SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/strigg/Desktop/Salmo_Calig/8C_32psu_1_S5_L001_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.0 Cutadapt version: 2.4 Number of cores used for trimming: 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 All Read 1 sequences will be trimmed by 5 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 5 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Users/strigg/Desktop/Salmo_Calig/TRIM/FASTQC Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.6.8 Command line parameters: -j 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /Users/strigg/Desktop/Salmo_Calig/8C_32psu_1_S5_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 446.69 s (32 us/read; 1.88 M reads/minute). === Summary === Total reads processed: 14,000,021 Reads with adapters: 12,585,652 (89.9%) Reads written (passing filters): 14,000,021 (100.0%) Total basepairs processed: 2,100,003,150 bp Quality-trimmed: 3,933,676 bp (0.2%) Total written (filtered): 1,383,592,146 bp (65.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12585652 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.5% C: 15.4% G: 21.7% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 794832 3500005.2 0 794832 2 137499 875001.3 0 137499 3 88574 218750.3 0 88574 4 55463 54687.6 0 55463 5 52467 13671.9 0 52467 6 51009 3418.0 0 51009 7 43440 854.5 0 43440 8 53882 213.6 0 53882 9 54563 53.4 0 53971 592 10 51819 13.4 1 49209 2610 11 57911 3.3 1 53768 4143 12 56442 0.8 1 53088 3354 13 57081 0.2 1 53583 3498 14 60408 0.2 1 56320 4088 15 62034 0.2 1 58378 3656 16 63250 0.2 1 58624 4626 17 76887 0.2 1 70864 6023 18 66288 0.2 1 62429 3859 19 56979 0.2 1 53412 3567 20 69709 0.2 1 65411 4298 21 77411 0.2 1 72341 5070 22 66479 0.2 1 62829 3650 23 78177 0.2 1 73134 5043 24 74482 0.2 1 68678 5804 25 80818 0.2 1 75690 5128 26 74228 0.2 1 70119 4109 27 83394 0.2 1 77679 5715 28 82403 0.2 1 76936 5467 29 90670 0.2 1 83444 7226 30 98605 0.2 1 93586 5019 31 72678 0.2 1 68276 4402 32 92171 0.2 1 86613 5558 33 90475 0.2 1 84682 5793 34 99774 0.2 1 93593 6181 35 93327 0.2 1 87313 6014 36 107093 0.2 1 100026 7067 37 103597 0.2 1 96127 7470 38 104511 0.2 1 98484 6027 39 106907 0.2 1 100401 6506 40 106662 0.2 1 100220 6442 41 122253 0.2 1 114028 8225 42 104346 0.2 1 96706 7640 43 169940 0.2 1 161783 8157 44 58164 0.2 1 53449 4715 45 118320 0.2 1 111612 6708 46 116293 0.2 1 109496 6797 47 124205 0.2 1 117076 7129 48 123424 0.2 1 116139 7285 49 135448 0.2 1 126575 8873 50 119092 0.2 1 112535 6557 51 128971 0.2 1 121071 7900 52 136415 0.2 1 127168 9247 53 146369 0.2 1 138214 8155 54 119815 0.2 1 112779 7036 55 143900 0.2 1 135212 8688 56 174050 0.2 1 164777 9273 57 117416 0.2 1 109615 7801 58 150456 0.2 1 142969 7487 59 132324 0.2 1 124478 7846 60 149629 0.2 1 140649 8980 61 147926 0.2 1 139679 8247 62 163513 0.2 1 154547 8966 63 134239 0.2 1 125798 8441 64 148604 0.2 1 140497 8107 65 167908 0.2 1 158298 9610 66 177387 0.2 1 167350 10037 67 194374 0.2 1 180373 14001 68 370239 0.2 1 354139 16100 69 62415 0.2 1 57251 5164 70 26365 0.2 1 22180 4185 71 101894 0.2 1 96350 5544 72 143779 0.2 1 135850 7929 73 154356 0.2 1 145962 8394 74 154436 0.2 1 145829 8607 75 155208 0.2 1 146440 8768 76 154614 0.2 1 146122 8492 77 156184 0.2 1 147502 8682 78 149615 0.2 1 141324 8291 79 149903 0.2 1 141513 8390 80 146761 0.2 1 138705 8056 81 147739 0.2 1 139495 8244 82 146032 0.2 1 137919 8113 83 142429 0.2 1 134446 7983 84 139641 0.2 1 132001 7640 85 137362 0.2 1 129737 7625 86 134899 0.2 1 127375 7524 87 130083 0.2 1 122670 7413 88 129596 0.2 1 122229 7367 89 124621 0.2 1 117492 7129 90 125612 0.2 1 118454 7158 91 119798 0.2 1 113079 6719 92 115717 0.2 1 109150 6567 93 109774 0.2 1 103564 6210 94 107743 0.2 1 101578 6165 95 101804 0.2 1 95988 5816 96 96724 0.2 1 91079 5645 97 92176 0.2 1 86874 5302 98 87424 0.2 1 82235 5189 99 86913 0.2 1 81280 5633 100 78985 0.2 1 74394 4591 101 75410 0.2 1 70955 4455 102 69075 0.2 1 64932 4143 103 64987 0.2 1 61075 3912 104 61751 0.2 1 58031 3720 105 55260 0.2 1 51879 3381 106 50545 0.2 1 47309 3236 107 46617 0.2 1 43701 2916 108 44206 0.2 1 41370 2836 109 39556 0.2 1 36926 2630 110 36531 0.2 1 34163 2368 111 32673 0.2 1 30562 2111 112 28896 0.2 1 26907 1989 113 25292 0.2 1 23480 1812 114 22657 0.2 1 21036 1621 115 19857 0.2 1 18470 1387 116 17394 0.2 1 16192 1202 117 14695 0.2 1 13605 1090 118 12814 0.2 1 11815 999 119 11036 0.2 1 10138 898 120 9387 0.2 1 8609 778 121 8006 0.2 1 7333 673 122 6428 0.2 1 5956 472 123 5508 0.2 1 5035 473 124 4687 0.2 1 4248 439 125 3879 0.2 1 3508 371 126 3097 0.2 1 2779 318 127 2720 0.2 1 2457 263 128 2100 0.2 1 1898 202 129 1767 0.2 1 1595 172 130 1354 0.2 1 1200 154 131 1174 0.2 1 1057 117 132 1133 0.2 1 1029 104 133 1115 0.2 1 1004 111 134 1260 0.2 1 1149 111 135 611 0.2 1 547 64 136 316 0.2 1 271 45 137 241 0.2 1 219 22 138 161 0.2 1 140 21 139 107 0.2 1 93 14 140 137 0.2 1 117 20 141 53 0.2 1 47 6 142 47 0.2 1 41 6 143 37 0.2 1 32 5 144 37 0.2 1 26 11 145 44 0.2 1 34 10 146 50 0.2 1 46 4 147 126 0.2 1 111 15 148 84 0.2 1 69 15 149 71 0.2 1 62 9 150 642 0.2 1 568 74 RUN STATISTICS FOR INPUT FILE: /Users/strigg/Desktop/Salmo_Calig/8C_32psu_1_S5_L001_R1_001.fastq.gz ============================================= 14000021 sequences processed in total