Segmentation fault

Question

Segmentation fault

Johnsonzcode opened this issue 4 years ago · comments

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

I am wondering that whether my assembly is finished ?
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 · Answer 1 · Tue Dec 15 2020 22:41:13 GMT+0800 (China Standard Time)

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

johnsonz · Answer 2 · Tue Dec 15 2020 22:48:02 GMT+0800 (China Standard Time)

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.
......

Hu Jiang · Answer 3 · Wed Dec 16 2020 09:10:40 GMT+0800 (China Standard Time)

Try to set rewrite = yes

johnsonz · Answer 4 · Wed Dec 16 2020 09:28:31 GMT+0800 (China Standard Time)

Try to set rewrite = yes

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

johnsonz · Answer 5 · Wed Dec 16 2020 09:38:35 GMT+0800 (China Standard Time)

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

Hu Jiang · Answer 6 · Wed Dec 16 2020 10:20:10 GMT+0800 (China Standard Time)

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?

johnsonz · Answer 7 · Wed Dec 16 2020 10:22:53 GMT+0800 (China Standard Time)

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.

Hu Jiang · Answer 8 · Wed Dec 16 2020 10:28:41 GMT+0800 (China Standard Time)

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?

johnsonz · Answer 9 · Wed Dec 16 2020 10:29:33 GMT+0800 (China Standard Time)

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

johnsonz · Answer 10 · Wed Dec 16 2020 10:31:25 GMT+0800 (China Standard Time)

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

Hu Jiang · Answer 11 · Wed Dec 16 2020 10:45:19 GMT+0800 (China Standard Time)

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.

johnsonz · Answer 12 · Wed Dec 16 2020 10:53:30 GMT+0800 (China Standard Time)

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.

Hu Jiang · Answer 13 · Wed Dec 16 2020 11:02:35 GMT+0800 (China Standard Time)

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.

johnsonz · Answer 14 · Wed Dec 16 2020 11:33:45 GMT+0800 (China Standard Time)

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

johnsonz · Answer 15 · Fri Dec 18 2020 10:07:44 GMT+0800 (China Standard Time)

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.