using Nextpolish and after polished ,produce more contigs

[guang-xi]

Hi
i used Nextpolish to polish my primary contigs fasta finished by Canu2.0. I followed the tutoral——using PE-short reads and Pacbio long reads for two rounds each.
here is my code:
########################################################
job_type = local
job_prefix = nextPolish
task = best
rewrite = yes
rerun = 3
parallel_jobs = 8
multithread_jobs = 8
genome =genome.contigs.fasta
genome_size = auto
workdir = ./01_rundir
polish_options = -p 8

[sgs_option]
sgs_fofn = ./sgs.fofn
sgs_options = -max_depth 100

[lgs_option]
lgs_fofn = ./lgs.fofn
lgs_options = -min_read_len 10k -max_read_len 150k -max_depth 60
lgs_minimap2_options = -x map-ont -t 8
########################################################
but after i polished my genome contigs ,i found that the contigs numbers increased highly,following figures are my genome.contigs.fasta、genome.nextpolish.contigs.fasta consequences statistics

could you tell me how to deal with it?

[moold]

what is the version of NextPolish you are using? Could you paste some seq IDs in the polished genome while not existed in the original genome?

[guang-xi]

the version is V1.2.4

[moold]

I guess the short reads contain N, see FAQ vi. BTW, pls update to the latest version.

[guang-xi]

ok,thank you ,ill try and feedback the result