SUMMARISING RUN PARAMETERS ========================== Input filename: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_1_S1_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_32psu_1_S1_L002_R1_001.fastq.gz Processing reads on 1 core in single-end mode ... Finished in 755.54 s (39 us/read; 1.55 M reads/minute). === Summary === Total reads processed: 19,571,235 Reads with adapters: 16,407,295 (83.8%) Reads written (passing filters): 19,571,235 (100.0%) Total basepairs processed: 2,935,685,250 bp Quality-trimmed: 8,266,740 bp (0.3%) Total written (filtered): 2,130,672,037 bp (72.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16407295 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.6% C: 14.6% G: 21.1% T: 34.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1871205 4892808.8 0 1871205 2 281413 1223202.2 0 281413 3 165620 305800.5 0 165620 4 102750 76450.1 0 102750 5 91621 19112.5 0 91621 6 89878 4778.1 0 89878 7 72653 1194.5 0 72653 8 92540 298.6 0 92540 9 93344 74.7 0 92169 1175 10 86372 18.7 1 80800 5572 11 99125 4.7 1 90406 8719 12 93690 1.2 1 86859 6831 13 96288 0.3 1 88938 7350 14 98016 0.3 1 89939 8077 15 102285 0.3 1 94257 8028 16 101242 0.3 1 92425 8817 17 123641 0.3 1 112025 11616 18 107224 0.3 1 99543 7681 19 90677 0.3 1 83921 6756 20 111453 0.3 1 102938 8515 21 124864 0.3 1 115203 9661 22 102217 0.3 1 95257 6960 23 124937 0.3 1 115301 9636 24 113499 0.3 1 102977 10522 25 124401 0.3 1 114862 9539 26 112120 0.3 1 104445 7675 27 128185 0.3 1 117570 10615 28 125849 0.3 1 115930 9919 29 134332 0.3 1 122337 11995 30 144690 0.3 1 135178 9512 31 111404 0.3 1 103047 8357 32 135894 0.3 1 125650 10244 33 131757 0.3 1 121043 10714 34 143190 0.3 1 131548 11642 35 157418 0.3 1 142743 14675 36 129247 0.3 1 119787 9460 37 149221 0.3 1 138285 10936 38 145468 0.3 1 133187 12281 39 172504 0.3 1 157173 15331 40 134071 0.3 1 124322 9749 41 180864 0.3 1 164818 16046 42 137219 0.3 1 124408 12811 43 239349 0.3 1 223461 15888 44 74486 0.3 1 66856 7630 45 161688 0.3 1 148747 12941 46 191505 0.3 1 176273 15232 47 179273 0.3 1 166898 12375 48 140851 0.3 1 128229 12622 49 208539 0.3 1 192459 16080 50 127958 0.3 1 118792 9166 51 162484 0.3 1 150649 11835 52 227313 0.3 1 208878 18435 53 230954 0.3 1 217665 13289 54 127985 0.3 1 117878 10107 55 190088 0.3 1 177776 12312 56 183666 0.3 1 171198 12468 57 212537 0.3 1 198874 13663 58 133097 0.3 1 125108 7989 59 104505 0.3 1 95591 8914 60 206694 0.3 1 193657 13037 61 190421 0.3 1 179352 11069 62 144000 0.3 1 134103 9897 63 180563 0.3 1 168547 12016 64 155217 0.3 1 145289 9928 65 158098 0.3 1 147007 11091 66 188945 0.3 1 175941 13004 67 211986 0.3 1 194786 17200 68 378408 0.3 1 357096 21312 69 162579 0.3 1 151778 10801 70 55965 0.3 1 49649 6316 71 63814 0.3 1 58189 5625 72 145461 0.3 1 136394 9067 73 166164 0.3 1 155484 10680 74 168411 0.3 1 157197 11214 75 167596 0.3 1 156098 11498 76 166388 0.3 1 154457 11931 77 167040 0.3 1 155459 11581 78 159704 0.3 1 148462 11242 79 158706 0.3 1 147370 11336 80 154542 0.3 1 143508 11034 81 154753 0.3 1 143966 10787 82 150886 0.3 1 140115 10771 83 145780 0.3 1 135596 10184 84 142086 0.3 1 132138 9948 85 137811 0.3 1 128196 9615 86 134898 0.3 1 125576 9322 87 129676 0.3 1 120849 8827 88 128629 0.3 1 119738 8891 89 123313 0.3 1 114615 8698 90 123132 0.3 1 114553 8579 91 117637 0.3 1 109407 8230 92 112493 0.3 1 104754 7739 93 106111 0.3 1 98757 7354 94 103337 0.3 1 96126 7211 95 95958 0.3 1 89095 6863 96 91266 0.3 1 84746 6520 97 86736 0.3 1 80632 6104 98 81864 0.3 1 75993 5871 99 80342 0.3 1 74325 6017 100 73408 0.3 1 68128 5280 101 68599 0.3 1 63783 4816 102 64339 0.3 1 59627 4712 103 59235 0.3 1 54992 4243 104 55526 0.3 1 51587 3939 105 49435 0.3 1 45975 3460 106 45302 0.3 1 42055 3247 107 41568 0.3 1 38569 2999 108 39344 0.3 1 36429 2915 109 35142 0.3 1 32532 2610 110 32440 0.3 1 30035 2405 111 29201 0.3 1 26917 2284 112 25771 0.3 1 23691 2080 113 22359 0.3 1 20490 1869 114 19994 0.3 1 18373 1621 115 17421 0.3 1 16000 1421 116 15295 0.3 1 14082 1213 117 13006 0.3 1 11960 1046 118 11522 0.3 1 10599 923 119 9598 0.3 1 8847 751 120 7795 0.3 1 7132 663 121 6634 0.3 1 6018 616 122 5895 0.3 1 5383 512 123 4806 0.3 1 4352 454 124 4169 0.3 1 3804 365 125 3459 0.3 1 3117 342 126 3006 0.3 1 2739 267 127 2458 0.3 1 2229 229 128 1849 0.3 1 1632 217 129 1614 0.3 1 1454 160 130 1309 0.3 1 1172 137 131 1113 0.3 1 990 123 132 1037 0.3 1 938 99 133 1203 0.3 1 1080 123 134 1440 0.3 1 1347 93 135 651 0.3 1 599 52 136 330 0.3 1 299 31 137 262 0.3 1 226 36 138 169 0.3 1 150 19 139 125 0.3 1 105 20 140 97 0.3 1 85 12 141 76 0.3 1 66 10 142 39 0.3 1 32 7 143 36 0.3 1 31 5 144 28 0.3 1 23 5 145 62 0.3 1 55 7 146 39 0.3 1 35 4 147 138 0.3 1 123 15 148 73 0.3 1 68 5 149 57 0.3 1 50 7 150 745 0.3 1 637 108 RUN STATISTICS FOR INPUT FILE: /Volumes/web/metacarcinus/Salmo_Calig/FASTQS/UW_Trigg_190718_done/16C_32psu_1_S1_L002_R1_001.fastq.gz ============================================= 19571235 sequences processed in total Sequences removed because they became shorter than the length cutoff of 20 bp: 7786 (0.0%)