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.
1/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L001_R1_001_val_1_val_1.fastq
2/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L001_R2_001_val_2_val_2.fastq
3/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L002_R1_001_val_1_val_1.fastq
4/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L002_R2_001_val_2_val_2.fastq
5/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L001_R1_001_val_1_val_1.fastq
6/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L001_R2_001_val_2_val_2.fastq
7/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L002_R1_001_val_1_val_1.fastq
8/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L002_R2_001_val_2_val_2.fastq
9/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L001_R1_001_val_1_val_1.fastq
10/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L001_R2_001_val_2_val_2.fastq
11/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L002_R1_001_val_1_val_1.fastq
12/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L002_R2_001_val_2_val_2.fastq
13/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L001_R1_001_val_1_val_1.fastq
14/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L001_R2_001_val_2_val_2.fastq
15/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L002_R1_001_val_1_val_1.fastq
16/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L002_R2_001_val_2_val_2.fastq
17/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L001_R1_001_val_1_val_1.fastq
18/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L001_R2_001_val_2_val_2.fastq
19/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L002_R1_001_val_1_val_1.fastq
20/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L002_R2_001_val_2_val_2.fastq
21/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L001_R1_001_val_1_val_1.fastq
22/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L001_R2_001_val_2_val_2.fastq
23/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L002_R1_001_val_1_val_1.fastq
24/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L002_R2_001_val_2_val_2.fastq
25/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L001_R1_001_val_1_val_1.fastq
26/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L001_R2_001_val_2_val_2.fastq
27/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L002_R1_001_val_1_val_1.fastq
28/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L002_R2_001_val_2_val_2.fastq
29/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L001_R1_001_val_1_val_1.fastq
30/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L001_R2_001_val_2_val_2.fastq
31/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L002_R1_001_val_1_val_1.fastq
32/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L002_R2_001_val_2_val_2.fastq
33/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L001_R1_001_val_1_val_1.fastq
34/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L001_R2_001_val_2_val_2.fastq
35/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L002_R1_001_val_1_val_1.fastq
36/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L002_R2_001_val_2_val_2.fastq
37/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_1.fastq
Reading: 50000000
38/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_2.fastq
Reading: 100000000
Reading: 150000000
39/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_1.fastq
Reading: 200000000
Reading: 250000000
40/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_2.fastq
Reading: 300000000
41/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_1.fastq
Reading: 350000000
Reading: 400000000
42/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_2.fastq
Reading: 450000000
43/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_1.fastq
Reading: 500000000
Reading: 550000000
44/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_2.fastq
Reading: 600000000
45/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_1.fastq
Reading: 650000000
46/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_2.fastq
Reading: 700000000
47/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_1.fastq
Reading: 750000000
Reading: 800000000
48/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_2.fastq
Reading: 850000000
49/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_1.fastq
Reading: 900000000
50/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_2.fastq
Reading: 950000000
51/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_1.fastq
Reading: 1000000000
Reading: 1050000000
52/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_2.fastq
Reading: 1100000000
53/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_1.fastq
Reading: 1150000000
54/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_2.fastq
55/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-1_S1_L001_R1_001_val_1.fastq
Reading: 1200000000
Reading: 1250000000
Reading: 1300000000
Reading: 1350000000
Reading: 1400000000
Reading: 1450000000
56/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-1_S1_L001_R2_001_val_2.fastq
Reading: 1500000000
Reading: 1550000000
Reading: 1600000000
Reading: 1650000000
Reading: 1700000000
Reading: 1750000000
57/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2_S5_L002_R1_001_val_1.fastq
Reading: 1800000000
Reading: 1850000000
Reading: 1900000000
Reading: 1950000000
Reading: 2000000000
Reading: 2050000000
58/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2_S5_L002_R2_001_val_2.fastq
Reading: 2100000000
Reading: 2150000000
Reading: 2200000000
Reading: 2250000000
Reading: 2300000000
Reading: 2350000000
59/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R1_001_val_1.fastq
60/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R2_001_val_2.fastq
61/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R1_001_val_1.fastq
62/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R2_001_val_2.fastq
63/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R1_001_val_1.fastq
Reading: 2400000000
Reading: 2450000000
Reading: 2500000000
Reading: 2550000000
Reading: 2600000000
Reading: 2650000000
64/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R2_001_val_2.fastq
Reading: 2700000000
Reading: 2750000000
Reading: 2800000000
Reading: 2850000000
Reading: 2900000000
65/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R1_001_val_1.fastq
Reading: 2950000000
Reading: 3000000000
Reading: 3050000000
Reading: 3100000000
Reading: 3150000000
Reading: 3200000000
66/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R2_001_val_2.fastq
Reading: 3250000000
Reading: 3300000000
Reading: 3350000000
Reading: 3400000000
Reading: 3450000000
Reading: 3500000000
67/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R1_001_val_1.fastq
68/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R2_001_val_2.fastq
69/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R1_001_val_1.fastq
70/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R2_001_val_2.fastq
71/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R1_001_val_1.fastq
72/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R2_001_val_2.fastq
73/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R1_001_val_1.fastq
74/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R2_001_val_2.fastq
75/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-3_S9_L003_R1_001_val_1.fastq
76/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-3_S9_L003_R2_001_val_2.fastq
77/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-4_S13_L004_R1_001_val_1.fastq
78/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-4_S13_L004_R2_001_val_2.fastq
79/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5_S17_L005_R1_001_val_1.fastq
80/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5_S17_L005_R2_001_val_2.fastq
81/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R1_001_val_1.fastq
82/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R2_001_val_2.fastq
83/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R1_001_val_1.fastq
84/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R2_001_val_2.fastq
85/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R1_001_val_1.fastq
86/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R2_001_val_2.fastq
87/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R1_001_val_1.fastq
88/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R2_001_val_2.fastq
89/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R1_001_val_1.fastq
Reading: 3550000000
Reading: 3600000000
Reading: 3650000000
Reading: 3700000000
Reading: 3750000000
90/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R2_001_val_2.fastq
Reading: 3800000000
Reading: 3850000000
Reading: 3900000000
Reading: 3950000000
91/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R1_001_val_1.fastq
Reading: 4000000000
Reading: 4050000000
Reading: 4100000000
Reading: 4150000000
Reading: 4200000000
92/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R2_001_val_2.fastq
Reading: 4250000000
Reading: 4300000000
Reading: 4350000000
Reading: 4400000000
Reading: 4450000000
93/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R1_001_val_1.fastq
94/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R2_001_val_2.fastq
95/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R1_001_val_1.fastq
96/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R2_001_val_2.fastq
97/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-6_S21_L006_R1_001_val_1.fastq
98/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-6_S21_L006_R2_001_val_2.fastq
99/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-7_S25_L007_R1_001_val_1.fastq
100/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-7_S25_L007_R2_001_val_2.fastq
101/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8_S29_L008_R1_001_val_1.fastq
102/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8_S29_L008_R2_001_val_2.fastq
103/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R1_001_val_1.fastq
104/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R2_001_val_2.fastq
105/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R1_001_val_1.fastq
106/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R2_001_val_2.fastq
107/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R1_001_val_1.fastq
108/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R2_001_val_2.fastq
109/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R1_001_val_1.fastq
110/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R2_001_val_2.fastq
111/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R1_001_val_1.fastq
112/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R2_001_val_2.fastq
113/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R1_001_val_1.fastq
114/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R2_001_val_2.fastq
115/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R1_001_val_1.fastq
Reading: 4500000000
Reading: 4550000000
Reading: 4600000000
Reading: 4650000000
Reading: 4700000000
Reading: 4750000000
116/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R2_001_val_2.fastq
Reading: 4800000000
Reading: 4850000000
Reading: 4900000000
Reading: 4950000000
Reading: 5000000000
117/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R1_001_val_1.fastq
Reading: 5050000000
Reading: 5100000000
Reading: 5150000000
Reading: 5200000000
Reading: 5250000000
Reading: 5300000000
118/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R2_001_val_2.fastq
Reading: 5350000000
Reading: 5400000000
Reading: 5450000000
Reading: 5500000000
Reading: 5550000000
Reading: 5600000000
Scan finished.
