Segmentation fault

[Johnsonzcode]

Question or Expected behavior After "ctg_graph done", there is "Segmentation fault" :

[INFO] 2020-12-15 19:19:56,915 start...
[INFO] 2020-12-15 19:19:56,915 logfile: pid47854.log.info
[WARNING] 2020-12-15 19:19:56,916 Change task "all" to "assemble", becasue the input_type is "corrected"
[INFO] 2020-12-15 19:19:56,916 options:
[INFO] 2020-12-15 19:19:56,917 {'job_type': 'local', 'job_prefix': 'nextDenovo_chicken', 'task': 'assemble', 'rewrite': 0, 'deltmp': 1, '
rerun': 3, 'parallel_jobs': '20', 'workdir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken', 'input_t
ype': 'corrected', 'read_cutoff': '1k', 'blocksize': '10g', 'pa_correction': '20', 'nodelist': '', 'cluster_options': '', 'sge_queue': ''
, 'seed_cutfiles': '20', 'correction_options': '-p 20 -max_lq_length 10000 -min_len_seed 17142', 'sort_options': '-m 200g -t 10 -k 40', '
_random_round_with_less_accuracy': 0, 'minimap2_options_cns': '-x ava-ont -t 8 -k17 -w17 --minlen 2000 --maxhan1 5000', 'minimap2_options
_map': ' -x map-ont', 'ctg_cns_options': ' -p 20', 'input_fofn': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenov
o/input.fofn', 'seed_cutoff': '34285', 'minimap2_options_raw': '-x ava-ont -t 8', 'nextgraph_options': '-a 1', 'raw_aligndir': '/storage-
01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/01.raw_align', 'cns_aligndir': '/storage-01/poultrylab1/zhaoqiang
sen/GenomeAssembly/chicken/3.nextdenovo/chicken/02.cns_align', 'ctg_graphdir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chick
en/3.nextdenovo/chicken/03.ctg_graph', 'sort_threads': 10, 'sort_mem': '200g', 'minimap2_threads': (8, 8), 'cns_threads': 20, 'map_thread
s': 20}
[INFO] 2020-12-15 19:19:56,917 mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken
[INFO] 2020-12-15 19:19:56,917 mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/01.raw_align
[INFO] 2020-12-15 19:19:56,917 mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/02.cns_align
[INFO] 2020-12-15 19:19:56,917 mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph
[INFO] 2020-12-15 19:19:56,918 analysis tasks done
[INFO] 2020-12-15 19:20:01,926 total jobs: 1
[INFO] 2020-12-15 19:20:01,928 Throw jobID:[47960] jobCmd:[/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chick
en/02.cns_align/01.split_seed.sh.work/split_seed0/nextDenovo_chicken.sh] in the local_cycle.
[INFO] 2020-12-15 19:22:55,193 split_seed done
[INFO] 2020-12-15 19:22:55,196 analysis tasks done
[INFO] 2020-12-15 19:22:55,272 total jobs: 45
[INFO] 2020-12-15 19:22:55,273 Throw jobID:[49788] jobCmd:[/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chick
en/02.cns_align/02.cns_align.sh.work/cns_align00/nextDenovo_chicken.sh] in the local_cycle.
......
[INFO] 2020-12-16 04:03:24,649 cns_align done
[INFO] 2020-12-16 04:03:24,650 analysis tasks done
[INFO] 2020-12-16 04:03:29,658 total jobs: 1
[INFO] 2020-12-16 04:03:29,659 Throw jobID:[81531] jobCmd:[/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo_chicken.sh] in the local_cycle.
[INFO] 2020-12-16 04:04:10,292 ctg_graph done
nextdenovo.sh: line 6: 47854 Segmentation fault      (core dumped) ./NextDenovo/nextDenovo run.cfg

1. I am wondering that whether my assembly is finished ?
2. If not, how to fix it and continue to run this assembly ?

Operating system

# cat /etc/redhat-release
CentOS Linux release 7.8.2003 (Core)

GCC gcc version 9.2.0 (GCC)

Python Python 3.6.11

NextDenovo 2.3.1

Additional context (Optional) run.cfg : [General] job_type = local job_prefix = nextDenovo_chicken task = all # 'all', 'correct', 'assemble' rewrite = no # yes/no # deltmp = yes rerun = 3 parallel_jobs = 20 input_type = corrected # input_fofn = input.fofn workdir = chicken

