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.
Building the sparse k-mer graph, round: 1
1/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fastq
Reading: 10000000
Memory used: 184 MB.
Reading time: 11641 secs.
Reading: 20000000
Memory used: 503 MB.
Reading time: 11899 secs.
Reading: 30000000
Memory used: 874 MB.
Reading time: 12154 secs.
Reading: 40000000
Memory used: 1254 MB.
Reading time: 12407 secs.
Reading: 50000000
Memory used: 1608 MB.
Reading time: 12662 secs.
Reading: 60000000
Memory used: 1958 MB.
Reading time: 12916 secs.
Reading: 70000000
Memory used: 2276 MB.
Reading time: 13170 secs.
Reading: 90000000
Memory used: 2839 MB.
Reading time: 13685 secs.
Reading: 100000000
Memory used: 3090 MB.
Reading time: 13950 secs.
Reading: 110000000
Memory used: 3309 MB.
Reading time: 14216 secs.
Reading: 120000000
Memory used: 3516 MB.
Reading time: 14484 secs.
Reading: 130000000
Memory used: 3698 MB.
Reading time: 14755 secs.
Reading: 140000000
Memory used: 3864 MB.
Reading time: 15028 secs.
Reading: 150000000
Memory used: 4010 MB.
Reading time: 15302 secs.
Reading: 160000000
Memory used: 4148 MB.
Reading time: 15576 secs.
2/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fastq
Reading: 170000000
Memory used: 4268 MB.
Reading time: 15859 secs.
Reading: 190000000
Memory used: 4483 MB.
Reading time: 16454 secs.
Reading: 220000000
Memory used: 4751 MB.
Reading time: 17354 secs.
Reading: 230000000
Memory used: 4827 MB.
Reading time: 17655 secs.
Reading: 250000000
Memory used: 4966 MB.
Reading time: 18264 secs.
Reading: 270000000
Memory used: 5081 MB.
Reading time: 18888 secs.
Reading: 280000000
Memory used: 5137 MB.
Reading time: 19196 secs.
Reading: 290000000
Memory used: 5189 MB.
Reading time: 19504 secs.
Reading: 300000000
Memory used: 5240 MB.
Reading time: 19813 secs.
Reading: 310000000
Memory used: 5288 MB.
Reading time: 20121 secs.
Reading: 320000000
Memory used: 5335 MB.
Reading time: 20430 secs.
Reading: 330000000
Memory used: 5379 MB.
Reading time: 20741 secs.
3/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fastq
Reading: 340000000
Memory used: 5422 MB.
Reading time: 21046 secs.
Reading: 350000000
Memory used: 5463 MB.
Reading time: 21350 secs.
Reading: 360000000
Memory used: 5500 MB.
Reading time: 21655 secs.
Reading: 380000000
Memory used: 5569 MB.
Reading time: 22267 secs.
Reading: 390000000
Memory used: 5601 MB.
Reading time: 22576 secs.
Reading: 400000000
Memory used: 5632 MB.
Reading time: 22883 secs.
Reading: 410000000
Memory used: 5661 MB.
Reading time: 23190 secs.
Reading: 420000000
Memory used: 5689 MB.
Reading time: 23499 secs.
Reading: 430000000
Memory used: 5716 MB.
Reading time: 23807 secs.
Reading: 440000000
Memory used: 5742 MB.
Reading time: 24117 secs.
Reading: 450000000
Memory used: 5767 MB.
Reading time: 24428 secs.
Reading: 460000000
Memory used: 5792 MB.
Reading time: 24737 secs.
Reading: 470000000
Memory used: 5817 MB.
Reading time: 25050 secs.
Reading: 480000000
Memory used: 5841 MB.
Reading time: 25361 secs.
Reading: 490000000
Memory used: 5864 MB.
Reading time: 25673 secs.
Reading: 500000000
Memory used: 5886 MB.
Reading time: 25986 secs.
Reading: 510000000
Memory used: 5909 MB.
Reading time: 26299 secs.
Reading: 520000000
Memory used: 5932 MB.
Reading time: 26613 secs.
4/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fastq
Reading: 570000000
Memory used: 6045 MB.
Reading time: 28230 secs.
Reading: 580000000
Memory used: 6069 MB.
Reading time: 28563 secs.
Reading: 600000000
Memory used: 6117 MB.
Reading time: 29211 secs.
Reading: 640000000
Memory used: 6214 MB.
Reading time: 30489 secs.
Reading: 650000000
Memory used: 6239 MB.
Reading time: 30808 secs.
Reading: 660000000
Memory used: 6264 MB.
Reading time: 31133 secs.
Reading: 670000000
Memory used: 6289 MB.
Reading time: 31458 secs.
Reading: 680000000
Memory used: 6315 MB.
Reading time: 31781 secs.
Reading: 700000000
Memory used: 6365 MB.
Reading time: 32422 secs.
Reading: 710000000
Memory used: 6389 MB.
Reading time: 32743 secs.
Reading: 720000000
Memory used: 6414 MB.
Reading time: 33060 secs.
Reading: 730000000
Memory used: 6439 MB.
Reading time: 33374 secs.
Reading: 740000000
Memory used: 6463 MB.
Reading time: 33688 secs.
Reading: 750000000
Memory used: 6488 MB.
Reading time: 33999 secs.
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
Reading: 760000000
Memory used: 6529 MB.
Reading time: 34325 secs.
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: 770000000
Memory used: 6573 MB.
Reading time: 34659 secs.
Reading: 780000000
Memory used: 6594 MB.
Reading time: 34965 secs.
Reading: 790000000
Memory used: 6615 MB.
Reading time: 35269 secs.
Reading: 800000000
Memory used: 6636 MB.
Reading time: 35572 secs.
Reading: 810000000
Memory used: 6658 MB.
Reading time: 35876 secs.
Reading: 820000000
Memory used: 6680 MB.
Reading time: 36182 secs.
Reading: 830000000
Memory used: 6701 MB.
Reading time: 36487 secs.
Reading: 840000000
Memory used: 6723 MB.
Reading time: 36790 secs.
Reading: 860000000
Memory used: 6771 MB.
Reading time: 37405 secs.
Reading: 890000000
Memory used: 6840 MB.
Reading time: 38322 secs.
Reading: 900000000
Memory used: 6864 MB.
Reading time: 38629 secs.
Reading: 910000000
Memory used: 6887 MB.
Reading time: 38935 secs.
Reading: 920000000
Memory used: 6911 MB.
Reading time: 39240 secs.
Reading: 930000000
Memory used: 6936 MB.
Reading time: 39550 secs.
Reading: 950000000
Memory used: 6984 MB.
Reading time: 40173 secs.
Reading: 970000000
Memory used: 7034 MB.
Reading time: 40800 secs.
Reading: 980000000
Memory used: 7059 MB.
Reading time: 41113 secs.
Reading: 990000000
Memory used: 7083 MB.
Reading time: 41424 secs.
Reading: 1000000000
Memory used: 7108 MB.
Reading time: 41736 secs.
Reading: 1010000000
Memory used: 7134 MB.
Reading time: 42050 secs.
Reading: 1020000000
Memory used: 7159 MB.
Reading time: 42363 secs.
Reading: 1040000000
Memory used: 7211 MB.
Reading time: 42992 secs.
Reading: 1050000000
Memory used: 7238 MB.
Reading time: 43306 secs.
Reading: 1060000000
Memory used: 7264 MB.
Reading time: 43620 secs.
Reading: 1070000000
Memory used: 7290 MB.
Reading time: 43934 secs.
18/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fastq
Reading: 1080000000
Memory used: 7318 MB.
Reading time: 44252 secs.
Reading: 1100000000
Memory used: 7384 MB.
Reading time: 44926 secs.
Reading: 1110000000
Memory used: 7417 MB.
Reading time: 45263 secs.
Reading: 1130000000
Memory used: 7487 MB.
Reading time: 45938 secs.
Reading: 1140000000
Memory used: 7522 MB.
Reading time: 46275 secs.
Reading: 1160000000
Memory used: 7594 MB.
Reading time: 46952 secs.
Reading: 1170000000
Memory used: 7631 MB.
Reading time: 47291 secs.
Reading: 1180000000
Memory used: 7667 MB.
Reading time: 47628 secs.
Reading: 1190000000
Memory used: 7704 MB.
Reading time: 47965 secs.
Reading: 1210000000
Memory used: 7779 MB.
Reading time: 48643 secs.
Reading: 1230000000
Memory used: 7854 MB.
Reading time: 49321 secs.
Reading: 1250000000
Memory used: 7933 MB.
Reading time: 50022 secs.
Reading: 1260000000
Memory used: 7972 MB.
Reading time: 50373 secs.
Reading: 1270000000
Memory used: 8013 MB.
Reading time: 50723 secs.
Reading: 1280000000
Memory used: 8053 MB.
Reading time: 51074 secs.
Reading: 1290000000
Memory used: 8094 MB.
Reading time: 51416 secs.
Reading: 1300000000
Memory used: 8134 MB.
Reading time: 51754 secs.
Reading: 1310000000
Memory used: 8176 MB.
Reading time: 52095 secs.
Reading: 1320000000
Memory used: 8219 MB.
Reading time: 52439 secs.
Reading: 1330000000
Memory used: 8261 MB.
Reading time: 52782 secs.
Reading: 1340000000
Memory used: 8304 MB.
Reading time: 53126 secs.
Reading: 1350000000
Memory used: 8347 MB.
Reading time: 53472 secs.
Reading: 1360000000
Memory used: 8390 MB.
Reading time: 53816 secs.
Reading: 1370000000
Memory used: 8433 MB.
Reading time: 54162 secs.
19/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fastq
Reading: 1390000000
Memory used: 8519 MB.
