prophage fasta file

[mujiezhang]

Hi,
I am using PhiSpy to predict prophages from bacteria. But the prophage fasta file have been masked with Ns. You say it is trivial to convert this format into separate contigs without the Ns but it is more complex to go from separate contigs back to a single joined contig. So how can I simply convert the format into separate contigs without Ns? Or does the PhiSpy.py have the option to do that?
And I have another question. I got an error like
''No bases were counted for orf {'start': 1570484, 'stop': 1570485, 'phmm': 0.0, 'peg': 'peg', 'is_phage': 0} from 1570484 to 1570485
This error is usually thrown with an exceptionally short ORF that is only a few bases. You should check this ORF and confirm it is real!"
and I checked the gbk file. This gene looks like this
" gene join(1570484..1570485,1..994)
/locus_tag="SMAR_RS00005"
/old_locus_tag="Smar_0001"
/db_xref="GeneID:4907656"
CDS join(1570484..1570485,1..994)
/locus_tag="SMAR_RS00005"
/old_locus_tag="Smar_0001"
/inference="COORDINATES: similar to AA
sequence:RefSeq:WP_013143107.1"
/note="Derived by automated computational analysis using
gene prediction method: Protein Homology."
/codon_start=1
/transl_table=11
/product="TIGR00269 family protein"
/protein_id="WP_052833761.1"
/db_xref="GeneID:4907656"
/translation="MVNCSICGRPAVYVNRISGQAYCKKHFLEYFDKKVRRTIRKYKM
FSSREHIVVAVSGGKDSLSLLHYLYNLSKRVPGWKITALLIDEGIGGYRDITKKDFLR
VVNELGVNYKIASFKEYLGYTLDEIVRIGREKGLPYLPCSYCGVFRRYLLNKVARDLG
GTVLATAHNLDDVIQTYVMNIINNSWDKILRLAPVTGPLDHPKFVRRAKPFYEILEKE
TTLYSILNNLYPKFVECPYARFNIRWMIRRQLNELEEKYPGTKYSLLRSLLRIISILS
KHRDEIIQGEIKTCKVCGEPSAHEICRACLYRYELGIMREDERKIVEEVLGKKKK"
"
So how can I solve this problem?
Sorry for my ignorance...I am a new bird...