SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308521_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: 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_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1417.456 s (15.951 µs/read; 3.76 M reads/minute). === Summary === Total reads processed: 88,863,684 Reads with adapters: 42,275,077 (47.6%) Reads written (passing filters): 88,863,684 (100.0%) Total basepairs processed: 13,418,416,284 bp Quality-trimmed: 40,326,442 bp (0.3%) Total written (filtered): 12,951,775,064 bp (96.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 42275077 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.0% C: 1.7% G: 16.7% T: 45.5% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 22982020 22215921.0 0 22982020 2 3980571 5553980.2 0 3980571 3 1811778 1388495.1 0 1811778 4 869219 347123.8 0 869219 5 361192 86780.9 0 361192 6 308399 21695.2 0 308399 7 300134 5423.8 0 300134 8 335328 1356.0 0 335328 9 287829 339.0 0 286369 1460 10 311347 84.7 1 285515 25832 11 330422 21.2 1 294298 36124 12 339775 5.3 1 306930 32845 13 292088 1.3 1 267933 24155 14 302085 1.3 1 269445 32640 15 308989 1.3 1 282286 26703 16 287818 1.3 1 256661 31157 17 323902 1.3 1 286293 37609 18 359517 1.3 1 332320 27197 19 178528 1.3 1 165316 13212 20 270286 1.3 1 248774 21512 21 285546 1.3 1 261916 23630 22 240253 1.3 1 221879 18374 23 281587 1.3 1 258453 23134 24 249378 1.3 1 221663 27715 25 257965 1.3 1 239464 18501 26 211472 1.3 1 197711 13761 27 249586 1.3 1 230105 19481 28 228145 1.3 1 212922 15223 29 234514 1.3 1 213486 21028 30 265242 1.3 1 248338 16904 31 148135 1.3 1 139100 9035 32 214813 1.3 1 201557 13256 33 191289 1.3 1 177483 13806 34 213192 1.3 1 195695 17497 35 176408 1.3 1 167237 9171 36 190493 1.3 1 177847 12646 37 175246 1.3 1 160639 14607 38 189670 1.3 1 175859 13811 39 165017 1.3 1 156972 8045 40 178918 1.3 1 167429 11489 41 144558 1.3 1 131473 13085 42 141444 1.3 1 134432 7012 43 190770 1.3 1 174492 16278 44 112484 1.3 1 104399 8085 45 215842 1.3 1 205972 9870 46 48383 1.3 1 44333 4050 47 118871 1.3 1 112697 6174 48 150958 1.3 1 142412 8546 49 90322 1.3 1 85706 4616 50 112659 1.3 1 105490 7169 51 110256 1.3 1 103266 6990 52 101902 1.3 1 96341 5561 53 96434 1.3 1 91525 4909 54 103166 1.3 1 96072 7094 55 126347 1.3 1 120137 6210 56 51827 1.3 1 48952 2875 57 101245 1.3 1 96340 4905 58 103280 1.3 1 99106 4174 59 41008 1.3 1 38305 2703 60 80673 1.3 1 78113 2560 61 45045 1.3 1 42901 2144 62 70333 1.3 1 66541 3792 63 80418 1.3 1 77248 3170 64 56265 1.3 1 54268 1997 65 32613 1.3 1 30870 1743 66 58562 1.3 1 55886 2676 67 60100 1.3 1 57447 2653 68 62099 1.3 1 59382 2717 69 51004 1.3 1 48272 2732 70 86167 1.3 1 82460 3707 71 6566 1.3 1 5989 577 72 7946 1.3 1 7478 468 73 21743 1.3 1 20818 925 74 28093 1.3 1 26921 1172 75 29435 1.3 1 28124 1311 76 29256 1.3 1 27880 1376 77 27056 1.3 1 25830 1226 78 26292 1.3 1 25081 1211 79 24670 1.3 1 23560 1110 80 23172 1.3 1 22104 1068 81 21887 1.3 1 20892 995 82 20119 1.3 1 19209 910 83 19068 1.3 1 18138 930 84 17841 1.3 1 17039 802 85 16685 1.3 1 15901 784 86 15404 1.3 1 14719 685 87 14498 1.3 1 13850 648 88 13447 1.3 1 12832 615 89 12522 1.3 1 11956 566 90 11581 1.3 1 11045 536 91 10794 1.3 1 10313 481 92 10130 1.3 1 9701 429 93 9230 1.3 1 8881 349 94 8476 1.3 1 8087 389 95 8074 1.3 1 7688 386 96 7382 1.3 1 7044 338 97 6843 1.3 1 6494 349 98 6474 1.3 1 6182 292 99 5871 1.3 1 5615 256 100 5364 1.3 1 5117 247 101 5004 1.3 1 4773 231 102 4491 1.3 1 4304 187 103 4330 1.3 1 4120 210 104 3809 1.3 1 3637 172 105 3595 1.3 1 3420 175 106 3177 1.3 1 3020 157 107 2761 1.3 1 2628 133 108 2658 1.3 1 2538 120 109 2366 1.3 1 2225 141 110 2061 1.3 1 1970 91 111 1988 1.3 1 1887 101 112 1753 1.3 1 1674 79 113 1486 1.3 1 1380 106 114 1333 1.3 1 1253 80 115 1160 1.3 1 1082 78 116 978 1.3 1 907 71 117 873 1.3 1 815 58 118 746 1.3 1 696 50 119 638 1.3 1 599 39 120 833 1.3 1 793 40 121 713 1.3 1 671 42 122 407 1.3 1 369 38 123 337 1.3 1 303 34 124 269 1.3 1 237 32 125 271 1.3 1 227 44 126 237 1.3 1 197 40 127 148 1.3 1 127 21 128 142 1.3 1 115 27 129 129 1.3 1 108 21 130 104 1.3 1 80 24 131 109 1.3 1 77 32 132 97 1.3 1 67 30 133 90 1.3 1 71 19 134 79 1.3 1 62 17 135 89 1.3 1 66 23 136 92 1.3 1 67 25 137 75 1.3 1 62 13 138 65 1.3 1 48 17 139 68 1.3 1 46 22 140 59 1.3 1 41 18 141 55 1.3 1 39 16 142 65 1.3 1 34 31 143 57 1.3 1 29 28 144 51 1.3 1 23 28 145 57 1.3 1 27 30 146 62 1.3 1 36 26 147 64 1.3 1 33 31 148 43 1.3 1 24 19 149 49 1.3 1 27 22 150 90 1.3 1 12 78 151 25814 1.3 1 55 25759 RUN STATISTICS FOR INPUT FILE: ERR12308521_1.fastq.gz ============================================= 88863684 sequences processed in total