Reading time: 54853 secs.
Reading: 1400000000
Memory used: 8552 MB.
Reading time: 55185 secs.
Reading: 1410000000
Memory used: 8583 MB.
Reading time: 55515 secs.
Reading: 1420000000
Memory used: 8613 MB.
Reading time: 55845 secs.
Reading: 1440000000
Memory used: 8673 MB.
Reading time: 56504 secs.
Reading: 1450000000
Memory used: 8702 MB.
Reading time: 56833 secs.
Reading: 1460000000
Memory used: 8731 MB.
Reading time: 57158 secs.
Reading: 1470000000
Memory used: 8759 MB.
Reading time: 57481 secs.
Reading: 1490000000
Memory used: 8820 MB.
Reading time: 58131 secs.
Reading: 1500000000
Memory used: 8849 MB.
Reading time: 58458 secs.
Reading: 1510000000
Memory used: 8877 MB.
Reading time: 58783 secs.
Reading: 1520000000
Memory used: 8906 MB.
Reading time: 59108 secs.
Reading: 1530000000
Memory used: 8935 MB.
Reading time: 59433 secs.
Reading: 1540000000
Memory used: 8963 MB.
Reading time: 59761 secs.
Reading: 1550000000
Memory used: 8991 MB.
Reading time: 60088 secs.
Reading: 1560000000
Memory used: 9020 MB.
Reading time: 60416 secs.
Reading: 1570000000
Memory used: 9049 MB.
Reading time: 60743 secs.
Reading: 1590000000
Memory used: 9107 MB.
Reading time: 61408 secs.
Reading: 1600000000
Memory used: 9136 MB.
Reading time: 61740 secs.
Reading: 1610000000
Memory used: 9166 MB.
Reading time: 62071 secs.
Reading: 1620000000
Memory used: 9196 MB.
Reading time: 62402 secs.
Reading: 1630000000
Memory used: 9228 MB.
Reading time: 62737 secs.
Reading: 1650000000
Memory used: 9288 MB.
Reading time: 63404 secs.
Reading: 1660000000
Memory used: 9317 MB.
Reading time: 63738 secs.
Reading: 1670000000
Memory used: 9347 MB.
Reading time: 64071 secs.
Reading: 1680000000
Memory used: 9375 MB.
Reading time: 64407 secs.
Reading: 1690000000
Memory used: 9403 MB.
Reading time: 64743 secs.
Reading: 1700000000
Memory used: 9434 MB.
Reading time: 65078 secs.
Reading: 1710000000
Memory used: 9463 MB.
Reading time: 65413 secs.
Reading: 1720000000
Memory used: 9495 MB.
Reading time: 65752 secs.
Reading: 1730000000
Memory used: 9525 MB.
Reading time: 66094 secs.
Reading: 1740000000
Memory used: 9554 MB.
Reading time: 66433 secs.
Reading: 1750000000
Memory used: 9582 MB.
Reading time: 66770 secs.
Reading: 1760000000
Memory used: 9610 MB.
Reading time: 67108 secs.
20/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fastq
Reading: 1770000000
Memory used: 9643 MB.
Reading time: 67452 secs.
Reading: 1780000000
Memory used: 9682 MB.
Reading time: 67808 secs.
Reading: 1790000000
Memory used: 9721 MB.
Reading time: 68162 secs.
Reading: 1800000000
Memory used: 9761 MB.
Reading time: 68517 secs.
Reading: 1810000000
Memory used: 9802 MB.
Reading time: 68871 secs.
Reading: 1820000000
Memory used: 9842 MB.
Reading time: 69228 secs.
Reading: 1830000000
Memory used: 9882 MB.
Reading time: 69586 secs.
Reading: 1840000000
Memory used: 9922 MB.
Reading time: 69942 secs.
Reading: 1850000000
Memory used: 9962 MB.
Reading time: 70300 secs.
Reading: 1860000000
Memory used: 10005 MB.
Reading time: 70659 secs.
Reading: 1870000000
Memory used: 10045 MB.
Reading time: 71019 secs.
Reading: 1880000000
Memory used: 10086 MB.
Reading time: 71379 secs.
Reading: 1890000000
Memory used: 10126 MB.
Reading time: 71738 secs.
Reading: 1900000000
Memory used: 10167 MB.
Reading time: 72098 secs.
Reading: 1910000000
Memory used: 10209 MB.
Reading time: 72459 secs.
Reading: 1920000000
Memory used: 10249 MB.
Reading time: 72822 secs.
Reading: 1930000000
Memory used: 10290 MB.
Reading time: 73185 secs.
Reading: 1950000000
Memory used: 10374 MB.
Reading time: 73914 secs.
Reading: 1960000000
Memory used: 10417 MB.
Reading time: 74282 secs.
Reading: 1970000000
Memory used: 10461 MB.
Reading time: 74648 secs.
Reading: 1980000000
Memory used: 10504 MB.
Reading time: 75009 secs.
Reading: 1990000000
Memory used: 10550 MB.
Reading time: 75377 secs.
Reading: 2000000000
Memory used: 10596 MB.
Reading time: 75742 secs.
Reading: 2010000000
Memory used: 10639 MB.
Reading time: 76104 secs.
Reading: 2040000000
Memory used: 10768 MB.
Reading time: 77194 secs.
Reading: 2060000000
Memory used: 10854 MB.
Reading time: 77921 secs.
Reading: 2070000000
Memory used: 10896 MB.
Reading time: 78286 secs.
Reading: 2080000000
Memory used: 10938 MB.
Reading time: 78650 secs.
Reading: 2090000000
Memory used: 10981 MB.
Reading time: 79015 secs.
Reading: 2100000000
Memory used: 11026 MB.
Reading time: 79382 secs.
Reading: 2110000000
Memory used: 11068 MB.
Reading time: 79750 secs.
Reading: 2120000000
Memory used: 11111 MB.
Reading time: 80118 secs.
Reading: 2130000000
Memory used: 11153 MB.
Reading time: 80484 secs.
21/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R1_001_val_1_val_1.fastq
Reading: 2150000000
Memory used: 11237 MB.
Reading time: 81194 secs.
Reading: 2170000000
Memory used: 11302 MB.
Reading time: 81824 secs.
Reading: 2180000000
Memory used: 11335 MB.
Reading time: 82135 secs.
Reading: 2190000000
Memory used: 11367 MB.
Reading time: 82445 secs.
Reading: 2200000000
Memory used: 11398 MB.
Reading time: 82755 secs.
Reading: 2220000000
Memory used: 11464 MB.
Reading time: 83372 secs.
Reading: 2230000000
Memory used: 11498 MB.
Reading time: 83679 secs.
Reading: 2270000000
Memory used: 11637 MB.
Reading time: 84924 secs.
Reading: 2280000000
Memory used: 11671 MB.
Reading time: 85235 secs.
Reading: 2300000000
Memory used: 11739 MB.
Reading time: 85858 secs.
Reading: 2310000000
Memory used: 11775 MB.
Reading time: 86168 secs.
Reading: 2330000000
Memory used: 11849 MB.
Reading time: 86787 secs.
Reading: 2350000000
Memory used: 11934 MB.
Reading time: 87423 secs.
Reading: 2360000000
Memory used: 11971 MB.
Reading time: 87737 secs.
Reading: 2370000000
Memory used: 12009 MB.
Reading time: 88051 secs.
Reading: 2380000000
Memory used: 12046 MB.
Reading time: 88365 secs.
Reading: 2390000000
Memory used: 12083 MB.
Reading time: 88680 secs.
Reading: 2400000000
Memory used: 12120 MB.
Reading time: 88992 secs.
Reading: 2420000000
Memory used: 12197 MB.
Reading time: 89614 secs.
Reading: 2430000000
Memory used: 12236 MB.
Reading time: 89929 secs.
Reading: 2440000000
Memory used: 12275 MB.
Reading time: 90246 secs.
Reading: 2450000000
Memory used: 12316 MB.
Reading time: 90562 secs.
Reading: 2460000000
Memory used: 12355 MB.
Reading time: 90876 secs.
Reading: 2470000000
Memory used: 12395 MB.
Reading time: 91191 secs.
Reading: 2480000000
Memory used: 12433 MB.
Reading time: 91509 secs.
Reading: 2490000000
Memory used: 12471 MB.
Reading time: 91823 secs.
Reading: 2500000000
Memory used: 12510 MB.
Reading time: 92139 secs.
Reading: 2510000000
Memory used: 12550 MB.
Reading time: 92452 secs.
Reading: 2520000000
Memory used: 12592 MB.
Reading time: 92765 secs.
Reading: 2530000000
Memory used: 12638 MB.
Reading time: 93089 secs.
Reading: 2540000000
Memory used: 12679 MB.
Reading time: 93418 secs.
Reading: 2550000000
Memory used: 12720 MB.
Reading time: 93744 secs.
Reading: 2560000000
Memory used: 12761 MB.
Reading time: 94071 secs.
Reading: 2570000000
Memory used: 12801 MB.
Reading time: 94400 secs.
Reading: 2580000000
Memory used: 12842 MB.
Reading time: 94729 secs.
Reading: 2590000000
Memory used: 12883 MB.
Reading time: 95056 secs.
Reading: 2600000000
Memory used: 12925 MB.
Reading time: 95382 secs.
Reading: 2610000000
Memory used: 12967 MB.
Reading time: 95708 secs.
Reading: 2620000000
Memory used: 13012 MB.
Reading time: 96037 secs.
Reading: 2650000000
Memory used: 13140 MB.
Reading time: 97033 secs.
Reading: 2660000000
Memory used: 13181 MB.
Reading time: 97365 secs.
Reading: 2670000000
Memory used: 13223 MB.
