SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_2_S6_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/8C_32psu_2_S6_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 536.72 s (41 us/read; 1.45 M reads/minute). === Summary === Total reads processed: 12,939,154 Reads with adapters: 10,288,624 (79.5%) Reads written (passing filters): 12,939,154 (100.0%) Total basepairs processed: 1,940,873,100 bp Quality-trimmed: 9,202,420 bp (0.5%) Total written (filtered): 1,495,378,762 bp (77.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10288624 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.2% C: 13.0% G: 23.8% T: 34.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1595771 3234788.5 0 1595771 2 240375 808697.1 0 240375 3 138443 202174.3 0 138443 4 81428 50543.6 0 81428 5 75038 12635.9 0 75038 6 64775 3159.0 0 64775 7 52085 789.7 0 52085 8 75127 197.4 0 75127 9 60527 49.4 0 60355 172 10 65326 12.3 1 62475 2851 11 69712 3.1 1 65682 4030 12 70487 0.8 1 66516 3971 13 78320 0.2 1 74147 4173 14 73989 0.2 1 69268 4721 15 60342 0.2 1 57080 3262 16 88180 0.2 1 83244 4936 17 69750 0.2 1 65392 4358 18 67540 0.2 1 63841 3699 19 85313 0.2 1 80354 4959 20 79769 0.2 1 75478 4291 21 70275 0.2 1 66324 3951 22 79177 0.2 1 74939 4238 23 82659 0.2 1 78081 4578 24 81915 0.2 1 77232 4683 25 93464 0.2 1 88557 4907 26 77147 0.2 1 72835 4312 27 85811 0.2 1 80374 5437 28 80396 0.2 1 76862 3534 29 85946 0.2 1 81104 4842 30 85726 0.2 1 81647 4079 31 92050 0.2 1 87288 4762 32 83804 0.2 1 79934 3870 33 92087 0.2 1 87200 4887 34 119466 0.2 1 113056 6410 35 67982 0.2 1 64809 3173 36 94466 0.2 1 89392 5074 37 100368 0.2 1 95090 5278 38 94027 0.2 1 89878 4149 39 91028 0.2 1 87016 4012 40 101155 0.2 1 95949 5206 41 98098 0.2 1 93343 4755 42 100747 0.2 1 96031 4716 43 92371 0.2 1 88129 4242 44 106061 0.2 1 101051 5010 45 109648 0.2 1 104507 5141 46 85668 0.2 1 81729 3939 47 104356 0.2 1 99808 4548 48 101281 0.2 1 96981 4300 49 106782 0.2 1 101997 4785 50 100514 0.2 1 95958 4556 51 125782 0.2 1 120079 5703 52 90772 0.2 1 86983 3789 53 109598 0.2 1 105306 4292 54 83322 0.2 1 79849 3473 55 107016 0.2 1 102862 4154 56 110967 0.2 1 106233 4734 57 104357 0.2 1 100229 4128 58 100691 0.2 1 96894 3797 59 102578 0.2 1 98489 4089 60 106303 0.2 1 102044 4259 61 108531 0.2 1 104028 4503 62 118161 0.2 1 113451 4710 63 158201 0.2 1 152213 5988 64 129612 0.2 1 125287 4325 65 83984 0.2 1 80809 3175 66 91901 0.2 1 88385 3516 67 89742 0.2 1 86128 3614 68 91530 0.2 1 88057 3473 69 90402 0.2 1 86917 3485 70 96053 0.2 1 92305 3748 71 99803 0.2 1 96104 3699 72 94159 0.2 1 90619 3540 73 98787 0.2 1 95125 3662 74 90680 0.2 1 87379 3301 75 86705 0.2 1 83434 3271 76 84928 0.2 1 81792 3136 77 84096 0.2 1 80874 3222 78 80178 0.2 1 77109 3069 79 77254 0.2 1 74397 2857 80 77028 0.2 1 74180 2848 81 75249 0.2 1 72550 2699 82 72339 0.2 1 69794 2545 83 70398 0.2 1 67790 2608 84 68189 0.2 1 65635 2554 85 66784 0.2 1 64244 2540 86 65482 0.2 1 63096 2386 87 67016 0.2 1 64553 2463 88 64151 0.2 1 61741 2410 89 57363 0.2 1 55205 2158 90 54985 0.2 1 52902 2083 91 52080 0.2 1 50216 1864 92 48422 0.2 1 46687 1735 93 47310 0.2 1 45600 1710 94 45459 0.2 1 43795 1664 95 43150 0.2 1 41608 1542 96 40380 0.2 1 38964 1416 97 36752 0.2 1 35440 1312 98 33446 0.2 1 32251 1195 99 33482 0.2 1 32255 1227 100 30657 0.2 1 29566 1091 101 28785 0.2 1 27832 953 102 27470 0.2 1 26566 904 103 25360 0.2 1 24494 866 104 23640 0.2 1 22887 753 105 21192 0.2 1 20482 710 106 19098 0.2 1 18446 652 107 16996 0.2 1 16368 628 108 15172 0.2 1 14616 556 109 14001 0.2 1 13446 555 110 12575 0.2 1 12154 421 111 11902 0.2 1 11531 371 112 10341 0.2 1 9986 355 113 8669 0.2 1 8372 297 114 7690 0.2 1 7405 285 115 6634 0.2 1 6377 257 116 5717 0.2 1 5480 237 117 4541 0.2 1 4344 197 118 4158 0.2 1 3977 181 119 3510 0.2 1 3351 159 120 2896 0.2 1 2771 125 121 2680 0.2 1 2560 120 122 2179 0.2 1 2075 104 123 1805 0.2 1 1731 74 124 1586 0.2 1 1495 91 125 1276 0.2 1 1206 70 126 1153 0.2 1 1112 41 127 891 0.2 1 852 39 128 721 0.2 1 684 37 129 559 0.2 1 529 30 130 484 0.2 1 453 31 131 369 0.2 1 355 14 132 299 0.2 1 280 19 133 268 0.2 1 245 23 134 297 0.2 1 280 17 135 162 0.2 1 155 7 136 110 0.2 1 102 8 137 81 0.2 1 76 5 138 67 0.2 1 59 8 139 34 0.2 1 30 4 140 26 0.2 1 23 3 141 15 0.2 1 15 142 15 0.2 1 15 143 8 0.2 1 8 144 6 0.2 1 4 2 145 17 0.2 1 15 2 146 13 0.2 1 12 1 147 33 0.2 1 27 6 148 14 0.2 1 14 149 8 0.2 1 6 2 150 114 0.2 1 107 7 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_2_S6_L001_R2_001.fastq.gz ============================================= 12939154 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 15624 (0.1%)