Genome size is much smaller than expected

[2benaszq]

Hello, dear teacher,
I really hope you can help me,
The size of my assembled genome is seriously smaller than expected, but the process ends normally.
The following is my parameter configuration：
##############################################################
[General]
job_type = sge
job_prefix = test
task = all # 'all', 'correct', 'assemble'
rewrite = yes # yes/no
deltmp = no
rerun = 3
parallel_jobs = 36
input_type = raw
read_type = ont # clr, ont, hifi
input_fofn = input.fofn
workdir = test_nd_run
submit = qsub -cwd -l vf=60g,q=all.q {script} #for sge

[correct_option]
read_cutoff = 1k
genome_size = 1741M
pa_correction = 51
sort_options = -m 43g -t 18 -k 40
minimap2_options_raw = -t 21
correction_options = -p 15

[assemble_option]
minimap2_options_cns = -t 21 -k17 -w17
nextgraph_options = -a 1
##############################################################
However I noticed that many nd.asm.f.part*.fasta files in my 03.ctg_graph/03.ctg_cns.sh.work directory are empty，If these files were generated properly, it would be about the size of the genome I expected.
The intermediate result for this part is as follows：
##############################################################
ll ctg_cns20 ctg_cns25
ctg_cns20:
total 24564
-rw-rw-r-- 1 25146734 May 21 04:10 nd.asm.f.part019.fasta
-rwxr--r-- 1 957 May 21 04:04 test.sh
-rw-rw-r-- 1 0 May 21 04:10 test.sh.done

ctg_cns25:
total 4
-rw-rw-r-- 1 0 May 21 04:05 nd.asm.f.part024.fasta
-rwxr--r-- 1 957 May 21 04:04 test.sh
-rw-rw-r-- 1 0 May 21 04:05 test.sh.done

##############################################################
However, even if the generated nd.asm.f.part024.fasta file is empty, the process still works；
The following is the log file delivered to the sge cluster
##############################################################
hostname

• hostname
  cd /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns25
• cd /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns25
  time /public/apps/miniconda3/bin/python /public/pipline/GenomicAnalysis/01.assemble/01.nextdenovo/NextDenovo_v2.5.0/NextDenovo/lib/ctg_cns.py -p 15 -g /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta -b /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta.blc -i 24 -r ont -l /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.input.bams -o nd.asm.f.part024.fasta
• /public/apps/miniconda3/bin/python /public/pipline/GenomicAnalysis/01.assemble/01.nextdenovo/NextDenovo_v2.5.0/NextDenovo/lib/ctg_cns.py -p 15 -g /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta -b /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta.blc -i 24 -r ont -l /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.input.bams -o nd.asm.f.part024.fasta
  [232296 INFO] 2022-05-21 04:06:33 Corrected step options:
  [232296 INFO] 2022-05-21 04:06:33
  split: 1
  auto: True
  process: 15
  read_type: 1
  block_index: 24
  window: 5000000
  uppercase: False
  alignment_score_ratio: 0.8
  out: nd.asm.f.part024.fasta
  alignment_identity_ratio: 0.8
  bam_list: /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.input.bams
  genome: /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta
  block: /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta.blc
  [232301 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232301 from parent 232296
  [232304 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232304 from parent 232296
  [232306 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232306 from parent 232296
  [232307 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232307 from parent 232296
  [232309 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232309 from parent 232296
  [232311 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232311 from parent 232296
  [232313 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232313 from parent 232296
  [232315 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232315 from parent 232296
  [232317 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232317 from parent 232296
  [232319 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232319 from parent 232296
  [232321 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232321 from parent 232296
  [232323 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232323 from parent 232296
  [232325 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232325 from parent 232296
  [232328 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232328 from parent 232296
  [232330 INFO] 2022-05-21 04:06:36 Start a corrected worker in 232330 from parent 232296

real 0m2.634s
user 0m1.851s
sys 0m0.672s
touch /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns25/test.sh.done

• touch /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns25/test.sh.done
  ##############################################################
  I would like to know how to resize the genome to be in line with my expectations and why the nd.asm.f.part*.fasta file size is 0；
  Thank you again sincerely！

[2benaszq]

By the way, the assembled size is 906Mb, but the busco evaluation is normal, 96.8%

[moold]

Hi, could you paste the main log to here? what is the file size of test_nd_run//03.ctg_graph/nd.asm.fasta and test_nd_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta?

