SUMMARISING RUN PARAMETERS ========================== Input filename: /Users/strigg/Desktop/Salmo_Calig/16C_26psu_3_S15_L002_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/16C_26psu_3_S15_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 554.96 s (38 us/read; 1.58 M reads/minute). === Summary === Total reads processed: 14,622,552 Reads with adapters: 11,026,853 (75.4%) Reads written (passing filters): 14,622,552 (100.0%) Total basepairs processed: 2,193,382,800 bp Quality-trimmed: 5,795,035 bp (0.3%) Total written (filtered): 1,756,312,964 bp (80.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11026853 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.2% C: 18.2% G: 19.4% T: 32.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2255035 3655638.0 0 2255035 2 341709 913909.5 0 341709 3 202869 228477.4 0 202869 4 99930 57119.3 0 99930 5 74502 14279.8 0 74502 6 72604 3570.0 0 72604 7 55151 892.5 0 55151 8 72986 223.1 0 72986 9 72897 55.8 0 71832 1065 10 66371 13.9 1 61637 4734 11 77738 3.5 1 70168 7570 12 72088 0.9 1 66222 5866 13 72584 0.2 1 66413 6171 14 75037 0.2 1 68093 6944 15 77546 0.2 1 70821 6725 16 76138 0.2 1 68711 7427 17 96440 0.2 1 86428 10012 18 77278 0.2 1 71237 6041 19 65884 0.2 1 60354 5530 20 80966 0.2 1 74091 6875 21 91593 0.2 1 83562 8031 22 72795 0.2 1 67343 5452 23 89502 0.2 1 81872 7630 24 80431 0.2 1 72300 8131 25 87978 0.2 1 80303 7675 26 79303 0.2 1 73214 6089 27 90256 0.2 1 81812 8444 28 88151 0.2 1 80669 7482 29 90769 0.2 1 81855 8914 30 100156 0.2 1 92655 7501 31 70749 0.2 1 65028 5721 32 94056 0.2 1 86125 7931 33 85223 0.2 1 77723 7500 34 93938 0.2 1 85684 8254 35 95264 0.2 1 85673 9591 36 98487 0.2 1 89904 8583 37 91367 0.2 1 84496 6871 38 91067 0.2 1 83299 7768 39 98566 0.2 1 90240 8326 40 98669 0.2 1 89677 8992 41 109128 0.2 1 98383 10745 42 90124 0.2 1 81722 8402 43 141587 0.2 1 131681 9906 44 48458 0.2 1 43335 5123 45 101474 0.2 1 92754 8720 46 96951 0.2 1 88935 8016 47 101587 0.2 1 93762 7825 48 93451 0.2 1 85286 8165 49 109864 0.2 1 100369 9495 50 86419 0.2 1 80081 6338 51 97144 0.2 1 89290 7854 52 106661 0.2 1 96904 9757 53 115583 0.2 1 107526 8057 54 81720 0.2 1 74951 6769 55 103125 0.2 1 94975 8150 56 119342 0.2 1 110505 8837 57 94296 0.2 1 86511 7785 58 95906 0.2 1 89537 6369 59 78497 0.2 1 71935 6562 60 103672 0.2 1 95850 7822 61 99103 0.2 1 91989 7114 62 98519 0.2 1 91357 7162 63 92047 0.2 1 85069 6978 64 87141 0.2 1 80859 6282 65 98035 0.2 1 90511 7524 66 104856 0.2 1 96876 7980 67 112499 0.2 1 102554 9945 68 203504 0.2 1 191009 12495 69 62594 0.2 1 57415 5179 70 23252 0.2 1 19824 3428 71 45182 0.2 1 41443 3739 72 77078 0.2 1 71850 5228 73 85031 0.2 1 79046 5985 74 84254 0.2 1 78257 5997 75 83996 0.2 1 77711 6285 76 82731 0.2 1 76446 6285 77 82380 0.2 1 76363 6017 78 77279 0.2 1 71312 5967 79 77209 0.2 1 71223 5986 80 74817 0.2 1 69029 5788 81 73406 0.2 1 67839 5567 82 72738 0.2 1 67207 5531 83 69208 0.2 1 64025 5183 84 68393 0.2 1 63216 5177 85 66034 0.2 1 60887 5147 86 63919 0.2 1 59135 4784 87 60801 0.2 1 56313 4488 88 60788 0.2 1 56093 4695 89 57692 0.2 1 53269 4423 90 56584 0.2 1 52478 4106 91 53589 0.2 1 49546 4043 92 51833 0.2 1 47890 3943 93 48199 0.2 1 44575 3624 94 46944 0.2 1 43278 3666 95 43653 0.2 1 40307 3346 96 41698 0.2 1 38443 3255 97 38960 0.2 1 36083 2877 98 36779 0.2 1 33843 2936 99 34473 0.2 1 31757 2716 100 32693 0.2 1 30095 2598 101 30447 0.2 1 28045 2402 102 27845 0.2 1 25608 2237 103 26414 0.2 1 24289 2125 104 24929 0.2 1 23050 1879 105 21773 0.2 1 20195 1578 106 20226 0.2 1 18586 1640 107 18400 0.2 1 16897 1503 108 17326 0.2 1 15891 1435 109 15645 0.2 1 14342 1303 110 14020 0.2 1 12816 1204 111 12849 0.2 1 11744 1105 112 11234 0.2 1 10286 948 113 9985 0.2 1 9120 865 114 8637 0.2 1 7820 817 115 7857 0.2 1 7138 719 116 6705 0.2 1 6073 632 117 6037 0.2 1 5491 546 118 5126 0.2 1 4659 467 119 4476 0.2 1 4067 409 120 3856 0.2 1 3446 410 121 3506 0.2 1 3100 406 122 2914 0.2 1 2611 303 123 2582 0.2 1 2308 274 124 2250 0.2 1 1996 254 125 1869 0.2 1 1644 225 126 1660 0.2 1 1451 209 127 1486 0.2 1 1318 168 128 1135 0.2 1 1016 119 129 1048 0.2 1 958 90 130 730 0.2 1 642 88 131 781 0.2 1 698 83 132 769 0.2 1 708 61 133 1082 0.2 1 1006 76 134 1977 0.2 1 1867 110 135 796 0.2 1 751 45 136 320 0.2 1 290 30 137 204 0.2 1 187 17 138 179 0.2 1 161 18 139 112 0.2 1 104 8 140 111 0.2 1 94 17 141 71 0.2 1 68 3 142 79 0.2 1 67 12 143 106 0.2 1 93 13 144 63 0.2 1 61 2 145 233 0.2 1 213 20 146 995 0.2 1 960 35 147 4990 0.2 1 4774 216 148 3265 0.2 1 3135 130 149 1955 0.2 1 1846 109 150 16845 0.2 1 15820 1025 RUN STATISTICS FOR INPUT FILE: /Users/strigg/Desktop/Salmo_Calig/16C_26psu_3_S15_L002_R1_001.fastq.gz ============================================= 14622552 sequences processed in total