SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308522_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: 44462). Second best hit was smallRNA (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 ERR12308522_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1761.836 s (20.951 µs/read; 2.86 M reads/minute). === Summary === Total reads processed: 84,093,597 Reads with adapters: 42,694,947 (50.8%) Reads written (passing filters): 84,093,597 (100.0%) Total basepairs processed: 12,698,133,147 bp Quality-trimmed: 77,155,029 bp (0.6%) Total written (filtered): 12,436,322,495 bp (97.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 42694947 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.4% C: 18.3% G: 1.3% T: 29.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 36463319 21023399.2 0 36463319 2 578984 5255849.8 0 578984 3 304463 1313962.5 0 304463 4 197430 328490.6 0 197430 5 199192 82122.7 0 199192 6 172468 20530.7 0 172468 7 162166 5132.7 0 162166 8 193071 1283.2 0 193071 9 108398 320.8 0 108069 329 10 161899 80.2 1 142004 19895 11 142986 20.0 1 125930 17056 12 153147 5.0 1 130290 22857 13 141860 1.3 1 121478 20382 14 169750 1.3 1 142381 27369 15 110637 1.3 1 95167 15470 16 128192 1.3 1 110286 17906 17 157964 1.3 1 136813 21151 18 87326 1.3 1 75321 12005 19 133741 1.3 1 113736 20005 20 131159 1.3 1 113270 17889 21 81470 1.3 1 70747 10723 22 108201 1.3 1 93190 15011 23 104421 1.3 1 89932 14489 24 124044 1.3 1 104869 19175 25 114671 1.3 1 99530 15141 26 77554 1.3 1 66507 11047 27 73460 1.3 1 63587 9873 28 94892 1.3 1 83000 11892 29 75462 1.3 1 66294 9168 30 89498 1.3 1 77520 11978 31 71343 1.3 1 62308 9035 32 80394 1.3 1 69542 10852 33 78772 1.3 1 68638 10134 34 76446 1.3 1 67360 9086 35 62548 1.3 1 54659 7889 36 62835 1.3 1 55776 7059 37 66489 1.3 1 58788 7701 38 52047 1.3 1 45813 6234 39 59962 1.3 1 52995 6967 40 55772 1.3 1 49362 6410 41 51411 1.3 1 45825 5586 42 58996 1.3 1 52233 6763 43 42155 1.3 1 37370 4785 44 49331 1.3 1 43385 5946 45 50883 1.3 1 44868 6015 46 41867 1.3 1 36988 4879 47 43138 1.3 1 38576 4562 48 39285 1.3 1 34993 4292 49 38972 1.3 1 34545 4427 50 36539 1.3 1 32792 3747 51 34336 1.3 1 30881 3455 52 34415 1.3 1 31017 3398 53 33028 1.3 1 29804 3224 54 37326 1.3 1 33628 3698 55 23813 1.3 1 21526 2287 56 29875 1.3 1 26686 3189 57 39985 1.3 1 35888 4097 58 18805 1.3 1 16821 1984 59 21796 1.3 1 19743 2053 60 27508 1.3 1 24880 2628 61 24586 1.3 1 22260 2326 62 18425 1.3 1 16706 1719 63 38703 1.3 1 35306 3397 64 16823 1.3 1 15139 1684 65 13336 1.3 1 12151 1185 66 12543 1.3 1 11367 1176 67 20205 1.3 1 18536 1669 68 17483 1.3 1 15884 1599 69 14578 1.3 1 13314 1264 70 16006 1.3 1 14793 1213 71 14563 1.3 1 13378 1185 72 14522 1.3 1 13286 1236 73 18404 1.3 1 16949 1455 74 13612 1.3 1 12379 1233 75 13195 1.3 1 12183 1012 76 7697 1.3 1 7083 614 77 7404 1.3 1 6833 571 78 8174 1.3 1 7519 655 79 7797 1.3 1 7194 603 80 7844 1.3 1 7227 617 81 7486 1.3 1 6882 604 82 7200 1.3 1 6635 565 83 7053 1.3 1 6476 577 84 6564 1.3 1 6060 504 85 6310 1.3 1 5829 481 86 5882 1.3 1 5412 470 87 5601 1.3 1 5148 453 88 5130 1.3 1 4780 350 89 4892 1.3 1 4532 360 90 4928 1.3 1 4578 350 91 4435 1.3 1 4117 318 92 4298 1.3 1 3977 321 93 4221 1.3 1 3903 318 94 3768 1.3 1 3523 245 95 3603 1.3 1 3332 271 96 3386 1.3 1 3133 253 97 3237 1.3 1 2975 262 98 3341 1.3 1 3083 258 99 2982 1.3 1 2779 203 100 2961 1.3 1 2741 220 101 2539 1.3 1 2366 173 102 2355 1.3 1 2202 153 103 2156 1.3 1 1985 171 104 2050 1.3 1 1906 144 105 1879 1.3 1 1770 109 106 1765 1.3 1 1644 121 107 1645 1.3 1 1545 100 108 1543 1.3 1 1430 113 109 1361 1.3 1 1249 112 110 1251 1.3 1 1160 91 111 1157 1.3 1 1071 86 112 1062 1.3 1 991 71 113 920 1.3 1 855 65 114 825 1.3 1 762 63 115 725 1.3 1 679 46 116 680 1.3 1 625 55 117 616 1.3 1 558 58 118 513 1.3 1 454 59 119 474 1.3 1 415 59 120 521 1.3 1 474 47 121 402 1.3 1 357 45 122 323 1.3 1 287 36 123 244 1.3 1 197 47 124 249 1.3 1 219 30 125 240 1.3 1 201 39 126 191 1.3 1 158 33 127 163 1.3 1 132 31 128 133 1.3 1 97 36 129 122 1.3 1 106 16 130 120 1.3 1 99 21 131 122 1.3 1 97 25 132 93 1.3 1 77 16 133 117 1.3 1 97 20 134 88 1.3 1 67 21 135 82 1.3 1 64 18 136 74 1.3 1 62 12 137 75 1.3 1 52 23 138 59 1.3 1 41 18 139 72 1.3 1 55 17 140 68 1.3 1 45 23 141 61 1.3 1 40 21 142 49 1.3 1 32 17 143 52 1.3 1 28 24 144 44 1.3 1 24 20 145 49 1.3 1 29 20 146 52 1.3 1 27 25 147 70 1.3 1 41 29 148 49 1.3 1 30 19 149 69 1.3 1 48 21 150 38 1.3 1 24 14 151 265 1.3 1 58 207 RUN STATISTICS FOR INPUT FILE: ERR12308522_1.fastq.gz ============================================= 84093597 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 84093597 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 66994 (0.08%)