SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308512_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Python version: could not detect Number of cores used for trimming: 2 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 150927). Second best hit was Nextera (count: 0) Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp Output file will be GZIP compressed This is cutadapt 4.2 with Python 3.10.8 Command line parameters: -j 2 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC ERR12308512_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1399.784 s (17.368 µs/read; 3.45 M reads/minute). === Summary === Total reads processed: 80,593,414 Reads with adapters: 46,724,975 (58.0%) Reads written (passing filters): 80,593,414 (100.0%) Total basepairs processed: 12,169,605,514 bp Quality-trimmed: 68,340,455 bp (0.6%) Total written (filtered): 11,549,362,881 bp (94.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46724975 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.6% C: 20.1% G: 2.3% T: 28.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 29572166 20148353.5 0 29572166 2 816060 5037088.4 0 816060 3 529947 1259272.1 0 529947 4 374256 314818.0 0 374256 5 403014 78704.5 0 403014 6 358955 19676.1 0 358955 7 335448 4919.0 0 335448 8 411346 1229.8 0 411346 9 244533 307.4 0 243971 562 10 354578 76.9 1 317022 37556 11 318827 19.2 1 285831 32996 12 345523 4.8 1 299574 45949 13 337596 1.2 1 293392 44204 14 391871 1.2 1 335374 56497 15 277741 1.2 1 243860 33881 16 323780 1.2 1 282720 41060 17 404407 1.2 1 355623 48784 18 222832 1.2 1 195020 27812 19 385548 1.2 1 334402 51146 20 325249 1.2 1 286287 38962 21 184970 1.2 1 162130 22840 22 283656 1.2 1 247575 36081 23 282659 1.2 1 246722 35937 24 351769 1.2 1 303427 48342 25 318339 1.2 1 280465 37874 26 225101 1.2 1 196392 28709 27 226618 1.2 1 197892 28726 28 288217 1.2 1 255940 32277 29 232673 1.2 1 206974 25699 30 264976 1.2 1 233508 31468 31 227765 1.2 1 201685 26080 32 238672 1.2 1 210337 28335 33 238645 1.2 1 209770 28875 34 222165 1.2 1 199219 22946 35 271269 1.2 1 243137 28132 36 165660 1.2 1 147027 18633 37 223341 1.2 1 199119 24222 38 251623 1.2 1 225422 26201 39 230733 1.2 1 208256 22477 40 137313 1.2 1 121550 15763 41 198408 1.2 1 177970 20438 42 202082 1.2 1 181447 20635 43 166471 1.2 1 149265 17206 44 180890 1.2 1 161549 19341 45 190582 1.2 1 169696 20886 46 172898 1.2 1 154356 18542 47 168006 1.2 1 152164 15842 48 161147 1.2 1 145050 16097 49 163618 1.2 1 147128 16490 50 154685 1.2 1 140472 14213 51 145518 1.2 1 132035 13483 52 147003 1.2 1 133035 13968 53 139355 1.2 1 126662 12693 54 156852 1.2 1 142762 14090 55 110443 1.2 1 100888 9555 56 135157 1.2 1 122321 12836 57 171202 1.2 1 155316 15886 58 93056 1.2 1 84389 8667 59 107256 1.2 1 98603 8653 60 128415 1.2 1 117308 11107 61 119309 1.2 1 109343 9966 62 90672 1.2 1 83061 7611 63 176010 1.2 1 161706 14304 64 86370 1.2 1 79324 7046 65 67883 1.2 1 62198 5685 66 63686 1.2 1 58449 5237 67 100022 1.2 1 92685 7337 68 90193 1.2 1 83377 6816 69 75457 1.2 1 69738 5719 70 82210 1.2 1 76529 5681 71 74135 1.2 1 68853 5282 72 73436 1.2 1 68189 5247 73 94659 1.2 1 88350 6309 74 67085 1.2 1 62279 4806 75 67714 1.2 1 63153 4561 76 37402 1.2 1 34737 2665 77 36649 1.2 1 34085 2564 78 39327 1.2 1 36687 2640 79 38080 1.2 1 35456 2624 80 37370 1.2 1 34795 2575 81 36047 1.2 1 33560 2487 82 34009 1.2 1 31773 2236 83 33279 1.2 1 30924 2355 84 31019 1.2 1 28922 2097 85 30211 1.2 1 28265 1946 86 26753 1.2 1 25030 1723 87 25188 1.2 1 23603 1585 88 23351 1.2 1 21938 1413 89 22013 1.2 1 20646 1367 90 21242 1.2 1 19959 1283 91 19216 1.2 1 18012 1204 92 17891 1.2 1 16765 1126 93 16954 1.2 1 15951 1003 94 15182 1.2 1 14230 952 95 14256 1.2 1 13354 902 96 13465 1.2 1 12630 835 97 12342 1.2 1 11569 773 98 11578 1.2 1 10865 713 99 11366 1.2 1 10640 726 100 10720 1.2 1 10083 637 101 9128 1.2 1 8599 529 102 8089 1.2 1 7605 484 103 7479 1.2 1 7034 445 104 6659 1.2 1 6260 399 105 6282 1.2 1 5911 371 106 5576 1.2 1 5239 337 107 5226 1.2 1 4910 316 108 4711 1.2 1 4432 279 109 4236 1.2 1 3983 253 110 3865 1.2 1 3615 250 111 3522 1.2 1 3310 212 112 3184 1.2 1 2998 186 113 2766 1.2 1 2585 181 114 2342 1.2 1 2173 169 115 2079 1.2 1 1929 150 116 1732 1.2 1 1632 100 117 1571 1.2 1 1454 117 118 1390 1.2 1 1288 102 119 1192 1.2 1 1089 103 120 1421 1.2 1 1323 98 121 1063 1.2 1 979 84 122 700 1.2 1 620 80 123 618 1.2 1 547 71 124 493 1.2 1 442 51 125 406 1.2 1 351 55 126 308 1.2 1 262 46 127 287 1.2 1 237 50 128 221 1.2 1 181 40 129 189 1.2 1 156 33 130 148 1.2 1 123 25 131 134 1.2 1 109 25 132 106 1.2 1 90 16 133 123 1.2 1 102 21 134 81 1.2 1 65 16 135 94 1.2 1 78 16 136 58 1.2 1 54 4 137 78 1.2 1 67 11 138 54 1.2 1 45 9 139 67 1.2 1 49 18 140 42 1.2 1 34 8 141 59 1.2 1 43 16 142 33 1.2 1 19 14 143 33 1.2 1 24 9 144 39 1.2 1 22 17 145 47 1.2 1 31 16 146 31 1.2 1 17 14 147 35 1.2 1 18 17 148 26 1.2 1 19 7 149 56 1.2 1 29 27 150 36 1.2 1 22 14 151 224 1.2 1 43 181 RUN STATISTICS FOR INPUT FILE: ERR12308512_2.fastq.gz ============================================= 80593414 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 80593414 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 46309 (0.06%)