SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_2_S2_L001_R2_001.fastq.gz Trimming mode: single-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; user defined) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length before a sequence gets removed: 20 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /Volumes/web/metacarcinus/Salmo_Calig/analyses/20190722/TRIM_adapt/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 /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_2_S2_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 700.79 s (40 us/read; 1.52 M reads/minute). === Summary === Total reads processed: 17,734,461 Reads with adapters: 14,708,042 (82.9%) Reads written (passing filters): 17,734,461 (100.0%) Total basepairs processed: 2,660,169,150 bp Quality-trimmed: 13,508,119 bp (0.5%) Total written (filtered): 1,965,332,665 bp (73.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14708042 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.9% C: 12.0% G: 24.7% T: 34.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1823726 4433615.2 0 1823726 2 284755 1108403.8 0 284755 3 172034 277101.0 0 172034 4 100056 69275.2 0 100056 5 94653 17318.8 0 94653 6 82500 4329.7 0 82500 7 67622 1082.4 0 67622 8 96831 270.6 0 96831 9 76935 67.7 0 76693 242 10 84917 16.9 1 81330 3587 11 89902 4.2 1 84914 4988 12 90846 1.1 1 85794 5052 13 101679 0.3 1 96540 5139 14 96092 0.3 1 90143 5949 15 77319 0.3 1 73208 4111 16 114151 0.3 1 107904 6247 17 91752 0.3 1 86386 5366 18 88174 0.3 1 83679 4495 19 112277 0.3 1 105925 6352 20 105306 0.3 1 99944 5362 21 93914 0.3 1 89017 4897 22 106559 0.3 1 101114 5445 23 110793 0.3 1 104912 5881 24 108885 0.3 1 102936 5949 25 124131 0.3 1 117742 6389 26 104655 0.3 1 98869 5786 27 118794 0.3 1 111576 7218 28 109018 0.3 1 104356 4662 29 118362 0.3 1 112044 6318 30 117104 0.3 1 111822 5282 31 127211 0.3 1 120779 6432 32 116001 0.3 1 110611 5390 33 128546 0.3 1 121947 6599 34 164203 0.3 1 155704 8499 35 96279 0.3 1 92057 4222 36 133909 0.3 1 126861 7048 37 140147 0.3 1 132941 7206 38 132076 0.3 1 126615 5461 39 129476 0.3 1 124081 5395 40 145043 0.3 1 137854 7189 41 140152 0.3 1 133933 6219 42 149889 0.3 1 143207 6682 43 127335 0.3 1 121774 5561 44 151174 0.3 1 144187 6987 45 157069 0.3 1 149770 7299 46 127123 0.3 1 121787 5336 47 151889 0.3 1 145363 6526 48 148136 0.3 1 142156 5980 49 155657 0.3 1 148850 6807 50 151455 0.3 1 144647 6808 51 188717 0.3 1 180540 8177 52 134588 0.3 1 129312 5276 53 165157 0.3 1 158982 6175 54 125197 0.3 1 120399 4798 55 161733 0.3 1 155845 5888 56 166592 0.3 1 159894 6698 57 159442 0.3 1 153722 5720 58 155066 0.3 1 149532 5534 59 156693 0.3 1 150794 5899 60 162642 0.3 1 156571 6071 61 166749 0.3 1 160204 6545 62 183711 0.3 1 176590 7121 63 247983 0.3 1 239379 8604 64 207871 0.3 1 201612 6259 65 131895 0.3 1 127166 4729 66 143535 0.3 1 138546 4989 67 143350 0.3 1 137946 5404 68 144808 0.3 1 139662 5146 69 143872 0.3 1 138552 5320 70 149770 0.3 1 144363 5407 71 159740 0.3 1 154143 5597 72 151950 0.3 1 146385 5565 73 160797 0.3 1 155248 5549 74 148028 0.3 1 142917 5111 75 141398 0.3 1 136490 4908 76 138432 0.3 1 133692 4740 77 138578 0.3 1 133680 4898 78 133953 0.3 1 129214 4739 79 129618 0.3 1 125018 4600 80 128335 0.3 1 124016 4319 81 126134 0.3 1 121892 4242 82 121190 0.3 1 117136 4054 83 117273 0.3 1 113373 3900 84 113306 0.3 1 109397 3909 85 112548 0.3 1 108604 3944 86 113235 0.3 1 109296 3939 87 114063 0.3 1 110237 3826 88 110699 0.3 1 106931 3768 89 99019 0.3 1 95692 3327 90 94514 0.3 1 91234 3280 91 89156 0.3 1 86055 3101 92 83513 0.3 1 80693 2820 93 80899 0.3 1 78065 2834 94 78488 0.3 1 75830 2658 95 74185 0.3 1 71733 2452 96 70096 0.3 1 67821 2275 97 63309 0.3 1 61201 2108 98 59315 0.3 1 57291 2024 99 56316 0.3 1 54360 1956 100 50955 0.3 1 49217 1738 101 47839 0.3 1 46277 1562 102 45011 0.3 1 43553 1458 103 42598 0.3 1 41263 1335 104 41495 0.3 1 40193 1302 105 36516 0.3 1 35305 1211 106 32285 0.3 1 31286 999 107 28907 0.3 1 27939 968 108 26521 0.3 1 25551 970 109 23377 0.3 1 22637 740 110 20921 0.3 1 20208 713 111 19648 0.3 1 19007 641 112 16880 0.3 1 16303 577 113 14733 0.3 1 14236 497 114 12634 0.3 1 12219 415 115 10616 0.3 1 10211 405 116 8792 0.3 1 8474 318 117 7302 0.3 1 7031 271 118 6324 0.3 1 6071 253 119 5278 0.3 1 5066 212 120 4245 0.3 1 4065 180 121 3766 0.3 1 3593 173 122 3122 0.3 1 2986 136 123 2579 0.3 1 2463 116 124 2054 0.3 1 1977 77 125 1702 0.3 1 1630 72 126 1444 0.3 1 1379 65 127 1157 0.3 1 1113 44 128 945 0.3 1 906 39 129 732 0.3 1 690 42 130 636 0.3 1 596 40 131 486 0.3 1 462 24 132 421 0.3 1 393 28 133 391 0.3 1 380 11 134 460 0.3 1 437 23 135 244 0.3 1 230 14 136 145 0.3 1 134 11 137 97 0.3 1 92 5 138 61 0.3 1 60 1 139 51 0.3 1 44 7 140 41 0.3 1 36 5 141 18 0.3 1 15 3 142 19 0.3 1 18 1 143 6 0.3 1 6 144 18 0.3 1 16 2 145 49 0.3 1 42 7 146 32 0.3 1 31 1 147 61 0.3 1 61 148 55 0.3 1 53 2 149 39 0.3 1 37 2 150 364 0.3 1 342 22 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_2_S2_L001_R2_001.fastq.gz ============================================= 17734461 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 21505 (0.1%)