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 Reading: 50000000 Reading: 100000000 Reading: 150000000 2/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L001_R2_001_val_2_val_2.fastq Reading: 200000000 Reading: 250000000 Reading: 300000000 3/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L002_R1_001_val_1_val_1.fastq Reading: 350000000 Reading: 400000000 Reading: 450000000 Reading: 500000000 4/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/AD002_S9_L002_R2_001_val_2_val_2.fastq Reading: 550000000 Reading: 600000000 Reading: 650000000 Reading: 700000000 Reading: 750000000 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 Reading: 800000000 Reading: 850000000 Reading: 900000000 Reading: 950000000 Reading: 1000000000 Reading: 1050000000 18/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L001_R2_001_val_2_val_2.fastq Reading: 1100000000 Reading: 1150000000 Reading: 1200000000 Reading: 1250000000 Reading: 1300000000 Reading: 1350000000 19/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L002_R1_001_val_1_val_1.fastq Reading: 1400000000 Reading: 1450000000 Reading: 1500000000 Reading: 1550000000 Reading: 1600000000 Reading: 1650000000 Reading: 1700000000 Reading: 1750000000 20/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR013_AD013_S2_L002_R2_001_val_2_val_2.fastq Reading: 1800000000 Reading: 1850000000 Reading: 1900000000 Reading: 1950000000 Reading: 2000000000 Reading: 2050000000 Reading: 2100000000 21/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L001_R1_001_val_1_val_1.fastq Reading: 2150000000 Reading: 2200000000 Reading: 2250000000 Reading: 2300000000 Reading: 2350000000 Reading: 2400000000 Reading: 2450000000 Reading: 2500000000 Reading: 2550000000 Reading: 2600000000 Reading: 2650000000 Reading: 2700000000 Reading: 2750000000 Reading: 2800000000 Reading: 2850000000 22/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L001_R2_001_val_2_val_2.fastq Reading: 2900000000 Reading: 2950000000 Reading: 3000000000 Reading: 3050000000 Reading: 3100000000 Reading: 3150000000 Reading: 3200000000 Reading: 3250000000 Reading: 3300000000 Reading: 3350000000 Reading: 3400000000 Reading: 3450000000 Reading: 3500000000 Reading: 3550000000 Reading: 3600000000 23/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L002_R1_001_val_1_val_1.fastq Reading: 3650000000 Reading: 3700000000 Reading: 3750000000 Reading: 3800000000 Reading: 3850000000 Reading: 3900000000 Reading: 3950000000 Reading: 4000000000 Reading: 4050000000 Reading: 4100000000 Reading: 4150000000 Reading: 4200000000 Reading: 4250000000 Reading: 4300000000 Reading: 4350000000 Reading: 4400000000 Reading: 4450000000 Reading: 4500000000 24/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR014_AD014_S5_L002_R2_001_val_2_val_2.fastq Reading: 4550000000 Reading: 4600000000 Reading: 4650000000 Reading: 4700000000 Reading: 4750000000 Reading: 4800000000 Reading: 4850000000 Reading: 4900000000 Reading: 4950000000 Reading: 5000000000 Reading: 5050000000 Reading: 5100000000 Reading: 5150000000 Reading: 5200000000 Reading: 5250000000 Reading: 5300000000 Reading: 5350000000 25/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L001_R1_001_val_1_val_1.fastq Reading: 5400000000 Reading: 5450000000 Reading: 5500000000 Reading: 5550000000 Reading: 5600000000 Reading: 5650000000 26/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L001_R2_001_val_2_val_2.fastq Reading: 5700000000 Reading: 5750000000 Reading: 5800000000 Reading: 5850000000 Reading: 5900000000 27/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L002_R1_001_val_1_val_1.fastq Reading: 5950000000 Reading: 6000000000 Reading: 6050000000 Reading: 6100000000 Reading: 6150000000 Reading: 6200000000 28/118 files. Processing file: /gscratch/scrubbed/samwhite/20180129_trimgalore_geoduck_novaseq/NR015_AD015_S6_L002_R2_001_val_2_val_2.fastq Reading: 6250000000 Reading: 6300000000 Reading: 6350000000 Reading: 6400000000 Reading: 6450000000 Reading: 6500000000 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: 6550000000 Reading: 6600000000 38/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L1_wHAIPI023989-79_2.fastq Reading: 6650000000 Reading: 6700000000 