SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_1_S1_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/16C_32psu_1_S1_L002_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 791.00 s (40 us/read; 1.48 M reads/minute). === Summary === Total reads processed: 19,571,235 Reads with adapters: 16,271,535 (83.1%) Reads written (passing filters): 19,571,235 (100.0%) Total basepairs processed: 2,935,685,250 bp Quality-trimmed: 14,968,782 bp (0.5%) Total written (filtered): 2,137,866,393 bp (72.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16271535 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.4% C: 12.6% G: 25.1% T: 33.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1934443 4892808.8 0 1934443 2 292006 1223202.2 0 292006 3 180981 305800.5 0 180981 4 103045 76450.1 0 103045 5 98608 19112.5 0 98608 6 87562 4778.1 0 87562 7 69739 1194.5 0 69739 8 101138 298.6 0 101138 9 80590 74.7 0 80291 299 10 87083 18.7 1 80903 6180 11 94744 4.7 1 86859 7885 12 93509 1.2 1 85833 7676 13 107672 0.3 1 99050 8622 14 100767 0.3 1 91771 8996 15 81145 0.3 1 74763 6382 16 119727 0.3 1 109867 9860 17 101003 0.3 1 92682 8321 18 90163 0.3 1 83122 7041 19 118403 0.3 1 108874 9529 20 111750 0.3 1 103085 8665 21 98369 0.3 1 90814 7555 22 111808 0.3 1 103242 8566 23 118255 0.3 1 109009 9246 24 118284 0.3 1 108899 9385 25 134913 0.3 1 125516 9397 26 111710 0.3 1 102736 8974 27 124043 0.3 1 113612 10431 28 113048 0.3 1 105567 7481 29 126854 0.3 1 117529 9325 30 124172 0.3 1 115653 8519 31 138567 0.3 1 128798 9769 32 118532 0.3 1 110581 7951 33 139520 0.3 1 129113 10407 34 182115 0.3 1 169415 12700 35 97650 0.3 1 90702 6948 36 141232 0.3 1 130648 10584 37 151183 0.3 1 140571 10612 38 140794 0.3 1 131792 9002 39 135094 0.3 1 126791 8303 40 155470 0.3 1 144881 10589 41 152110 0.3 1 142307 9803 42 156034 0.3 1 145893 10141 43 140408 0.3 1 131398 9010 44 166488 0.3 1 155279 11209 45 176759 0.3 1 165212 11547 46 127616 0.3 1 119430 8186 47 162788 0.3 1 153156 9632 48 159821 0.3 1 150024 9797 49 167515 0.3 1 156791 10724 50 162854 0.3 1 152416 10438 51 201852 0.3 1 189155 12697 52 145803 0.3 1 136773 9030 53 181599 0.3 1 171435 10164 54 132563 0.3 1 124771 7792 55 175847 0.3 1 165921 9926 56 182238 0.3 1 170952 11286 57 175759 0.3 1 166454 9305 58 168899 0.3 1 159768 9131 59 170487 0.3 1 160788 9699 60 179591 0.3 1 169442 10149 61 183203 0.3 1 173168 10035 62 201509 0.3 1 189650 11859 63 267932 0.3 1 254493 13439 64 223354 0.3 1 213922 9432 65 145944 0.3 1 138249 7695 66 160488 0.3 1 151671 8817 67 160429 0.3 1 151245 9184 68 163626 0.3 1 154620 9006 69 162388 0.3 1 153192 9196 70 171183 0.3 1 161721 9462 71 179954 0.3 1 170347 9607 72 173057 0.3 1 163544 9513 73 181347 0.3 1 171665 9682 74 168687 0.3 1 159362 9325 75 161354 0.3 1 152554 8800 76 158086 0.3 1 149538 8548 77 158408 0.3 1 149654 8754 78 152524 0.3 1 144195 8329 79 148468 0.3 1 140463 8005 80 146791 0.3 1 138965 7826 81 146914 0.3 1 138951 7963 82 140738 0.3 1 133245 7493 83 136720 0.3 1 129557 7163 84 133340 0.3 1 126399 6941 85 131509 0.3 1 124949 6560 86 131725 0.3 1 125074 6651 87 132992 0.3 1 126515 6477 88 130544 0.3 1 124131 6413 89 118247 0.3 1 112246 6001 90 114880 0.3 1 109042 5838 91 108202 0.3 1 102767 5435 92 102465 0.3 1 97298 5167 93 99313 0.3 1 94369 4944 94 96247 0.3 1 91557 4690 95 90355 0.3 1 85764 4591 96 86105 0.3 1 81859 4246 97 80863 0.3 1 77002 3861 98 76806 0.3 1 73205 3601 99 77725 0.3 1 74014 3711 100 71514 0.3 1 68090 3424 101 67122 0.3 1 63869 3253 102 62547 0.3 1 59630 2917 103 55990 0.3 1 53291 2699 104 53130 0.3 1 50496 2634 105 47112 0.3 1 44737 2375 106 43436 0.3 1 41396 2040 107 39313 0.3 1 37430 1883 108 36083 0.3 1 34294 1789 109 32958 0.3 1 31374 1584 110 30549 0.3 1 29023 1526 111 28680 0.3 1 27349 1331 112 25012 0.3 1 23754 1258 113 21932 0.3 1 20848 1084 114 19318 0.3 1 18424 894 115 16367 0.3 1 15528 839 116 14214 0.3 1 13511 703 117 11890 0.3 1 11258 632 118 10558 0.3 1 10008 550 119 8964 0.3 1 8531 433 120 7160 0.3 1 6810 350 121 6260 0.3 1 5925 335 122 5526 0.3 1 5261 265 123 4601 0.3 1 4388 213 124 3924 0.3 1 3711 213 125 3337 0.3 1 3153 184 126 2851 0.3 1 2683 168 127 2269 0.3 1 2147 122 128 1715 0.3 1 1615 100 129 1527 0.3 1 1454 73 130 1240 0.3 1 1181 59 131 1038 0.3 1 985 53 132 992 0.3 1 936 56 133 1237 0.3 1 1180 57 134 1424 0.3 1 1372 52 135 637 0.3 1 603 34 136 325 0.3 1 316 9 137 239 0.3 1 218 21 138 165 0.3 1 161 4 139 114 0.3 1 104 10 140 92 0.3 1 87 5 141 71 0.3 1 68 3 142 32 0.3 1 29 3 143 33 0.3 1 28 5 144 26 0.3 1 21 5 145 62 0.3 1 60 2 146 42 0.3 1 41 1 147 127 0.3 1 113 14 148 65 0.3 1 60 5 149 42 0.3 1 37 5 150 529 0.3 1 500 29 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_1_S1_L002_R2_001.fastq.gz ============================================= 19571235 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 29241 (0.1%)