SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_4_S12_L002_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_26psu_4_S12_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 557.67 s (45 us/read; 1.34 M reads/minute). === Summary === Total reads processed: 12,486,748 Reads with adapters: 8,772,809 (70.3%) Reads written (passing filters): 12,486,748 (100.0%) Total basepairs processed: 1,873,012,200 bp Quality-trimmed: 12,376,106 bp (0.7%) Total written (filtered): 1,558,147,987 bp (83.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8772809 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.4% C: 12.6% G: 20.8% T: 36.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2358875 3121687.0 0 2358875 2 288344 780421.8 0 288344 3 173054 195105.4 0 173054 4 87112 48776.4 0 87112 5 64247 12194.1 0 64247 6 55212 3048.5 0 55212 7 41727 762.1 0 41727 8 62151 190.5 0 62151 9 50342 47.6 0 50157 185 10 52158 11.9 1 48148 4010 11 57855 3.0 1 52397 5458 12 56897 0.7 1 51566 5331 13 64575 0.2 1 58979 5596 14 59154 0.2 1 53315 5839 15 47002 0.2 1 42866 4136 16 69658 0.2 1 63405 6253 17 57386 0.2 1 52045 5341 18 51929 0.2 1 47327 4602 19 66863 0.2 1 60907 5956 20 62288 0.2 1 57071 5217 21 55272 0.2 1 50547 4725 22 61984 0.2 1 56766 5218 23 65026 0.2 1 59587 5439 24 63838 0.2 1 58214 5624 25 72434 0.2 1 66848 5586 26 60587 0.2 1 55112 5475 27 67754 0.2 1 61588 6166 28 59366 0.2 1 54979 4387 29 67701 0.2 1 62118 5583 30 62432 0.2 1 57688 4744 31 72162 0.2 1 66403 5759 32 60976 0.2 1 56497 4479 33 69840 0.2 1 64116 5724 34 91102 0.2 1 84079 7023 35 47382 0.2 1 43590 3792 36 69435 0.2 1 63655 5780 37 74003 0.2 1 67997 6006 38 68560 0.2 1 63793 4767 39 65708 0.2 1 61286 4422 40 74240 0.2 1 68710 5530 41 72214 0.2 1 67124 5090 42 72980 0.2 1 67853 5127 43 66699 0.2 1 62062 4637 44 76923 0.2 1 71373 5550 45 80740 0.2 1 74874 5866 46 58943 0.2 1 54854 4089 47 73645 0.2 1 68927 4718 48 72329 0.2 1 67389 4940 49 74646 0.2 1 69490 5156 50 70816 0.2 1 65987 4829 51 86746 0.2 1 80793 5953 52 63282 0.2 1 59102 4180 53 76728 0.2 1 71964 4764 54 55670 0.2 1 52124 3546 55 73350 0.2 1 68943 4407 56 76024 0.2 1 70858 5166 57 71982 0.2 1 67849 4133 58 68868 0.2 1 64881 3987 59 68360 0.2 1 64151 4209 60 71518 0.2 1 67054 4464 61 73466 0.2 1 69155 4311 62 79595 0.2 1 74642 4953 63 103748 0.2 1 97894 5854 64 85376 0.2 1 81260 4116 65 55857 0.2 1 52588 3269 66 61954 0.2 1 58405 3549 67 59930 0.2 1 56159 3771 68 60490 0.2 1 56878 3612 69 60452 0.2 1 56708 3744 70 61904 0.2 1 58197 3707 71 65599 0.2 1 61887 3712 72 62591 0.2 1 58936 3655 73 64906 0.2 1 61091 3815 74 60780 0.2 1 57167 3613 75 57385 0.2 1 53955 3430 76 55285 0.2 1 51973 3312 77 55087 0.2 1 51740 3347 78 52962 0.2 1 49812 3150 79 51023 0.2 1 48174 2849 80 50358 0.2 1 47516 2842 81 49364 0.2 1 46484 2880 82 47242 0.2 1 44529 2713 83 45686 0.2 1 43106 2580 84 44410 0.2 1 41863 2547 85 43592 0.2 1 41103 2489 86 43331 0.2 1 40952 2379 87 42675 0.2 1 40428 2247 88 42372 0.2 1 40023 2349 89 37747 0.2 1 35602 2145 90 37018 0.2 1 34943 2075 91 33562 0.2 1 31712 1850 92 31899 0.2 1 30215 1684 93 30547 0.2 1 28874 1673 94 30566 0.2 1 28886 1680 95 28277 0.2 1 26704 1573 96 27180 0.2 1 25709 1471 97 24703 0.2 1 23381 1322 98 23174 0.2 1 21893 1281 99 21741 0.2 1 20527 1214 100 19732 0.2 1 18608 1124 101 17665 0.2 1 16698 967 102 16908 0.2 1 15954 954 103 15998 0.2 1 15059 939 104 15634 0.2 1 14747 887 105 13889 0.2 1 13156 733 106 12626 0.2 1 11933 693 107 11469 0.2 1 10791 678 108 10122 0.2 1 9581 541 109 9139 0.2 1 8610 529 110 8759 0.2 1 8236 523 111 8023 0.2 1 7545 478 112 7113 0.2 1 6705 408 113 6235 0.2 1 5883 352 114 5409 0.2 1 5057 352 115 4485 0.2 1 4203 282 116 3795 0.2 1 3556 239 117 3367 0.2 1 3120 247 118 2891 0.2 1 2702 189 119 2519 0.2 1 2367 152 120 2120 0.2 1 1963 157 121 1866 0.2 1 1743 123 122 1561 0.2 1 1440 121 123 1426 0.2 1 1322 104 124 1196 0.2 1 1106 90 125 1010 0.2 1 943 67 126 988 0.2 1 920 68 127 903 0.2 1 840 63 128 611 0.2 1 560 51 129 510 0.2 1 470 40 130 453 0.2 1 423 30 131 514 0.2 1 467 47 132 553 0.2 1 529 24 133 1090 0.2 1 1032 58 134 2641 0.2 1 2566 75 135 828 0.2 1 794 34 136 185 0.2 1 169 16 137 110 0.2 1 95 15 138 79 0.2 1 73 6 139 44 0.2 1 40 4 140 39 0.2 1 36 3 141 22 0.2 1 17 5 142 20 0.2 1 14 6 143 16 0.2 1 15 1 144 54 0.2 1 47 7 145 219 0.2 1 204 15 146 229 0.2 1 213 16 147 1254 0.2 1 1201 53 148 756 0.2 1 716 40 149 417 0.2 1 400 17 150 2389 0.2 1 2234 155 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_4_S12_L002_R2_001.fastq.gz ============================================= 12486748 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 29715 (0.2%)