Reading time: 97696 secs.
Reading: 2690000000
Memory used: 13308 MB.
Reading time: 98352 secs.
Reading: 2700000000
Memory used: 13352 MB.
Reading time: 98679 secs.
Reading: 2710000000
Memory used: 13398 MB.
Reading time: 99015 secs.
Reading: 2730000000
Memory used: 13485 MB.
Reading time: 99688 secs.
Reading: 2740000000
Memory used: 13529 MB.
Reading time: 100018 secs.
Reading: 2760000000
Memory used: 13616 MB.
Reading time: 100673 secs.
Reading: 2770000000
Memory used: 13665 MB.
Reading time: 101001 secs.
Reading: 2780000000
Memory used: 13711 MB.
Reading time: 101325 secs.
Reading: 2790000000
Memory used: 13757 MB.
Reading time: 101649 secs.
Reading: 2850000000
Memory used: 14035 MB.
Reading time: 103631 secs.
Reading: 2860000000
Memory used: 14081 MB.
Reading time: 103959 secs.
Reading: 2870000000
Memory used: 14129 MB.
Reading time: 104287 secs.
Reading: 2890000000
Memory used: 14227 MB.
Reading time: 104946 secs.
22/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L001_R2_001_val_2_val_2.fastq
Reading: 2900000000
Memory used: 14286 MB.
Reading time: 105307 secs.
Reading: 2910000000
Memory used: 14343 MB.
Reading time: 105665 secs.
Reading: 2920000000
Memory used: 14400 MB.
Reading time: 106025 secs.
Reading: 2930000000
Memory used: 14457 MB.
Reading time: 106384 secs.
Reading: 2940000000
Memory used: 14514 MB.
Reading time: 106746 secs.
Reading: 2960000000
Memory used: 14631 MB.
Reading time: 107471 secs.
Reading: 2970000000
Memory used: 14692 MB.
Reading time: 107831 secs.
Reading: 2980000000
Memory used: 14755 MB.
Reading time: 108189 secs.
Reading: 2990000000
Memory used: 14818 MB.
Reading time: 108546 secs.
Reading: 3000000000
Memory used: 14878 MB.
Reading time: 108900 secs.
Reading: 3010000000
Memory used: 14938 MB.
Reading time: 109251 secs.
Reading: 3020000000
Memory used: 14999 MB.
Reading time: 109600 secs.
Reading: 3030000000
Memory used: 15060 MB.
Reading time: 109952 secs.
Reading: 3050000000
Memory used: 15182 MB.
Reading time: 110657 secs.
Reading: 3060000000
Memory used: 15246 MB.
Reading time: 111007 secs.
Reading: 3070000000
Memory used: 15311 MB.
Reading time: 111357 secs.
Reading: 3090000000
Memory used: 15443 MB.
Reading time: 112070 secs.
Reading: 3110000000
Memory used: 15571 MB.
Reading time: 112781 secs.
Reading: 3120000000
Memory used: 15635 MB.
Reading time: 113139 secs.
Reading: 3130000000
Memory used: 15698 MB.
Reading time: 113496 secs.
Reading: 3160000000
Memory used: 15893 MB.
Reading time: 114563 secs.
Reading: 3170000000
Memory used: 15962 MB.
Reading time: 114923 secs.
Reading: 3200000000
Memory used: 16163 MB.
Reading time: 116006 secs.
Reading: 3210000000
Memory used: 16229 MB.
Reading time: 116367 secs.
Reading: 3230000000
Memory used: 16360 MB.
Reading time: 117095 secs.
Reading: 3240000000
Memory used: 16427 MB.
Reading time: 117456 secs.
Reading: 3250000000
Memory used: 16495 MB.
Reading time: 117818 secs.
Reading: 3260000000
Memory used: 16564 MB.
Reading time: 118179 secs.
Reading: 3280000000
Memory used: 16709 MB.
Reading time: 118921 secs.
Reading: 3290000000
Memory used: 16780 MB.
Reading time: 119296 secs.
Reading: 3300000000
Memory used: 16851 MB.
Reading time: 119673 secs.
Reading: 3320000000
Memory used: 16992 MB.
Reading time: 120433 secs.
Reading: 3340000000
Memory used: 17138 MB.
Reading time: 121190 secs.
Reading: 3350000000
Memory used: 17212 MB.
Reading time: 121566 secs.
Reading: 3360000000
Memory used: 17287 MB.
Reading time: 121949 secs.
Reading: 3380000000
Memory used: 17430 MB.
Reading time: 122706 secs.
Reading: 3390000000
Memory used: 17502 MB.
Reading time: 123086 secs.
Reading: 3400000000
Memory used: 17573 MB.
Reading time: 123466 secs.
Reading: 3420000000
Memory used: 17715 MB.
Reading time: 124231 secs.
Reading: 3450000000
Memory used: 17941 MB.
Reading time: 125376 secs.
Reading: 3460000000
Memory used: 18018 MB.
Reading time: 125766 secs.
Reading: 3470000000
Memory used: 18093 MB.
Reading time: 126152 secs.
Reading: 3480000000
Memory used: 18167 MB.
Reading time: 126538 secs.
Reading: 3500000000
Memory used: 18318 MB.
Reading time: 127316 secs.
Reading: 3510000000
Memory used: 18395 MB.
Reading time: 127706 secs.
Reading: 3520000000
Memory used: 18471 MB.
Reading time: 128086 secs.
Reading: 3530000000
Memory used: 18550 MB.
Reading time: 128463 secs.
Reading: 3540000000
Memory used: 18629 MB.
Reading time: 128839 secs.
Reading: 3550000000
Memory used: 18706 MB.
Reading time: 129220 secs.
Reading: 3560000000
Memory used: 18782 MB.
Reading time: 129598 secs.
Reading: 3570000000
Memory used: 18858 MB.
Reading time: 129976 secs.
Reading: 3580000000
Memory used: 18937 MB.
Reading time: 130358 secs.
Reading: 3590000000
Memory used: 19011 MB.
Reading time: 130740 secs.
Reading: 3600000000
Memory used: 19085 MB.
Reading time: 131121 secs.
Reading: 3610000000
Memory used: 19164 MB.
Reading time: 131504 secs.
Reading: 3620000000
Memory used: 19246 MB.
Reading time: 131887 secs.
Reading: 3630000000
Memory used: 19328 MB.
Reading time: 132269 secs.
23/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fastq
Reading: 3640000000
Memory used: 19403 MB.
Reading time: 132656 secs.
Reading: 3650000000
Memory used: 19463 MB.
Reading time: 133042 secs.
Reading: 3660000000
Memory used: 19514 MB.
Reading time: 133421 secs.
Reading: 3670000000
Memory used: 19563 MB.
Reading time: 133801 secs.
Reading: 3680000000
Memory used: 19611 MB.
Reading time: 134179 secs.
Reading: 3710000000
Memory used: 19757 MB.
Reading time: 135315 secs.
Reading: 3720000000
Memory used: 19806 MB.
Reading time: 135693 secs.
Reading: 3740000000
Memory used: 19906 MB.
Reading time: 136451 secs.
Reading: 3750000000
Memory used: 19956 MB.
Reading time: 136834 secs.
Reading: 3760000000
Memory used: 20002 MB.
Reading time: 137220 secs.
Reading: 3770000000
Memory used: 20050 MB.
Reading time: 137609 secs.
Reading: 3790000000
Memory used: 20145 MB.
Reading time: 138376 secs.
Reading: 3820000000
Memory used: 20289 MB.
Reading time: 139502 secs.
Reading: 3840000000
Memory used: 20386 MB.
Reading time: 140241 secs.
Reading: 3850000000
Memory used: 20439 MB.
Reading time: 140606 secs.
Reading: 3870000000
Memory used: 20548 MB.
Reading time: 141349 secs.
Reading: 3880000000
Memory used: 20595 MB.
Reading time: 141722 secs.
Reading: 3890000000
Memory used: 20643 MB.
Reading time: 142095 secs.
Reading: 3900000000
Memory used: 20690 MB.
Reading time: 142467 secs.
Reading: 3910000000
Memory used: 20737 MB.
Reading time: 142838 secs.
Reading: 3920000000
Memory used: 20785 MB.
Reading time: 143209 secs.
Reading: 3930000000
Memory used: 20833 MB.
Reading time: 143582 secs.
Reading: 3940000000
Memory used: 20881 MB.
Reading time: 143954 secs.
Reading: 3950000000
Memory used: 20930 MB.
Reading time: 144325 secs.
Reading: 3960000000
Memory used: 20981 MB.
Reading time: 144698 secs.
Reading: 3970000000
Memory used: 21031 MB.
Reading time: 145073 secs.
Reading: 3980000000
Memory used: 21077 MB.
Reading time: 145454 secs.
Reading: 4000000000
Memory used: 21171 MB.
Reading time: 146216 secs.
Reading: 4020000000
Memory used: 21267 MB.
Reading time: 146975 secs.
Reading: 4030000000
Memory used: 21316 MB.
Reading time: 147354 secs.
Reading: 4050000000
Memory used: 21413 MB.
Reading time: 148114 secs.
Reading: 4060000000
Memory used: 21462 MB.
Reading time: 148492 secs.
Reading: 4070000000
Memory used: 21514 MB.
Reading time: 148869 secs.
Reading: 4080000000
Memory used: 21563 MB.
Reading time: 149251 secs.
Reading: 4090000000
Memory used: 21612 MB.
Reading time: 149637 secs.
Reading: 4100000000
Memory used: 21661 MB.
Reading time: 150023 secs.
Reading: 4110000000
Memory used: 21710 MB.
Reading time: 150407 secs.
Reading: 4120000000
Memory used: 21758 MB.
