SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308509_1.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: 100878). Second best hit was Nextera (count: 1) 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 ERR12308509_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1505.505 s (19.135 µs/read; 3.14 M reads/minute). === Summary === Total reads processed: 78,676,948 Reads with adapters: 43,352,280 (55.1%) Reads written (passing filters): 78,676,948 (100.0%) Total basepairs processed: 11,880,219,148 bp Quality-trimmed: 61,959,171 bp (0.5%) Total written (filtered): 11,459,778,898 bp (96.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43352280 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.6% C: 18.4% G: 1.2% T: 29.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 32130062 19669237.0 0 32130062 2 548571 4917309.2 0 548571 3 359852 1229327.3 0 359852 4 266033 307331.8 0 266033 5 278263 76833.0 0 278263 6 245426 19208.2 0 245426 7 229648 4802.1 0 229648 8 274308 1200.5 0 274308 9 180393 300.1 0 180037 356 10 241052 75.0 1 215203 25849 11 231542 18.8 1 204864 26678 12 234719 4.7 1 194047 40672 13 227447 1.2 1 185810 41637 14 258212 1.2 1 208876 49336 15 188728 1.2 1 155775 32953 16 215291 1.2 1 176271 39020 17 267271 1.2 1 221919 45352 18 145545 1.2 1 118878 26667 19 272968 1.2 1 224227 48741 20 215110 1.2 1 176902 38208 21 122033 1.2 1 99876 22157 22 195830 1.2 1 160980 34850 23 193778 1.2 1 158819 34959 24 252139 1.2 1 206524 45615 25 220292 1.2 1 182273 38019 26 140366 1.2 1 115354 25012 27 131893 1.2 1 108420 23473 28 190671 1.2 1 160024 30647 29 152941 1.2 1 127873 25068 30 169665 1.2 1 141404 28261 31 162570 1.2 1 135515 27055 32 170804 1.2 1 143445 27359 33 148103 1.2 1 123651 24452 34 152745 1.2 1 129021 23724 35 149787 1.2 1 126104 23683 36 165716 1.2 1 138377 27339 37 144311 1.2 1 120673 23638 38 128622 1.2 1 109184 19438 39 136127 1.2 1 115707 20420 40 156303 1.2 1 133251 23052 41 104123 1.2 1 88115 16008 42 135390 1.2 1 115728 19662 43 111939 1.2 1 95095 16844 44 120992 1.2 1 103288 17704 45 126434 1.2 1 107334 19100 46 108880 1.2 1 92455 16425 47 107845 1.2 1 93262 14583 48 104337 1.2 1 89458 14879 49 99714 1.2 1 85283 14431 50 96210 1.2 1 83395 12815 51 91882 1.2 1 78914 12968 52 91840 1.2 1 79420 12420 53 88217 1.2 1 76360 11857 54 100070 1.2 1 87043 13027 55 65507 1.2 1 56856 8651 56 81640 1.2 1 70483 11157 57 79593 1.2 1 69029 10564 58 70283 1.2 1 61048 9235 59 69160 1.2 1 60404 8756 60 72666 1.2 1 63878 8788 61 70294 1.2 1 61278 9016 62 53944 1.2 1 46944 7000 63 96417 1.2 1 85274 11143 64 55285 1.2 1 48468 6817 65 38971 1.2 1 34272 4699 66 37108 1.2 1 32586 4522 67 56571 1.2 1 50390 6181 68 50179 1.2 1 44447 5732 69 42201 1.2 1 37512 4689 70 44946 1.2 1 40094 4852 71 41790 1.2 1 37262 4528 72 40982 1.2 1 36677 4305 73 52834 1.2 1 47217 5617 74 36715 1.2 1 32884 3831 75 37214 1.2 1 33594 3620 76 21862 1.2 1 19681 2181 77 20234 1.2 1 18089 2145 78 21356 1.2 1 19213 2143 79 20801 1.2 1 18755 2046 80 19965 1.2 1 18052 1913 81 19457 1.2 1 17553 1904 82 18540 1.2 1 16743 1797 83 18128 1.2 1 16310 1818 84 16881 1.2 1 15327 1554 85 16244 1.2 1 14681 1563 86 14629 1.2 1 13288 1341 87 13406 1.2 1 12152 1254 88 12387 1.2 1 11309 1078 89 11896 1.2 1 10797 1099 90 11212 1.2 1 10273 939 91 10453 1.2 1 9572 881 92 9576 1.2 1 8763 813 93 8951 1.2 1 8252 699 94 7943 1.2 1 7270 673 95 7551 1.2 1 6943 608 96 7000 1.2 1 6472 528 97 6398 1.2 1 5915 483 98 6054 1.2 1 5562 492 99 5932 1.2 1 5442 490 100 5497 1.2 1 5059 438 101 4620 1.2 1 4253 367 102 4097 1.2 1 3811 286 103 3738 1.2 1 3458 280 104 3176 1.2 1 2967 209 105 3193 1.2 1 2981 212 106 2735 1.2 1 2568 167 107 2484 1.2 1 2296 188 108 2238 1.2 1 2083 155 109 1904 1.2 1 1767 137 110 1803 1.2 1 1698 105 111 1616 1.2 1 1513 103 112 1395 1.2 1 1313 82 113 1132 1.2 1 1041 91 114 1027 1.2 1 961 66 115 894 1.2 1 818 76 116 780 1.2 1 721 59 117 593 1.2 1 540 53 118 546 1.2 1 497 49 119 485 1.2 1 445 40 120 446 1.2 1 399 47 121 453 1.2 1 416 37 122 293 1.2 1 259 34 123 252 1.2 1 220 32 124 222 1.2 1 204 18 125 208 1.2 1 170 38 126 205 1.2 1 172 33 127 186 1.2 1 153 33 128 198 1.2 1 163 35 129 170 1.2 1 148 22 130 123 1.2 1 97 26 131 133 1.2 1 111 22 132 85 1.2 1 76 9 133 106 1.2 1 101 5 134 89 1.2 1 78 11 135 96 1.2 1 80 16 136 80 1.2 1 68 12 137 88 1.2 1 75 13 138 79 1.2 1 70 9 139 66 1.2 1 48 18 140 52 1.2 1 40 12 141 65 1.2 1 49 16 142 40 1.2 1 27 13 143 39 1.2 1 31 8 144 30 1.2 1 16 14 145 43 1.2 1 39 4 146 36 1.2 1 20 16 147 47 1.2 1 30 17 148 47 1.2 1 31 16 149 54 1.2 1 33 21 150 34 1.2 1 16 18 151 96 1.2 1 34 62 RUN STATISTICS FOR INPUT FILE: ERR12308509_1.fastq.gz ============================================= 78676948 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 78676948 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 29795 (0.04%)