SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_1_S1_L001_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_L001_R2_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 777.07 s (40 us/read; 1.52 M reads/minute). === Summary === Total reads processed: 19,624,894 Reads with adapters: 16,339,161 (83.3%) Reads written (passing filters): 19,624,894 (100.0%) Total basepairs processed: 2,943,734,100 bp Quality-trimmed: 15,599,605 bp (0.5%) Total written (filtered): 2,144,342,165 bp (72.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16339161 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.5% C: 12.6% G: 25.0% T: 33.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1942196 4906223.5 0 1942196 2 299564 1226555.9 0 299564 3 177742 306639.0 0 177742 4 105333 76659.7 0 105333 5 100538 19164.9 0 100538 6 87955 4791.2 0 87955 7 71440 1197.8 0 71440 8 102524 299.5 0 102524 9 81367 74.9 0 81047 320 10 89669 18.7 1 85117 4552 11 95729 4.7 1 89915 5814 12 95768 1.2 1 89687 6081 13 108234 0.3 1 101948 6286 14 103335 0.3 1 96341 6994 15 82616 0.3 1 77316 5300 16 121595 0.3 1 114016 7579 17 98896 0.3 1 92218 6678 18 93415 0.3 1 87589 5826 19 120547 0.3 1 112557 7990 20 113077 0.3 1 106404 6673 21 99743 0.3 1 93549 6194 22 113380 0.3 1 106586 6794 23 116836 0.3 1 109692 7144 24 119139 0.3 1 111646 7493 25 135500 0.3 1 127577 7923 26 112154 0.3 1 104938 7216 27 122636 0.3 1 114199 8437 28 117975 0.3 1 111836 6139 29 125073 0.3 1 117359 7714 30 127096 0.3 1 120402 6694 31 137659 0.3 1 129729 7930 32 123762 0.3 1 117342 6420 33 138965 0.3 1 130590 8375 34 180950 0.3 1 170447 10503 35 102752 0.3 1 97235 5517 36 141525 0.3 1 133105 8420 37 151296 0.3 1 142475 8821 38 141804 0.3 1 134802 7002 39 139699 0.3 1 132682 7017 40 156245 0.3 1 147123 9122 41 150848 0.3 1 143057 7791 42 156523 0.3 1 148491 8032 43 142855 0.3 1 135344 7511 44 166066 0.3 1 157102 8964 45 178466 0.3 1 169227 9239 46 128203 0.3 1 121604 6599 47 163666 0.3 1 155525 8141 48 161229 0.3 1 153502 7727 49 169595 0.3 1 161041 8554 50 162191 0.3 1 153908 8283 51 204248 0.3 1 193780 10468 52 147164 0.3 1 140471 6693 53 177383 0.3 1 169465 7918 54 135474 0.3 1 129206 6268 55 177540 0.3 1 169636 7904 56 183270 0.3 1 174617 8653 57 175273 0.3 1 167802 7471 58 168130 0.3 1 160997 7133 59 172563 0.3 1 164868 7695 60 179506 0.3 1 171470 8036 61 186851 0.3 1 178181 8670 62 203675 0.3 1 194173 9502 63 273998 0.3 1 262527 11471 64 226808 0.3 1 218491 8317 65 147108 0.3 1 140746 6362 66 160644 0.3 1 153693 6951 67 159286 0.3 1 152193 7093 68 161933 0.3 1 155050 6883 69 160655 0.3 1 153681 6974 70 170416 0.3 1 162996 7420 71 179225 0.3 1 171910 7315 72 171231 0.3 1 163925 7306 73 181424 0.3 1 173901 7523 74 167534 0.3 1 160668 6866 75 160295 0.3 1 153643 6652 76 157715 0.3 1 151296 6419 77 157679 0.3 1 150903 6776 78 152483 0.3 1 146130 6353 79 147737 0.3 1 141492 6245 80 146667 0.3 1 140666 6001 81 145920 0.3 1 140003 5917 82 140689 0.3 1 134853 5836 83 136034 0.3 1 130439 5595 84 133908 0.3 1 128250 5658 85 131675 0.3 1 126012 5663 86 131672 0.3 1 126197 5475 87 133848 0.3 1 128384 5464 88 129850 0.3 1 124580 5270 89 116878 0.3 1 112187 4691 90 113165 0.3 1 108451 4714 91 107851 0.3 1 103636 4215 92 101212 0.3 1 97187 4025 93 98995 0.3 1 94995 4000 94 95394 0.3 1 91542 3852 95 90020 0.3 1 86380 3640 96 85913 0.3 1 82550 3363 97 80493 0.3 1 77312 3181 98 75879 0.3 1 72925 2954 99 77605 0.3 1 74598 3007 100 70637 0.3 1 67912 2725 101 67043 0.3 1 64475 2568 102 62076 0.3 1 59759 2317 103 56002 0.3 1 53869 2133 104 53213 0.3 1 51172 2041 105 47322 0.3 1 45493 1829 106 43803 0.3 1 42161 1642 107 39428 0.3 1 37938 1490 108 36024 0.3 1 34621 1403 109 33005 0.3 1 31801 1204 110 30413 0.3 1 29223 1190 111 28718 0.3 1 27704 1014 112 24826 0.3 1 23909 917 113 22246 0.3 1 21395 851 114 19255 0.3 1 18504 751 115 16125 0.3 1 15460 665 116 14013 0.3 1 13452 561 117 11755 0.3 1 11314 441 118 10504 0.3 1 10075 429 119 8740 0.3 1 8381 359 120 7099 0.3 1 6789 310 121 6395 0.3 1 6127 268 122 5283 0.3 1 5086 197 123 4656 0.3 1 4456 200 124 3824 0.3 1 3672 152 125 3323 0.3 1 3181 142 126 2821 0.3 1 2694 127 127 2334 0.3 1 2219 115 128 1727 0.3 1 1654 73 129 1502 0.3 1 1423 79 130 1215 0.3 1 1157 58 131 1055 0.3 1 1002 53 132 1009 0.3 1 967 42 133 1312 0.3 1 1260 52 134 1503 0.3 1 1462 41 135 647 0.3 1 618 29 136 354 0.3 1 338 16 137 216 0.3 1 209 7 138 150 0.3 1 140 10 139 114 0.3 1 110 4 140 64 0.3 1 60 4 141 66 0.3 1 61 5 142 51 0.3 1 49 2 143 40 0.3 1 37 3 144 27 0.3 1 25 2 145 50 0.3 1 45 5 146 38 0.3 1 37 1 147 120 0.3 1 112 8 148 74 0.3 1 68 6 149 76 0.3 1 73 3 150 581 0.3 1 559 22 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_1_S1_L001_R2_001.fastq.gz ============================================= 19624894 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 31376 (0.2%)