Reading time: 150794 secs.
Reading: 4130000000
Memory used: 21807 MB.
Reading time: 151179 secs.
Reading: 4150000000
Memory used: 21909 MB.
Reading time: 151948 secs.
Reading: 4160000000
Memory used: 21961 MB.
Reading time: 152333 secs.
Reading: 4170000000
Memory used: 22013 MB.
Reading time: 152718 secs.
Reading: 4180000000
Memory used: 22067 MB.
Reading time: 153103 secs.
Reading: 4190000000
Memory used: 22124 MB.
Reading time: 153496 secs.
Reading: 4210000000
Memory used: 22224 MB.
Reading time: 154281 secs.
Reading: 4220000000
Memory used: 22277 MB.
Reading time: 154674 secs.
Reading: 4230000000
Memory used: 22328 MB.
Reading time: 155066 secs.
Reading: 4240000000
Memory used: 22377 MB.
Reading time: 155459 secs.
Reading: 4250000000
Memory used: 22427 MB.
Reading time: 155847 secs.
Reading: 4270000000
Memory used: 22525 MB.
Reading time: 156633 secs.
Reading: 4290000000
Memory used: 22627 MB.
Reading time: 157418 secs.
Reading: 4300000000
Memory used: 22675 MB.
Reading time: 157812 secs.
Reading: 4320000000
Memory used: 22768 MB.
Reading time: 158612 secs.
Reading: 4330000000
Memory used: 22815 MB.
Reading time: 159010 secs.
Reading: 4350000000
Memory used: 22911 MB.
Reading time: 159810 secs.
Reading: 4360000000
Memory used: 22965 MB.
Reading time: 160209 secs.
Reading: 4370000000
Memory used: 23014 MB.
Reading time: 160602 secs.
Reading: 4380000000
Memory used: 23062 MB.
Reading time: 160991 secs.
Reading: 4390000000
Memory used: 23112 MB.
Reading time: 161380 secs.
Reading: 4400000000
Memory used: 23163 MB.
Reading time: 161769 secs.
Reading: 4410000000
Memory used: 23223 MB.
Reading time: 162165 secs.
Reading: 4420000000
Memory used: 23276 MB.
Reading time: 162561 secs.
Reading: 4430000000
Memory used: 23323 MB.
Reading time: 162958 secs.
Reading: 4440000000
Memory used: 23369 MB.
Reading time: 163353 secs.
Reading: 4470000000
Memory used: 23510 MB.
Reading time: 164538 secs.
Reading: 4480000000
Memory used: 23557 MB.
Reading time: 164932 secs.
Reading: 4490000000
Memory used: 23604 MB.
Reading time: 165327 secs.
Reading: 4500000000
Memory used: 23651 MB.
Reading time: 165723 secs.
Reading: 4510000000
Memory used: 23700 MB.
Reading time: 166121 secs.
24/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fastq
Reading: 4520000000
Memory used: 23764 MB.
Reading time: 166535 secs.
Reading: 4530000000
Memory used: 23833 MB.
Reading time: 166957 secs.
Reading: 4540000000
Memory used: 23900 MB.
Reading time: 167379 secs.
Reading: 4560000000
Memory used: 24035 MB.
Reading time: 168219 secs.
Reading: 4580000000
Memory used: 24174 MB.
Reading time: 169061 secs.
Reading: 4590000000
Memory used: 24244 MB.
Reading time: 169483 secs.
Reading: 4600000000
Memory used: 24314 MB.
Reading time: 169905 secs.
Reading: 4610000000
Memory used: 24387 MB.
Reading time: 170327 secs.
Reading: 4620000000
Memory used: 24461 MB.
Reading time: 170750 secs.
Reading: 4630000000
Memory used: 24531 MB.
Reading time: 171176 secs.
Reading: 4640000000
Memory used: 24599 MB.
Reading time: 171605 secs.
Reading: 4650000000
Memory used: 24667 MB.
Reading time: 172034 secs.
Reading: 4660000000
Memory used: 24734 MB.
Reading time: 172462 secs.
Reading: 4670000000
Memory used: 24803 MB.
Reading time: 172891 secs.
Reading: 4680000000
Memory used: 24872 MB.
Reading time: 173318 secs.
Reading: 4710000000
Memory used: 25082 MB.
Reading time: 174578 secs.
Reading: 4720000000
Memory used: 25154 MB.
Reading time: 174994 secs.
Reading: 4730000000
Memory used: 25232 MB.
Reading time: 175408 secs.
Reading: 4740000000
Memory used: 25303 MB.
Reading time: 175825 secs.
Reading: 4750000000
Memory used: 25371 MB.
Reading time: 176243 secs.
Reading: 4760000000
Memory used: 25438 MB.
Reading time: 176662 secs.
Reading: 4780000000
Memory used: 25574 MB.
Reading time: 177501 secs.
Reading: 4800000000
Memory used: 25712 MB.
Reading time: 178341 secs.
Reading: 4810000000
Memory used: 25781 MB.
Reading time: 178764 secs.
Reading: 4820000000
Memory used: 25850 MB.
Reading time: 179185 secs.
Reading: 4830000000
Memory used: 25921 MB.
Reading time: 179608 secs.
Reading: 4840000000
Memory used: 25995 MB.
Reading time: 180031 secs.
Reading: 4850000000
Memory used: 26066 MB.
Reading time: 180458 secs.
Reading: 4860000000
Memory used: 26133 MB.
Reading time: 180888 secs.
Reading: 4870000000
Memory used: 26201 MB.
Reading time: 181317 secs.
Reading: 4890000000
Memory used: 26340 MB.
Reading time: 182179 secs.
Reading: 4900000000
Memory used: 26411 MB.
Reading time: 182611 secs.
Reading: 4910000000
Memory used: 26481 MB.
Reading time: 183043 secs.
Reading: 4930000000
Memory used: 26623 MB.
Reading time: 183911 secs.
Reading: 4940000000
Memory used: 26695 MB.
Reading time: 184344 secs.
Reading: 4950000000
Memory used: 26770 MB.
Reading time: 184776 secs.
Reading: 4960000000
Memory used: 26841 MB.
Reading time: 185214 secs.
Reading: 4970000000
Memory used: 26915 MB.
Reading time: 185655 secs.
Reading: 4980000000
Memory used: 26991 MB.
Reading time: 186099 secs.
Reading: 4990000000
Memory used: 27065 MB.
Reading time: 186539 secs.
Reading: 5000000000
Memory used: 27137 MB.
Reading time: 186977 secs.
Reading: 5010000000
Memory used: 27212 MB.
Reading time: 187417 secs.
Reading: 5020000000
Memory used: 27291 MB.
Reading time: 187860 secs.
Reading: 5040000000
Memory used: 27450 MB.
Reading time: 188748 secs.
Reading: 5050000000
Memory used: 27529 MB.
Reading time: 189193 secs.
Reading: 5060000000
Memory used: 27610 MB.
Reading time: 189640 secs.
Reading: 5070000000
Memory used: 27681 MB.
Reading time: 190084 secs.
Reading: 5080000000
Memory used: 27751 MB.
Reading time: 190532 secs.
Reading: 5090000000
Memory used: 27820 MB.
Reading time: 190978 secs.
Reading: 5100000000
Memory used: 27890 MB.
Reading time: 191426 secs.
Reading: 5110000000
Memory used: 27960 MB.
Reading time: 191872 secs.
Reading: 5120000000
Memory used: 28032 MB.
Reading time: 192317 secs.
Reading: 5130000000
Memory used: 28105 MB.
Reading time: 192765 secs.
Reading: 5140000000
Memory used: 28177 MB.
Reading time: 193219 secs.
Reading: 5150000000
Memory used: 28249 MB.
Reading time: 193672 secs.
Reading: 5170000000
Memory used: 28401 MB.
Reading time: 194586 secs.
Reading: 5180000000
Memory used: 28470 MB.
Reading time: 195041 secs.
Reading: 5200000000
Memory used: 28604 MB.
Reading time: 195957 secs.
Reading: 5210000000
Memory used: 28673 MB.
Reading time: 196410 secs.
Reading: 5220000000
Memory used: 28741 MB.
Reading time: 196860 secs.
Reading: 5230000000
Memory used: 28811 MB.
Reading time: 197304 secs.
Reading: 5240000000
Memory used: 28880 MB.
Reading time: 197752 secs.
Reading: 5250000000
Memory used: 28950 MB.
Reading time: 198206 secs.
Reading: 5260000000
Memory used: 29020 MB.
Reading time: 198659 secs.
Reading: 5270000000
Memory used: 29093 MB.
Reading time: 199113 secs.
Reading: 5280000000
Memory used: 29170 MB.
Reading time: 199572 secs.
Reading: 5290000000
Memory used: 29241 MB.
Reading time: 200029 secs.
Reading: 5300000000
Memory used: 29310 MB.
Reading time: 200493 secs.
Reading: 5310000000
Memory used: 29379 MB.
Reading time: 200956 secs.
Reading: 5320000000
Memory used: 29449 MB.
Reading time: 201419 secs.
Reading: 5330000000
Memory used: 29519 MB.
Reading time: 201877 secs.
Reading: 5340000000
Memory used: 29588 MB.
Reading time: 202332 secs.
Reading: 5350000000
Memory used: 29657 MB.
Reading time: 202795 secs.
Reading: 5360000000
Memory used: 29725 MB.
Reading time: 203254 secs.
Reading: 5370000000
Memory used: 29793 MB.
Reading time: 203713 secs.
Reading: 5380000000
Memory used: 29864 MB.
Reading time: 204174 secs.
25/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fastq
Reading: 5390000000
Memory used: 29937 MB.
Reading time: 204638 secs.