Building the sparse k-mer graph, round: 1
1/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L001_R1_001_val_1_val_1.fastq
2/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L001_R2_001_val_2_val_2.fastq
3/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L002_R1_001_val_1_val_1.fastq
4/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L002_R2_001_val_2_val_2.fastq
5/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L001_R1_001_val_1_val_1.fastq
6/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L001_R2_001_val_2_val_2.fastq
7/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L002_R1_001_val_1_val_1.fastq
8/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L002_R2_001_val_2_val_2.fastq
9/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L001_R1_001_val_1_val_1.fastq
10/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L001_R2_001_val_2_val_2.fastq
11/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L002_R1_001_val_1_val_1.fastq
12/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L002_R2_001_val_2_val_2.fastq
13/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L001_R1_001_val_1_val_1.fastq
14/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L001_R2_001_val_2_val_2.fastq
15/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L002_R1_001_val_1_val_1.fastq
16/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L002_R2_001_val_2_val_2.fastq
17/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L001_R1_001_val_1_val_1.fastq
18/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L001_R2_001_val_2_val_2.fastq
19/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L002_R1_001_val_1_val_1.fastq
20/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L002_R2_001_val_2_val_2.fastq
21/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L001_R1_001_val_1_val_1.fastq
22/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L001_R2_001_val_2_val_2.fastq
23/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L002_R1_001_val_1_val_1.fastq
24/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L002_R2_001_val_2_val_2.fastq
25/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L001_R1_001_val_1_val_1.fastq
26/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L001_R2_001_val_2_val_2.fastq
27/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L002_R1_001_val_1_val_1.fastq
28/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L002_R2_001_val_2_val_2.fastq
29/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L001_R1_001_val_1_val_1.fastq
30/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L001_R2_001_val_2_val_2.fastq
31/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L002_R1_001_val_1_val_1.fastq
32/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L002_R2_001_val_2_val_2.fastq
33/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L001_R1_001_val_1_val_1.fastq
34/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L001_R2_001_val_2_val_2.fastq
35/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L002_R1_001_val_1_val_1.fastq
36/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L002_R2_001_val_2_val_2.fastq
37/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_1.fastq
Reading: 10000000
Memory used: 196 MB.
Reading time: 9885 secs.
Reading: 20000000
Memory used: 599 MB.
Reading time: 10128 secs.
Reading: 30000000
Memory used: 1088 MB.
Reading time: 10368 secs.
Reading: 40000000
Memory used: 1621 MB.
Reading time: 10602 secs.
Reading: 50000000
Memory used: 2145 MB.
Reading time: 10838 secs.
Reading: 60000000
Memory used: 2656 MB.
Reading time: 11074 secs.
Reading: 70000000
Memory used: 3138 MB.
Reading time: 11310 secs.
Reading: 80000000
Memory used: 3593 MB.
Reading time: 11553 secs.
Reading: 90000000
Memory used: 4007 MB.
Reading time: 11788 secs.
38/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_2.fastq
Reading: 100000000
Memory used: 4363 MB.
Reading time: 12028 secs.
Reading: 110000000
Memory used: 4671 MB.
Reading time: 12273 secs.
Reading: 120000000
Memory used: 4946 MB.
Reading time: 12520 secs.
Reading: 130000000
Memory used: 5210 MB.
Reading time: 12768 secs.
Reading: 140000000
Memory used: 5448 MB.
Reading time: 13019 secs.
Reading: 150000000
Memory used: 5654 MB.
Reading time: 13276 secs.
Reading: 160000000
Memory used: 5852 MB.
Reading time: 13531 secs.
Reading: 170000000
Memory used: 6042 MB.
Reading time: 13786 secs.
Reading: 180000000
Memory used: 6203 MB.
Reading time: 14047 secs.
39/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_1.fastq
Reading: 190000000
Memory used: 6364 MB.
Reading time: 14305 secs.
Reading: 200000000
Memory used: 6533 MB.
Reading time: 14562 secs.
Reading: 210000000
Memory used: 6683 MB.
Reading time: 14832 secs.
Reading: 220000000
Memory used: 6826 MB.
Reading time: 15103 secs.
Reading: 230000000
Memory used: 6956 MB.
Reading time: 15362 secs.
Reading: 240000000
Memory used: 7076 MB.
Reading time: 15621 secs.
Reading: 250000000
Memory used: 7185 MB.
Reading time: 15883 secs.
Reading: 260000000
Memory used: 7286 MB.
Reading time: 16144 secs.
40/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_2.fastq
Reading: 270000000
Memory used: 7362 MB.
Reading time: 16413 secs.
Reading: 280000000
Memory used: 7430 MB.
Reading time: 16686 secs.
Reading: 290000000
Memory used: 7498 MB.
Reading time: 16964 secs.
Reading: 300000000
Memory used: 7561 MB.
Reading time: 17239 secs.
Reading: 310000000
Memory used: 7623 MB.
Reading time: 17512 secs.
Reading: 320000000
Memory used: 7680 MB.
Reading time: 17787 secs.
Reading: 330000000
Memory used: 7734 MB.
Reading time: 18074 secs.
41/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_1.fastq
Reading: 340000000
Memory used: 7807 MB.
Reading time: 18342 secs.
Reading: 350000000
Memory used: 7889 MB.
Reading time: 18607 secs.
Reading: 360000000
Memory used: 7964 MB.
Reading time: 18871 secs.
Reading: 370000000
Memory used: 8034 MB.
Reading time: 19135 secs.
Reading: 380000000
Memory used: 8103 MB.
Reading time: 19409 secs.
Reading: 390000000
Memory used: 8162 MB.
Reading time: 19675 secs.
Reading: 400000000
Memory used: 8217 MB.
Reading time: 19941 secs.
Reading: 410000000
Memory used: 8269 MB.
Reading time: 20204 secs.
42/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_2.fastq
Reading: 420000000
Memory used: 8307 MB.
Reading time: 20479 secs.
Reading: 430000000
Memory used: 8345 MB.
Reading time: 20752 secs.
Reading: 440000000
Memory used: 8382 MB.
Reading time: 21026 secs.
Reading: 450000000
Memory used: 8420 MB.
Reading time: 21297 secs.
Reading: 460000000
Memory used: 8453 MB.
Reading time: 21578 secs.
Reading: 470000000
Memory used: 8488 MB.
Reading time: 21859 secs.
Reading: 480000000
Memory used: 8524 MB.
Reading time: 22146 secs.
43/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_1.fastq
44/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_2.fastq
45/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_1.fastq
46/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_2.fastq
47/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_1.fastq
48/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_2.fastq
49/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_1.fastq
50/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_2.fastq
51/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_1.fastq
52/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_2.fastq
53/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_1.fastq
54/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_2.fastq
55/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-1_S1_L001_R1_001_val_1.fastq
Reading: 1200000000
Memory used: 8571 MB.
Reading time: 23261 secs.
Reading: 1210000000
Memory used: 8607 MB.
Reading time: 23449 secs.
Reading: 1220000000
Memory used: 8639 MB.
Reading time: 23636 secs.
Reading: 1230000000
Memory used: 8670 MB.
Reading time: 23824 secs.
Reading: 1250000000
Memory used: 8725 MB.
Reading time: 24199 secs.
Reading: 1260000000
Memory used: 8750 MB.
Reading time: 24385 secs.
Reading: 1280000000
Memory used: 8796 MB.
Reading time: 24758 secs.
Reading: 1340000000
Memory used: 8908 MB.
Reading time: 25860 secs.
Reading: 1350000000
Memory used: 8924 MB.
Reading time: 26043 secs.
Reading: 1360000000
Memory used: 8941 MB.
Reading time: 26225 secs.
Reading: 1370000000
Memory used: 8960 MB.
Reading time: 26412 secs.
Reading: 1380000000
Memory used: 8978 MB.
Reading time: 26595 secs.
Reading: 1390000000
Memory used: 8997 MB.
Reading time: 26782 secs.
Reading: 1400000000
Memory used: 9016 MB.
Reading time: 26967 secs.
Reading: 1420000000
Memory used: 9052 MB.
Reading time: 27340 secs.
Reading: 1430000000
Memory used: 9066 MB.
Reading time: 27524 secs.
Reading: 1440000000
Memory used: 9079 MB.
Reading time: 27706 secs.
Reading: 1450000000
Memory used: 9092 MB.
Reading time: 27890 secs.
Reading: 1470000000
Memory used: 9117 MB.
Reading time: 28258 secs.
Reading: 1480000000
Memory used: 9128 MB.
Reading time: 28443 secs.
56/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-1_S1_L001_R2_001_val_2.fastq
Reading: 1490000000
Memory used: 9140 MB.
Reading time: 28625 secs.
Reading: 1500000000
Memory used: 9153 MB.
Reading time: 28801 secs.
Reading: 1510000000
Memory used: 9166 MB.
Reading time: 28979 secs.
Reading: 1550000000
Memory used: 9223 MB.
Reading time: 29684 secs.
Reading: 1560000000
Memory used: 9238 MB.
Reading time: 29860 secs.
Reading: 1570000000
Memory used: 9254 MB.
Reading time: 30038 secs.
Reading: 1580000000
Memory used: 9271 MB.
Reading time: 30217 secs.
Reading: 1590000000
Memory used: 9288 MB.
Reading time: 30398 secs.
Reading: 1600000000
Memory used: 9305 MB.
Reading time: 30579 secs.
Reading: 1610000000
Memory used: 9323 MB.
Reading time: 30762 secs.
Reading: 1620000000
Memory used: 9340 MB.
Reading time: 30942 secs.
Reading: 1630000000
Memory used: 9357 MB.
Reading time: 31122 secs.
Reading: 1640000000
Memory used: 9375 MB.
Reading time: 31302 secs.
Reading: 1670000000
Memory used: 9426 MB.
Reading time: 31810 secs.
Reading: 1680000000
Memory used: 9445 MB.
Reading time: 32000 secs.
Reading: 1690000000
Memory used: 9465 MB.
Reading time: 32194 secs.
Reading: 1700000000
Memory used: 9487 MB.
Reading time: 32382 secs.
Reading: 1730000000
Memory used: 9549 MB.
Reading time: 32926 secs.