[2benaszq]

Hi, could you paste the main log to here? what is the file size of test_nd_run//03.ctg_graph/nd.asm.fasta and test_nd_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta?

Hello, Mr. Hu；
this is my file size；
ll -h test_nd_run/03.ctg_graph/nd.asm.fasta test_nd_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta
-rw-rw-r-- 1 858M May 21 03:11 test_nd_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/nd.asm.p.fasta
-rw-rw-r-- 1 865M May 21 04:16 test_nd_run/03.ctg_graph/nd.asm.fasta
##############################################################
this is my main log;
Since the log file is a bit long, I omitted some repeated and parallel task logs here, they are all delivered normally。
##############################################################
[54495 INFO] 2022-05-18 13:11:53 NextDenovo start...
[54495 INFO] 2022-05-18 13:11:53 version:v2.5.0 logfile:pid54495.log.info
[54495 WARNING] 2022-05-18 13:11:53 Re-write workdir
[54495 INFO] 2022-05-18 13:11:53 skip mkdir: /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run
[54495 INFO] 2022-05-18 13:11:53 skip mkdir: /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/01.raw_align
[54495 INFO] 2022-05-18 13:11:53 skip mkdir: /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/02.cns_align
[54495 INFO] 2022-05-18 13:11:53 skip mkdir: /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph
[54495 INFO] 2022-05-18 13:11:53 skip step: db_stat
[54495 INFO] 2022-05-18 13:11:53 updated options:
rerun: 3
task: all
rewrite: 1
job_type: sge
read_type: ont
input_type: raw
read_cutoff: 1k
seed_depth: 45.0
parallel_jobs: 36
pa_correction: 36
seed_cutfiles: 51
job_prefix: test
genome_size: 1741M
seed_cutoff: 38807
blocksize: 14651854901
ctg_cns_options: -p 15
nextgraph_options: -a 1
minimap2_options_map: -x map-ont
sort_options: -m 43g -t 18 -k 40 -k 40
minimap2_options_raw: -t 21 -x ava-ont
submit: qsub -cwd -l vf=60g,q=all.q {script}
correction_options: -p 15 -max_lq_length 10000 -min_len_seed 19403
minimap2_options_cns: -t 21 -k17 -w17 -x ava-ont -k 17 -w 17 --minlen 2000 --maxhan1 5000
workdir: /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run
input_fofn: /calculate/home/user/test/03.test/01.assembly/workdir/input.fofn
raw_aligndir: /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/01.raw_align
cns_aligndir: /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/02.cns_align
ctg_graphdir: /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph
[54495 INFO] 2022-05-18 13:11:53 summary of input data:
file:�[35m /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/01.raw_align/input.reads.stat �[0m
[Read length stat]
Types Count (#) Length (bp)
N10 168826 80724
N20 394168 65563
N30 666133 54863
N40 991161 45748
N50 1385178 37238
N60 1880321 28892
N70 2545544 20489
N80 3578377 11813
N90 5764807 4824

Types Count (#) Bases (bp) Depth (X)
Raw 14209923 163797508129 94.08
Filtered 1763560 994638699 0.57
Clean 12446363 162802869430 93.51

