SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245600_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 85632). 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 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR18245600_2.fastq.gz Processing single-end reads on 1 core ... Finished in 4348.625 s (52.027 µs/read; 1.15 M reads/minute). === Summary === Total reads processed: 83,583,654 Reads with adapters: 46,853,808 (56.1%) Reads written (passing filters): 83,583,654 (100.0%) Total basepairs processed: 12,537,548,100 bp Quality-trimmed: 31,957,347 bp (0.3%) Total written (filtered): 12,115,098,156 bp (96.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46853808 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.4% C: 19.3% G: 0.4% T: 32.8% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 36176572 20895913.5 0 36176572 2 357580 5223978.4 0 357580 3 354137 1305994.6 0 354137 4 326586 326498.6 0 326586 5 299117 81624.7 0 299117 6 277471 20406.2 0 277471 7 280631 5101.5 0 280631 8 294437 1275.4 0 294437 9 230171 318.8 0 229139 1032 10 264299 79.7 1 249365 14934 11 250698 19.9 1 233391 17307 12 253328 5.0 1 235903 17425 13 231456 1.2 1 216944 14512 14 242479 1.2 1 225571 16908 15 212989 1.2 1 199187 13802 16 215302 1.2 1 200617 14685 17 240218 1.2 1 224489 15729 18 167174 1.2 1 156675 10499 19 211715 1.2 1 197437 14278 20 200763 1.2 1 188125 12638 21 159948 1.2 1 148999 10949 22 174524 1.2 1 163898 10626 23 167030 1.2 1 156908 10122 24 189094 1.2 1 176480 12614 25 177005 1.2 1 167062 9943 26 127060 1.2 1 118978 8082 27 135100 1.2 1 125511 9589 28 144668 1.2 1 136858 7810 29 131554 1.2 1 123124 8430 30 135682 1.2 1 127842 7840 31 121540 1.2 1 114546 6994 32 121577 1.2 1 114748 6829 33 133263 1.2 1 125118 8145 34 108938 1.2 1 101772 7166 35 106272 1.2 1 100403 5869 36 115648 1.2 1 109392 6256 37 97971 1.2 1 92583 5388 38 94953 1.2 1 89908 5045 39 102738 1.2 1 97426 5312 40 81686 1.2 1 77441 4245 41 89489 1.2 1 84866 4623 42 123320 1.2 1 117591 5729 43 56475 1.2 1 52238 4237 44 141380 1.2 1 135015 6365 45 97634 1.2 1 92578 5056 46 59171 1.2 1 54123 5048 47 166726 1.2 1 162418 4308 48 19713 1.2 1 17453 2260 49 63503 1.2 1 60560 2943 50 23935 1.2 1 22537 1398 51 36316 1.2 1 34399 1917 52 24834 1.2 1 23180 1654 53 59318 1.2 1 56471 2847 54 93916 1.2 1 90703 3213 55 22765 1.2 1 20825 1940 56 60407 1.2 1 55940 4467 57 205524 1.2 1 200616 4908 58 32954 1.2 1 30757 2197 59 17640 1.2 1 15551 2089 60 122329 1.2 1 118822 3507 61 21866 1.2 1 20562 1304 62 16806 1.2 1 14853 1953 63 109485 1.2 1 105383 4102 64 133820 1.2 1 130678 3142 65 11148 1.2 1 10046 1102 66 26036 1.2 1 24791 1245 67 17882 1.2 1 17134 748 68 9909 1.2 1 9158 751 69 16706 1.2 1 15837 869 70 25582 1.2 1 24665 917 71 9281 1.2 1 8715 566 72 9237 1.2 1 8706 531 73 11486 1.2 1 10816 670 74 12090 1.2 1 11403 687 75 17240 1.2 1 16382 858 76 21092 1.2 1 20068 1024 77 23977 1.2 1 22939 1038 78 26327 1.2 1 25273 1054 79 26403 1.2 1 25348 1055 80 26523 1.2 1 25447 1076 81 26556 1.2 1 25547 1009 82 26481 1.2 1 25372 1109 83 27859 1.2 1 26736 1123 84 27128 1.2 1 25995 1133 85 27953 1.2 1 26826 1127 86 25745 1.2 1 24737 1008 87 24352 1.2 1 23360 992 88 23021 1.2 1 22092 929 89 22862 1.2 1 22001 861 90 22509 1.2 1 21668 841 91 21646 1.2 1 20878 768 92 21096 1.2 1 20279 817 93 21111 1.2 1 20318 793 94 20259 1.2 1 19500 759 95 20193 1.2 1 19476 717 96 19565 1.2 1 18912 653 97 19419 1.2 1 18672 747 98 19530 1.2 1 18844 686 99 19933 1.2 1 19171 762 100 20125 1.2 1 19430 695 101 18470 1.2 1 17803 667 102 17752 1.2 1 17095 657 103 16958 1.2 1 16322 636 104 16451 1.2 1 15873 578 105 16518 1.2 1 15910 608 106 16175 1.2 1 15574 601 107 16095 1.2 1 15435 660 108 15752 1.2 1 15175 577 109 15746 1.2 1 15209 537 110 15755 1.2 1 15210 545 111 15875 1.2 1 15282 593 112 15818 1.2 1 15266 552 113 14827 1.2 1 14294 533 114 14730 1.2 1 14178 552 115 14075 1.2 1 13588 487 116 14190 1.2 1 13689 501 117 14086 1.2 1 13577 509 118 14040 1.2 1 13551 489 119 13976 1.2 1 13427 549 120 13737 1.2 1 13161 576 121 13517 1.2 1 12922 595 122 13082 1.2 1 12415 667 123 13294 1.2 1 12439 855 124 12601 1.2 1 11742 859 125 12703 1.2 1 11533 1170 126 12106 1.2 1 10743 1363 127 11527 1.2 1 9957 1570 128 11056 1.2 1 9432 1624 129 11067 1.2 1 9137 1930 130 10244 1.2 1 8138 2106 131 10256 1.2 1 7792 2464 132 9922 1.2 1 7163 2759 133 9684 1.2 1 6405 3279 134 9055 1.2 1 5847 3208 135 8348 1.2 1 5191 3157 136 7403 1.2 1 4431 2972 137 6238 1.2 1 4235 2003 138 5801 1.2 1 4365 1436 139 5198 1.2 1 4056 1142 140 5073 1.2 1 4165 908 141 5745 1.2 1 4975 770 142 4793 1.2 1 4246 547 143 4499 1.2 1 3943 556 144 6564 1.2 1 5679 885 145 8341 1.2 1 7181 1160 146 4213 1.2 1 3456 757 147 443 1.2 1 301 142 148 4650 1.2 1 3824 826 149 1838 1.2 1 1467 371 150 42559 1.2 1 36799 5760 RUN STATISTICS FOR INPUT FILE: SRR18245600_2.fastq.gz ============================================= 83583654 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 83583654 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 183730 (0.22%)