SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_4_S8_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_32psu_4_S8_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 658.84 s (45 us/read; 1.33 M reads/minute). === Summary === Total reads processed: 14,607,942 Reads with adapters: 10,984,887 (75.2%) Reads written (passing filters): 14,607,942 (100.0%) Total basepairs processed: 2,191,191,300 bp Quality-trimmed: 8,040,292 bp (0.4%) Total written (filtered): 1,774,637,805 bp (81.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10984887 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.9% C: 11.2% G: 23.3% T: 36.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2154515 3651985.5 0 2154515 2 307769 912996.4 0 307769 3 171355 228249.1 0 171355 4 100114 57062.3 0 100114 5 89281 14265.6 0 89281 6 78941 3566.4 0 78941 7 64482 891.6 0 64482 8 90895 222.9 0 90895 9 71519 55.7 0 71259 260 10 77769 13.9 1 72602 5167 11 81991 3.5 1 75629 6362 12 81945 0.9 1 75457 6488 13 93276 0.2 1 85901 7375 14 86548 0.2 1 79069 7479 15 71575 0.2 1 66062 5513 16 101873 0.2 1 93937 7936 17 86756 0.2 1 79766 6990 18 75151 0.2 1 69487 5664 19 100031 0.2 1 92361 7670 20 92540 0.2 1 85573 6967 21 80563 0.2 1 74553 6010 22 91001 0.2 1 84166 6835 23 96186 0.2 1 88873 7313 24 95097 0.2 1 87831 7266 25 107490 0.2 1 100206 7284 26 89500 0.2 1 82469 7031 27 97464 0.2 1 89433 8031 28 89257 0.2 1 83469 5788 29 97776 0.2 1 90646 7130 30 94678 0.2 1 88320 6358 31 104562 0.2 1 97122 7440 32 90375 0.2 1 84247 6128 33 104255 0.2 1 96395 7860 34 131765 0.2 1 122731 9034 35 71827 0.2 1 67071 4756 36 101000 0.2 1 93594 7406 37 108384 0.2 1 100841 7543 38 100305 0.2 1 93893 6412 39 96265 0.2 1 90338 5927 40 108609 0.2 1 101413 7196 41 105469 0.2 1 98528 6941 42 108491 0.2 1 101465 7026 43 97504 0.2 1 91262 6242 44 114735 0.2 1 107039 7696 45 119691 0.2 1 111821 7870 46 85524 0.2 1 79914 5610 47 107169 0.2 1 100947 6222 48 104472 0.2 1 98077 6395 49 109888 0.2 1 102993 6895 50 104895 0.2 1 98149 6746 51 128024 0.2 1 120005 8019 52 92440 0.2 1 86601 5839 53 114005 0.2 1 107513 6492 54 82023 0.2 1 77215 4808 55 107798 0.2 1 101620 6178 56 110208 0.2 1 103344 6864 57 105022 0.2 1 99470 5552 58 100686 0.2 1 95258 5428 59 100045 0.2 1 94333 5712 60 103616 0.2 1 97757 5859 61 106446 0.2 1 100410 6036 62 115794 0.2 1 108819 6975 63 149726 0.2 1 142046 7680 64 116619 0.2 1 111405 5214 65 80564 0.2 1 76264 4300 66 87049 0.2 1 82185 4864 67 86779 0.2 1 81921 4858 68 87371 0.2 1 82619 4752 69 85219 0.2 1 80357 4862 70 93639 0.2 1 88366 5273 71 91437 0.2 1 86289 5148 72 86910 0.2 1 81943 4967 73 89655 0.2 1 84810 4845 74 82770 0.2 1 78094 4676 75 77878 0.2 1 73550 4328 76 75167 0.2 1 70959 4208 77 74827 0.2 1 70567 4260 78 71263 0.2 1 67257 4006 79 68082 0.2 1 64314 3768 80 66978 0.2 1 63430 3548 81 67480 0.2 1 63757 3723 82 63500 0.2 1 60093 3407 83 60414 0.2 1 57170 3244 84 57646 0.2 1 54576 3070 85 56216 0.2 1 53261 2955 86 55705 0.2 1 52806 2899 87 54555 0.2 1 51737 2818 88 52657 0.2 1 49839 2818 89 47083 0.2 1 44512 2571 90 45017 0.2 1 42539 2478 91 42292 0.2 1 40068 2224 92 39093 0.2 1 37073 2020 93 36824 0.2 1 34979 1845 94 35114 0.2 1 33278 1836 95 33006 0.2 1 31281 1725 96 30878 0.2 1 29246 1632 97 28202 0.2 1 26749 1453 98 25663 0.2 1 24339 1324 99 24079 0.2 1 22771 1308 100 21840 0.2 1 20690 1150 101 19586 0.2 1 18574 1012 102 18375 0.2 1 17447 928 103 16706 0.2 1 15871 835 104 15675 0.2 1 14815 860 105 13756 0.2 1 13047 709 106 12568 0.2 1 11946 622 107 10619 0.2 1 10045 574 108 9793 0.2 1 9277 516 109 8520 0.2 1 8082 438 110 7642 0.2 1 7254 388 111 7055 0.2 1 6693 362 112 5993 0.2 1 5692 301 113 5089 0.2 1 4789 300 114 4335 0.2 1 4087 248 115 3576 0.2 1 3383 193 116 2943 0.2 1 2759 184 117 2497 0.2 1 2342 155 118 2119 0.2 1 1989 130 119 1740 0.2 1 1643 97 120 1465 0.2 1 1354 111 121 1235 0.2 1 1152 83 122 1011 0.2 1 954 57 123 812 0.2 1 749 63 124 706 0.2 1 655 51 125 559 0.2 1 512 47 126 438 0.2 1 415 23 127 439 0.2 1 406 33 128 306 0.2 1 286 20 129 222 0.2 1 208 14 130 202 0.2 1 190 12 131 161 0.2 1 148 13 132 146 0.2 1 132 14 133 137 0.2 1 126 11 134 210 0.2 1 203 7 135 81 0.2 1 72 9 136 43 0.2 1 38 5 137 44 0.2 1 36 8 138 25 0.2 1 22 3 139 23 0.2 1 23 140 5 0.2 1 5 141 9 0.2 1 9 142 12 0.2 1 11 1 143 2 0.2 1 2 144 10 0.2 1 7 3 145 5 0.2 1 5 146 6 0.2 1 6 147 23 0.2 1 22 1 148 13 0.2 1 13 149 11 0.2 1 10 1 150 112 0.2 1 105 7 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_32psu_4_S8_L002_R2_001.fastq.gz ============================================= 14607942 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 10571 (0.1%)