Reading: 1750000000
Memory used: 9588 MB.
Reading time: 33278 secs.
Reading: 1760000000
Memory used: 9609 MB.
Reading time: 33459 secs.
57/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2_S5_L002_R1_001_val_1.fastq
Reading: 1780000000
Memory used: 9649 MB.
Reading time: 33824 secs.
Reading: 1800000000
Memory used: 9685 MB.
Reading time: 34198 secs.
Reading: 1810000000
Memory used: 9702 MB.
Reading time: 34385 secs.
Reading: 1830000000
Memory used: 9731 MB.
Reading time: 34759 secs.
Reading: 1850000000
Memory used: 9758 MB.
Reading time: 35134 secs.
Reading: 1860000000
Memory used: 9771 MB.
Reading time: 35321 secs.
Reading: 1870000000
Memory used: 9783 MB.
Reading time: 35507 secs.
Reading: 1880000000
Memory used: 9795 MB.
Reading time: 35694 secs.
Reading: 1890000000
Memory used: 9807 MB.
Reading time: 35882 secs.
Reading: 1900000000
Memory used: 9818 MB.
Reading time: 36068 secs.
Reading: 1910000000
Memory used: 9829 MB.
Reading time: 36256 secs.
Reading: 1920000000
Memory used: 9839 MB.
Reading time: 36442 secs.
Reading: 1930000000
Memory used: 9850 MB.
Reading time: 36631 secs.
Reading: 1940000000
Memory used: 9861 MB.
Reading time: 36817 secs.
Reading: 1970000000
Memory used: 9890 MB.
Reading time: 37376 secs.
Reading: 1980000000
Memory used: 9900 MB.
Reading time: 37563 secs.
Reading: 1990000000
Memory used: 9910 MB.
Reading time: 37751 secs.
Reading: 2000000000
Memory used: 9919 MB.
Reading time: 37939 secs.
Reading: 2010000000
Memory used: 9929 MB.
Reading time: 38127 secs.
Reading: 2020000000
Memory used: 9939 MB.
Reading time: 38314 secs.
Reading: 2030000000
Memory used: 9949 MB.
Reading time: 38501 secs.
Reading: 2040000000
Memory used: 9958 MB.
Reading time: 38688 secs.
Reading: 2050000000
Memory used: 9967 MB.
Reading time: 38875 secs.
Reading: 2060000000
Memory used: 9981 MB.
Reading time: 39066 secs.
Reading: 2070000000
Memory used: 9992 MB.
Reading time: 39255 secs.
58/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2_S5_L002_R2_001_val_2.fastq
Reading: 2080000000
Memory used: 10004 MB.
Reading time: 39440 secs.
Reading: 2110000000
Memory used: 10053 MB.
Reading time: 39982 secs.
Reading: 2130000000
Memory used: 10090 MB.
Reading time: 40348 secs.
Reading: 2140000000
Memory used: 10108 MB.
Reading time: 40526 secs.
Reading: 2160000000
Memory used: 10147 MB.
Reading time: 40886 secs.
Reading: 2170000000
Memory used: 10168 MB.
Reading time: 41068 secs.
Reading: 2230000000
Memory used: 10297 MB.
Reading time: 42179 secs.
Reading: 2240000000
Memory used: 10319 MB.
Reading time: 42363 secs.
Reading: 2260000000
Memory used: 10366 MB.
Reading time: 42736 secs.
Reading: 2270000000
Memory used: 10387 MB.
Reading time: 42905 secs.
Reading: 2280000000
Memory used: 10410 MB.
Reading time: 43091 secs.
Reading: 2290000000
Memory used: 10434 MB.
Reading time: 43273 secs.
Reading: 2310000000
Memory used: 10483 MB.
Reading time: 43642 secs.
Reading: 2360000000
Memory used: 10620 MB.
Reading time: 44571 secs.
Reading: 2370000000
Memory used: 10646 MB.
Reading time: 44753 secs.
59/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R1_001_val_1.fastq
60/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R2_001_val_2.fastq
61/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R1_001_val_1.fastq
62/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R2_001_val_2.fastq
63/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R1_001_val_1.fastq
Reading: 2380000000
Memory used: 10671 MB.
Reading time: 44943 secs.
Reading: 2390000000
Memory used: 10693 MB.
Reading time: 45135 secs.
Reading: 2400000000
Memory used: 10713 MB.
Reading time: 45328 secs.
Reading: 2410000000
Memory used: 10731 MB.
Reading time: 45519 secs.
Reading: 2430000000
Memory used: 10766 MB.
Reading time: 45905 secs.
Reading: 2440000000
Memory used: 10782 MB.
Reading time: 46102 secs.
Reading: 2450000000
Memory used: 10797 MB.
Reading time: 46293 secs.
Reading: 2460000000
Memory used: 10813 MB.
Reading time: 46484 secs.
Reading: 2470000000
Memory used: 10827 MB.
Reading time: 46677 secs.
Reading: 2480000000
Memory used: 10841 MB.
Reading time: 46870 secs.
Reading: 2500000000
Memory used: 10868 MB.
Reading time: 47255 secs.
Reading: 2530000000
Memory used: 10915 MB.
Reading time: 47839 secs.
Reading: 2540000000
Memory used: 10933 MB.
Reading time: 48036 secs.
Reading: 2550000000
Memory used: 10950 MB.
Reading time: 48231 secs.
Reading: 2560000000
Memory used: 10965 MB.
Reading time: 48427 secs.
Reading: 2570000000
Memory used: 10979 MB.
Reading time: 48581 secs.
Reading: 2580000000
Memory used: 10993 MB.
Reading time: 48787 secs.
Reading: 2590000000
Memory used: 11006 MB.
Reading time: 48995 secs.
Reading: 2610000000
Memory used: 11032 MB.
Reading time: 49382 secs.
Reading: 2620000000
Memory used: 11045 MB.
Reading time: 49576 secs.
Reading: 2630000000
Memory used: 11062 MB.
Reading time: 49773 secs.
Reading: 2640000000
Memory used: 11075 MB.
Reading time: 49966 secs.
Reading: 2650000000
Memory used: 11089 MB.
Reading time: 50161 secs.
64/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R2_001_val_2.fastq
Reading: 2660000000
Memory used: 11103 MB.
Reading time: 50351 secs.
Reading: 2680000000
Memory used: 11148 MB.
Reading time: 50721 secs.
Reading: 2690000000
Memory used: 11171 MB.
Reading time: 50907 secs.
Reading: 2700000000
Memory used: 11195 MB.
Reading time: 51093 secs.
Reading: 2710000000
Memory used: 11220 MB.
Reading time: 51279 secs.
Reading: 2720000000
Memory used: 11245 MB.
Reading time: 51462 secs.
Reading: 2740000000
Memory used: 11296 MB.
Reading time: 51832 secs.
Reading: 2750000000
Memory used: 11323 MB.
Reading time: 52018 secs.
Reading: 2780000000
Memory used: 11405 MB.
Reading time: 52581 secs.
Reading: 2790000000
Memory used: 11433 MB.
Reading time: 52768 secs.
Reading: 2800000000
Memory used: 11461 MB.
Reading time: 52957 secs.
Reading: 2810000000
Memory used: 11492 MB.
Reading time: 53143 secs.
Reading: 2820000000
Memory used: 11523 MB.
Reading time: 53330 secs.
Reading: 2830000000
Memory used: 11558 MB.
Reading time: 53524 secs.
Reading: 2840000000
Memory used: 11588 MB.
Reading time: 53710 secs.
Reading: 2850000000
Memory used: 11620 MB.
Reading time: 53898 secs.
Reading: 2860000000
Memory used: 11657 MB.
Reading time: 54092 secs.
Reading: 2870000000
Memory used: 11691 MB.
Reading time: 54283 secs.
Reading: 2880000000
Memory used: 11723 MB.
Reading time: 54472 secs.
Reading: 2910000000
Memory used: 11819 MB.
Reading time: 55039 secs.
Reading: 2920000000
Memory used: 11850 MB.
Reading time: 55228 secs.
Reading: 2930000000
Memory used: 11882 MB.
Reading time: 55417 secs.
Reading: 2940000000
Memory used: 11914 MB.
Reading time: 55603 secs.
65/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R1_001_val_1.fastq
Reading: 2950000000
Memory used: 11941 MB.
Reading time: 55796 secs.
Reading: 2960000000
Memory used: 11964 MB.
Reading time: 55991 secs.
Reading: 2970000000
Memory used: 11986 MB.
Reading time: 56185 secs.
Reading: 2980000000
Memory used: 12006 MB.
Reading time: 56379 secs.
Reading: 2990000000
Memory used: 12025 MB.
Reading time: 56574 secs.
Reading: 3000000000
Memory used: 12043 MB.
Reading time: 56769 secs.
Reading: 3010000000
Memory used: 12061 MB.
Reading time: 56965 secs.
Reading: 3020000000
Memory used: 12079 MB.
Reading time: 57161 secs.
Reading: 3030000000
Memory used: 12098 MB.
Reading time: 57357 secs.
Reading: 3040000000
Memory used: 12115 MB.
Reading time: 57554 secs.
Reading: 3050000000
Memory used: 12132 MB.
