SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245603_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: 91211). 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 SRR18245603_2.fastq.gz Processing single-end reads on 1 core ... Finished in 4391.014 s (50.981 µs/read; 1.18 M reads/minute). === Summary === Total reads processed: 86,130,397 Reads with adapters: 48,843,847 (56.7%) Reads written (passing filters): 86,130,397 (100.0%) Total basepairs processed: 12,919,559,550 bp Quality-trimmed: 46,455,224 bp (0.4%) Total written (filtered): 12,445,844,014 bp (96.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 48843847 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.9% C: 17.9% G: 0.4% T: 32.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 38175894 21532599.2 0 38175894 2 294559 5383149.8 0 294559 3 299926 1345787.5 0 299926 4 270247 336446.9 0 270247 5 238081 84111.7 0 238081 6 226673 21027.9 0 226673 7 236773 5257.0 0 236773 8 244890 1314.2 0 244890 9 192435 328.6 0 191653 782 10 227183 82.1 1 214906 12277 11 210762 20.5 1 197560 13202 12 221597 5.1 1 206552 15045 13 198713 1.3 1 186785 11928 14 216657 1.3 1 201362 15295 15 191107 1.3 1 178698 12409 16 190360 1.3 1 178112 12248 17 218037 1.3 1 203468 14569 18 157208 1.3 1 147422 9786 19 233111 1.3 1 218206 14905 20 154715 1.3 1 145324 9391 21 143515 1.3 1 134987 8528 22 165308 1.3 1 155375 9933 23 163359 1.3 1 153419 9940 24 197746 1.3 1 184351 13395 25 171464 1.3 1 162454 9010 26 123579 1.3 1 115795 7784 27 126489 1.3 1 117925 8564 28 152228 1.3 1 143915 8313 29 126718 1.3 1 119330 7388 30 146155 1.3 1 138173 7982 31 118846 1.3 1 112364 6482 32 127624 1.3 1 120721 6903 33 126245 1.3 1 118866 7379 34 124763 1.3 1 117698 7065 35 117665 1.3 1 110525 7140 36 128870 1.3 1 122352 6518 37 99044 1.3 1 92932 6112 38 122705 1.3 1 116130 6575 39 135830 1.3 1 129286 6544 40 71573 1.3 1 66814 4759 41 91481 1.3 1 86861 4620 42 122630 1.3 1 116830 5800 43 85867 1.3 1 78518 7349 44 365541 1.3 1 353464 12077 45 106211 1.3 1 100590 5621 46 36200 1.3 1 32468 3732 47 118450 1.3 1 115011 3439 48 20133 1.3 1 17998 2135 49 61670 1.3 1 59071 2599 50 17058 1.3 1 15721 1337 51 32455 1.3 1 30843 1612 52 16520 1.3 1 15092 1428 53 65703 1.3 1 62769 2934 54 106861 1.3 1 103471 3390 55 31912 1.3 1 29637 2275 56 67331 1.3 1 63279 4052 57 168214 1.3 1 163706 4508 58 47062 1.3 1 44629 2433 59 32941 1.3 1 30136 2805 60 145702 1.3 1 141541 4161 61 48021 1.3 1 46033 1988 62 19516 1.3 1 17438 2078 63 116667 1.3 1 111466 5201 64 225516 1.3 1 220564 4952 65 32007 1.3 1 30151 1856 66 39948 1.3 1 38335 1613 67 27648 1.3 1 26689 959 68 10810 1.3 1 10114 696 69 17076 1.3 1 16133 943 70 27763 1.3 1 26825 938 71 10840 1.3 1 10313 527 72 9958 1.3 1 9409 549 73 12537 1.3 1 12001 536 74 13739 1.3 1 13112 627 75 18894 1.3 1 18125 769 76 24985 1.3 1 24047 938 77 25169 1.3 1 24009 1160 78 32479 1.3 1 31248 1231 79 34819 1.3 1 33491 1328 80 35634 1.3 1 34212 1422 81 35688 1.3 1 34263 1425 82 36154 1.3 1 34682 1472 83 38645 1.3 1 37133 1512 84 37249 1.3 1 35742 1507 85 39132 1.3 1 37636 1496 86 35411 1.3 1 33956 1455 87 33278 1.3 1 31955 1323 88 32448 1.3 1 31159 1289 89 31375 1.3 1 30097 1278 90 31846 1.3 1 30557 1289 91 30700 1.3 1 29482 1218 92 29826 1.3 1 28639 1187 93 29870 1.3 1 28756 1114 94 28112 1.3 1 27020 1092 95 27690 1.3 1 26618 1072 96 27706 1.3 1 26639 1067 97 27380 1.3 1 26307 1073 98 27664 1.3 1 26585 1079 99 27932 1.3 1 26866 1066 100 27920 1.3 1 26838 1082 101 25425 1.3 1 24412 1013 102 23972 1.3 1 22965 1007 103 23176 1.3 1 22213 963 104 22385 1.3 1 21444 941 105 22560 1.3 1 21670 890 106 22028 1.3 1 21126 902 107 21498 1.3 1 20599 899 108 21073 1.3 1 20198 875 109 19926 1.3 1 19084 842 110 19639 1.3 1 18821 818 111 19541 1.3 1 18740 801 112 19612 1.3 1 18735 877 113 18849 1.3 1 18077 772 114 18992 1.3 1 18188 804 115 17032 1.3 1 16334 698 116 16193 1.3 1 15457 736 117 15797 1.3 1 15080 717 118 15369 1.3 1 14666 703 119 14978 1.3 1 14290 688 120 14478 1.3 1 13698 780 121 13918 1.3 1 13156 762 122 12633 1.3 1 11851 782 123 12481 1.3 1 11561 920 124 11765 1.3 1 10666 1099 125 11273 1.3 1 10040 1233 126 10725 1.3 1 9204 1521 127 10124 1.3 1 8548 1576 128 9365 1.3 1 7631 1734 129 8624 1.3 1 6923 1701 130 7768 1.3 1 6133 1635 131 7221 1.3 1 5586 1635 132 6739 1.3 1 5065 1674 133 6261 1.3 1 4484 1777 134 5515 1.3 1 3799 1716 135 4863 1.3 1 3114 1749 136 4241 1.3 1 2694 1547 137 3560 1.3 1 2484 1076 138 3335 1.3 1 2516 819 139 2949 1.3 1 2350 599 140 2981 1.3 1 2415 566 141 3416 1.3 1 2921 495 142 2734 1.3 1 2318 416 143 2507 1.3 1 2122 385 144 3809 1.3 1 3198 611 145 4764 1.3 1 3868 896 146 2308 1.3 1 1798 510 147 244 1.3 1 142 102 148 2905 1.3 1 2174 731 149 1107 1.3 1 819 288 150 22541 1.3 1 18077 4464 RUN STATISTICS FOR INPUT FILE: SRR18245603_2.fastq.gz ============================================= 86130397 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 86130397 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 111870 (0.13%)