I am using wgsim to simulate reads from randomly selected genome regions (hg19):

1. bedtools shuffleBed to randomly permute location (1Mb);
2. wgsim (0.3.1-r13) to simulate reads.

Noticed that sometimes wgsim stops (works fine for some fasta files and for specific fasta produces empty <out.read1.fq> <out.read2.fq> files and does nothing else).

Checked those 1Mb fasta files and they are all N's

   >Chr_random
   NNNNNNNNNNNNNNN
   ...
   NNNNNNNNNNNNNNN

Question:

• How can solve this wgsim problem?
  Or
• How can I filter out N rich fasta files?

NB: wgsim "chromosome specif bias" was reported before - Short Read Simulator For Cnv Indel? Don't know if I am encountering the same problem here.

Edit

I simply used grep but their might be more elegant way.