Reading time: 57750 secs.
Reading: 3060000000
Memory used: 12148 MB.
Reading time: 57947 secs.
Reading: 3070000000
Memory used: 12164 MB.
Reading time: 58145 secs.
Reading: 3080000000
Memory used: 12180 MB.
Reading time: 58344 secs.
Reading: 3090000000
Memory used: 12196 MB.
Reading time: 58543 secs.
Reading: 3100000000
Memory used: 12215 MB.
Reading time: 58741 secs.
Reading: 3110000000
Memory used: 12234 MB.
Reading time: 58943 secs.
Reading: 3120000000
Memory used: 12258 MB.
Reading time: 59148 secs.
Reading: 3140000000
Memory used: 12304 MB.
Reading time: 59555 secs.
Reading: 3150000000
Memory used: 12323 MB.
Reading time: 59755 secs.
Reading: 3160000000
Memory used: 12339 MB.
Reading time: 59956 secs.
Reading: 3170000000
Memory used: 12356 MB.
Reading time: 60154 secs.
Reading: 3180000000
Memory used: 12374 MB.
Reading time: 60354 secs.
Reading: 3190000000
Memory used: 12389 MB.
Reading time: 60553 secs.
Reading: 3210000000
Memory used: 12421 MB.
Reading time: 60953 secs.
Reading: 3220000000
Memory used: 12437 MB.
Reading time: 61154 secs.
Reading: 3230000000
Memory used: 12452 MB.
Reading time: 61352 secs.
66/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R2_001_val_2.fastq
Reading: 3240000000
Memory used: 12482 MB.
Reading time: 61543 secs.
Reading: 3250000000
Memory used: 12512 MB.
Reading time: 61733 secs.
Reading: 3260000000
Memory used: 12542 MB.
Reading time: 61924 secs.
Reading: 3280000000
Memory used: 12605 MB.
Reading time: 62310 secs.
Reading: 3300000000
Memory used: 12669 MB.
Reading time: 62694 secs.
Reading: 3310000000
Memory used: 12702 MB.
Reading time: 62885 secs.
Reading: 3320000000
Memory used: 12736 MB.
Reading time: 63076 secs.
Reading: 3330000000
Memory used: 12770 MB.
Reading time: 63269 secs.
Reading: 3340000000
Memory used: 12805 MB.
Reading time: 63464 secs.
Reading: 3350000000
Memory used: 12839 MB.
Reading time: 63660 secs.
Reading: 3360000000
Memory used: 12874 MB.
Reading time: 63855 secs.
Reading: 3380000000
Memory used: 12948 MB.
Reading time: 64244 secs.
Reading: 3410000000
Memory used: 13077 MB.
Reading time: 64848 secs.
Reading: 3430000000
Memory used: 13177 MB.
Reading time: 65257 secs.
Reading: 3440000000
Memory used: 13229 MB.
Reading time: 65458 secs.
Reading: 3460000000
Memory used: 13314 MB.
Reading time: 65857 secs.
Reading: 3470000000
Memory used: 13355 MB.
Reading time: 66054 secs.
Reading: 3500000000
Memory used: 13473 MB.
Reading time: 66640 secs.
Reading: 3510000000
Memory used: 13513 MB.
Reading time: 66834 secs.
67/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R1_001_val_1.fastq
68/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R2_001_val_2.fastq
69/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R1_001_val_1.fastq
70/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R2_001_val_2.fastq
71/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R1_001_val_1.fastq
72/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R2_001_val_2.fastq
73/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R1_001_val_1.fastq
Reading: 3520000000
Memory used: 13552 MB.
Reading time: 67026 secs.
74/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R2_001_val_2.fastq
75/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-3_S9_L003_R1_001_val_1.fastq
76/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-3_S9_L003_R2_001_val_2.fastq
77/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-4_S13_L004_R1_001_val_1.fastq
78/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-4_S13_L004_R2_001_val_2.fastq
79/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5_S17_L005_R1_001_val_1.fastq
80/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5_S17_L005_R2_001_val_2.fastq
81/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R1_001_val_1.fastq
82/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R2_001_val_2.fastq
83/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R1_001_val_1.fastq
84/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R2_001_val_2.fastq
85/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R1_001_val_1.fastq
86/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R2_001_val_2.fastq
87/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R1_001_val_1.fastq
88/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R2_001_val_2.fastq
89/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R1_001_val_1.fastq
Reading: 3530000000
Memory used: 13583 MB.
Reading time: 67211 secs.
Reading: 3540000000
Memory used: 13605 MB.
Reading time: 67390 secs.
Reading: 3570000000
Memory used: 13666 MB.
Reading time: 67924 secs.
Reading: 3580000000
Memory used: 13684 MB.
Reading time: 68104 secs.
Reading: 3590000000
Memory used: 13703 MB.
Reading time: 68284 secs.
Reading: 3610000000
Memory used: 13739 MB.
Reading time: 68641 secs.
Reading: 3620000000
Memory used: 13756 MB.
Reading time: 68821 secs.
Reading: 3630000000
Memory used: 13773 MB.
Reading time: 69001 secs.
Reading: 3640000000
Memory used: 13790 MB.
Reading time: 69179 secs.
Reading: 3660000000
Memory used: 13822 MB.
Reading time: 69537 secs.
Reading: 3670000000
Memory used: 13841 MB.
Reading time: 69718 secs.
Reading: 3680000000
Memory used: 13876 MB.
Reading time: 69907 secs.
Reading: 3690000000
Memory used: 13899 MB.
Reading time: 70091 secs.
Reading: 3710000000
Memory used: 13938 MB.
Reading time: 70456 secs.
Reading: 3720000000
Memory used: 13965 MB.
Reading time: 70643 secs.
Reading: 3730000000
Memory used: 13983 MB.
Reading time: 70825 secs.
Reading: 3740000000
Memory used: 13999 MB.
Reading time: 71006 secs.
Reading: 3750000000
Memory used: 14015 MB.
Reading time: 71187 secs.
90/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R2_001_val_2.fastq
Reading: 3770000000
Memory used: 14065 MB.
Reading time: 71539 secs.
Reading: 3800000000
Memory used: 14162 MB.
Reading time: 72057 secs.
Reading: 3810000000
Memory used: 14195 MB.
Reading time: 72231 secs.
Reading: 3820000000
Memory used: 14229 MB.
Reading time: 72405 secs.
Reading: 3830000000
Memory used: 14263 MB.
Reading time: 72578 secs.
Reading: 3880000000
Memory used: 14438 MB.
Reading time: 73448 secs.
Reading: 3890000000
Memory used: 14474 MB.
Reading time: 73621 secs.
Reading: 3900000000
Memory used: 14510 MB.
Reading time: 73795 secs.
Reading: 3920000000
Memory used: 14604 MB.
Reading time: 74161 secs.
Reading: 3930000000
Memory used: 14655 MB.
Reading time: 74342 secs.
Reading: 3950000000
Memory used: 14751 MB.
Reading time: 74703 secs.
Reading: 3970000000
Memory used: 14834 MB.
Reading time: 75053 secs.
Reading: 3980000000
Memory used: 14873 MB.
Reading time: 75226 secs.
91/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R1_001_val_1.fastq
Reading: 4010000000
Memory used: 14982 MB.
Reading time: 75765 secs.
Reading: 4020000000
Memory used: 15006 MB.
Reading time: 75946 secs.
Reading: 4030000000
Memory used: 15028 MB.
Reading time: 76127 secs.
Reading: 4040000000
Memory used: 15049 MB.
Reading time: 76309 secs.
Reading: 4060000000
Memory used: 15090 MB.
Reading time: 76672 secs.
Reading: 4080000000
Memory used: 15131 MB.
Reading time: 77035 secs.
Reading: 4090000000
Memory used: 15150 MB.
Reading time: 77216 secs.
Reading: 4130000000
Memory used: 15224 MB.
Reading time: 77945 secs.
Reading: 4140000000
Memory used: 15243 MB.
Reading time: 78128 secs.
Reading: 4150000000
Memory used: 15261 MB.
Reading time: 78312 secs.
Reading: 4160000000
Memory used: 15292 MB.
Reading time: 78502 secs.
Reading: 4170000000
Memory used: 15335 MB.
Reading time: 78697 secs.
Reading: 4200000000
Memory used: 15428 MB.
Reading time: 79230 secs.
Reading: 4210000000
Memory used: 15466 MB.
Reading time: 79423 secs.
Reading: 4220000000
Memory used: 15487 MB.
Reading time: 79605 secs.
Reading: 4230000000
Memory used: 15511 MB.
Reading time: 79790 secs.
92/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R2_001_val_2.fastq
Reading: 4240000000
Memory used: 15545 MB.
Reading time: 79965 secs.
Reading: 4250000000
Memory used: 15584 MB.
Reading time: 80138 secs.
Reading: 4260000000
Memory used: 15623 MB.
Reading time: 80313 secs.
Reading: 4270000000
Memory used: 15662 MB.
Reading time: 80488 secs.
Reading: 4280000000
Memory used: 15702 MB.
Reading time: 80662 secs.
Reading: 4310000000
Memory used: 15824 MB.