[correct_option] read_cutoff = 1k seed_cutoff = 34285 # blocksize = 10g # pa_correction = 20 seed_cutfiles = 20 sort_options = -m 200g -t 10 -k 40 minimap2_options_raw = -x ava-ont -t 8 correction_options = -p 20 #

[assemble_option] minimap2_options_cns = -x ava-ont -t 8 -k17 -w17 nextgraph_options = -a 1

[X-WJ]

I think Your assembly is unfinished.Your final assembly file should be at 03.ctg_graph/nd.asm.fasta . Try to rerun ./NextDenovo/nextDenovo run.cfg

[Johnsonzcode]

If I rerun nextDenovo according to run.cfg, It seems restart the assembly because it backups the old folder and mkdir new one :

[INFO] 2020-12-16 06:34:13,496 start...
[INFO] 2020-12-16 06:34:13,497 logfile: pid335182.log.info
[WARNING] 2020-12-16 06:34:13,498 Change task "all" to "assemble", becasue the input_type is "corrected"
[INFO] 2020-12-16 06:34:13,498 options:
[INFO] 2020-12-16 06:34:13,498 {'job_type': 'local', 'job_prefix': 'nextDenovo_chicken', 'task': 'assemble', 'rewrite': 0, 'deltmp': 1, 'rerun': 3, 'parallel_jobs': '20', 'workdir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken', 'input_type': 'corrected', 'read_cutoff': '1k', 'blocksize': '10g', 'pa_correction': '20', 'nodelist': '', 'cluster_options': '', 'sge_queue': '', 'seed_cutfiles': '20', 'correction_options': '-p 20 -max_lq_length 10000 -min_len_seed 17142', 'sort_options': '-m 200g -t 10 -k 40', '_random_round_with_less_accuracy': 0, 'minimap2_options_cns': '-x ava-ont -t 8 -k17 -w17 --minlen 2000 --maxhan1 5000', 'minimap2_options_map': ' -x map-ont', 'ctg_cns_options': ' -p 20', 'input_fofn': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/input.fofn', 'seed_cutoff': '34285', 'minimap2_options_raw': '-x ava-ont -t 8', 'nextgraph_options': '-a 1', 'raw_aligndir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/01.raw_align', 'cns_aligndir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/02.cns_align', 'ctg_graphdir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph', 'sort_threads': 10, 'sort_mem': '200g', 'minimap2_threads': (8, 8), 'cns_threads': 20, 'map_threads': 20}
[INFO] 2020-12-16 06:34:13,498 skip mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken
[WARNING] 2020-12-16 06:34:13,498 backup /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/01.raw_align to /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/01.raw_align.backup.v0
[INFO] 2020-12-16 06:34:13,498 mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/01.raw_align
[WARNING] 2020-12-16 06:34:13,499 backup /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/02.cns_align to /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/02.cns_align.backup.v0
[INFO] 2020-12-16 06:34:13,499 mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/02.cns_align
[WARNING] 2020-12-16 06:34:13,499 backup /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph to /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph.backup.v0
[INFO] 2020-12-16 06:34:13,499 mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph
[INFO] 2020-12-16 06:34:13,500 analysis tasks done
[INFO] 2020-12-16 06:34:18,508 total jobs: 1
[INFO] 2020-12-16 06:34:18,510 Throw jobID:[335288] jobCmd:[/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/02.cns_align/01.split_seed.sh.work/split_seed0/nextDenovo_chicken.sh] in the local_cycle.
......

[moold]

Try to set rewrite = yes

[Johnsonzcode]

Try to set rewrite = yes

If set rewrite = yes, there won't be Segmentation fault, right ?

[Johnsonzcode]

I try as you say. Thank you for your reply but it appears same Segmentation fault

