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SSPACE fasta output doesn't contain undefined nucleotides (NNNNNNN nucleotides )

Hello Biostar ! I hope you all doing well , please i have question in scaffolding

i used sspace for scaffolding using this command line 

GapFiller.pl -l Gap_Filler_Library   -x 1 -k 10 -n 30  -T 4  -s contigs.fa -m 30 -b GapFiller_RESULTS -t

the contigs file was obtained by assembly of Miseq (length =200 ) data using spades ,

the library file contain this informations

Lib1 bowtie R_1_Miseq.fastq R_2_Miseq.fastq 400 0.25 FR

The problem is in the fasta output of sspace , i didn't find any undefined nucleotides (NNNNNN ) when i used Hiseq data , it gives fasta output containing NNN nucleotides , i don't know why i obtained this results in Miseq data , can you please tell if theres any explanation for this results or if i did something wrong in the paramaters

Thank you very much !

assembly sequence software error alignment
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written by Bioinfo • Bioinfo

Hi, I also run into this situation, have you found the reason, could you give me some suggestions?

Thank you very much!

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written by dukecomeback • dukecomeback

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