39/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_1.fastq Reading: 6750000000 Reading: 6800000000 40/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151114_I191_FCH3Y35BCXX_L2_wHAMPI023988-81_2.fastq Reading: 6850000000 41/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_1.fastq Reading: 6900000000 Reading: 6950000000 42/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/151122_I136_FCH3L2FBBXX_L7_wHAXPI023990-97_2.fastq Reading: 7000000000 43/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_1.fastq Reading: 7050000000 44/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L3_WHPANwalDDAADWAAPEI-101_2.fastq Reading: 7100000000 Reading: 7150000000 45/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_1.fastq Reading: 7200000000 46/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L4_WHPANwalDDAADWAAPEI-101_2.fastq Reading: 7250000000 47/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_1.fastq Reading: 7300000000 Reading: 7350000000 48/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDABDLAAPEI-100_2.fastq Reading: 7400000000 49/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_1.fastq Reading: 7450000000 50/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L5_WHPANwalDDACDTAAPEI-102_2.fastq Reading: 7500000000 51/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_1.fastq Reading: 7550000000 52/118 files. Processing file: /gscratch/scrubbed/samwhite/bgi_geoduck/160103_I137_FCH3V5YBBXX_L6_WHPANwalDDABDLAAPEI-100_2.fastq Reading: 7600000000 Reading: 7650000000 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 Reading: 7700000000 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: 7750000000 Reading: 7800000000 Reading: 7850000000 Reading: 7900000000 Reading: 7950000000 Reading: 8000000000 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: 8050000000 Reading: 8100000000 Reading: 8150000000 Reading: 8200000000 Reading: 8250000000 Reading: 8300000000 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: 8350000000 Reading: 8400000000 Reading: 8450000000 Reading: 8500000000 Reading: 8550000000 Reading: 8600000000 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: 8650000000 Reading: 8700000000 Reading: 8750000000 Reading: 8800000000 Reading: 8850000000 Reading: 8900000000 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: 8950000000 Reading: 9000000000 Reading: 9050000000 Reading: 9100000000 Reading: 9150000000 Reading: 9200000000 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: 9250000000 Reading: 9300000000 Reading: 9350000000 Reading: 9400000000 Reading: 9450000000 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: 9500000000 Reading: 9550000000 Reading: 9600000000 Reading: 9650000000 Reading: 9700000000 Reading: 9750000000 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: 9800000000 Reading: 9850000000 Reading: 9900000000 Reading: 9950000000 Reading: 10000000000 Reading: 10050000000 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: 10100000000 Reading: 10150000000 Reading: 10200000000 Reading: 10250000000 Reading: 10300000000 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: 10350000000 Reading: 10400000000 Reading: 10450000000 Reading: 10500000000 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: 10550000000 Reading: 10600000000 Reading: 10650000000 Reading: 10700000000 Reading: 10750000000 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: 10800000000 Reading: 10850000000 Reading: 10900000000 Reading: 10950000000 Reading: 11000000000 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: 11050000000 Reading: 11100000000 Reading: 11150000000 Reading: 11200000000 Reading: 11250000000 Reading: 11300000000 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: 11350000000 Reading: 11400000000 Reading: 11450000000 Reading: 11500000000 Reading: 11550000000 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: 11600000000 Reading: 11650000000 Reading: 11700000000 Reading: 11750000000 Reading: 11800000000 Reading: 11850000000 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: 11900000000 Reading: 11950000000 Reading: 12000000000 Reading: 12050000000 Reading: 12100000000 Reading: 12150000000 Scan finished. Error! K-mer size too large!