Some contigs are not scaffolded

[rknx]

I have a plasmid that I am trying to stitch together. Based on molecular work and homology, I'm fairly certain two contigs (NODE_001 and NODE_051) below are part of same plasmid. However, in the final results, NODE_051 does not seem to be scaffolded with NODE_001.

Command

ragtag.py scaffold -C --debug -t 4 -d 250000 --aligner nucmer -o ragtag/qry ref.fa qry.fa

Please find relevant parts of debug outputs that may be of use:

ragtag.scaffold.debug.query.info.txt

NODE_001	CP018729.1	1.0	1.0	1.0
NODE_051	CP018729.1	1.0	1.0	1.0
NODE_130	CP018729.1	1.0	1.0	1.0
NODE_141	CP018729.1	1.0	1.0	1.0
NODE_165	CP018729.1	1.0	1.0	1.0

ragtag.scaffold.debug.unfiltered.paf

NODE_001	165349	16993	165349	+	CP018729.1	211336	0	148354	148339	148356	0
NODE_001	165349	80	16993	+	CP018729.1	211336	194424	211336	16912	16913	0
NODE_051	40607	37844	39333	-	CP018729.1	211336	152188	153677	1446	1489	0
NODE_051	40607	72	32458	-	CP018729.1	211336	162034	194428	32308	32395	0
NODE_130	5747	0	3339	+	CP018729.1	211336	156050	159389	3339	3339	0
NODE_141	3861	0	3861	-	CP018729.1	211336	148692	152553	3861	3861	0
NODE_165	524	0	524	-	CP018729.1	211336	155185	155709	524	524	0

ragtag.scaffold.debug.filtered.paf

NODE_001	165349	16993	165349	+	CP018729.1	211336	0	148354	148339	148356	0
NODE_001	165349	80	16993	+	CP018729.1	211336	194424	211336	16912	16913	0
NODE_051	40607	37844	39333	-	CP018729.1	211336	152188	153677	1446	1489	0
NODE_051	40607	72	32458	-	CP018729.1	211336	162034	194428	32308	32395	0
NODE_130	5747	0	3339	+	CP018729.1	211336	156050	159389	3339	3339	0
NODE_141	3861	0	3861	-	CP018729.1	211336	148692	152553	3861	3861	0
NODE_165	524	0	524	-	CP018729.1	211336	155185	155709	524	524	0

ragtag.scaffold.asm.paf

NODE_001	165349	16993	165349	+	CP018729.1	211336	0	148354	148339	148356	0	NM:i:17	cg:Z:61867M1I59022M1I27465M
NODE_001	165349	80	16993	+	CP018729.1	211336	194424	211336	16912	16913	0	NM:i:1	cg:Z:15091M1I1821M
NODE_051	40607	37844	39333	-	CP018729.1	211336	152188	153677	1446	1489	0	NM:i:43	cg:Z:1489M
NODE_051	40607	72	32458	-	CP018729.1	211336	162034	194428	32308	32395	0	NM:i:87	cg:Z:27321M2D1M3D16M1D87M3D3189M1I1771M
NODE_130	5747	0	3339	+	CP018729.1	211336	156050	159389	3339	3339	0	NM:i:0	cg:Z:3339M
NODE_141	3861	0	3861	-	CP018729.1	211336	148692	152553	3861	3861	0	NM:i:0	cg:Z:3861M
NODE_165	524	0	524	-	CP018729.1	211336	155185	155709	524	524	0	NM:i:0	cg:Z:524M

But in the end, it appears that NODE_051 is not scaffolded together with NODE_001 in CP018729.1.

ragtag.scaffold.agp

CP018729.1_RagTag	1	165349	1	W	NODE_001	1	165349	+
Chr0_RagTag	50040	90646	43	W	NODE_051	1	40607	+
Chr0_RagTag	90647	90746	44	U	100	contig	no	na

rragtag.scaffold.stats

placed_sequences	placed_bp	unplaced_sequences	unplaced_bp	gap_bp	gap_sequences
145	5285728	23	108456	16400	164

Why is NODE_051 not a part of the scaffold, and what parameters should I change to include it? Please let me know if you'd like the input files. Thanks.