SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_2_S6_L002_R1_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_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 519.98 s (40 us/read; 1.48 M reads/minute). === Summary === Total reads processed: 12,868,767 Reads with adapters: 10,286,843 (79.9%) Reads written (passing filters): 12,868,767 (100.0%) Total basepairs processed: 1,930,315,050 bp Quality-trimmed: 3,674,826 bp (0.2%) Total written (filtered): 1,483,181,496 bp (76.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10286843 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.8% C: 14.7% G: 20.5% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1541222 3217191.8 0 1541222 2 228030 804297.9 0 228030 3 129528 201074.5 0 129528 4 78688 50268.6 0 78688 5 67124 12567.2 0 67124 6 66330 3141.8 0 66330 7 52508 785.4 0 52508 8 67652 196.4 0 67652 9 67615 49.1 0 66819 796 10 63063 12.3 1 59213 3850 11 71894 3.1 1 65954 5940 12 67897 0.8 1 62829 5068 13 71151 0.2 1 65849 5302 14 69055 0.2 1 63709 5346 15 75069 0.2 1 69302 5767 16 71424 0.2 1 65420 6004 17 86810 0.2 1 79021 7789 18 77955 0.2 1 72600 5355 19 63383 0.2 1 58809 4574 20 78965 0.2 1 73063 5902 21 85485 0.2 1 79014 6471 22 72855 0.2 1 68021 4834 23 85346 0.2 1 78944 6402 24 80318 0.2 1 73301 7017 25 85430 0.2 1 78969 6461 26 78740 0.2 1 73485 5255 27 88451 0.2 1 81474 6977 28 85790 0.2 1 79338 6452 29 91791 0.2 1 83845 7946 30 95449 0.2 1 89482 5967 31 75838 0.2 1 70423 5415 32 92731 0.2 1 85851 6880 33 86762 0.2 1 80055 6707 34 99437 0.2 1 91057 8380 35 85081 0.2 1 79384 5697 36 99297 0.2 1 91300 7997 37 101918 0.2 1 94163 7755 38 96379 0.2 1 88997 7382 39 103865 0.2 1 95226 8639 40 94376 0.2 1 87615 6761 41 104329 0.2 1 95123 9206 42 94892 0.2 1 86892 8000 43 148535 0.2 1 139624 8911 44 48085 0.2 1 43529 4556 45 105311 0.2 1 97887 7424 46 95734 0.2 1 88889 6845 47 101958 0.2 1 94804 7154 48 102091 0.2 1 94808 7283 49 112404 0.2 1 104035 8369 50 93295 0.2 1 87104 6191 51 104120 0.2 1 96595 7525 52 107257 0.2 1 99149 8108 53 113672 0.2 1 105961 7711 54 91213 0.2 1 85172 6041 55 107994 0.2 1 100085 7909 56 133513 0.2 1 124815 8698 57 81884 0.2 1 75254 6630 58 110562 0.2 1 103755 6807 59 98179 0.2 1 91032 7147 60 104453 0.2 1 97116 7337 61 104191 0.2 1 97239 6952 62 114950 0.2 1 107431 7519 63 89541 0.2 1 82900 6641 64 101345 0.2 1 94868 6477 65 113295 0.2 1 105436 7859 66 116379 0.2 1 108386 7993 67 124994 0.2 1 114943 10051 68 229157 0.2 1 217120 12037 69 41354 0.2 1 37561 3793 70 17861 0.2 1 14972 2889 71 66015 0.2 1 61819 4196 72 88699 0.2 1 83225 5474 73 92274 0.2 1 86536 5738 74 90496 0.2 1 84396 6100 75 91072 0.2 1 84946 6126 76 89676 0.2 1 83357 6319 77 89231 0.2 1 83068 6163 78 83699 0.2 1 77980 5719 79 83174 0.2 1 77470 5704 80 80873 0.2 1 75140 5733 81 79905 0.2 1 74411 5494 82 77850 0.2 1 72450 5400 83 75463 0.2 1 70383 5080 84 72909 0.2 1 67760 5149 85 70237 0.2 1 65392 4845 86 67846 0.2 1 63270 4576 87 65212 0.2 1 60837 4375 88 63724 0.2 1 59434 4290 89 60287 0.2 1 56154 4133 90 60221 0.2 1 55941 4280 91 56630 0.2 1 52736 3894 92 53891 0.2 1 50132 3759 93 50029 0.2 1 46571 3458 94 48812 0.2 1 45399 3413 95 45157 0.2 1 41906 3251 96 42860 0.2 1 39861 2999 97 40400 0.2 1 37713 2687 98 37633 0.2 1 34970 2663 99 36386 0.2 1 33717 2669 100 32744 0.2 1 30375 2369 101 30684 0.2 1 28451 2233 102 28336 0.2 1 26275 2061 103 26125 0.2 1 24257 1868 104 24496 0.2 1 22774 1722 105 21603 0.2 1 20114 1489 106 19703 0.2 1 18252 1451 107 18114 0.2 1 16740 1374 108 16491 0.2 1 15275 1216 109 15050 0.2 1 13866 1184 110 13423 0.2 1 12430 993 111 12182 0.2 1 11225 957 112 10547 0.2 1 9689 858 113 9161 0.2 1 8400 761 114 7859 0.2 1 7209 650 115 6948 0.2 1 6344 604 116 6269 0.2 1 5743 526 117 5202 0.2 1 4768 434 118 4673 0.2 1 4242 431 119 3797 0.2 1 3484 313 120 3288 0.2 1 2990 298 121 2786 0.2 1 2513 273 122 2451 0.2 1 2220 231 123 1988 0.2 1 1766 222 124 1684 0.2 1 1506 178 125 1280 0.2 1 1137 143 126 1164 0.2 1 1040 124 127 900 0.2 1 789 111 128 728 0.2 1 654 74 129 628 0.2 1 547 81 130 442 0.2 1 393 49 131 450 0.2 1 380 70 132 321 0.2 1 277 44 133 283 0.2 1 243 40 134 293 0.2 1 262 31 135 181 0.2 1 154 27 136 135 0.2 1 102 33 137 78 0.2 1 61 17 138 63 0.2 1 56 7 139 49 0.2 1 46 3 140 36 0.2 1 28 8 141 27 0.2 1 20 7 142 11 0.2 1 8 3 143 11 0.2 1 10 1 144 9 0.2 1 4 5 145 13 0.2 1 10 3 146 15 0.2 1 11 4 147 27 0.2 1 25 2 148 26 0.2 1 23 3 149 15 0.2 1 15 150 143 0.2 1 117 26 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_2_S6_L002_R1_001.fastq.gz ============================================= 12868767 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 2224 (0.0%)