Reading time: 81189 secs.
Reading: 4330000000
Memory used: 15906 MB.
Reading time: 81544 secs.
Reading: 4350000000
Memory used: 15989 MB.
Reading time: 81898 secs.
Reading: 4360000000
Memory used: 16030 MB.
Reading time: 82074 secs.
Reading: 4370000000
Memory used: 16072 MB.
Reading time: 82251 secs.
Reading: 4380000000
Memory used: 16114 MB.
Reading time: 82430 secs.
Reading: 4390000000
Memory used: 16157 MB.
Reading time: 82609 secs.
Reading: 4410000000
Memory used: 16282 MB.
Reading time: 82986 secs.
Reading: 4420000000
Memory used: 16343 MB.
Reading time: 83173 secs.
Reading: 4430000000
Memory used: 16404 MB.
Reading time: 83359 secs.
Reading: 4440000000
Memory used: 16456 MB.
Reading time: 83542 secs.
Reading: 4450000000
Memory used: 16522 MB.
Reading time: 83732 secs.
93/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R1_001_val_1.fastq
94/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R2_001_val_2.fastq
95/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R1_001_val_1.fastq
96/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R2_001_val_2.fastq
97/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-6_S21_L006_R1_001_val_1.fastq
98/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-6_S21_L006_R2_001_val_2.fastq
99/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-7_S25_L007_R1_001_val_1.fastq
100/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-7_S25_L007_R2_001_val_2.fastq
101/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8_S29_L008_R1_001_val_1.fastq
102/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8_S29_L008_R2_001_val_2.fastq
103/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R1_001_val_1.fastq
104/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R2_001_val_2.fastq
105/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R1_001_val_1.fastq
106/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R2_001_val_2.fastq
107/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R1_001_val_1.fastq
108/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R2_001_val_2.fastq
109/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R1_001_val_1.fastq
110/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R2_001_val_2.fastq
111/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R1_001_val_1.fastq
112/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R2_001_val_2.fastq
113/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R1_001_val_1.fastq
114/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R2_001_val_2.fastq
115/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R1_001_val_1.fastq
Reading: 4490000000
Memory used: 16678 MB.
Reading time: 84496 secs.
Reading: 4500000000
Memory used: 16702 MB.
Reading time: 84697 secs.
Reading: 4510000000
Memory used: 16724 MB.
Reading time: 84898 secs.
Reading: 4520000000
Memory used: 16746 MB.
Reading time: 85098 secs.
Reading: 4530000000
Memory used: 16767 MB.
Reading time: 85301 secs.
Reading: 4540000000
Memory used: 16788 MB.
Reading time: 85504 secs.
Reading: 4550000000
Memory used: 16809 MB.
Reading time: 85705 secs.
Reading: 4560000000
Memory used: 16829 MB.
Reading time: 85907 secs.
Reading: 4580000000
Memory used: 16867 MB.
Reading time: 86309 secs.
Reading: 4600000000
Memory used: 16904 MB.
Reading time: 86711 secs.
Reading: 4620000000
Memory used: 16940 MB.
Reading time: 87112 secs.
Reading: 4630000000
Memory used: 16957 MB.
Reading time: 87315 secs.
Reading: 4640000000
Memory used: 16981 MB.
Reading time: 87515 secs.
Reading: 4650000000
Memory used: 17005 MB.
Reading time: 87717 secs.
Reading: 4660000000
Memory used: 17035 MB.
Reading time: 87923 secs.
Reading: 4680000000
Memory used: 17074 MB.
Reading time: 88327 secs.
Reading: 4690000000
Memory used: 17092 MB.
Reading time: 88527 secs.
Reading: 4700000000
Memory used: 17110 MB.
Reading time: 88727 secs.
Reading: 4710000000
Memory used: 17130 MB.
Reading time: 88928 secs.
Reading: 4720000000
Memory used: 17149 MB.
Reading time: 89128 secs.
Reading: 4730000000
Memory used: 17167 MB.
Reading time: 89329 secs.
Reading: 4740000000
Memory used: 17185 MB.
Reading time: 89530 secs.
Reading: 4750000000
Memory used: 17203 MB.
Reading time: 89729 secs.
116/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R2_001_val_2.fastq
Reading: 4760000000
Memory used: 17235 MB.
Reading time: 89925 secs.
Reading: 4780000000
Memory used: 17323 MB.
Reading time: 90307 secs.
Reading: 4790000000
Memory used: 17366 MB.
Reading time: 90500 secs.
Reading: 4820000000
Memory used: 17500 MB.
Reading time: 91080 secs.
Reading: 4830000000
Memory used: 17547 MB.
Reading time: 91271 secs.
Reading: 4840000000
Memory used: 17594 MB.
Reading time: 91465 secs.
Reading: 4850000000
Memory used: 17642 MB.
Reading time: 91658 secs.
Reading: 4860000000
Memory used: 17688 MB.
Reading time: 91855 secs.
Reading: 4870000000
Memory used: 17735 MB.
Reading time: 92050 secs.
Reading: 4890000000
Memory used: 17829 MB.
Reading time: 92437 secs.
Reading: 4900000000
Memory used: 17876 MB.
Reading time: 92632 secs.
Reading: 4910000000
Memory used: 17937 MB.
Reading time: 92833 secs.
Reading: 4920000000
Memory used: 17995 MB.
Reading time: 93023 secs.
Reading: 4930000000
Memory used: 18051 MB.
Reading time: 93217 secs.
Reading: 4940000000
Memory used: 18113 MB.
Reading time: 93415 secs.
Reading: 4950000000
Memory used: 18166 MB.
Reading time: 93609 secs.
Reading: 4960000000
Memory used: 18217 MB.
Reading time: 93800 secs.
Reading: 4970000000
Memory used: 18267 MB.
Reading time: 93990 secs.
Reading: 4980000000
Memory used: 18318 MB.
Reading time: 94182 secs.
Reading: 5000000000
Memory used: 18425 MB.
Reading time: 94559 secs.
Reading: 5010000000
Memory used: 18476 MB.
Reading time: 94752 secs.
Reading: 5020000000
Memory used: 18531 MB.
Reading time: 94942 secs.
Reading: 5030000000
Memory used: 18592 MB.
Reading time: 95136 secs.
117/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R1_001_val_1.fastq
Reading: 5060000000
Memory used: 18692 MB.
Reading time: 95735 secs.
Reading: 5070000000
Memory used: 18715 MB.
Reading time: 95937 secs.
Reading: 5080000000
Memory used: 18737 MB.
Reading time: 96141 secs.
Reading: 5100000000
Memory used: 18779 MB.
Reading time: 96545 secs.
Reading: 5110000000
Memory used: 18800 MB.
Reading time: 96748 secs.
Reading: 5120000000
Memory used: 18820 MB.
Reading time: 96951 secs.
Reading: 5130000000
Memory used: 18841 MB.
Reading time: 97154 secs.
Reading: 5140000000
Memory used: 18860 MB.
Reading time: 97356 secs.
Reading: 5160000000
Memory used: 18897 MB.
Reading time: 97763 secs.
Reading: 5170000000
Memory used: 18914 MB.
Reading time: 97967 secs.
Reading: 5200000000
Memory used: 18966 MB.
Reading time: 98578 secs.
Reading: 5210000000
Memory used: 18985 MB.
Reading time: 98782 secs.
Reading: 5240000000
Memory used: 19037 MB.
Reading time: 99394 secs.
Reading: 5260000000
Memory used: 19098 MB.
Reading time: 99813 secs.
Reading: 5270000000
Memory used: 19130 MB.
Reading time: 100022 secs.
Reading: 5280000000
Memory used: 19166 MB.
Reading time: 100229 secs.
Reading: 5300000000
Memory used: 19219 MB.
Reading time: 100640 secs.
Reading: 5310000000
Memory used: 19244 MB.
Reading time: 100847 secs.
Reading: 5320000000
Memory used: 19263 MB.
Reading time: 101053 secs.
118/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R2_001_val_2.fastq
Reading: 5330000000
Memory used: 19308 MB.
Reading time: 101249 secs.
Reading: 5340000000
Memory used: 19360 MB.
Reading time: 101444 secs.
Reading: 5350000000
Memory used: 19411 MB.
Reading time: 101641 secs.
Reading: 5360000000
Memory used: 19461 MB.
Reading time: 101839 secs.
Reading: 5370000000
Memory used: 19513 MB.
Reading time: 102036 secs.
Reading: 5380000000
Memory used: 19565 MB.
Reading time: 102232 secs.
Reading: 5390000000
Memory used: 19617 MB.
Reading time: 102428 secs.
Reading: 5430000000
Memory used: 19839 MB.
Reading time: 103229 secs.
Reading: 5440000000
Memory used: 19895 MB.
Reading time: 103431 secs.
Reading: 5460000000
Memory used: 20005 MB.
Reading time: 103832 secs.
Reading: 5480000000
Memory used: 20111 MB.
Reading time: 104230 secs.
Reading: 5500000000
Memory used: 20219 MB.
Reading time: 104628 secs.
Reading: 5520000000
Memory used: 20326 MB.
Reading time: 105028 secs.
Reading: 5550000000
Memory used: 20493 MB.
