SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684005_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: 221306). 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 ERR10684005_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1581.006 s (18.619 µs/read; 3.22 M reads/minute). === Summary === Total reads processed: 84,913,702 Reads with adapters: 55,966,429 (65.9%) Reads written (passing filters): 84,913,702 (100.0%) Total basepairs processed: 12,821,969,002 bp Quality-trimmed: 47,638,317 bp (0.4%) Total written (filtered): 11,916,470,578 bp (92.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 55966429 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.2% C: 19.3% G: 1.0% T: 27.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 28608414 21228425.5 0 28608414 2 1171453 5307106.4 0 1171453 3 739344 1326776.6 0 739344 4 623514 331694.1 0 623514 5 645756 82923.5 0 645756 6 631196 20730.9 0 631196 7 641576 5182.7 0 641576 8 768751 1295.7 0 768751 9 478795 323.9 0 476594 2201 10 644126 81.0 1 572755 71371 11 554965 20.2 1 500545 54420 12 583353 5.1 1 508754 74599 13 546586 1.3 1 475947 70639 14 647267 1.3 1 558412 88855 15 423284 1.3 1 373132 50152 16 530792 1.3 1 469026 61766 17 718729 1.3 1 632884 85845 18 362691 1.3 1 319672 43019 19 673923 1.3 1 590236 83687 20 499726 1.3 1 441851 57875 21 354407 1.3 1 315571 38836 22 449771 1.3 1 398382 51389 23 435654 1.3 1 384822 50832 24 508999 1.3 1 441469 67530 25 493545 1.3 1 438190 55355 26 370454 1.3 1 329608 40846 27 329451 1.3 1 290710 38741 28 491667 1.3 1 437217 54450 29 387091 1.3 1 346048 41043 30 544726 1.3 1 487158 57568 31 294821 1.3 1 262522 32299 32 427942 1.3 1 379215 48727 33 339633 1.3 1 303803 35830 34 259711 1.3 1 232827 26884 35 320204 1.3 1 285906 34298 36 385921 1.3 1 344728 41193 37 245095 1.3 1 220347 24748 38 391355 1.3 1 351171 40184 39 333320 1.3 1 301093 32227 40 250851 1.3 1 226597 24254 41 311448 1.3 1 280846 30602 42 302077 1.3 1 272169 29908 43 230872 1.3 1 209345 21527 44 240571 1.3 1 216381 24190 45 250011 1.3 1 225004 25007 46 240331 1.3 1 218480 21851 47 231193 1.3 1 208456 22737 48 228655 1.3 1 207633 21022 49 254469 1.3 1 230928 23541 50 227359 1.3 1 207405 19954 51 219908 1.3 1 200466 19442 52 207946 1.3 1 189857 18089 53 197330 1.3 1 179300 18030 54 220416 1.3 1 200214 20202 55 138811 1.3 1 126671 12140 56 176373 1.3 1 160494 15879 57 207302 1.3 1 188057 19245 58 145306 1.3 1 132583 12723 59 180395 1.3 1 165913 14482 60 197263 1.3 1 180645 16618 61 184521 1.3 1 169576 14945 62 157976 1.3 1 144855 13121 63 223898 1.3 1 205560 18338 64 111679 1.3 1 102157 9522 65 122177 1.3 1 113030 9147 66 91848 1.3 1 84422 7426 67 130252 1.3 1 119908 10344 68 130648 1.3 1 120426 10222 69 121429 1.3 1 112028 9401 70 130694 1.3 1 120957 9737 71 129743 1.3 1 119919 9824 72 126307 1.3 1 116688 9619 73 148665 1.3 1 137909 10756 74 120787 1.3 1 112250 8537 75 108314 1.3 1 101231 7083 76 70794 1.3 1 65897 4897 77 65090 1.3 1 60101 4989 78 68857 1.3 1 63845 5012 79 69297 1.3 1 64301 4996 80 71387 1.3 1 66399 4988 81 71567 1.3 1 66490 5077 82 66559 1.3 1 61900 4659 83 62694 1.3 1 58362 4332 84 57915 1.3 1 53853 4062 85 55239 1.3 1 51379 3860 86 50986 1.3 1 47497 3489 87 47996 1.3 1 44772 3224 88 46276 1.3 1 43255 3021 89 45363 1.3 1 42361 3002 90 44945 1.3 1 42112 2833 91 42492 1.3 1 39722 2770 92 40655 1.3 1 38034 2621 93 38102 1.3 1 35750 2352 94 34269 1.3 1 32159 2110 95 31514 1.3 1 29471 2043 96 29120 1.3 1 27389 1731 97 27138 1.3 1 25426 1712 98 25602 1.3 1 24084 1518 99 24965 1.3 1 23424 1541 100 24046 1.3 1 22616 1430 101 21580 1.3 1 20282 1298 102 19595 1.3 1 18447 1148 103 18047 1.3 1 16966 1081 104 16159 1.3 1 15278 881 105 14713 1.3 1 13930 783 106 13334 1.3 1 12619 715 107 12082 1.3 1 11354 728 108 11017 1.3 1 10421 596 109 9533 1.3 1 9020 513 110 8678 1.3 1 8216 462 111 7979 1.3 1 7547 432 112 7000 1.3 1 6664 336 113 6448 1.3 1 6113 335 114 5258 1.3 1 5011 247 115 4354 1.3 1 4136 218 116 3464 1.3 1 3266 198 117 3119 1.3 1 2976 143 118 2575 1.3 1 2442 133 119 2140 1.3 1 2014 126 120 3443 1.3 1 3277 166 121 1537 1.3 1 1460 77 122 1086 1.3 1 1025 61 123 799 1.3 1 753 46 124 610 1.3 1 567 43 125 403 1.3 1 371 32 126 405 1.3 1 377 28 127 264 1.3 1 242 22 128 179 1.3 1 153 26 129 171 1.3 1 149 22 130 118 1.3 1 94 24 131 135 1.3 1 115 20 132 76 1.3 1 69 7 133 110 1.3 1 92 18 134 74 1.3 1 57 17 135 99 1.3 1 83 16 136 73 1.3 1 56 17 137 100 1.3 1 79 21 138 56 1.3 1 43 13 139 65 1.3 1 52 13 140 56 1.3 1 41 15 141 90 1.3 1 68 22 142 50 1.3 1 30 20 143 65 1.3 1 45 20 144 39 1.3 1 21 18 145 48 1.3 1 32 16 146 47 1.3 1 26 21 147 58 1.3 1 43 15 148 46 1.3 1 24 22 149 72 1.3 1 42 30 150 27 1.3 1 13 14 151 252 1.3 1 183 69 RUN STATISTICS FOR INPUT FILE: ERR10684005_1.fastq.gz ============================================= 84913702 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 84913702 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 67011 (0.08%)