Reading: 5400000000
Memory used: 29989 MB.
Reading time: 205091 secs.
Reading: 5420000000
Memory used: 30090 MB.
Reading time: 205991 secs.
Reading: 5430000000
Memory used: 30142 MB.
Reading time: 206442 secs.
Reading: 5470000000
Memory used: 30359 MB.
Reading time: 208245 secs.
Reading: 5480000000
Memory used: 30412 MB.
Reading time: 208691 secs.
Reading: 5490000000
Memory used: 30467 MB.
Reading time: 209140 secs.
Reading: 5500000000
Memory used: 30521 MB.
Reading time: 209589 secs.
Reading: 5510000000
Memory used: 30573 MB.
Reading time: 210037 secs.
Reading: 5520000000
Memory used: 30633 MB.
Reading time: 210490 secs.
Reading: 5530000000
Memory used: 30688 MB.
Reading time: 210949 secs.
Reading: 5540000000
Memory used: 30743 MB.
Reading time: 211407 secs.
Reading: 5550000000
Memory used: 30802 MB.
Reading time: 211859 secs.
Reading: 5560000000
Memory used: 30859 MB.
Reading time: 212311 secs.
Reading: 5570000000
Memory used: 30913 MB.
Reading time: 212759 secs.
Reading: 5580000000
Memory used: 30972 MB.
Reading time: 213201 secs.
Reading: 5590000000
Memory used: 31028 MB.
Reading time: 213642 secs.
Reading: 5600000000
Memory used: 31087 MB.
Reading time: 214078 secs.
Reading: 5610000000
Memory used: 31149 MB.
Reading time: 214507 secs.
Reading: 5620000000
Memory used: 31208 MB.
Reading time: 214937 secs.
Reading: 5630000000
Memory used: 31264 MB.
Reading time: 215368 secs.
26/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fastq
Reading: 5640000000
Memory used: 31327 MB.
Reading time: 215797 secs.
Reading: 5650000000
Memory used: 31413 MB.
Reading time: 216265 secs.
Reading: 5660000000
Memory used: 31496 MB.
Reading time: 216732 secs.
Reading: 5690000000
Memory used: 31753 MB.
Reading time: 218128 secs.
Reading: 5700000000
Memory used: 31840 MB.
Reading time: 218591 secs.
Reading: 5710000000
Memory used: 31931 MB.
Reading time: 219060 secs.
Reading: 5720000000
Memory used: 32016 MB.
Reading time: 219528 secs.
Reading: 5730000000
Memory used: 32102 MB.
Reading time: 219992 secs.
Reading: 5740000000
Memory used: 32193 MB.
Reading time: 220461 secs.
Reading: 5750000000
Memory used: 32279 MB.
Reading time: 220928 secs.
Reading: 5760000000
Memory used: 32364 MB.
Reading time: 221394 secs.
Reading: 5770000000
Memory used: 32458 MB.
Reading time: 221868 secs.
Reading: 5780000000
Memory used: 32555 MB.
Reading time: 222352 secs.
Reading: 5790000000
Memory used: 32651 MB.
Reading time: 222833 secs.
Reading: 5800000000
Memory used: 32749 MB.
Reading time: 223313 secs.
Reading: 5810000000
Memory used: 32842 MB.
Reading time: 223792 secs.
Reading: 5820000000
Memory used: 32933 MB.
Reading time: 224268 secs.
Reading: 5830000000
Memory used: 33032 MB.
Reading time: 224746 secs.
Reading: 5840000000
Memory used: 33128 MB.
Reading time: 225228 secs.
Reading: 5850000000
Memory used: 33225 MB.
Reading time: 225708 secs.
Reading: 5860000000
Memory used: 33324 MB.
Reading time: 226189 secs.
Reading: 5870000000
Memory used: 33420 MB.
Reading time: 226672 secs.
Reading: 5880000000
Memory used: 33514 MB.
Reading time: 227155 secs.
27/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L002_R1_001_val_1_val_1.fastq
Reading: 5900000000
Memory used: 33682 MB.
Reading time: 228110 secs.
Reading: 5910000000
Memory used: 33736 MB.
Reading time: 228574 secs.
Reading: 5920000000
Memory used: 33790 MB.
Reading time: 229037 secs.
Reading: 5930000000
Memory used: 33844 MB.
Reading time: 229503 secs.
Reading: 5950000000
Memory used: 33948 MB.
Reading time: 230442 secs.
Reading: 5960000000
Memory used: 34003 MB.
Reading time: 230908 secs.
Reading: 5970000000
Memory used: 34060 MB.
Reading time: 231380 secs.
Reading: 5990000000
Memory used: 34162 MB.
Reading time: 232322 secs.
Reading: 6000000000
Memory used: 34215 MB.
Reading time: 232790 secs.
Reading: 6020000000
Memory used: 34315 MB.
Reading time: 233739 secs.
Reading: 6040000000
Memory used: 34420 MB.
Reading time: 234691 secs.
Reading: 6050000000
Memory used: 34471 MB.
Reading time: 235170 secs.
Reading: 6060000000
Memory used: 34526 MB.
Reading time: 235647 secs.
Reading: 6080000000
Memory used: 34638 MB.
Reading time: 236606 secs.
Reading: 6090000000
Memory used: 34691 MB.
Reading time: 237079 secs.
Reading: 6100000000
Memory used: 34742 MB.
Reading time: 237548 secs.
Reading: 6120000000
Memory used: 34841 MB.
Reading time: 238479 secs.
Reading: 6130000000
Memory used: 34894 MB.
Reading time: 238946 secs.
Reading: 6140000000
Memory used: 34948 MB.
Reading time: 239414 secs.
Reading: 6150000000
Memory used: 35001 MB.
Reading time: 239886 secs.
Reading: 6160000000
Memory used: 35049 MB.
Reading time: 240356 secs.
Reading: 6170000000
Memory used: 35096 MB.
Reading time: 240823 secs.
28/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fastq
Reading: 6180000000
Memory used: 35159 MB.
Reading time: 241306 secs.
Reading: 6190000000
Memory used: 35235 MB.
Reading time: 241801 secs.
Reading: 6200000000
Memory used: 35312 MB.
Reading time: 242295 secs.
Reading: 6210000000
Memory used: 35391 MB.
Reading time: 242788 secs.
Reading: 6220000000
Memory used: 35469 MB.
Reading time: 243286 secs.
Reading: 6230000000
Memory used: 35544 MB.
Reading time: 243784 secs.
Reading: 6240000000
Memory used: 35621 MB.
Reading time: 244280 secs.
Reading: 6260000000
Memory used: 35777 MB.
Reading time: 245283 secs.
Reading: 6270000000
Memory used: 35853 MB.
Reading time: 245783 secs.
Reading: 6280000000
Memory used: 35929 MB.
Reading time: 246283 secs.
Reading: 6290000000
Memory used: 36007 MB.
Reading time: 246787 secs.
Reading: 6300000000
Memory used: 36084 MB.
Reading time: 247294 secs.
Reading: 6310000000
Memory used: 36162 MB.
Reading time: 247801 secs.
Reading: 6320000000
Memory used: 36241 MB.
Reading time: 248308 secs.
Reading: 6330000000
Memory used: 36326 MB.
Reading time: 248821 secs.
Reading: 6340000000
Memory used: 36410 MB.
Reading time: 249333 secs.
Reading: 6350000000
Memory used: 36499 MB.
Reading time: 249846 secs.
Reading: 6360000000
Memory used: 36582 MB.
Reading time: 250359 secs.
Reading: 6370000000
Memory used: 36658 MB.
Reading time: 250870 secs.
Reading: 6400000000
Memory used: 36892 MB.
Reading time: 252405 secs.
Reading: 6420000000
Memory used: 37044 MB.
Reading time: 253434 secs.
Reading: 6430000000
Memory used: 37124 MB.
Reading time: 253952 secs.
Reading: 6440000000
Memory used: 37201 MB.
Reading time: 254471 secs.
Reading: 6450000000
Memory used: 37275 MB.
Reading time: 254990 secs.
Reading: 6460000000
Memory used: 37352 MB.
Reading time: 255506 secs.
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
Reading: 6470000000
Memory used: 37463 MB.
Reading time: 256122 secs.
36/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fastq
Total bases: 788272581018
Total nodes in round 1: 983395345
Reading time: 258031 secs.
Building the sparse k-mer graph, round: 2
1/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R1_001_val_1_val_1.fastq
Reading: 10000000
Reading time: 258490 secs.
Reading: 20000000
Reading time: 258938 secs.
Reading: 30000000
Reading time: 259381 secs.
Reading: 40000000
Reading time: 259819 secs.
Reading: 50000000
Reading time: 260264 secs.
Reading: 60000000
Reading time: 260704 secs.
Reading: 70000000
Reading time: 261142 secs.
Reading: 90000000
Reading time: 262019 secs.
Reading: 100000000
Reading time: 262462 secs.
Reading: 110000000
Reading time: 262902 secs.
Reading: 120000000
Reading time: 263340 secs.
Reading: 130000000
Reading time: 263779 secs.
Reading: 140000000
Reading time: 264215 secs.
Reading: 150000000
Reading time: 264646 secs.
Reading: 160000000
Reading time: 265078 secs.
2/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L001_R2_001_val_2_val_2.fastq
Reading: 170000000
Reading time: 265520 secs.
Reading: 190000000
Reading time: 266425 secs.
Reading: 220000000
Reading time: 267760 secs.
Reading: 230000000
Reading time: 268197 secs.
Reading: 250000000
Reading time: 269066 secs.
Reading: 270000000
Reading time: 269935 secs.
Reading: 280000000
Reading time: 270368 secs.
Reading: 290000000
Reading time: 270796 secs.