Reading time: 105607 secs.
Reading: 5580000000
Memory used: 20731 MB.
Reading time: 106237 secs.
Total bases: 656494834234
Total nodes in round 1: 392058825
Reading time: 107929 secs.
Building the sparse k-mer graph, round: 2
1/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L001_R1_001_val_1_val_1.fastq
2/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L001_R2_001_val_2_val_2.fastq
3/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L002_R1_001_val_1_val_1.fastq
4/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L002_R2_001_val_2_val_2.fastq
5/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L001_R1_001_val_1_val_1.fastq
6/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L001_R2_001_val_2_val_2.fastq
7/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L002_R1_001_val_1_val_1.fastq
8/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR005_S4_L002_R2_001_val_2_val_2.fastq
9/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L001_R1_001_val_1_val_1.fastq
10/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L001_R2_001_val_2_val_2.fastq
11/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L002_R1_001_val_1_val_1.fastq
12/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR006_S3_L002_R2_001_val_2_val_2.fastq
13/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L001_R1_001_val_1_val_1.fastq
14/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L001_R2_001_val_2_val_2.fastq
15/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L002_R1_001_val_1_val_1.fastq
16/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR012_S1_L002_R2_001_val_2_val_2.fastq
17/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L001_R1_001_val_1_val_1.fastq
18/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L001_R2_001_val_2_val_2.fastq
19/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L002_R1_001_val_1_val_1.fastq
20/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L002_R2_001_val_2_val_2.fastq
21/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L001_R1_001_val_1_val_1.fastq
22/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L001_R2_001_val_2_val_2.fastq
23/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L002_R1_001_val_1_val_1.fastq
24/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L002_R2_001_val_2_val_2.fastq
25/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L001_R1_001_val_1_val_1.fastq
26/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L001_R2_001_val_2_val_2.fastq
27/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L002_R1_001_val_1_val_1.fastq
28/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L002_R2_001_val_2_val_2.fastq
29/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L001_R1_001_val_1_val_1.fastq
30/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L001_R2_001_val_2_val_2.fastq
31/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L002_R1_001_val_1_val_1.fastq
32/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR019_S7_L002_R2_001_val_2_val_2.fastq
33/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L001_R1_001_val_1_val_1.fastq
34/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L001_R2_001_val_2_val_2.fastq
35/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L002_R1_001_val_1_val_1.fastq
36/118 files.
Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR021_S8_L002_R2_001_val_2_val_2.fastq
37/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_1.fastq
Reading: 10000000
Reading time: 108207 secs.
Reading: 20000000
Reading time: 108482 secs.
Reading: 30000000
Reading time: 108757 secs.
Reading: 40000000
Reading time: 109034 secs.
Reading: 50000000
Reading time: 109310 secs.
Reading: 60000000
Reading time: 109588 secs.
Reading: 70000000
Reading time: 109865 secs.
Reading: 80000000
Reading time: 110143 secs.
Reading: 90000000
Reading time: 110423 secs.
38/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_2.fastq
Reading: 100000000
Reading time: 110701 secs.
Reading: 110000000
Reading time: 110976 secs.
Reading: 120000000
Reading time: 111253 secs.
Reading: 130000000
Reading time: 111530 secs.
Reading: 140000000
Reading time: 111805 secs.
Reading: 150000000
Reading time: 112081 secs.
Reading: 160000000
Reading time: 112357 secs.
Reading: 170000000
Reading time: 112636 secs.
Reading: 180000000
Reading time: 112912 secs.
39/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_1.fastq
Reading: 190000000
Reading time: 113190 secs.
Reading: 200000000
Reading time: 113470 secs.
Reading: 210000000
Reading time: 113749 secs.
Reading: 220000000
Reading time: 114030 secs.
Reading: 230000000
Reading time: 114312 secs.
Reading: 240000000
Reading time: 114593 secs.
Reading: 250000000
Reading time: 114873 secs.
Reading: 260000000
Reading time: 115154 secs.
40/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_2.fastq
Reading: 270000000
Reading time: 115437 secs.
Reading: 280000000
Reading time: 115716 secs.
Reading: 290000000
Reading time: 115993 secs.
Reading: 300000000
Reading time: 116271 secs.
Reading: 310000000
Reading time: 116547 secs.
Reading: 320000000
Reading time: 116823 secs.
Reading: 330000000
Reading time: 117098 secs.
41/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_1.fastq
Reading: 340000000
Reading time: 117373 secs.
Reading: 350000000
Reading time: 117652 secs.
Reading: 360000000
Reading time: 117925 secs.
Reading: 370000000
Reading time: 118198 secs.
Reading: 380000000
Reading time: 118466 secs.
Reading: 390000000
Reading time: 118732 secs.
Reading: 400000000
Reading time: 119002 secs.
Reading: 410000000
Reading time: 119269 secs.
42/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_2.fastq
Reading: 420000000
Reading time: 119533 secs.
Reading: 430000000
Reading time: 119795 secs.
Reading: 440000000
Reading time: 120057 secs.
Reading: 450000000
Reading time: 120319 secs.
Reading: 460000000
Reading time: 120573 secs.
Reading: 470000000
Reading time: 120828 secs.
Reading: 480000000
Reading time: 121095 secs.
43/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_1.fastq
44/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_2.fastq
45/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_1.fastq
46/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_2.fastq
47/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_1.fastq
48/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_2.fastq
49/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_1.fastq
50/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_2.fastq
51/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_1.fastq
52/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_2.fastq
53/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_1.fastq
54/118 files.
Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDACDTAAPEI-102_2.fastq
55/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-1_S1_L001_R1_001_val_1.fastq
Reading: 1200000000
Reading time: 122169 secs.
Reading: 1210000000
Reading time: 122360 secs.
Reading: 1220000000
Reading time: 122548 secs.
Reading: 1230000000
Reading time: 122735 secs.
Reading: 1250000000
Reading time: 123110 secs.
Reading: 1260000000
Reading time: 123299 secs.
Reading: 1280000000
Reading time: 123675 secs.
Reading: 1340000000
Reading time: 124792 secs.
Reading: 1350000000
Reading time: 124976 secs.
Reading: 1360000000
Reading time: 125160 secs.
Reading: 1370000000
Reading time: 125344 secs.
Reading: 1380000000
Reading time: 125528 secs.
Reading: 1390000000
Reading time: 125712 secs.
Reading: 1400000000
Reading time: 125897 secs.
Reading: 1420000000
Reading time: 126263 secs.
Reading: 1430000000
Reading time: 126446 secs.
Reading: 1440000000
Reading time: 126631 secs.
Reading: 1450000000
Reading time: 126815 secs.
Reading: 1470000000
Reading time: 127184 secs.
Reading: 1480000000
Reading time: 127368 secs.
56/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-1_S1_L001_R2_001_val_2.fastq
Reading: 1490000000
Reading time: 127545 secs.
Reading: 1500000000
Reading time: 127707 secs.
Reading: 1510000000
Reading time: 127873 secs.
Reading: 1550000000
Reading time: 128523 secs.
Reading: 1560000000
Reading time: 128685 secs.
Reading: 1570000000
Reading time: 128850 secs.
Reading: 1580000000
Reading time: 129015 secs.
Reading: 1590000000
Reading time: 129183 secs.
Reading: 1600000000
Reading time: 129350 secs.
Reading: 1610000000
Reading time: 129517 secs.
Reading: 1620000000
Reading time: 129682 secs.
Reading: 1630000000
Reading time: 129843 secs.
Reading: 1640000000
Reading time: 130007 secs.
Reading: 1670000000
Reading time: 130464 secs.
Reading: 1680000000
Reading time: 130625 secs.
Reading: 1690000000
Reading time: 130786 secs.
Reading: 1700000000
Reading time: 130946 secs.
Reading: 1730000000
Reading time: 131434 secs.
Reading: 1750000000
Reading time: 131751 secs.
Reading: 1760000000
Reading time: 131916 secs.
57/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2_S5_L002_R1_001_val_1.fastq
Reading: 1780000000
Reading time: 132244 secs.
Reading: 1800000000
Reading time: 132603 secs.
Reading: 1810000000
Reading time: 132781 secs.
Reading: 1830000000
Reading time: 133137 secs.
Reading: 1850000000
Reading time: 133492 secs.
Reading: 1860000000
Reading time: 133670 secs.
Reading: 1870000000
Reading time: 133847 secs.
Reading: 1880000000
Reading time: 134025 secs.
Reading: 1890000000
Reading time: 134203 secs.
Reading: 1900000000
Reading time: 134381 secs.
Reading: 1910000000
Reading time: 134559 secs.
Reading: 1920000000
Reading time: 134737 secs.
Reading: 1930000000
Reading time: 134916 secs.
Reading: 1940000000
Reading time: 135093 secs.
Reading: 1970000000
Reading time: 135626 secs.
Reading: 1980000000
Reading time: 135804 secs.
Reading: 1990000000
Reading time: 135981 secs.
Reading: 2000000000
Reading time: 136158 secs.
Reading: 2010000000
Reading time: 136336 secs.
Reading: 2020000000
Reading time: 136514 secs.
Reading: 2030000000
Reading time: 136692 secs.