[INFO] 2020-12-16 17:25:43,332 start...
[INFO] 2020-12-16 17:25:43,333 logfile: pid377773.log.info
[WARNING] 2020-12-16 17:25:43,334 Re-write workdir
[WARNING] 2020-12-16 17:25:43,334 Change task "all" to "assemble", becasue the input_type is "corrected"
[INFO] 2020-12-16 17:25:43,334 options:
[INFO] 2020-12-16 17:25:43,334 {'job_type': 'local', 'job_prefix': 'nextDenovo_chicken', 'task': 'assemble', 'rewrite': 1, 'deltmp': 1, 'rerun': 3, 'parallel_jobs': '20', 'workdir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken', 'input_type': 'corrected', 'read_cutoff': '1k', 'blocksize': '10g', 'pa_correction': '20', 'nodelist': '', 'cluster_options': '', 'sge_queue': '', 'seed_cutfiles': '20', 'correction_options': '-p 20 -max_lq_length 10000 -min_len_seed 17142', 'sort_options': '-m 200g -t 10 -k 40', '_random_round_with_less_accuracy': 0, 'minimap2_options_cns': '-x ava-ont -t 8 -k17 -w17 --minlen 2000 --maxhan1 5000', 'minimap2_options_map': ' -x map-ont', 'ctg_cns_options': ' -p 20', 'input_fofn': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/input.fofn', 'seed_cutoff': '34285', 'minimap2_options_raw': '-x ava-ont -t 8', 'nextgraph_options': '-a 1', 'raw_aligndir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/01.raw_align', 'cns_aligndir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/02.cns_align', 'ctg_graphdir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph', 'sort_threads': 10, 'sort_mem': '200g', 'minimap2_threads': (8, 8), 'cns_threads': 20, 'map_threads': 20}
[INFO] 2020-12-16 17:25:43,334 skip mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken
[INFO] 2020-12-16 17:25:43,335 skip mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/01.raw_align
[INFO] 2020-12-16 17:25:43,335 skip mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/02.cns_align
[INFO] 2020-12-16 17:25:43,335 skip mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph
[INFO] 2020-12-16 17:25:43,336 analysis tasks done
[INFO] 2020-12-16 17:25:43,336 skip step: split_seed
[INFO] 2020-12-16 17:25:43,338 analysis tasks done
[INFO] 2020-12-16 17:25:43,339 skip step: cns_align
[INFO] 2020-12-16 17:25:43,339 analysis tasks done
[INFO] 2020-12-16 17:25:43,339 skip step: ctg_graph
nextdenovo.sh: line 6: 377773 Segmentation fault      (core dumped) ./NextDenovo/nextDenovo run.cfg

[moold]

You can check whether the output of /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo_chicken.sh is correct?

[Johnsonzcode]

nextDenovo_chicken.sh looks like:

#!/bin/bash
set -xve
hostname
cd /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0
time /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/NextDenovo/bin/nextgraph -a 1 -f /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.input.seqs /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta;
touch /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo_chicken.sh.done

where nextDenovo_chicken.sh.done exits. It means that nextDenovo_chicken.sh finished. But I don't know how to check nd.asm.p.fasta is correct :

# ls -lh
 1014M Dec 16 14:34 nd.asm.p.fasta

If it is final assembly, the size of nd.asm.p.fasta seems correct. I set 1g in run.cfg.

[moold]

Could you paste the content of /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo_chicken.sh.e to here?

[Johnsonzcode]

Of course :

hostname
+ hostname
cd /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0
+ cd /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0
time /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/NextDenovo/bin/nextgraph -a 1 -f /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.input.seqs /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta;
+ /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/NextDenovo/bin/nextgraph -a 1 -f /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.input.seqs /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.input.ovls -o nd.asm.p.fasta
[INFO] 2020-12-16 14:33:50 Initialize graph and reading...
[INFO] 2020-12-16 14:34:13 Initial Node(s): 261692, Edge(s): 2220758
[INFO] 2020-12-16 14:34:14 Depth stat, Mid: 57.000 Max: 114000.000 Repeat: 85.500 L:N:H: 0.182:0.800:0.018
[INFO] 2020-12-16 14:34:14 Outdegree stat, Mid: 9.000 Max: 18000.000 Repeat: 13.500 L:N:H: 0.181:0.819:0.000
[INFO] 2020-12-16 14:34:15 Chimeric node ratio: 0.199% (candidate: 0.639%)
[INFO] 2020-12-16 14:34:21 Assembly done and outputting...
[INFO] 2020-12-16 14:34:26 Assembly stat:
Type           Length (bp)            Count (#)
N10             90931881                    2
N20             81289399                    3
N30             76172526                    4
N40             47812504                    6
N50             27316320                    9
N60             19614968                   13
N70             14095085                   19
N80              9306926                   28
N90              5843368                   42

Min.               58226                    -
Max.            98600593                    -
Ave.             4887846                    -
Total         1060662579                  217
[INFO] 2020-12-16 14:34:26 CMD:
 /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/NextDenovo/bin/nextgraph -a 1 -f /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.input.seqs -o nd.asm.p.fasta /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.input.ovls
[INFO] 2020-12-16 14:34:26 Real time: 35.344 sec; CPU: 35.060 sec; Peak RSS: 0.598 GB

real    0m35.372s
user    0m32.308s
sys     0m2.753s
touch /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo_chicken.sh.done
+ touch /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph0/nextDenovo_chicken.sh.done

[Johnsonzcode]

It seems finished correctly but I am not sure. So in the top of this topic I wondering whether my assembly is finished.

