SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_4_S16_L002_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/16C_26psu_4_S16_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 696.49 s (40 us/read; 1.48 M reads/minute). === Summary === Total reads processed: 17,208,353 Reads with adapters: 13,674,200 (79.5%) Reads written (passing filters): 17,208,353 (100.0%) Total basepairs processed: 2,581,252,950 bp Quality-trimmed: 5,331,759 bp (0.2%) Total written (filtered): 1,977,555,409 bp (76.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13674200 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.9% C: 17.1% G: 19.6% T: 33.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2124508 4302088.2 0 2124508 2 313423 1075522.1 0 313423 3 180126 268880.5 0 180126 4 103470 67220.1 0 103470 5 86090 16805.0 0 86090 6 84599 4201.3 0 84599 7 66757 1050.3 0 66757 8 88962 262.6 0 88962 9 83630 65.6 0 82470 1160 10 80181 16.4 1 74703 5478 11 92233 4.1 1 83672 8561 12 86362 1.0 1 79524 6838 13 87841 0.3 1 80589 7252 14 90274 0.3 1 82360 7914 15 93818 0.3 1 85881 7937 16 92355 0.3 1 83764 8591 17 113048 0.3 1 101963 11085 18 96642 0.3 1 89228 7414 19 80013 0.3 1 73649 6364 20 99407 0.3 1 91339 8068 21 111176 0.3 1 101662 9514 22 92147 0.3 1 85457 6690 23 107114 0.3 1 98360 8754 24 102847 0.3 1 93006 9841 25 109576 0.3 1 100448 9128 26 99232 0.3 1 91712 7520 27 112349 0.3 1 102540 9809 28 109676 0.3 1 100710 8966 29 116787 0.3 1 105939 10848 30 125526 0.3 1 116820 8706 31 91212 0.3 1 83997 7215 32 117558 0.3 1 108076 9482 33 110064 0.3 1 101072 8992 34 118132 0.3 1 107623 10509 35 118711 0.3 1 108495 10216 36 135621 0.3 1 122255 13366 37 140972 0.3 1 130809 10163 38 95392 0.3 1 87779 7613 39 130577 0.3 1 118922 11655 40 131214 0.3 1 119601 11613 41 152494 0.3 1 139337 13157 42 102460 0.3 1 93074 9386 43 197072 0.3 1 184157 12915 44 54139 0.3 1 48245 5894 45 131336 0.3 1 121138 10198 46 127690 0.3 1 117856 9834 47 129086 0.3 1 119565 9521 48 131921 0.3 1 121440 10481 49 145001 0.3 1 133240 11761 50 116964 0.3 1 108432 8532 51 131690 0.3 1 121283 10407 52 137379 0.3 1 125946 11433 53 148180 0.3 1 137434 10746 54 113408 0.3 1 104863 8545 55 140308 0.3 1 129251 11057 56 175262 0.3 1 162851 12411 57 103098 0.3 1 94387 8711 58 143210 0.3 1 133468 9742 59 125785 0.3 1 116067 9718 60 133778 0.3 1 123739 10039 61 134602 0.3 1 124844 9758 62 150181 0.3 1 139349 10832 63 115498 0.3 1 106236 9262 64 129364 0.3 1 120287 9077 65 148548 0.3 1 137651 10897 66 150760 0.3 1 139512 11248 67 160846 0.3 1 146823 14023 68 302542 0.3 1 285033 17509 69 61997 0.3 1 56378 5619 70 24824 0.3 1 20506 4318 71 82321 0.3 1 76477 5844 72 114537 0.3 1 107064 7473 73 122133 0.3 1 114073 8060 74 121733 0.3 1 113185 8548 75 121574 0.3 1 112683 8891 76 119912 0.3 1 110967 8945 77 120383 0.3 1 111732 8651 78 113881 0.3 1 105452 8429 79 111936 0.3 1 103610 8326 80 109761 0.3 1 101635 8126 81 108328 0.3 1 100397 7931 82 105284 0.3 1 97525 7759 83 103557 0.3 1 95997 7560 84 99896 0.3 1 92540 7356 85 96863 0.3 1 89671 7192 86 94827 0.3 1 87870 6957 87 90622 0.3 1 84095 6527 88 89624 0.3 1 82896 6728 89 85693 0.3 1 79392 6301 90 85156 0.3 1 79011 6145 91 80919 0.3 1 74951 5968 92 77468 0.3 1 71924 5544 93 72342 0.3 1 67111 5231 94 71272 0.3 1 66088 5184 95 65969 0.3 1 61048 4921 96 63375 0.3 1 58785 4590 97 59353 0.3 1 55151 4202 98 55614 0.3 1 51400 4214 99 54309 0.3 1 50115 4194 100 49832 0.3 1 46148 3684 101 46196 0.3 1 42723 3473 102 43375 0.3 1 40084 3291 103 40365 0.3 1 37360 3005 104 37934 0.3 1 35154 2780 105 33958 0.3 1 31403 2555 106 31440 0.3 1 29092 2348 107 28594 0.3 1 26406 2188 108 27035 0.3 1 24984 2051 109 24211 0.3 1 22261 1950 110 22056 0.3 1 20350 1706 111 20216 0.3 1 18643 1573 112 17663 0.3 1 16163 1500 113 15323 0.3 1 14109 1214 114 13594 0.3 1 12500 1094 115 12178 0.3 1 11179 999 116 10756 0.3 1 9835 921 117 9186 0.3 1 8396 790 118 8066 0.3 1 7378 688 119 6801 0.3 1 6177 624 120 5605 0.3 1 5122 483 121 5036 0.3 1 4635 401 122 4356 0.3 1 3917 439 123 3703 0.3 1 3365 338 124 3136 0.3 1 2845 291 125 2679 0.3 1 2426 253 126 2221 0.3 1 2017 204 127 1848 0.3 1 1642 206 128 1384 0.3 1 1237 147 129 1223 0.3 1 1070 153 130 986 0.3 1 889 97 131 829 0.3 1 741 88 132 691 0.3 1 626 65 133 780 0.3 1 701 79 134 1086 0.3 1 1026 60 135 511 0.3 1 480 31 136 248 0.3 1 207 41 137 178 0.3 1 152 26 138 125 0.3 1 113 12 139 79 0.3 1 67 12 140 60 0.3 1 49 11 141 36 0.3 1 30 6 142 37 0.3 1 26 11 143 39 0.3 1 35 4 144 23 0.3 1 20 3 145 36 0.3 1 29 7 146 37 0.3 1 31 6 147 101 0.3 1 92 9 148 53 0.3 1 44 9 149 35 0.3 1 29 6 150 573 0.3 1 484 89 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_26psu_4_S16_L002_R1_001.fastq.gz ============================================= 17208353 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 5621 (0.0%)