SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308521_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: 107580). 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 ERR12308521_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1495.773 s (16.832 µs/read; 3.56 M reads/minute). === Summary === Total reads processed: 88,863,684 Reads with adapters: 49,317,821 (55.5%) Reads written (passing filters): 88,863,684 (100.0%) Total basepairs processed: 13,418,416,284 bp Quality-trimmed: 76,421,576 bp (0.6%) Total written (filtered): 12,926,121,837 bp (96.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 49317821 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.7% C: 19.4% G: 1.5% T: 28.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 35341073 22215921.0 0 35341073 2 696627 5553980.2 0 696627 3 458480 1388495.1 0 458480 4 359503 347123.8 0 359503 5 374975 86780.9 0 374975 6 332678 21695.2 0 332678 7 320052 5423.8 0 320052 8 398797 1356.0 0 398797 9 204508 339.0 0 204012 496 10 339555 84.7 1 299334 40221 11 295551 21.2 1 264214 31337 12 315895 5.3 1 261326 54569 13 304523 1.3 1 248670 55853 14 356832 1.3 1 286399 70433 15 249469 1.3 1 206289 43180 16 284356 1.3 1 233713 50643 17 372201 1.3 1 308754 63447 18 181091 1.3 1 148607 32484 19 368966 1.3 1 301505 67461 20 281714 1.3 1 232843 48871 21 157671 1.3 1 130608 27063 22 259408 1.3 1 213962 45446 23 254385 1.3 1 208870 45515 24 347150 1.3 1 283221 63929 25 298798 1.3 1 248067 50731 26 175444 1.3 1 144720 30724 27 148914 1.3 1 123190 25724 28 255788 1.3 1 214287 41501 29 184471 1.3 1 155151 29320 30 258049 1.3 1 215365 42684 31 164092 1.3 1 136927 27165 32 241218 1.3 1 201599 39619 33 157078 1.3 1 132193 24885 34 199276 1.3 1 166971 32305 35 192592 1.3 1 163107 29485 36 172758 1.3 1 146407 26351 37 219611 1.3 1 183493 36118 38 174717 1.3 1 148764 25953 39 143322 1.3 1 122084 21238 40 146845 1.3 1 124038 22807 41 152828 1.3 1 131046 21782 42 152909 1.3 1 130935 21974 43 131464 1.3 1 111950 19514 44 139552 1.3 1 118575 20977 45 147772 1.3 1 125086 22686 46 127109 1.3 1 108321 18788 47 126003 1.3 1 108687 17316 48 110874 1.3 1 95467 15407 49 116883 1.3 1 100204 16679 50 106698 1.3 1 92677 14021 51 103504 1.3 1 89435 14069 52 102524 1.3 1 88573 13951 53 96651 1.3 1 83986 12665 54 108223 1.3 1 94212 14011 55 73932 1.3 1 64583 9349 56 88694 1.3 1 76929 11765 57 111039 1.3 1 96375 14664 58 59570 1.3 1 51783 7787 59 65312 1.3 1 57629 7683 60 80422 1.3 1 70554 9868 61 73070 1.3 1 64125 8945 62 53059 1.3 1 46825 6234 63 108419 1.3 1 95820 12599 64 50326 1.3 1 44166 6160 65 38955 1.3 1 34318 4637 66 37138 1.3 1 32772 4366 67 57712 1.3 1 51558 6154 68 49439 1.3 1 44020 5419 69 41369 1.3 1 36864 4505 70 45358 1.3 1 40770 4588 71 41426 1.3 1 37155 4271 72 39854 1.3 1 35797 4057 73 51388 1.3 1 46374 5014 74 35570 1.3 1 32137 3433 75 35013 1.3 1 31757 3256 76 19964 1.3 1 18005 1959 77 19115 1.3 1 17244 1871 78 20983 1.3 1 18900 2083 79 20249 1.3 1 18381 1868 80 19605 1.3 1 17816 1789 81 18780 1.3 1 17072 1708 82 17622 1.3 1 16017 1605 83 17386 1.3 1 15810 1576 84 16181 1.3 1 14803 1378 85 15739 1.3 1 14281 1458 86 14147 1.3 1 12920 1227 87 12997 1.3 1 11838 1159 88 11996 1.3 1 10988 1008 89 11525 1.3 1 10532 993 90 10905 1.3 1 10084 821 91 9867 1.3 1 9050 817 92 9416 1.3 1 8688 728 93 8691 1.3 1 8034 657 94 7715 1.3 1 7093 622 95 7572 1.3 1 6973 599 96 6988 1.3 1 6440 548 97 6415 1.3 1 5950 465 98 6301 1.3 1 5842 459 99 5950 1.3 1 5534 416 100 5515 1.3 1 5116 399 101 4816 1.3 1 4478 338 102 4180 1.3 1 3903 277 103 3999 1.3 1 3729 270 104 3473 1.3 1 3232 241 105 3302 1.3 1 3068 234 106 2931 1.3 1 2755 176 107 2619 1.3 1 2447 172 108 2560 1.3 1 2400 160 109 2181 1.3 1 2027 154 110 1923 1.3 1 1811 112 111 1892 1.3 1 1762 130 112 1690 1.3 1 1600 90 113 1444 1.3 1 1343 101 114 1284 1.3 1 1193 91 115 1149 1.3 1 1068 81 116 942 1.3 1 887 55 117 854 1.3 1 784 70 118 697 1.3 1 647 50 119 645 1.3 1 590 55 120 986 1.3 1 938 48 121 689 1.3 1 641 48 122 414 1.3 1 362 52 123 336 1.3 1 310 26 124 258 1.3 1 229 29 125 261 1.3 1 226 35 126 219 1.3 1 194 25 127 168 1.3 1 145 23 128 130 1.3 1 109 21 129 139 1.3 1 111 28 130 102 1.3 1 77 25 131 99 1.3 1 78 21 132 81 1.3 1 71 10 133 93 1.3 1 72 21 134 73 1.3 1 56 17 135 74 1.3 1 65 9 136 85 1.3 1 66 19 137 78 1.3 1 62 16 138 61 1.3 1 46 15 139 55 1.3 1 43 12 140 49 1.3 1 37 12 141 51 1.3 1 44 7 142 49 1.3 1 33 16 143 40 1.3 1 27 13 144 36 1.3 1 23 13 145 45 1.3 1 27 18 146 56 1.3 1 37 19 147 47 1.3 1 32 15 148 29 1.3 1 23 6 149 34 1.3 1 24 10 150 20 1.3 1 9 11 151 267 1.3 1 51 216 RUN STATISTICS FOR INPUT FILE: ERR12308521_2.fastq.gz ============================================= 88863684 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 88863684 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 53909 (0.06%)