SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.9.1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Output file will be GZIP compressed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001_val_2.fq.gz Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 106.50 s (27 us/read; 2.25 M reads/minute). === Summary === Total reads processed: 3,996,315 Reads with adapters: 2,365,417 (59.2%) Reads written (passing filters): 3,996,315 (100.0%) Total basepairs processed: 593,688,021 bp Quality-trimmed: 161,140 bp (0.0%) Total written (filtered): 568,208,959 bp (95.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 2365417 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.9% C: 23.9% G: 22.7% T: 22.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1092119 999078.8 0 1092119 2 237188 249769.7 0 237188 3 105726 62442.4 0 105726 4 70512 15610.6 0 70512 5 833 3902.7 0 833 6 25608 975.7 0 25608 7 24439 243.9 0 24439 8 30007 61.0 0 30007 9 19423 15.2 0 19324 99 10 27007 3.8 1 24438 2569 11 24193 1.0 1 21508 2685 12 49848 0.2 1 44992 4856 13 417 0.1 1 163 254 14 30409 0.1 1 26982 3427 15 41366 0.1 1 37549 3817 16 176 0.1 1 77 99 17 27857 0.1 1 25162 2695 18 16568 0.1 1 14861 1707 19 29519 0.1 1 26578 2941 20 21091 0.1 1 19067 2024 21 16792 0.1 1 14962 1830 22 20201 0.1 1 18364 1837 23 21276 0.1 1 19178 2098 24 37690 0.1 1 34176 3514 25 18430 0.1 1 16766 1664 26 17597 0.1 1 15864 1733 27 10354 0.1 1 8997 1357 28 28466 0.1 1 26325 2141 29 5853 0.1 1 4981 872 30 25322 0.1 1 23457 1865 31 8773 0.1 1 7711 1062 32 40024 0.1 1 37612 2412 33 15124 0.1 1 13686 1438 34 5040 0.1 1 4387 653 35 21707 0.1 1 20267 1440 36 7141 0.1 1 6402 739 37 9565 0.1 1 8710 855 38 5456 0.1 1 5052 404 39 7199 0.1 1 6631 568 40 2942 0.1 1 2733 209 41 9827 0.1 1 9198 629 42 12807 0.1 1 11985 822 43 5830 0.1 1 5380 450 44 8947 0.1 1 8286 661 45 14044 0.1 1 13176 868 46 7086 0.1 1 6524 562 47 4907 0.1 1 4585 322 48 12935 0.1 1 12161 774 49 5201 0.1 1 4855 346 50 2042 0.1 1 1867 175 51 8681 0.1 1 8150 531 52 11816 0.1 1 11253 563 53 4853 0.1 1 4571 282 54 5760 0.1 1 5434 326 55 3489 0.1 1 3286 203 56 1741 0.1 1 1609 132 57 2940 0.1 1 2759 181 58 3041 0.1 1 2850 191 59 1674 0.1 1 1550 124 60 1051 0.1 1 942 109 61 883 0.1 1 805 78 62 943 0.1 1 873 70 63 1034 0.1 1 960 74 64 1718 0.1 1 1633 85 65 1982 0.1 1 1863 119 66 1986 0.1 1 1876 110 67 1871 0.1 1 1749 122 68 1762 0.1 1 1657 105 69 1718 0.1 1 1620 98 70 1574 0.1 1 1476 98 71 1413 0.1 1 1317 96 72 1343 0.1 1 1269 74 73 1190 0.1 1 1122 68 74 1114 0.1 1 1048 66 75 1075 0.1 1 1009 66 76 935 0.1 1 881 54 77 910 0.1 1 852 58 78 809 0.1 1 773 36 79 788 0.1 1 753 35 80 783 0.1 1 742 41 81 682 0.1 1 644 38 82 640 0.1 1 583 57 83 582 0.1 1 557 25 84 530 0.1 1 496 34 85 475 0.1 1 450 25 86 434 0.1 1 407 27 87 422 0.1 1 396 26 88 440 0.1 1 409 31 89 363 0.1 1 343 20 90 367 0.1 1 338 29 91 370 0.1 1 350 20 92 288 0.1 1 265 23 93 266 0.1 1 246 20 94 285 0.1 1 268 17 95 198 0.1 1 180 18 96 259 0.1 1 242 17 97 224 0.1 1 206 18 98 211 0.1 1 201 10 99 195 0.1 1 180 15 100 179 0.1 1 160 19 101 176 0.1 1 157 19 102 129 0.1 1 118 11 103 144 0.1 1 128 16 104 130 0.1 1 119 11 105 99 0.1 1 92 7 106 105 0.1 1 94 11 107 98 0.1 1 92 6 108 78 0.1 1 70 8 109 101 0.1 1 92 9 110 71 0.1 1 67 4 111 92 0.1 1 89 3 112 81 0.1 1 72 9 113 95 0.1 1 91 4 114 53 0.1 1 45 8 115 80 0.1 1 69 11 116 66 0.1 1 56 10 117 54 0.1 1 46 8 118 77 0.1 1 69 8 119 60 0.1 1 53 7 120 77 0.1 1 69 8 121 55 0.1 1 46 9 122 73 0.1 1 68 5 123 54 0.1 1 49 5 124 66 0.1 1 59 7 125 73 0.1 1 69 4 126 97 0.1 1 89 8 127 62 0.1 1 60 2 128 116 0.1 1 104 12 129 102 0.1 1 90 12 130 77 0.1 1 66 11 131 97 0.1 1 83 14 132 85 0.1 1 81 4 133 93 0.1 1 83 10 134 94 0.1 1 76 18 135 95 0.1 1 81 14 136 77 0.1 1 69 8 137 107 0.1 1 99 8 138 79 0.1 1 72 7 139 95 0.1 1 79 16 140 45 0.1 1 33 12 141 49 0.1 1 34 15 142 67 0.1 1 43 24 143 52 0.1 1 38 14 144 30 0.1 1 15 15 145 27 0.1 1 16 11 146 60 0.1 1 13 47 147 42 0.1 1 21 21 148 106 0.1 1 62 44 149 32 0.1 1 21 11 150 21 0.1 1 14 7 151 252 0.1 1 185 67 RUN STATISTICS FOR INPUT FILE: /home/sam/data/geoduck_illumina/trimmed/NR021_S8_L001_R2_001_val_2.fq.gz ============================================= 3996315 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 3996315 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 27040 (0.68%)