[moold]

It seems everything is OK, I can not solve it because I can't reproduce this error except I can access your system to debug. Optional, you can use nd.asm.p.fasta as the final result, but it may contain more errors than the final result.

[Johnsonzcode]

Can I manually finish steps between nd.asm.p.fasta and final result ? In the beginning, although I use CCS reads to correct ONT reads and set input_type = corrected, I am not sure its quality. So if there is a way to avoid errors, I want to refine it manually.

[moold]

No, there must be an error when running, you cannot skip it. You can polish this genome using Hifi reads or short reads to improve the single-base accuracy, and you can use Bionano or Hic data to improve the structural accuracy.

[Johnsonzcode]

OK

(asm_practise) [poultrylab1@pbsnode01 3.nextdenovo]$ python NextDenovo/nextDenovo run.cfg
[INFO] 2020-12-16 19:17:20,477 start...
[INFO] 2020-12-16 19:17:20,477 logfile: pid30071.log.info
[WARNING] 2020-12-16 19:17:20,479 Re-write workdir
[INFO] 2020-12-16 19:17:20,479 options:
[INFO] 2020-12-16 19:17:20,479 {'job_type': 'local', 'job_prefix': 'nextDenovo_chicken', 'task': 'assemble', 'rewrite': 1, 'deltmp': 1, 'rerun': 3, 'parallel_jobs': '20', 'workdir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken', 'input_type': 'corrected', 'read_cutoff': '1k', 'blocksize': '10g', 'pa_correction': '20', 'nodelist': '', 'cluster_options': '', 'sge_queue': '', 'seed_cutfiles': '20', 'correction_options': '-p 20 -max_lq_length 10000 -min_len_seed 17142', 'sort_options': '-m 200g -t 10 -k 40', '_random_round_with_less_accuracy': 0, 'minimap2_options_cns': '-x ava-ont -t 8 -k17 -w17 --minlen 2000 --maxhan1 5000', 'minimap2_options_map': ' -x map-ont', 'ctg_cns_options': ' -p 20', 'input_fofn': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/input.fofn', 'seed_cutoff': '34285', 'minimap2_options_raw': '-x ava-ont -t 1', 'nextgraph_options': '-a 1', 'raw_aligndir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/01.raw_align', 'cns_aligndir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/02.cns_align', 'ctg_graphdir': '/storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph', 'sort_threads': 10, 'sort_mem': '200g', 'minimap2_threads': (1, 8), 'cns_threads': 20, 'map_threads': 20}
[INFO] 2020-12-16 19:17:20,479 skip mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken
[INFO] 2020-12-16 19:17:20,479 skip mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/01.raw_align
[INFO] 2020-12-16 19:17:20,479 skip mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/02.cns_align
[INFO] 2020-12-16 19:17:20,480 skip mkdir: /storage-01/poultrylab1/zhaoqiangsen/GenomeAssembly/chicken/3.nextdenovo/chicken/03.ctg_graph
[INFO] 2020-12-16 19:17:20,481 analysis tasks done
[INFO] 2020-12-16 19:17:20,481 skip step: split_seed
[INFO] 2020-12-16 19:17:20,483 analysis tasks done
[INFO] 2020-12-16 19:17:20,484 skip step: cns_align
[INFO] 2020-12-16 19:17:20,484 analysis tasks done
[INFO] 2020-12-16 19:17:20,484 skip step: ctg_graph
Segmentation fault (core dumped)

The same as before

[Johnsonzcode]

We fix it by modifying run.cfg like this :

run.cfg :
[General]
job_type = local
job_prefix = nextDenovo_chicken
task = all # 'all', 'correct', 'assemble'
rewrite = no # yes/no #
deltmp = yes
rerun = 3
parallel_jobs = 20
input_type = raw #
input_fofn = input.fofn
workdir = chicken

[correct_option]
read_cutoff = 1k
seed_cutoff = 34285 #
blocksize = 14g #
pa_correction = 20
seed_cutfiles = 20
sort_options = -m 20g -t 8 -k 40
minimap2_options_raw = -x ava-ont -t 8
correction_options = -p 8 #

minimap2_options_cns = -x ava-ont -t 8 -k17 -w17
nextgraph_options = -a 1

We think it may be a problem of resource allocation, [correct_option] and [assemble_option] just as part of nextDnovo, they should set smaller than we set before.