Reading: 300000000
Reading time: 271224 secs.
Reading: 310000000
Reading time: 271648 secs.
Reading: 320000000
Reading time: 272071 secs.
Reading: 330000000
Reading time: 272494 secs.
3/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R1_001_val_1_val_1.fastq
Reading: 340000000
Reading time: 272915 secs.
Reading: 350000000
Reading time: 273332 secs.
Reading: 360000000
Reading time: 273745 secs.
Reading: 380000000
Reading time: 274574 secs.
Reading: 390000000
Reading time: 274987 secs.
Reading: 400000000
Reading time: 275402 secs.
Reading: 410000000
Reading time: 275809 secs.
Reading: 420000000
Reading time: 276223 secs.
Reading: 430000000
Reading time: 276638 secs.
Reading: 440000000
Reading time: 277047 secs.
Reading: 450000000
Reading time: 277458 secs.
Reading: 460000000
Reading time: 277864 secs.
Reading: 470000000
Reading time: 278272 secs.
Reading: 480000000
Reading time: 278684 secs.
Reading: 490000000
Reading time: 279094 secs.
Reading: 500000000
Reading time: 279507 secs.
Reading: 510000000
Reading time: 279917 secs.
Reading: 520000000
Reading time: 280322 secs.
4/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/AD002_S9_L002_R2_001_val_2_val_2.fastq
Reading: 570000000
Reading time: 282375 secs.
Reading: 580000000
Reading time: 282790 secs.
Reading: 600000000
Reading time: 283618 secs.
Reading: 640000000
Reading time: 285274 secs.
Reading: 650000000
Reading time: 285686 secs.
Reading: 660000000
Reading time: 286097 secs.
Reading: 670000000
Reading time: 286505 secs.
Reading: 680000000
Reading time: 286914 secs.
Reading: 700000000
Reading time: 287731 secs.
Reading: 710000000
Reading time: 288139 secs.
Reading: 720000000
Reading time: 288548 secs.
Reading: 730000000
Reading time: 288956 secs.
Reading: 740000000
Reading time: 289367 secs.
Reading: 750000000
Reading time: 289777 secs.
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
Reading: 760000000
Reading time: 290210 secs.
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: 770000000
Reading time: 290668 secs.
Reading: 780000000
Reading time: 291070 secs.
Reading: 790000000
Reading time: 291471 secs.
Reading: 800000000
Reading time: 291870 secs.
Reading: 810000000
Reading time: 292266 secs.
Reading: 820000000
Reading time: 292662 secs.
Reading: 830000000
Reading time: 293064 secs.
Reading: 840000000
Reading time: 293462 secs.
Reading: 860000000
Reading time: 294259 secs.
Reading: 890000000
Reading time: 295447 secs.
Reading: 900000000
Reading time: 295843 secs.
Reading: 910000000
Reading time: 296240 secs.
Reading: 920000000
Reading time: 296633 secs.
Reading: 930000000
Reading time: 297030 secs.
Reading: 950000000
Reading time: 297834 secs.
Reading: 970000000
Reading time: 298633 secs.
Reading: 980000000
Reading time: 299033 secs.
Reading: 990000000
Reading time: 299433 secs.
Reading: 1000000000
Reading time: 299833 secs.
Reading: 1010000000
Reading time: 300231 secs.
Reading: 1020000000
Reading time: 300625 secs.
Reading: 1040000000
Reading time: 301404 secs.
Reading: 1050000000
Reading time: 301793 secs.
Reading: 1060000000
Reading time: 302181 secs.
Reading: 1070000000
Reading time: 302569 secs.
18/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L001_R2_001_val_2_val_2.fastq
Reading: 1080000000
Reading time: 302958 secs.
Reading: 1100000000
Reading time: 303772 secs.
Reading: 1110000000
Reading time: 304177 secs.
Reading: 1130000000
Reading time: 304986 secs.
Reading: 1140000000
Reading time: 305389 secs.
Reading: 1160000000
Reading time: 306194 secs.
Reading: 1170000000
Reading time: 306596 secs.
Reading: 1180000000
Reading time: 306999 secs.
Reading: 1190000000
Reading time: 307399 secs.
Reading: 1210000000
Reading time: 308200 secs.
Reading: 1230000000
Reading time: 309003 secs.
Reading: 1250000000
Reading time: 309805 secs.
Reading: 1260000000
Reading time: 310210 secs.
Reading: 1270000000
Reading time: 310610 secs.
Reading: 1280000000
Reading time: 311013 secs.
Reading: 1290000000
Reading time: 311415 secs.
Reading: 1300000000
Reading time: 311817 secs.
Reading: 1310000000
Reading time: 312216 secs.
Reading: 1320000000
Reading time: 312619 secs.
Reading: 1330000000
Reading time: 313020 secs.
Reading: 1340000000
Reading time: 313422 secs.
Reading: 1350000000
Reading time: 313821 secs.
Reading: 1360000000
Reading time: 314223 secs.
Reading: 1370000000
Reading time: 314623 secs.
19/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R1_001_val_1_val_1.fastq
Reading: 1390000000
Reading time: 315423 secs.
Reading: 1400000000
Reading time: 315820 secs.
Reading: 1410000000
Reading time: 316214 secs.
Reading: 1420000000
Reading time: 316607 secs.
Reading: 1440000000
Reading time: 317394 secs.
Reading: 1450000000
Reading time: 317791 secs.
Reading: 1460000000
Reading time: 318185 secs.
Reading: 1470000000
Reading time: 318577 secs.
Reading: 1490000000
Reading time: 319368 secs.
Reading: 1500000000
Reading time: 319765 secs.
Reading: 1510000000
Reading time: 320159 secs.
Reading: 1520000000
Reading time: 320552 secs.
Reading: 1530000000
Reading time: 320945 secs.
Reading: 1540000000
Reading time: 321353 secs.
Reading: 1550000000
Reading time: 321757 secs.
Reading: 1560000000
Reading time: 322159 secs.
Reading: 1570000000
Reading time: 322560 secs.
Reading: 1590000000
Reading time: 323371 secs.
Reading: 1600000000
Reading time: 323774 secs.
Reading: 1610000000
Reading time: 324177 secs.
Reading: 1620000000
Reading time: 324578 secs.
Reading: 1630000000
Reading time: 324985 secs.
Reading: 1650000000
Reading time: 325795 secs.
Reading: 1660000000
Reading time: 326199 secs.
Reading: 1670000000
Reading time: 326602 secs.
Reading: 1680000000
Reading time: 327008 secs.
Reading: 1690000000
Reading time: 327416 secs.
Reading: 1700000000
Reading time: 327823 secs.
Reading: 1710000000
Reading time: 328228 secs.
Reading: 1720000000
Reading time: 328634 secs.
Reading: 1730000000
Reading time: 329044 secs.
Reading: 1740000000
Reading time: 329452 secs.
Reading: 1750000000
Reading time: 329861 secs.
Reading: 1760000000
Reading time: 330267 secs.
20/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR013_AD013_S2_L002_R2_001_val_2_val_2.fastq
Reading: 1770000000
Reading time: 330678 secs.
Reading: 1780000000
Reading time: 331095 secs.
Reading: 1790000000
Reading time: 331510 secs.
Reading: 1800000000
Reading time: 331925 secs.
Reading: 1810000000
Reading time: 332338 secs.
Reading: 1820000000
Reading time: 332754 secs.
Reading: 1830000000
Reading time: 333170 secs.
Reading: 1840000000
Reading time: 333585 secs.
Reading: 1850000000
Reading time: 333999 secs.
Reading: 1860000000
Reading time: 334412 secs.
Reading: 1870000000
Reading time: 334828 secs.
Reading: 1880000000
Reading time: 335245 secs.
Reading: 1890000000
Reading time: 335659 secs.
Reading: 1900000000
Reading time: 336075 secs.
Reading: 1910000000
Reading time: 336491 secs.
Reading: 1920000000
Reading time: 336908 secs.
Reading: 1930000000
Reading time: 337325 secs.
Reading: 1950000000
Reading time: 338158 secs.
Reading: 1960000000
Reading time: 338575 secs.
Reading: 1970000000
Reading time: 338992 secs.
Reading: 1980000000
Reading time: 339408 secs.
Reading: 1990000000
Reading time: 339823 secs.
Reading: 2000000000
Reading time: 340236 secs.
Reading: 2010000000
Reading time: 340653 secs.
Reading: 2040000000
Reading time: 341899 secs.
Reading: 2060000000
Reading time: 342734 secs.
Reading: 2070000000
Reading time: 343152 secs.
Reading: 2080000000
Reading time: 343568 secs.
Reading: 2090000000
Reading time: 343984 secs.
Reading: 2100000000
Reading time: 344400 secs.
Reading: 2110000000
Reading time: 344819 secs.
Reading: 2120000000
Reading time: 345235 secs.
Reading: 2130000000
Reading time: 345651 secs.
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 time: 346454 secs.
Reading: 2170000000
Reading time: 347176 secs.
Reading: 2180000000
Reading time: 347537 secs.
Reading: 2190000000
Reading time: 347898 secs.
Reading: 2200000000
Reading time: 348258 secs.
Reading: 2220000000
Reading time: 348972 secs.
Reading: 2230000000
Reading time: 349325 secs.
Reading: 2270000000
Reading time: 350755 secs.
Reading: 2280000000
Reading time: 351112 secs.
Reading: 2300000000
Reading time: 351827 secs.
Reading: 2310000000
Reading time: 352178 secs.
Reading: 2330000000
Reading time: 352880 secs.
Reading: 2350000000
Reading time: 353595 secs.
Reading: 2360000000
Reading time: 353951 secs.
Reading: 2370000000
Reading time: 354308 secs.
