Command: 
Programfile g GAP_VALUE k KMER_SIZE LD LOAD_SKG GS GENOME_SIZE TrimN TRIM_READS_WITH_N f INPUT_FILE1 f INPUT_FILE2 i1 INWARD_PAIR_END1 i2 INWARD_PAIR_END2 o1 OUTWARD_PAIR_END1 o2 OUTWARD_PAIR_END2

Parameters:
k: kmer size, support 15~127.
g: number of skipped intermediate k-mers, support 1-25.
f: single end reads. Multiple inputs shall be independently imported with this parameter.
i1 & i2 (or p1 & p2): inward paired-end reads.
o1 & o2 (or l1 & l2): outward paired-end reads.
GS: genome size estimation in bp (used for memory pre-allocation), suggest a large value if possible.(e.g. ~ 2x genome size)
LD: load a saved k-mer graph. 
BC: 1: build contigs.0: don't build.
KmerTable: 1 if you want to output the kmer table.
NodeCovTh: coverage threshold for spurious k-mers, support 0-16. (default 1)
EdgeCovTh: coverage threshold for spurious links, support 0-16. (default 0)
PathCovTh: coverage threshold for spurious paths in the breadth-first search, support 0-100.
TrimLen: trim long sequences to this length.
TrimN: throw away reads with more than this number of Ns.
TrimQual: trim off tails with quality scores lower than this.
QualBase: lowest quality score value (in ASCII value) in the current fastq scoring system, default: '!'.

For error correction:
Denoise: use 1 to call the error correction module. (default 0)
H: hybrid mode. 0 (Default): reads will be trimmed at the ends to ensure denoising accuracy (*MUST* set 0 for the last round). 1: reads will not be trimmed at the ends; 
CovTh: coverage threshold for an error. A k-mer with coverage < this value will be checked. Setting 0 will allow the program to choose a value based on the coverage histogram.
CorrTh: coverage threshold for a correct k-mer candidate. A k-mer with coverage >= this value will be considered a candidate for correction. Setting 0 will allow the program to choose a value based on the coverage histogram.

For scaffolding:
ExpCov: expected average k-mer coverage in a unique contig. Used for scaffolding.
Scaffold: 1: scaffolding with paired reads. 0: single end assembly.
LinkCovTh: coverage threshold for spurious paired-end links, support 0-100. (default 5)
Iter_Scaffold: 1: iterative scaffolding using the already built scaffolds (/super contigs). 0: one round scaffolding.
For mate pair scaffolding:
InsertSize: estimated insert size of the current pair.
i1_mp & i2_mp: inward mate paired reads (large insert sizes >10k, for shorter libraries omit "_mp").
o1_mp & o2_mp : outward paired-end reads (large insert sizes >10k, for shorter libraries omit "_mp").

Scanning the dataset.
1/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fastq
Reading: 50000000
Reading: 100000000
Reading: 150000000
2/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fastq
Reading: 200000000
Reading: 250000000
Reading: 300000000
3/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fastq
Reading: 350000000
Reading: 400000000
Reading: 450000000
Reading: 500000000
4/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fastq
Reading: 550000000
Reading: 600000000
Reading: 650000000
Reading: 700000000
Reading: 750000000
5/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R1_001_val_1_val_1.fastq
6/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L001_R2_001_val_2_val_2.fastq
7/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R1_001_val_1_val_1.fastq
8/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR005_S4_L002_R2_001_val_2_val_2.fastq
9/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R1_001_val_1_val_1.fastq
10/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L001_R2_001_val_2_val_2.fastq
11/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R1_001_val_1_val_1.fastq
12/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR006_S3_L002_R2_001_val_2_val_2.fastq
13/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R1_001_val_1_val_1.fastq
14/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L001_R2_001_val_2_val_2.fastq
15/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R1_001_val_1_val_1.fastq
16/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR012_S1_L002_R2_001_val_2_val_2.fastq
17/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R1_001_val_1_val_1.fastq
Reading: 800000000
Reading: 850000000
Reading: 900000000
Reading: 950000000
Reading: 1000000000
Reading: 1050000000
18/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fastq
Reading: 1100000000
Reading: 1150000000
Reading: 1200000000
Reading: 1250000000
Reading: 1300000000
Reading: 1350000000
19/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fastq
Reading: 1400000000
Reading: 1450000000
Reading: 1500000000
Reading: 1550000000
Reading: 1600000000
Reading: 1650000000
Reading: 1700000000
Reading: 1750000000
20/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fastq
Reading: 1800000000
Reading: 1850000000
Reading: 1900000000
Reading: 1950000000
Reading: 2000000000
Reading: 2050000000
Reading: 2100000000
21/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fastq
Reading: 2150000000
Reading: 2200000000
Reading: 2250000000
Reading: 2300000000
Reading: 2350000000
Reading: 2400000000
Reading: 2450000000
Reading: 2500000000
Reading: 2550000000
Reading: 2600000000
Reading: 2650000000
Reading: 2700000000
Reading: 2750000000
Reading: 2800000000
Reading: 2850000000
22/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fastq
Reading: 2900000000
Reading: 2950000000
Reading: 3000000000
Reading: 3050000000
Reading: 3100000000
Reading: 3150000000
Reading: 3200000000
Reading: 3250000000
Reading: 3300000000
Reading: 3350000000
Reading: 3400000000
Reading: 3450000000
Reading: 3500000000
Reading: 3550000000
Reading: 3600000000
23/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fastq
Reading: 3650000000
Reading: 3700000000
Reading: 3750000000
Reading: 3800000000
Reading: 3850000000
Reading: 3900000000
Reading: 3950000000
Reading: 4000000000
Reading: 4050000000
Reading: 4100000000
Reading: 4150000000
Reading: 4200000000
Reading: 4250000000
Reading: 4300000000
Reading: 4350000000
Reading: 4400000000
Reading: 4450000000
Reading: 4500000000
24/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fastq
Reading: 4550000000
Reading: 4600000000
Reading: 4650000000
Reading: 4700000000
Reading: 4750000000
Reading: 4800000000
Reading: 4850000000
Reading: 4900000000
Reading: 4950000000
Reading: 5000000000
Reading: 5050000000
Reading: 5100000000
Reading: 5150000000
Reading: 5200000000
Reading: 5250000000
Reading: 5300000000
Reading: 5350000000
25/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fastq
Reading: 5400000000
Reading: 5450000000
Reading: 5500000000
Reading: 5550000000
Reading: 5600000000
26/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fastq
Reading: 5650000000
Reading: 5700000000
Reading: 5750000000
Reading: 5800000000
Reading: 5850000000
27/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1_val_1.fastq
Reading: 5900000000
Reading: 5950000000
Reading: 6000000000
Reading: 6050000000
Reading: 6100000000
Reading: 6150000000
28/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fastq
Reading: 6200000000
Reading: 6250000000
Reading: 6300000000
Reading: 6350000000
Reading: 6400000000
Reading: 6450000000
29/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L001_R1_001_val_1_val_1.fastq
30/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L001_R2_001_val_2_val_2.fastq
31/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L002_R1_001_val_1_val_1.fastq
32/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR019_S7_L002_R2_001_val_2_val_2.fastq
33/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L001_R1_001_val_1_val_1.fastq
34/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L001_R2_001_val_2_val_2.fastq
35/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L002_R1_001_val_1_val_1.fastq
36/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fastq
Scan finished.
Error! K-mer size too large!