SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_2_S10_L001_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_26psu_2_S10_L001_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 725.23 s (39 us/read; 1.53 M reads/minute). === Summary === Total reads processed: 18,482,577 Reads with adapters: 14,846,196 (80.3%) Reads written (passing filters): 18,482,577 (100.0%) Total basepairs processed: 2,772,386,550 bp Quality-trimmed: 5,236,502 bp (0.2%) Total written (filtered): 2,109,664,469 bp (76.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14846196 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.0% C: 14.7% G: 20.4% T: 35.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2201281 4620644.2 0 2201281 2 324820 1155161.1 0 324820 3 181187 288790.3 0 181187 4 111024 72197.6 0 111024 5 91444 18049.4 0 91444 6 89339 4512.3 0 89339 7 75499 1128.1 0 75499 8 92079 282.0 0 92079 9 94613 70.5 0 93305 1308 10 87393 17.6 1 82726 4667 11 97272 4.4 1 89821 7451 12 94618 1.1 1 88577 6041 13 94580 0.3 1 88291 6289 14 98608 0.3 1 91401 7207 15 100703 0.3 1 94036 6667 16 100759 0.3 1 93186 7573 17 122345 0.3 1 112475 9870 18 103137 0.3 1 96868 6269 19 89996 0.3 1 84224 5772 20 107642 0.3 1 100714 6928 21 118859 0.3 1 110501 8358 22 101938 0.3 1 96023 5915 23 117604 0.3 1 109853 7751 24 110878 0.3 1 101488 9390 25 118235 0.3 1 110039 8196 26 108371 0.3 1 101787 6584 27 121571 0.3 1 112662 8909 28 119395 0.3 1 110884 8511 29 129888 0.3 1 119161 10727 30 136399 0.3 1 128723 7676 31 101982 0.3 1 95349 6633 32 129923 0.3 1 121526 8397 33 121306 0.3 1 112461 8845 34 134618 0.3 1 125125 9493 35 135522 0.3 1 127399 8123 36 126532 0.3 1 116217 10315 37 132624 0.3 1 124414 8210 38 135436 0.3 1 126589 8847 39 144343 0.3 1 135079 9264 40 131706 0.3 1 123113 8593 41 147103 0.3 1 136472 10631 42 135693 0.3 1 124813 10880 43 208641 0.3 1 197928 10713 44 70084 0.3 1 63748 6336 45 146631 0.3 1 137638 8993 46 134243 0.3 1 125635 8608 47 148092 0.3 1 138684 9408 48 143207 0.3 1 133950 9257 49 157250 0.3 1 146216 11034 50 135654 0.3 1 127338 8316 51 145480 0.3 1 136047 9433 52 151730 0.3 1 141076 10654 53 160594 0.3 1 150536 10058 54 131608 0.3 1 123193 8415 55 153566 0.3 1 143551 10015 56 188903 0.3 1 177823 11080 57 122969 0.3 1 114039 8930 58 155982 0.3 1 147471 8511 59 136864 0.3 1 128026 8838 60 152804 0.3 1 142938 9866 61 149972 0.3 1 141027 8945 62 164460 0.3 1 154790 9670 63 131600 0.3 1 122512 9088 64 147097 0.3 1 138434 8663 65 163813 0.3 1 153627 10186 66 170976 0.3 1 160133 10843 67 181725 0.3 1 167572 14153 68 347424 0.3 1 330644 16780 69 53801 0.3 1 49133 4668 70 21119 0.3 1 17296 3823 71 93829 0.3 1 88082 5747 72 129343 0.3 1 121746 7597 73 137109 0.3 1 128961 8148 74 135639 0.3 1 127288 8351 75 134319 0.3 1 126050 8269 76 133485 0.3 1 125306 8179 77 133818 0.3 1 125641 8177 78 125826 0.3 1 118003 7823 79 124061 0.3 1 116366 7695 80 122381 0.3 1 114907 7474 81 121340 0.3 1 113873 7467 82 118564 0.3 1 111221 7343 83 114400 0.3 1 107282 7118 84 110060 0.3 1 103458 6602 85 107144 0.3 1 100729 6415 86 104597 0.3 1 98129 6468 87 99965 0.3 1 93811 6154 88 99634 0.3 1 93629 6005 89 94213 0.3 1 88311 5902 90 93784 0.3 1 87912 5872 91 88966 0.3 1 83468 5498 92 84640 0.3 1 79309 5331 93 79324 0.3 1 74386 4938 94 77199 0.3 1 72415 4784 95 72155 0.3 1 67634 4521 96 68840 0.3 1 64535 4305 97 64425 0.3 1 60326 4099 98 60153 0.3 1 56199 3954 99 58789 0.3 1 54783 4006 100 53231 0.3 1 49872 3359 101 49747 0.3 1 46474 3273 102 46514 0.3 1 43441 3073 103 42759 0.3 1 39961 2798 104 40408 0.3 1 37725 2683 105 35915 0.3 1 33458 2457 106 33343 0.3 1 31066 2277 107 30056 0.3 1 28019 2037 108 28759 0.3 1 26783 1976 109 25234 0.3 1 23454 1780 110 22936 0.3 1 21306 1630 111 20750 0.3 1 19240 1510 112 17996 0.3 1 16644 1352 113 15908 0.3 1 14749 1159 114 14075 0.3 1 12991 1084 115 12424 0.3 1 11459 965 116 10747 0.3 1 9910 837 117 9113 0.3 1 8333 780 118 8109 0.3 1 7445 664 119 6883 0.3 1 6316 567 120 5713 0.3 1 5209 504 121 5168 0.3 1 4711 457 122 4185 0.3 1 3804 381 123 3552 0.3 1 3218 334 124 3100 0.3 1 2796 304 125 2576 0.3 1 2315 261 126 2168 0.3 1 1937 231 127 1692 0.3 1 1526 166 128 1332 0.3 1 1165 167 129 1229 0.3 1 1107 122 130 923 0.3 1 838 85 131 751 0.3 1 663 88 132 654 0.3 1 579 75 133 679 0.3 1 607 72 134 1033 0.3 1 947 86 135 428 0.3 1 390 38 136 228 0.3 1 207 21 137 170 0.3 1 154 16 138 136 0.3 1 118 18 139 81 0.3 1 70 11 140 68 0.3 1 55 13 141 49 0.3 1 43 6 142 55 0.3 1 47 8 143 45 0.3 1 36 9 144 21 0.3 1 19 2 145 58 0.3 1 54 4 146 122 0.3 1 110 12 147 390 0.3 1 355 35 148 248 0.3 1 225 23 149 170 0.3 1 149 21 150 1709 0.3 1 1353 356 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/8C_26psu_2_S10_L001_R1_001.fastq.gz ============================================= 18482577 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 7148 (0.0%)