Reading: 2380000000
Reading time: 354663 secs.
Reading: 2390000000
Reading time: 355020 secs.
Reading: 2400000000
Reading time: 355371 secs.
Reading: 2420000000
Reading time: 356068 secs.
Reading: 2430000000
Reading time: 356417 secs.
Reading: 2440000000
Reading time: 356772 secs.
Reading: 2450000000
Reading time: 357124 secs.
Reading: 2460000000
Reading time: 357468 secs.
Reading: 2470000000
Reading time: 357811 secs.
Reading: 2480000000
Reading time: 358156 secs.
Reading: 2490000000
Reading time: 358498 secs.
Reading: 2500000000
Reading time: 358838 secs.
Reading: 2510000000
Reading time: 359178 secs.
Reading: 2520000000
Reading time: 359515 secs.
Reading: 2530000000
Reading time: 359861 secs.
Reading: 2540000000
Reading time: 360215 secs.
Reading: 2550000000
Reading time: 360568 secs.
Reading: 2560000000
Reading time: 360921 secs.
Reading: 2570000000
Reading time: 361275 secs.
Reading: 2580000000
Reading time: 361628 secs.
Reading: 2590000000
Reading time: 361978 secs.
Reading: 2600000000
Reading time: 362323 secs.
Reading: 2610000000
Reading time: 362669 secs.
Reading: 2620000000
Reading time: 363014 secs.
Reading: 2650000000
Reading time: 364069 secs.
Reading: 2660000000
Reading time: 364422 secs.
Reading: 2670000000
Reading time: 364773 secs.
Reading: 2690000000
Reading time: 365465 secs.
Reading: 2700000000
Reading time: 365809 secs.
Reading: 2710000000
Reading time: 366159 secs.
Reading: 2730000000
Reading time: 366858 secs.
Reading: 2740000000
Reading time: 367209 secs.
Reading: 2760000000
Reading time: 367913 secs.
Reading: 2770000000
Reading time: 368259 secs.
Reading: 2780000000
Reading time: 368603 secs.
Reading: 2790000000
Reading time: 368948 secs.
Reading: 2850000000
Reading time: 371021 secs.
Reading: 2860000000
Reading time: 371364 secs.
Reading: 2870000000
Reading time: 371703 secs.
Reading: 2890000000
Reading time: 372380 secs.
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 time: 372745 secs.
Reading: 2910000000
Reading time: 373109 secs.
Reading: 2920000000
Reading time: 373473 secs.
Reading: 2930000000
Reading time: 373838 secs.
Reading: 2940000000
Reading time: 374205 secs.
Reading: 2960000000
Reading time: 374934 secs.
Reading: 2970000000
Reading time: 375293 secs.
Reading: 2980000000
Reading time: 375651 secs.
Reading: 2990000000
Reading time: 376011 secs.
Reading: 3000000000
Reading time: 376374 secs.
Reading: 3010000000
Reading time: 376736 secs.
Reading: 3020000000
Reading time: 377098 secs.
Reading: 3030000000
Reading time: 377461 secs.
Reading: 3050000000
Reading time: 378184 secs.
Reading: 3060000000
Reading time: 378541 secs.
Reading: 3070000000
Reading time: 378896 secs.
Reading: 3090000000
Reading time: 379618 secs.
Reading: 3110000000
Reading time: 380339 secs.
Reading: 3120000000
Reading time: 380699 secs.
Reading: 3130000000
Reading time: 381061 secs.
Reading: 3160000000
Reading time: 382133 secs.
Reading: 3170000000
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Reading: 3200000000
Reading time: 383564 secs.
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Reading time: 383923 secs.
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Reading time: 386428 secs.
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Reading time: 386793 secs.
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Reading time: 387886 secs.
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Reading time: 388610 secs.
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Reading time: 388969 secs.
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Reading time: 389330 secs.
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Reading: 3390000000
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Reading time: 391507 secs.
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Reading time: 392944 secs.
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Reading time: 394757 secs.
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Reading time: 395116 secs.
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Reading time: 395473 secs.
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Reading time: 396193 secs.
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Reading time: 396556 secs.
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Reading time: 396917 secs.
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Reading time: 397278 secs.
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Reading time: 397640 secs.
Reading: 3600000000
Reading time: 398002 secs.
Reading: 3610000000
Reading time: 398362 secs.
Reading: 3620000000
Reading time: 398719 secs.
Reading: 3630000000
Reading time: 399074 secs.
23/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R1_001_val_1_val_1.fastq
Reading: 3640000000
Reading time: 399433 secs.
Reading: 3650000000
Reading time: 399795 secs.
Reading: 3660000000
Reading time: 400157 secs.
Reading: 3670000000
Reading time: 400517 secs.
Reading: 3680000000
Reading time: 400877 secs.
Reading: 3710000000
Reading time: 401954 secs.
Reading: 3720000000
Reading time: 402311 secs.
Reading: 3740000000
Reading time: 403022 secs.
Reading: 3750000000
Reading time: 403380 secs.
Reading: 3760000000
Reading time: 403742 secs.
Reading: 3770000000
Reading time: 404104 secs.
Reading: 3790000000
Reading time: 404826 secs.
Reading: 3820000000
Reading time: 405898 secs.
Reading: 3840000000
Reading time: 406613 secs.
Reading: 3850000000
Reading time: 406969 secs.
Reading: 3870000000
Reading time: 407691 secs.
Reading: 3880000000
Reading time: 408054 secs.
Reading: 3890000000
Reading time: 408418 secs.
Reading: 3900000000
Reading time: 408782 secs.
Reading: 3910000000
Reading time: 409143 secs.
Reading: 3920000000
Reading time: 409501 secs.
Reading: 3930000000
Reading time: 409861 secs.
Reading: 3940000000
Reading time: 410219 secs.
Reading: 3950000000
Reading time: 410579 secs.
Reading: 3960000000
Reading time: 410938 secs.
Reading: 3970000000
Reading time: 411300 secs.
Reading: 3980000000
Reading time: 411667 secs.
Reading: 4000000000
Reading time: 412400 secs.
Reading: 4020000000
Reading time: 413127 secs.
Reading: 4030000000
Reading time: 413490 secs.
Reading: 4050000000
Reading time: 414216 secs.
Reading: 4060000000
Reading time: 414581 secs.
Reading: 4070000000
Reading time: 414948 secs.
Reading: 4080000000
Reading time: 415315 secs.
Reading: 4090000000
Reading time: 415682 secs.
Reading: 4100000000
Reading time: 416045 secs.
Reading: 4110000000
Reading time: 416410 secs.
Reading: 4120000000
Reading time: 416773 secs.
Reading: 4130000000
Reading time: 417135 secs.
Reading: 4150000000
Reading time: 417858 secs.
Reading: 4160000000
Reading time: 418219 secs.
Reading: 4170000000
Reading time: 418580 secs.
Reading: 4180000000
Reading time: 418943 secs.
Reading: 4190000000
Reading time: 419309 secs.
Reading: 4210000000
Reading time: 420049 secs.
Reading: 4220000000
Reading time: 420417 secs.
Reading: 4230000000
Reading time: 420782 secs.
Reading: 4240000000
Reading time: 421147 secs.
Reading: 4250000000
Reading time: 421508 secs.
Reading: 4270000000
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Reading: 4290000000
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Reading: 4300000000
Reading time: 423320 secs.
Reading: 4320000000
Reading time: 424059 secs.
Reading: 4330000000
Reading time: 424427 secs.
Reading: 4350000000
Reading time: 425161 secs.
Reading: 4360000000
Reading time: 425527 secs.
Reading: 4370000000
Reading time: 425893 secs.
Reading: 4380000000
Reading time: 426258 secs.
Reading: 4390000000
Reading time: 426622 secs.
Reading: 4400000000
Reading time: 426987 secs.
Reading: 4410000000
Reading time: 427354 secs.
Reading: 4420000000
Reading time: 427726 secs.
Reading: 4430000000
Reading time: 428098 secs.
Reading: 4440000000
Reading time: 428466 secs.
Reading: 4470000000
Reading time: 429569 secs.
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Reading time: 429937 secs.
Reading: 4490000000
Reading time: 430304 secs.
Reading: 4500000000
Reading time: 430670 secs.
Reading: 4510000000
Reading time: 431037 secs.
24/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR014_AD014_S5_L002_R2_001_val_2_val_2.fastq
Reading: 4520000000
Reading time: 431412 secs.
Reading: 4530000000
Reading time: 431793 secs.
Reading: 4540000000
Reading time: 432172 secs.
Reading: 4560000000
Reading time: 432929 secs.
Reading: 4580000000
Reading time: 433679 secs.
Reading: 4590000000
Reading time: 434055 secs.
Reading: 4600000000
Reading time: 434431 secs.
Reading: 4610000000
Reading time: 434805 secs.
Reading: 4620000000
Reading time: 435177 secs.
Reading: 4630000000
Reading time: 435555 secs.
Reading: 4640000000
Reading time: 435936 secs.
Reading: 4650000000
Reading time: 436321 secs.
Reading: 4660000000
Reading time: 436703 secs.
Reading: 4670000000
Reading time: 437085 secs.
Reading: 4680000000
Reading time: 437465 secs.
Reading: 4710000000
Reading time: 438594 secs.
Reading: 4720000000
Reading time: 438969 secs.
Reading: 4730000000
Reading time: 439344 secs.
Reading: 4740000000
Reading time: 439721 secs.
Reading: 4750000000
Reading time: 440104 secs.
Reading: 4760000000
Reading time: 440484 secs.
Reading: 4780000000
Reading time: 441242 secs.
Reading: 4800000000
Reading time: 441997 secs.
Reading: 4810000000
Reading time: 442373 secs.