Reading: 2040000000
Reading time: 136869 secs.
Reading: 2050000000
Reading time: 137047 secs.
Reading: 2060000000
Reading time: 137224 secs.
Reading: 2070000000
Reading time: 137402 secs.
58/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2_S5_L002_R2_001_val_2.fastq
Reading: 2080000000
Reading time: 137571 secs.
Reading: 2110000000
Reading time: 138051 secs.
Reading: 2130000000
Reading time: 138373 secs.
Reading: 2140000000
Reading time: 138530 secs.
Reading: 2160000000
Reading time: 138845 secs.
Reading: 2170000000
Reading time: 139006 secs.
Reading: 2230000000
Reading time: 139991 secs.
Reading: 2240000000
Reading time: 140155 secs.
Reading: 2260000000
Reading time: 140480 secs.
Reading: 2270000000
Reading time: 140628 secs.
Reading: 2280000000
Reading time: 140792 secs.
Reading: 2290000000
Reading time: 140952 secs.
Reading: 2310000000
Reading time: 141278 secs.
Reading: 2360000000
Reading time: 142057 secs.
Reading: 2370000000
Reading time: 142217 secs.
59/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R1_001_val_1.fastq
60/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-1_S2_L001_R2_001_val_2.fastq
61/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R1_001_val_1.fastq
62/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-2_S6_L002_R2_001_val_2.fastq
63/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R1_001_val_1.fastq
Reading: 2380000000
Reading time: 142389 secs.
Reading: 2390000000
Reading time: 142568 secs.
Reading: 2400000000
Reading time: 142747 secs.
Reading: 2410000000
Reading time: 142927 secs.
Reading: 2430000000
Reading time: 143286 secs.
Reading: 2440000000
Reading time: 143466 secs.
Reading: 2450000000
Reading time: 143647 secs.
Reading: 2460000000
Reading time: 143825 secs.
Reading: 2470000000
Reading time: 144004 secs.
Reading: 2480000000
Reading time: 144185 secs.
Reading: 2500000000
Reading time: 144546 secs.
Reading: 2530000000
Reading time: 145084 secs.
Reading: 2540000000
Reading time: 145260 secs.
Reading: 2550000000
Reading time: 145437 secs.
Reading: 2560000000
Reading time: 145615 secs.
Reading: 2570000000
Reading time: 145753 secs.
Reading: 2580000000
Reading time: 145932 secs.
Reading: 2590000000
Reading time: 146113 secs.
Reading: 2610000000
Reading time: 146472 secs.
Reading: 2620000000
Reading time: 146650 secs.
Reading: 2630000000
Reading time: 146827 secs.
Reading: 2640000000
Reading time: 147006 secs.
Reading: 2650000000
Reading time: 147186 secs.
64/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-3_S10_L003_R2_001_val_2.fastq
Reading: 2660000000
Reading time: 147362 secs.
Reading: 2680000000
Reading time: 147685 secs.
Reading: 2690000000
Reading time: 147847 secs.
Reading: 2700000000
Reading time: 148012 secs.
Reading: 2710000000
Reading time: 148173 secs.
Reading: 2720000000
Reading time: 148333 secs.
Reading: 2740000000
Reading time: 148655 secs.
Reading: 2750000000
Reading time: 148817 secs.
Reading: 2780000000
Reading time: 149310 secs.
Reading: 2790000000
Reading time: 149472 secs.
Reading: 2800000000
Reading time: 149635 secs.
Reading: 2810000000
Reading time: 149797 secs.
Reading: 2820000000
Reading time: 149957 secs.
Reading: 2830000000
Reading time: 150117 secs.
Reading: 2840000000
Reading time: 150281 secs.
Reading: 2850000000
Reading time: 150442 secs.
Reading: 2860000000
Reading time: 150602 secs.
Reading: 2870000000
Reading time: 150761 secs.
Reading: 2880000000
Reading time: 150924 secs.
Reading: 2910000000
Reading time: 151412 secs.
Reading: 2920000000
Reading time: 151574 secs.
Reading: 2930000000
Reading time: 151735 secs.
Reading: 2940000000
Reading time: 151896 secs.
65/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R1_001_val_1.fastq
Reading: 2950000000
Reading time: 152069 secs.
Reading: 2960000000
Reading time: 152246 secs.
Reading: 2970000000
Reading time: 152426 secs.
Reading: 2980000000
Reading time: 152606 secs.
Reading: 2990000000
Reading time: 152785 secs.
Reading: 3000000000
Reading time: 152965 secs.
Reading: 3010000000
Reading time: 153146 secs.
Reading: 3020000000
Reading time: 153325 secs.
Reading: 3030000000
Reading time: 153504 secs.
Reading: 3040000000
Reading time: 153683 secs.
Reading: 3050000000
Reading time: 153863 secs.
Reading: 3060000000
Reading time: 154044 secs.
Reading: 3070000000
Reading time: 154221 secs.
Reading: 3080000000
Reading time: 154400 secs.
Reading: 3090000000
Reading time: 154579 secs.
Reading: 3100000000
Reading time: 154755 secs.
Reading: 3110000000
Reading time: 154933 secs.
Reading: 3120000000
Reading time: 155111 secs.
Reading: 3140000000
Reading time: 155463 secs.
Reading: 3150000000
Reading time: 155647 secs.
Reading: 3160000000
Reading time: 155826 secs.
Reading: 3170000000
Reading time: 156003 secs.
Reading: 3180000000
Reading time: 156181 secs.
Reading: 3190000000
Reading time: 156359 secs.
Reading: 3210000000
Reading time: 156714 secs.
Reading: 3220000000
Reading time: 156892 secs.
Reading: 3230000000
Reading time: 157070 secs.
66/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-4_S14_L004_R2_001_val_2.fastq
Reading: 3240000000
Reading time: 157229 secs.
Reading: 3250000000
Reading time: 157389 secs.
Reading: 3260000000
Reading time: 157548 secs.
Reading: 3280000000
Reading time: 157871 secs.
Reading: 3300000000
Reading time: 158189 secs.
Reading: 3310000000
Reading time: 158349 secs.
Reading: 3320000000
Reading time: 158511 secs.
Reading: 3330000000
Reading time: 158673 secs.
Reading: 3340000000
Reading time: 158837 secs.
Reading: 3350000000
Reading time: 158999 secs.
Reading: 3360000000
Reading time: 159161 secs.
Reading: 3380000000
Reading time: 159484 secs.
Reading: 3410000000
Reading time: 159962 secs.
Reading: 3430000000
Reading time: 160279 secs.
Reading: 3440000000
Reading time: 160434 secs.
Reading: 3460000000
Reading time: 160755 secs.
Reading: 3470000000
Reading time: 160916 secs.
Reading: 3500000000
Reading time: 161402 secs.
Reading: 3510000000
Reading time: 161560 secs.
67/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R1_001_val_1.fastq
68/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-5_S18_L005_R2_001_val_2.fastq
69/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R1_001_val_1.fastq
70/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-6_S22_L006_R2_001_val_2.fastq
71/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R1_001_val_1.fastq
72/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-7_S26_L007_R2_001_val_2.fastq
73/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R1_001_val_1.fastq
Reading: 3520000000
Reading time: 161720 secs.
74/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-2to4kb-8_S30_L008_R2_001_val_2.fastq
75/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-3_S9_L003_R1_001_val_1.fastq
76/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-3_S9_L003_R2_001_val_2.fastq
77/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-4_S13_L004_R1_001_val_1.fastq
78/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-4_S13_L004_R2_001_val_2.fastq
79/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5_S17_L005_R1_001_val_1.fastq
80/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5_S17_L005_R2_001_val_2.fastq
81/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R1_001_val_1.fastq
82/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-1_S3_L001_R2_001_val_2.fastq
83/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R1_001_val_1.fastq
84/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-2_S7_L002_R2_001_val_2.fastq
85/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R1_001_val_1.fastq
86/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-3_S11_L003_R2_001_val_2.fastq
87/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R1_001_val_1.fastq
88/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-4_S15_L004_R2_001_val_2.fastq
89/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R1_001_val_1.fastq
Reading: 3530000000
Reading time: 161879 secs.
Reading: 3540000000
Reading time: 162035 secs.
Reading: 3570000000
Reading time: 162506 secs.
Reading: 3580000000
Reading time: 162663 secs.
Reading: 3590000000
Reading time: 162820 secs.
Reading: 3610000000
Reading time: 163132 secs.
Reading: 3620000000
Reading time: 163290 secs.
Reading: 3630000000
Reading time: 163446 secs.
Reading: 3640000000
Reading time: 163601 secs.
Reading: 3660000000
Reading time: 163916 secs.
Reading: 3670000000
Reading time: 164073 secs.
Reading: 3680000000
Reading time: 164229 secs.
Reading: 3690000000
Reading time: 164387 secs.
Reading: 3710000000
Reading time: 164705 secs.
Reading: 3720000000
Reading time: 164862 secs.
Reading: 3730000000
Reading time: 165021 secs.
Reading: 3740000000
Reading time: 165181 secs.
Reading: 3750000000
Reading time: 165340 secs.
90/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-5_S19_L005_R2_001_val_2.fastq
Reading: 3770000000
Reading time: 165638 secs.
