SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308519_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: 99083). 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 ERR12308519_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1582.349 s (19.888 µs/read; 3.02 M reads/minute). === Summary === Total reads processed: 79,561,917 Reads with adapters: 44,170,257 (55.5%) Reads written (passing filters): 79,561,917 (100.0%) Total basepairs processed: 12,013,849,467 bp Quality-trimmed: 59,184,562 bp (0.5%) Total written (filtered): 11,587,120,274 bp (96.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 44170257 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.5% C: 19.5% G: 0.8% T: 29.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 32974594 19890479.2 0 32974594 2 437873 4972619.8 0 437873 3 339937 1243155.0 0 339937 4 270366 310788.7 0 270366 5 283862 77697.2 0 283862 6 251007 19424.3 0 251007 7 232432 4856.1 0 232432 8 287149 1214.0 0 287149 9 174341 303.5 0 173910 431 10 243760 75.9 1 221539 22221 11 225839 19.0 1 205404 20435 12 234911 4.7 1 193725 41186 13 231266 1.2 1 188045 43221 14 264049 1.2 1 213236 50813 15 188935 1.2 1 155625 33310 16 219358 1.2 1 179351 40007 17 274161 1.2 1 227243 46918 18 144578 1.2 1 118173 26405 19 260393 1.2 1 213412 46981 20 212754 1.2 1 174968 37786 21 124617 1.2 1 102122 22495 22 190105 1.2 1 156164 33941 23 188343 1.2 1 154065 34278 24 249478 1.2 1 204021 45457 25 228223 1.2 1 188375 39848 26 137223 1.2 1 112589 24634 27 120172 1.2 1 98655 21517 28 195859 1.2 1 164407 31452 29 141715 1.2 1 117863 23852 30 194887 1.2 1 162677 32210 31 125497 1.2 1 103765 21732 32 192479 1.2 1 160956 31523 33 156117 1.2 1 129985 26132 34 109825 1.2 1 91369 18456 35 150847 1.2 1 127409 23438 36 139618 1.2 1 117068 22550 37 149324 1.2 1 124602 24722 38 130788 1.2 1 110297 20491 39 151353 1.2 1 128895 22458 40 103810 1.2 1 87591 16219 41 128515 1.2 1 108399 20116 42 132614 1.2 1 112426 20188 43 107542 1.2 1 90690 16852 44 116595 1.2 1 98591 18004 45 123789 1.2 1 104268 19521 46 111674 1.2 1 94579 17095 47 107710 1.2 1 92420 15290 48 99269 1.2 1 84573 14696 49 105384 1.2 1 89636 15748 50 96897 1.2 1 83428 13469 51 94605 1.2 1 81113 13492 52 94387 1.2 1 80975 13412 53 89647 1.2 1 77354 12293 54 100174 1.2 1 86752 13422 55 72228 1.2 1 62370 9858 56 85922 1.2 1 74342 11580 57 107321 1.2 1 93290 14031 58 60412 1.2 1 51790 8622 59 67431 1.2 1 58691 8740 60 81157 1.2 1 70768 10389 61 74266 1.2 1 64782 9484 62 56251 1.2 1 49110 7141 63 111523 1.2 1 98634 12889 64 54912 1.2 1 47738 7174 65 41574 1.2 1 36459 5115 66 41259 1.2 1 36092 5167 67 62774 1.2 1 55699 7075 68 55597 1.2 1 48993 6604 69 47591 1.2 1 42065 5526 70 52263 1.2 1 46478 5785 71 47714 1.2 1 42263 5451 72 46287 1.2 1 41091 5196 73 60583 1.2 1 54279 6304 74 41880 1.2 1 37458 4422 75 40543 1.2 1 36437 4106 76 22942 1.2 1 20581 2361 77 23362 1.2 1 20933 2429 78 24839 1.2 1 22314 2525 79 24506 1.2 1 22037 2469 80 23807 1.2 1 21568 2239 81 22725 1.2 1 20502 2223 82 21722 1.2 1 19528 2194 83 21019 1.2 1 19013 2006 84 19425 1.2 1 17625 1800 85 19036 1.2 1 17285 1751 86 16988 1.2 1 15456 1532 87 15639 1.2 1 14288 1351 88 14561 1.2 1 13329 1232 89 13950 1.2 1 12684 1266 90 13028 1.2 1 11930 1098 91 11790 1.2 1 10801 989 92 11088 1.2 1 10167 921 93 10228 1.2 1 9384 844 94 9141 1.2 1 8368 773 95 8391 1.2 1 7765 626 96 7786 1.2 1 7208 578 97 7150 1.2 1 6601 549 98 6505 1.2 1 6058 447 99 6273 1.2 1 5811 462 100 5922 1.2 1 5549 373 101 4795 1.2 1 4463 332 102 4200 1.2 1 3946 254 103 3767 1.2 1 3520 247 104 3209 1.2 1 2993 216 105 3015 1.2 1 2824 191 106 2669 1.2 1 2532 137 107 2341 1.2 1 2186 155 108 1978 1.2 1 1864 114 109 1743 1.2 1 1641 102 110 1513 1.2 1 1438 75 111 1369 1.2 1 1297 72 112 1182 1.2 1 1116 66 113 883 1.2 1 839 44 114 731 1.2 1 674 57 115 594 1.2 1 563 31 116 494 1.2 1 451 43 117 447 1.2 1 413 34 118 367 1.2 1 338 29 119 332 1.2 1 309 23 120 313 1.2 1 300 13 121 255 1.2 1 225 30 122 199 1.2 1 178 21 123 160 1.2 1 151 9 124 152 1.2 1 136 16 125 115 1.2 1 90 25 126 123 1.2 1 108 15 127 94 1.2 1 83 11 128 114 1.2 1 100 14 129 100 1.2 1 85 15 130 93 1.2 1 86 7 131 79 1.2 1 67 12 132 69 1.2 1 59 10 133 68 1.2 1 60 8 134 75 1.2 1 65 10 135 68 1.2 1 58 10 136 42 1.2 1 33 9 137 55 1.2 1 50 5 138 36 1.2 1 27 9 139 31 1.2 1 28 3 140 44 1.2 1 30 14 141 57 1.2 1 46 11 142 42 1.2 1 26 16 143 21 1.2 1 11 10 144 47 1.2 1 30 17 145 32 1.2 1 25 7 146 31 1.2 1 16 15 147 34 1.2 1 25 9 148 29 1.2 1 20 9 149 34 1.2 1 23 11 150 19 1.2 1 7 12 151 39 1.2 1 13 26 RUN STATISTICS FOR INPUT FILE: ERR12308519_2.fastq.gz ============================================= 79561917 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 79561917 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 22160 (0.03%)