Reading: 4820000000
Reading time: 442751 secs.
Reading: 4830000000
Reading time: 443127 secs.
Reading: 4840000000
Reading time: 443501 secs.
Reading: 4850000000
Reading time: 443879 secs.
Reading: 4860000000
Reading time: 444259 secs.
Reading: 4870000000
Reading time: 444638 secs.
Reading: 4890000000
Reading time: 445395 secs.
Reading: 4900000000
Reading time: 445776 secs.
Reading: 4910000000
Reading time: 446155 secs.
Reading: 4930000000
Reading time: 446910 secs.
Reading: 4940000000
Reading time: 447286 secs.
Reading: 4950000000
Reading time: 447661 secs.
Reading: 4960000000
Reading time: 448041 secs.
Reading: 4970000000
Reading time: 448421 secs.
Reading: 4980000000
Reading time: 448800 secs.
Reading: 4990000000
Reading time: 449177 secs.
Reading: 5000000000
Reading time: 449554 secs.
Reading: 5010000000
Reading time: 449930 secs.
Reading: 5020000000
Reading time: 450306 secs.
Reading: 5040000000
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Reading: 5050000000
Reading time: 451433 secs.
Reading: 5060000000
Reading time: 451808 secs.
Reading: 5070000000
Reading time: 452187 secs.
Reading: 5080000000
Reading time: 452567 secs.
Reading: 5090000000
Reading time: 452948 secs.
Reading: 5100000000
Reading time: 453327 secs.
Reading: 5110000000
Reading time: 453705 secs.
Reading: 5120000000
Reading time: 454080 secs.
Reading: 5130000000
Reading time: 454457 secs.
Reading: 5140000000
Reading time: 454836 secs.
Reading: 5150000000
Reading time: 455214 secs.
Reading: 5170000000
Reading time: 455965 secs.
Reading: 5180000000
Reading time: 456341 secs.
Reading: 5200000000
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Reading time: 457865 secs.
Reading: 5230000000
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Reading time: 459001 secs.
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Reading: 5270000000
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Reading: 5280000000
Reading time: 460136 secs.
Reading: 5290000000
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Reading: 5300000000
Reading time: 460895 secs.
Reading: 5310000000
Reading time: 461277 secs.
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Reading: 5330000000
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Reading: 5340000000
Reading time: 462417 secs.
Reading: 5350000000
Reading time: 462796 secs.
Reading: 5360000000
Reading time: 463176 secs.
Reading: 5370000000
Reading time: 463554 secs.
Reading: 5380000000
Reading time: 463932 secs.
25/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R1_001_val_1_val_1.fastq
Reading: 5390000000
Reading time: 464309 secs.
Reading: 5400000000
Reading time: 464678 secs.
Reading: 5420000000
Reading time: 465407 secs.
Reading: 5430000000
Reading time: 465774 secs.
Reading: 5470000000
Reading time: 467232 secs.
Reading: 5480000000
Reading time: 467592 secs.
Reading: 5490000000
Reading time: 467953 secs.
Reading: 5500000000
Reading time: 468314 secs.
Reading: 5510000000
Reading time: 468674 secs.
Reading: 5520000000
Reading time: 469036 secs.
Reading: 5530000000
Reading time: 469405 secs.
Reading: 5540000000
Reading time: 469772 secs.
Reading: 5550000000
Reading time: 470136 secs.
Reading: 5560000000
Reading time: 470502 secs.
Reading: 5570000000
Reading time: 470866 secs.
Reading: 5580000000
Reading time: 471229 secs.
Reading: 5590000000
Reading time: 471594 secs.
Reading: 5600000000
Reading time: 471956 secs.
Reading: 5610000000
Reading time: 472317 secs.
Reading: 5620000000
Reading time: 472678 secs.
Reading: 5630000000
Reading time: 473041 secs.
26/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L001_R2_001_val_2_val_2.fastq
Reading: 5640000000
Reading time: 473399 secs.
Reading: 5650000000
Reading time: 473781 secs.
Reading: 5660000000
Reading time: 474163 secs.
Reading: 5690000000
Reading time: 475302 secs.
Reading: 5700000000
Reading time: 475678 secs.
Reading: 5710000000
Reading time: 476056 secs.
Reading: 5720000000
Reading time: 476435 secs.
Reading: 5730000000
Reading time: 476810 secs.
Reading: 5740000000
Reading time: 477186 secs.
Reading: 5750000000
Reading time: 477565 secs.
Reading: 5760000000
Reading time: 477940 secs.
Reading: 5770000000
Reading time: 478316 secs.
Reading: 5780000000
Reading time: 478696 secs.
Reading: 5790000000
Reading time: 479077 secs.
Reading: 5800000000
Reading time: 479454 secs.
Reading: 5810000000
Reading time: 479836 secs.
Reading: 5820000000
Reading time: 480214 secs.
Reading: 5830000000
Reading time: 480590 secs.
Reading: 5840000000
Reading time: 480967 secs.
Reading: 5850000000
Reading time: 481345 secs.
Reading: 5860000000
Reading time: 481719 secs.
Reading: 5870000000
Reading time: 482097 secs.
Reading: 5880000000
Reading time: 482477 secs.
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 time: 483227 secs.
Reading: 5910000000
Reading time: 483602 secs.
Reading: 5920000000
Reading time: 483973 secs.
Reading: 5930000000
Reading time: 484346 secs.
Reading: 5950000000
Reading time: 485094 secs.
Reading: 5960000000
Reading time: 485466 secs.
Reading: 5970000000
Reading time: 485841 secs.
Reading: 5990000000
Reading time: 486592 secs.
Reading: 6000000000
Reading time: 486965 secs.
Reading: 6020000000
Reading time: 487719 secs.
Reading: 6040000000
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Reading: 6050000000
Reading time: 488847 secs.
Reading: 6060000000
Reading time: 489222 secs.
Reading: 6080000000
Reading time: 489975 secs.
Reading: 6090000000
Reading time: 490352 secs.
Reading: 6100000000
Reading time: 490728 secs.
Reading: 6120000000
Reading time: 491485 secs.
Reading: 6130000000
Reading time: 491863 secs.
Reading: 6140000000
Reading time: 492240 secs.
Reading: 6150000000
Reading time: 492620 secs.
Reading: 6160000000
Reading time: 492998 secs.
Reading: 6170000000
Reading time: 493376 secs.
28/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR015_AD015_S6_L002_R2_001_val_2_val_2.fastq
Reading: 6180000000
Reading time: 493758 secs.
Reading: 6190000000
Reading time: 494147 secs.
Reading: 6200000000
Reading time: 494539 secs.
Reading: 6210000000
Reading time: 494932 secs.
Reading: 6220000000
Reading time: 495327 secs.
Reading: 6230000000
Reading time: 495722 secs.
Reading: 6240000000
Reading time: 496117 secs.
Reading: 6260000000
Reading time: 496910 secs.
Reading: 6270000000
Reading time: 497306 secs.
Reading: 6280000000
Reading time: 497702 secs.
Reading: 6290000000
Reading time: 498098 secs.
Reading: 6300000000
Reading time: 498496 secs.
Reading: 6310000000
Reading time: 498893 secs.
Reading: 6320000000
Reading time: 499288 secs.
Reading: 6330000000
Reading time: 499686 secs.
Reading: 6340000000
Reading time: 500082 secs.
Reading: 6350000000
Reading time: 500476 secs.
Reading: 6360000000
Reading time: 500871 secs.
Reading: 6370000000
Reading time: 501268 secs.
Reading: 6400000000
Reading time: 502457 secs.
Reading: 6420000000
Reading time: 503250 secs.
Reading: 6430000000
Reading time: 503646 secs.
Reading: 6440000000
Reading time: 504044 secs.
Reading: 6450000000
Reading time: 504441 secs.
Reading: 6460000000
Reading time: 504837 secs.
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
Reading: 6470000000
Reading time: 505312 secs.
36/36 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimmed_again/NR021_S8_L002_R2_001_val_2_val_2.fastq
Total nodes in round 2: 983395345
Total nodes: 983395345
Total edges in round 2: 1815880934
Reading time: 507061 secs.
Screening off weak nodes and edges...
Graph simplification...
Min searching depth: 5
Max searching depth: 15
Current depth: 5
10000000
20000000
30000000
40000000
50000000
60000000
70000000
80000000
90000000
100000000
110000000
120000000
130000000
140000000
150000000
160000000
170000000
180000000
190000000
200000000
210000000
220000000
230000000
240000000
250000000
260000000
270000000
280000000
290000000
300000000
310000000
320000000
330000000
Current depth: 8
10000000
20000000
30000000
40000000
50000000
60000000
70000000
80000000
90000000
100000000
110000000
120000000
130000000
140000000
150000000
160000000
170000000
180000000
190000000
200000000
210000000
220000000
230000000
240000000
250000000
260000000
270000000
280000000
290000000
300000000
310000000
320000000
330000000
Current depth: 11
10000000
20000000
30000000
40000000
50000000
60000000
70000000
80000000
90000000
100000000
110000000
120000000
130000000
140000000
150000000
160000000
170000000
180000000
190000000
200000000
210000000
220000000
230000000
240000000
250000000
260000000
270000000
280000000
290000000
300000000
310000000
320000000
330000000
Current depth: 14
10000000
20000000
30000000
40000000
50000000
60000000
70000000
80000000
90000000
100000000
110000000
120000000
130000000
140000000
150000000
160000000
170000000
180000000
190000000
200000000
210000000
220000000
230000000
240000000
250000000
260000000
270000000
280000000
290000000
300000000
310000000
320000000
330000000
Build contigs...
Contigs remapping.
Marking kmers...
Kmer marking time: 1401 secs.