Reading: 3800000000
Reading time: 166068 secs.
Reading: 3810000000
Reading time: 166209 secs.
Reading: 3820000000
Reading time: 166352 secs.
Reading: 3830000000
Reading time: 166496 secs.
Reading: 3880000000
Reading time: 167209 secs.
Reading: 3890000000
Reading time: 167353 secs.
Reading: 3900000000
Reading time: 167498 secs.
Reading: 3920000000
Reading time: 167784 secs.
Reading: 3930000000
Reading time: 167925 secs.
Reading: 3950000000
Reading time: 168211 secs.
Reading: 3970000000
Reading time: 168498 secs.
Reading: 3980000000
Reading time: 168642 secs.
91/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R1_001_val_1.fastq
Reading: 4010000000
Reading time: 169088 secs.
Reading: 4020000000
Reading time: 169245 secs.
Reading: 4030000000
Reading time: 169403 secs.
Reading: 4040000000
Reading time: 169560 secs.
Reading: 4060000000
Reading time: 169874 secs.
Reading: 4080000000
Reading time: 170187 secs.
Reading: 4090000000
Reading time: 170344 secs.
Reading: 4130000000
Reading time: 170976 secs.
Reading: 4140000000
Reading time: 171135 secs.
Reading: 4150000000
Reading time: 171294 secs.
Reading: 4160000000
Reading time: 171452 secs.
Reading: 4170000000
Reading time: 171609 secs.
Reading: 4200000000
Reading time: 172059 secs.
Reading: 4210000000
Reading time: 172217 secs.
Reading: 4220000000
Reading time: 172376 secs.
Reading: 4230000000
Reading time: 172536 secs.
92/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-6_S23_L006_R2_001_val_2.fastq
Reading: 4240000000
Reading time: 172681 secs.
Reading: 4250000000
Reading time: 172823 secs.
Reading: 4260000000
Reading time: 172967 secs.
Reading: 4270000000
Reading time: 173109 secs.
Reading: 4280000000
Reading time: 173252 secs.
Reading: 4310000000
Reading time: 173680 secs.
Reading: 4330000000
Reading time: 173968 secs.
Reading: 4350000000
Reading time: 174255 secs.
Reading: 4360000000
Reading time: 174398 secs.
Reading: 4370000000
Reading time: 174541 secs.
Reading: 4380000000
Reading time: 174684 secs.
Reading: 4390000000
Reading time: 174828 secs.
Reading: 4410000000
Reading time: 175112 secs.
Reading: 4420000000
Reading time: 175251 secs.
Reading: 4430000000
Reading time: 175392 secs.
Reading: 4440000000
Reading time: 175533 secs.
Reading: 4450000000
Reading time: 175674 secs.
93/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R1_001_val_1.fastq
94/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-7_S27_L007_R2_001_val_2.fastq
95/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R1_001_val_1.fastq
96/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-5to7kb-8_S31_L008_R2_001_val_2.fastq
97/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-6_S21_L006_R1_001_val_1.fastq
98/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-6_S21_L006_R2_001_val_2.fastq
99/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-7_S25_L007_R1_001_val_1.fastq
100/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-7_S25_L007_R2_001_val_2.fastq
101/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8_S29_L008_R1_001_val_1.fastq
102/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8_S29_L008_R2_001_val_2.fastq
103/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R1_001_val_1.fastq
104/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-1_S4_L001_R2_001_val_2.fastq
105/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R1_001_val_1.fastq
106/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-2_S8_L002_R2_001_val_2.fastq
107/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R1_001_val_1.fastq
108/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-3_S12_L003_R2_001_val_2.fastq
109/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R1_001_val_1.fastq
110/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-4_S16_L004_R2_001_val_2.fastq
111/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R1_001_val_1.fastq
112/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-5_S20_L005_R2_001_val_2.fastq
113/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R1_001_val_1.fastq
114/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-6_S24_L006_R2_001_val_2.fastq
115/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R1_001_val_1.fastq
Reading: 4490000000
Reading time: 176299 secs.
Reading: 4500000000
Reading time: 176469 secs.
Reading: 4510000000
Reading time: 176640 secs.
Reading: 4520000000
Reading time: 176811 secs.
Reading: 4530000000
Reading time: 176980 secs.
Reading: 4540000000
Reading time: 177148 secs.
Reading: 4550000000
Reading time: 177315 secs.
Reading: 4560000000
Reading time: 177485 secs.
Reading: 4580000000
Reading time: 177827 secs.
Reading: 4600000000
Reading time: 178165 secs.
Reading: 4620000000
Reading time: 178505 secs.
Reading: 4630000000
Reading time: 178674 secs.
Reading: 4640000000
Reading time: 178843 secs.
Reading: 4650000000
Reading time: 179012 secs.
Reading: 4660000000
Reading time: 179181 secs.
Reading: 4680000000
Reading time: 179522 secs.
Reading: 4690000000
Reading time: 179693 secs.
Reading: 4700000000
Reading time: 179862 secs.
Reading: 4710000000
Reading time: 180031 secs.
Reading: 4720000000
Reading time: 180202 secs.
Reading: 4730000000
Reading time: 180372 secs.
Reading: 4740000000
Reading time: 180543 secs.
Reading: 4750000000
Reading time: 180713 secs.
116/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-7_S28_L007_R2_001_val_2.fastq
Reading: 4760000000
Reading time: 180872 secs.
Reading: 4780000000
Reading time: 181178 secs.
Reading: 4790000000
Reading time: 181333 secs.
Reading: 4820000000
Reading time: 181798 secs.
Reading: 4830000000
Reading time: 181950 secs.
Reading: 4840000000
Reading time: 182104 secs.
Reading: 4850000000
Reading time: 182258 secs.
Reading: 4860000000
Reading time: 182412 secs.
Reading: 4870000000
Reading time: 182568 secs.
Reading: 4890000000
Reading time: 182877 secs.
Reading: 4900000000
Reading time: 183031 secs.
Reading: 4910000000
Reading time: 183186 secs.
Reading: 4920000000
Reading time: 183333 secs.
Reading: 4930000000
Reading time: 183485 secs.
Reading: 4940000000
Reading time: 183640 secs.
Reading: 4950000000
Reading time: 183793 secs.
Reading: 4960000000
Reading time: 183948 secs.
Reading: 4970000000
Reading time: 184103 secs.
Reading: 4980000000
Reading time: 184258 secs.
Reading: 5000000000
Reading time: 184560 secs.
Reading: 5010000000
Reading time: 184714 secs.
Reading: 5020000000
Reading time: 184866 secs.
Reading: 5030000000
Reading time: 185019 secs.
117/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R1_001_val_1.fastq
Reading: 5060000000
Reading time: 185519 secs.
Reading: 5070000000
Reading time: 185689 secs.
Reading: 5080000000
Reading time: 185860 secs.
Reading: 5100000000
Reading time: 186202 secs.
Reading: 5110000000
Reading time: 186373 secs.
Reading: 5120000000
Reading time: 186543 secs.
Reading: 5130000000
Reading time: 186714 secs.
Reading: 5140000000
Reading time: 186885 secs.
Reading: 5160000000
Reading time: 187226 secs.
Reading: 5170000000
Reading time: 187395 secs.
Reading: 5200000000
Reading time: 187906 secs.
Reading: 5210000000
Reading time: 188076 secs.
Reading: 5240000000
Reading time: 188589 secs.
Reading: 5260000000
Reading time: 188930 secs.
Reading: 5270000000
Reading time: 189101 secs.
Reading: 5280000000
Reading time: 189270 secs.
Reading: 5300000000
Reading time: 189609 secs.
Reading: 5310000000
Reading time: 189780 secs.
Reading: 5320000000
Reading time: 189951 secs.
118/118 files.
Processing file: /gscratch/scrubbed/samwhite/illumina_geoduck_hiseq/20180328_trim_galore_illumina_hiseq_geoduck/Geoduck-NMP-gDNA-8to10kb-8_S32_L008_R2_001_val_2.fastq
Reading: 5330000000
Reading time: 190108 secs.
Reading: 5340000000
Reading time: 190260 secs.
Reading: 5350000000
Reading time: 190414 secs.
Reading: 5360000000
Reading time: 190569 secs.
Reading: 5370000000
Reading time: 190722 secs.
Reading: 5380000000
Reading time: 190873 secs.
Reading: 5390000000
Reading time: 191025 secs.
Reading: 5430000000
Reading time: 191637 secs.
Reading: 5440000000
Reading time: 191793 secs.
Reading: 5460000000
Reading time: 192102 secs.
Reading: 5480000000
Reading time: 192408 secs.
Reading: 5500000000
Reading time: 192714 secs.
Reading: 5520000000
Reading time: 193022 secs.
Reading: 5550000000
Reading time: 193460 secs.
Reading: 5580000000
Reading time: 193916 secs.
Total nodes in round 2: 392058825
Total nodes: 392058825
Total edges in round 2: 602370576
Reading time: 195408 secs.
Screening off weak nodes and edges...
Graph simplification...
Min searching depth: 7
Max searching depth: 20
Current depth: 7
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: 15
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: 19
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: 787 secs.