Running: /projects/rwarren_prj2/LINKS/paper/links_v1.5/LINKS [v1.5]
-f rawapATlinks3.scaffolds.fa
-s pacbio.fof
-d 20000
-k 21
-e 0.1
-l 5
-a 0.3
-t 5
-o 10
-b rawapATlinks4
-r rawapATlinks1.bloom
-p 0.0001
-x 0

Checking pacbio.fasta...ok
Checking sequence target file rawapATlinks3.scaffolds.fa...ok
Checking Bloom filter file rawapATlinks1.bloom...ok
A Bloom filter was supplied (rawapATlinks1.bloom) and will be used instead of building a new one from -f rawapATlinks3.scaffolds.fa

=>Reading long reads, building hash table: Wed Jun 17 17:05:44 PDT 2015

Reads processed k=21, dist=20000, offset=10 nt, sliding step=5 nt:

Reads processed from file 1/1, pacbio.fasta:
3448228


Extracted 13943 total 21-mer pairs

=>Reading sequence contigs (to scaffold), tracking k-mer positions: Wed Jun 17 17:09:30 PDT 2015

Contigs processed k=21:
997


=>Scaffolding initiated: Wed Jun 17 17:11:13 PDT 2015

===========PAIRED K-MER STATS===========
Total number of pairs extracted from -s pacbio.fof: 13943
At least one sequence/pair missing from contigs: 0
Assembled pairs: 5554 (11108 sequences)
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 4058
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 286
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 256
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 46
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 908
	---
Total satisfied: 4104	unsatisfied: 1450

Breakdown by insert sizes:
--------Reads with 20000 bp inserts--------
MIN:18000 MAX:22000 as defined by 20000 * 0.1
At least one sequence/pair missing: 
Assembled pairs: 5554
	Satisfied in distance/logic within contigs (i.e. -> <-, distance on target: 4058
	Unsatisfied in distance within contigs (i.e. distance out-of-bounds): 286
	Unsatisfied pairing logic within contigs (i.e. illogical pairing ->->, <-<- or <-->): 256
	---
	Satisfied in distance/logic within a given contig pair (pre-scaffold): 46
	Unsatisfied in distance within a given contig pair (i.e. calculated distances out-of-bounds): 908
============================================
=>Scaffolding ended: Wed Jun 17 17:11:18 PDT 2015
=>Making FASTA file: Wed Jun 17 17:11:18 PDT 2015

Scaffolding executed normally Wed Jun 17 17:11:22 PDT 2015