SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_3_S11_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_3_S11_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 678.15 s (39 us/read; 1.52 M reads/minute). === Summary === Total reads processed: 17,175,482 Reads with adapters: 14,720,565 (85.7%) Reads written (passing filters): 17,175,482 (100.0%) Total basepairs processed: 2,576,322,300 bp Quality-trimmed: 12,927,719 bp (0.5%) Total written (filtered): 1,825,809,518 bp (70.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14720565 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 27.4% C: 12.3% G: 25.7% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1394679 4293870.5 0 1394679 2 231063 1073467.6 0 231063 3 146836 268366.9 0 146836 4 85160 67091.7 0 85160 5 83607 16772.9 0 83607 6 75270 4193.2 0 75270 7 59401 1048.3 0 59401 8 87249 262.1 0 87249 9 68581 65.5 0 68364 217 10 75306 16.4 1 69907 5399 11 81844 4.1 1 75220 6624 12 81567 1.0 1 74921 6646 13 94550 0.3 1 87043 7507 14 88612 0.3 1 80763 7849 15 71080 0.3 1 65748 5332 16 104508 0.3 1 96265 8243 17 90450 0.3 1 83158 7292 18 79309 0.3 1 73193 6116 19 106248 0.3 1 97745 8503 20 97943 0.3 1 90478 7465 21 87195 0.3 1 80598 6597 22 99625 0.3 1 92109 7516 23 105941 0.3 1 98004 7937 24 105924 0.3 1 97524 8400 25 120959 0.3 1 112658 8301 26 100855 0.3 1 92739 8116 27 111349 0.3 1 102191 9158 28 103794 0.3 1 97081 6713 29 115018 0.3 1 106647 8371 30 112098 0.3 1 104443 7655 31 125293 0.3 1 116600 8693 32 108268 0.3 1 101076 7192 33 127668 0.3 1 118305 9363 34 163116 0.3 1 151740 11376 35 90695 0.3 1 84564 6131 36 130252 0.3 1 120794 9458 37 137508 0.3 1 128167 9341 38 131385 0.3 1 123153 8232 39 125429 0.3 1 117971 7458 40 144394 0.3 1 134617 9777 41 142244 0.3 1 133129 9115 42 146211 0.3 1 136886 9325 43 130656 0.3 1 122570 8086 44 158062 0.3 1 147788 10274 45 169410 0.3 1 158451 10959 46 116471 0.3 1 109140 7331 47 153771 0.3 1 145129 8642 48 151126 0.3 1 142022 9104 49 158775 0.3 1 148794 9981 50 155083 0.3 1 145500 9583 51 193098 0.3 1 181154 11944 52 138930 0.3 1 130761 8169 53 172888 0.3 1 163380 9508 54 126226 0.3 1 118962 7264 55 168553 0.3 1 159300 9253 56 174469 0.3 1 163938 10531 57 166262 0.3 1 157805 8457 58 161940 0.3 1 153447 8493 59 163516 0.3 1 154551 8965 60 171750 0.3 1 162391 9359 61 176379 0.3 1 166983 9396 62 194831 0.3 1 183858 10973 63 257381 0.3 1 244702 12679 64 218615 0.3 1 209942 8673 65 141285 0.3 1 134011 7274 66 154574 0.3 1 146600 7974 67 155286 0.3 1 146846 8440 68 158519 0.3 1 150042 8477 69 156924 0.3 1 148115 8809 70 167343 0.3 1 158462 8881 71 174948 0.3 1 165808 9140 72 168193 0.3 1 159291 8902 73 175743 0.3 1 166626 9117 74 163090 0.3 1 154296 8794 75 155077 0.3 1 146999 8078 76 152837 0.3 1 144700 8137 77 152701 0.3 1 144644 8057 78 148868 0.3 1 140946 7922 79 143248 0.3 1 135788 7460 80 143729 0.3 1 136194 7535 81 142811 0.3 1 135360 7451 82 135758 0.3 1 128640 7118 83 132076 0.3 1 125333 6743 84 127993 0.3 1 121417 6576 85 127663 0.3 1 121292 6371 86 126712 0.3 1 120456 6256 87 127809 0.3 1 121761 6048 88 125518 0.3 1 119426 6092 89 112440 0.3 1 106917 5523 90 109295 0.3 1 103850 5445 91 103669 0.3 1 98616 5053 92 96386 0.3 1 91748 4638 93 94174 0.3 1 89557 4617 94 91197 0.3 1 86759 4438 95 86770 0.3 1 82553 4217 96 83121 0.3 1 79129 3992 97 76650 0.3 1 72963 3687 98 72211 0.3 1 68803 3408 99 70867 0.3 1 67509 3358 100 63540 0.3 1 60596 2944 101 60139 0.3 1 57240 2899 102 55801 0.3 1 53158 2643 103 50487 0.3 1 47969 2518 104 48235 0.3 1 45902 2333 105 42853 0.3 1 40742 2111 106 39140 0.3 1 37246 1894 107 35386 0.3 1 33624 1762 108 31865 0.3 1 30331 1534 109 29026 0.3 1 27576 1450 110 25978 0.3 1 24750 1228 111 24137 0.3 1 23015 1122 112 21305 0.3 1 20312 993 113 18391 0.3 1 17493 898 114 16197 0.3 1 15347 850 115 13468 0.3 1 12821 647 116 11291 0.3 1 10728 563 117 9599 0.3 1 9121 478 118 8211 0.3 1 7795 416 119 6772 0.3 1 6417 355 120 5885 0.3 1 5586 299 121 5082 0.3 1 4799 283 122 4085 0.3 1 3891 194 123 3540 0.3 1 3373 167 124 2933 0.3 1 2771 162 125 2424 0.3 1 2286 138 126 1979 0.3 1 1877 102 127 1585 0.3 1 1504 81 128 1307 0.3 1 1233 74 129 1065 0.3 1 999 66 130 818 0.3 1 765 53 131 695 0.3 1 661 34 132 692 0.3 1 651 41 133 1029 0.3 1 991 38 134 1555 0.3 1 1499 56 135 581 0.3 1 564 17 136 217 0.3 1 210 7 137 148 0.3 1 133 15 138 96 0.3 1 87 9 139 66 0.3 1 63 3 140 62 0.3 1 58 4 141 31 0.3 1 28 3 142 29 0.3 1 25 4 143 15 0.3 1 15 144 16 0.3 1 16 145 37 0.3 1 37 146 31 0.3 1 30 1 147 76 0.3 1 72 4 148 44 0.3 1 40 4 149 38 0.3 1 34 4 150 422 0.3 1 392 30 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_3_S11_L002_R2_001.fastq.gz ============================================= 17175482 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 24770 (0.1%)