Suggested seed_cutoff (genome size: 1741.00Mb, expected seed depth: 45, real seed depth: 45.00): 38807 bp
[54495 INFO] 2022-05-18 13:11:53 skip step: db_split
[54495 INFO] 2022-05-18 13:11:53 skip step: raw_align
[54495 INFO] 2022-05-18 13:12:27 skip step: sort_align
[54495 INFO] 2022-05-18 13:12:30 Total jobs: 17
[54495 INFO] 2022-05-18 13:12:30 Submitted jobID:[2701718] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/02.cns_align/01.seed_cns.sh.work/seed_cns35/test.sh] in the sge_cycle.
....................................................................................................................................
[54495 INFO] 2022-05-18 13:12:30 Submitted jobID:[2701734] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/02.cns_align/01.seed_cns.sh.work/seed_cns51/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-18 13:54:22 seed_cns done
[54495 INFO] 2022-05-18 13:54:22 seed_cns finished, and final corrected reads file:
[54495 INFO] 2022-05-18 13:54:22 �[35m /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/02.cns_align/01.seed_cns.sh.work/seed_cns/cns.fasta �[0m
[54495 INFO] 2022-05-18 13:54:38 Total jobs: 1326
[54495 INFO] 2022-05-18 13:54:38 Submitted jobID:[2701978] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/02.cns_align/02.cns_align.sh.work/cns_align0/cns_align0001/test.sh] in the sge_cycle.
....................................................................................................................................
[54495 INFO] 2022-05-20 22:19:47 Submitted jobID:[2739273] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/02.cns_align/02.cns_align.sh.work/cns_align4/cns_align1326/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 02:54:44 cns_align done
[54495 INFO] 2022-05-21 02:54:49 Total jobs: 1
[54495 INFO] 2022-05-21 02:54:49 Submitted jobID:[2755972] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/01.ctg_graph.sh.work/ctg_graph1/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 03:12:21 ctg_graph done
[54495 INFO] 2022-05-21 03:12:26 Total jobs: 51
[54495 INFO] 2022-05-21 03:12:26 Submitted jobID:[2762140] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/02.ctg_align.sh.work/ctg_align01/test.sh] in the sge_cycle.
....................................................................................................................................
[54495 INFO] 2022-05-21 03:39:57 Submitted jobID:[2764894] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/02.ctg_align.sh.work/ctg_align51/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:49 ctg_align done
[54495 INFO] 2022-05-21 04:05:53 Total jobs: 36
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769228] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns01/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769229] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns02/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769230] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns03/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769231] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns04/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769232] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns05/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769233] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns06/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769234] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns07/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769235] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns08/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769236] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns09/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769237] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns10/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769238] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns11/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769239] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns12/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769240] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns13/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769241] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns14/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769242] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns15/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769243] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns16/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769244] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns17/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769246] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns18/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769247] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns19/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769248] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns20/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769249] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns21/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769250] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns22/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769251] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns23/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769253] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns24/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769254] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns25/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769255] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns26/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769256] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns27/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769257] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns28/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769258] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns29/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769259] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns30/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769260] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns31/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769261] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns32/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769263] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns33/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769264] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns34/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769265] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns35/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:05:53 Submitted jobID:[2769266] jobCmd:[/calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/03.ctg_cns.sh.work/ctg_cns36/test.sh] in the sge_cycle.
[54495 INFO] 2022-05-21 04:17:02 ctg_cns done
[54495 INFO] 2022-05-21 04:17:11 nextDenovo finished
[54495 INFO] 2022-05-21 04:17:11 final assembly file:
[54495 INFO] 2022-05-21 04:17:11 �[35m /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/nd.asm.fasta �[0m
[54495 INFO] 2022-05-21 04:17:11 final stat file:
[54495 INFO] 2022-05-21 04:17:11 �[35m /calculate/home/user/test/03.test/01.assembly/workdir/test_nd_run/03.ctg_graph/nd.asm.fasta.stat �[0m
[54495 INFO] 2022-05-21 04:17:11 asm stat:
[54495 INFO] 2022-05-21 04:17:11
Type Length (bp) Count (#)
N10 65722573 2
N20 64762714 3
N30 43175573 5
N40 25769601 8
N50 24223420 11
N60 18614738 16
N70 9511832 23
N80 4147554 38
N90 971234 88

Min. 54156 -
Max. 69308906 -
Ave. 2581648 -
Total 906158747 351
##############################################################
Thank you，Mr. Hu！

[moold]

The log shows that nextdenovo has fininshed without errors. So if you are sure that the estimated genome size is right (the busco score is good, while the assembly size is only half of estimated genome size, so this is really weird), see FAQ to optimize assembly size.

[2benaszq]

The log shows that nextdenovo has fininshed without errors. So if you are sure that the estimated genome size is right (the busco score is good, while the assembly size is only half of estimated genome size, so this is really weird), see FAQ to optimize assembly size.

Ok, thank you Mr. Hu；
I think it may still be a problem of estimating the genome size, thank you for your suggestion