SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_2_S21_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/CTRL_16C_26psu_2_S21_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 526.48 s (39 us/read; 1.53 M reads/minute). === Summary === Total reads processed: 13,408,232 Reads with adapters: 11,603,960 (86.5%) Reads written (passing filters): 13,408,232 (100.0%) Total basepairs processed: 2,011,234,800 bp Quality-trimmed: 8,433,724 bp (0.4%) Total written (filtered): 1,430,263,611 bp (71.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11603960 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 11.7% G: 26.2% T: 34.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1017131 3352058.0 0 1017131 2 177058 838014.5 0 177058 3 112787 209503.6 0 112787 4 67003 52375.9 0 67003 5 66504 13094.0 0 66504 6 60966 3273.5 0 60966 7 50684 818.4 0 50684 8 71309 204.6 0 71309 9 56145 51.1 0 55917 228 10 61633 12.8 1 57525 4108 11 66766 3.2 1 61633 5133 12 66970 0.8 1 61817 5153 13 77136 0.2 1 71259 5877 14 74020 0.2 1 67910 6110 15 60571 0.2 1 56229 4342 16 86270 0.2 1 79871 6399 17 75982 0.2 1 70248 5734 18 65820 0.2 1 61090 4730 19 87582 0.2 1 81169 6413 20 81347 0.2 1 75534 5813 21 71738 0.2 1 66607 5131 22 82571 0.2 1 76726 5845 23 87855 0.2 1 81586 6269 24 88796 0.2 1 82344 6452 25 99857 0.2 1 93510 6347 26 83385 0.2 1 77300 6085 27 93625 0.2 1 86769 6856 28 85817 0.2 1 80874 4943 29 96248 0.2 1 90002 6246 30 93727 0.2 1 88168 5559 31 103646 0.2 1 97099 6547 32 90867 0.2 1 85391 5476 33 105892 0.2 1 98959 6933 34 137038 0.2 1 128489 8549 35 77044 0.2 1 72414 4630 36 105552 0.2 1 98517 7035 37 112682 0.2 1 105690 6992 38 106873 0.2 1 100867 6006 39 102355 0.2 1 96889 5466 40 117602 0.2 1 110487 7115 41 116162 0.2 1 109429 6733 42 121108 0.2 1 114095 7013 43 109639 0.2 1 103525 6114 44 129653 0.2 1 122002 7651 45 138376 0.2 1 130424 7952 46 97190 0.2 1 91779 5411 47 124803 0.2 1 118327 6476 48 124244 0.2 1 117667 6577 49 131343 0.2 1 123780 7563 50 128654 0.2 1 121411 7243 51 160151 0.2 1 151381 8770 52 116727 0.2 1 110469 6258 53 144929 0.2 1 137769 7160 54 104645 0.2 1 99281 5364 55 138649 0.2 1 131848 6801 56 142696 0.2 1 134983 7713 57 141410 0.2 1 134925 6485 58 134726 0.2 1 128298 6428 59 134797 0.2 1 128190 6607 60 140631 0.2 1 133581 7050 61 142568 0.2 1 135579 6989 62 160172 0.2 1 152064 8108 63 209874 0.2 1 200586 9288 64 163821 0.2 1 157603 6218 65 114086 0.2 1 108681 5405 66 126793 0.2 1 120700 6093 67 126587 0.2 1 120373 6214 68 128999 0.2 1 122868 6131 69 127101 0.2 1 121101 6000 70 133367 0.2 1 126848 6519 71 137940 0.2 1 131348 6592 72 133744 0.2 1 127253 6491 73 140847 0.2 1 134101 6746 74 131039 0.2 1 124610 6429 75 123648 0.2 1 117677 5971 76 121797 0.2 1 115805 5992 77 120668 0.2 1 114606 6062 78 116805 0.2 1 111027 5778 79 111250 0.2 1 105828 5422 80 110955 0.2 1 105751 5204 81 109348 0.2 1 104246 5102 82 103784 0.2 1 98831 4953 83 101052 0.2 1 96319 4733 84 98311 0.2 1 93628 4683 85 96878 0.2 1 92456 4422 86 95996 0.2 1 91571 4425 87 96605 0.2 1 92256 4349 88 93536 0.2 1 89501 4035 89 83632 0.2 1 79805 3827 90 80377 0.2 1 76751 3626 91 75608 0.2 1 72292 3316 92 71253 0.2 1 68176 3077 93 68064 0.2 1 65127 2937 94 65349 0.2 1 62356 2993 95 61296 0.2 1 58482 2814 96 57547 0.2 1 54961 2586 97 53666 0.2 1 51329 2337 98 50699 0.2 1 48576 2123 99 48177 0.2 1 46098 2079 100 43932 0.2 1 42005 1927 101 39615 0.2 1 37850 1765 102 35478 0.2 1 33828 1650 103 32345 0.2 1 30762 1583 104 30580 0.2 1 29207 1373 105 27062 0.2 1 25870 1192 106 24593 0.2 1 23539 1054 107 21633 0.2 1 20641 992 108 19150 0.2 1 18297 853 109 17101 0.2 1 16306 795 110 15550 0.2 1 14882 668 111 14159 0.2 1 13496 663 112 12046 0.2 1 11497 549 113 10553 0.2 1 10087 466 114 9330 0.2 1 8879 451 115 7323 0.2 1 7020 303 116 6173 0.2 1 5878 295 117 5159 0.2 1 4924 235 118 4546 0.2 1 4310 236 119 3676 0.2 1 3456 220 120 3075 0.2 1 2912 163 121 2608 0.2 1 2451 157 122 2115 0.2 1 1990 125 123 1712 0.2 1 1620 92 124 1534 0.2 1 1451 83 125 1259 0.2 1 1192 67 126 1123 0.2 1 1061 62 127 965 0.2 1 910 55 128 708 0.2 1 665 43 129 619 0.2 1 586 33 130 674 0.2 1 630 44 131 895 0.2 1 850 45 132 923 0.2 1 873 50 133 1446 0.2 1 1396 50 134 1648 0.2 1 1601 47 135 705 0.2 1 677 28 136 204 0.2 1 192 12 137 151 0.2 1 142 9 138 69 0.2 1 59 10 139 62 0.2 1 53 9 140 50 0.2 1 43 7 141 28 0.2 1 22 6 142 25 0.2 1 22 3 143 20 0.2 1 20 144 13 0.2 1 12 1 145 39 0.2 1 35 4 146 44 0.2 1 41 3 147 178 0.2 1 162 16 148 92 0.2 1 79 13 149 44 0.2 1 42 2 150 302 0.2 1 273 29 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/CTRL_16C_26psu_2_S21_L002_R2_001.fastq.gz ============================================= 13408232 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 17606 (0.1%)