3.ovl
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align3/input.seed.001.2bit.2.ovl
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align5/input.seed.001.2bit.4.ovl
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align6/input.seed.001.2bit.5.ovl
[397038 INFO] 2024-09-19 15:09:33 remove temporary result: /DATA/User/wangyuru/nd_test/01_rundir/01.raw_align/03.raw_align.sh.work/raw_align7/input.seed.001.2bit.6.ovl
[397038 INFO] 2024-09-19 15:09:38 Total jobs: 3
[397038 INFO] 2024-09-19 15:09:38 Submitted jobID:[411080] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns1/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:09:39 Submitted jobID:[411086] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns2/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:09:55 Submitted jobID:[411294] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns3/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:10:10 seed_cns done
[397038 INFO] 2024-09-19 15:10:10 seed_cns finished, and final corrected reads file:
[397038 INFO] 2024-09-19 15:10:10 /DATA/User/wangyuru/nd_test/./01_rundir/02.cns_align/01.seed_cns.sh.work/seed_cns/cns.fasta
[397038 INFO] 2024-09-19 15:10:10 Total jobs: 6
[397038 INFO] 2024-09-19 15:10:10 Submitted jobID:[411487] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align1/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:10:10 Submitted jobID:[411503] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align2/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:10:21 Submitted jobID:[411672] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align3/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:10:23 Submitted jobID:[411714] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align4/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:10:26 Submitted jobID:[411778] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align5/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:10:30 Submitted jobID:[411852] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align6/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:10:35 cns_align done
[397038 INFO] 2024-09-19 15:10:40 Total jobs: 1
[397038 INFO] 2024-09-19 15:10:40 Submitted jobID:[411993] jobCmd:[/DATA/User/wangyuru/nd_test/01_rundir/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nextDenovo.sh] in the local_cycle.
[397038 INFO] 2024-09-19 15:10:41 ctg_graph done
~/NextDenovo/test_data/01_rundir/02.cns_align/02.cns_align.sh.work/cns_align0/nextDenovo.sh.e

Genome characteristics
droper sheep, the whole genome is about 2.6GB

Input data
sheep cyclone data:
file1: total base count 1281725586
file2: total base count 2110087581

Config file
$cat run.cfg
[General]
job_type = local
job_prefix = nextDenovo
task = all # 'all', 'correct', 'assemble'
rewrite = yes # yes/no
deltmp = yes
rerun = 3
parallel_jobs = 2
input_type = raw
read_type = clr
input_fofn = ./input.fofn
workdir = ./01_rundir

[correct_option]
read_cutoff = 1k
genome_size = 308161
pa_correction = 2
sort_options = -m 1g -t 2
minimap2_options_raw = -t 8
correction_options = -p 15

[assemble_option]
minimap2_options_cns = -t 8
nextgraph_options = -a 1

Operating system
Which operating system and version are you using?
No LSB modules are available.
Distributor ID: Ubuntu
Description: Ubuntu 22.04.1 LTS
Release: 22.04
Codename: jammy

GCC
What version of GCC are you using?
gcc version 11.4.0 (Ubuntu 11.4.0-1ubuntu1~22.04)

Python
What version of Python are you using?
Python 3.12.2

NextDenovo
What version of NextDenovo are you using?
nextDenovo 2.5.2

[moold]

genome_size = 308161, is this genome size (bp) correct?