SUMMARISING RUN PARAMETERS ========================== Input filename: DE-5_trimmed_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.9 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 2826). Second best hit was Nextera (count: 12) 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 Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: -t 12 Output file will be GZIP compressed This is cutadapt 4.9 with Python 3.12.8 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC DE-5_trimmed_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 356.187 s (4.351 µs/read; 13.79 M reads/minute). === Summary === Total reads processed: 81,854,062 Reads with adapters: 22,682,130 (27.7%) Reads written (passing filters): 81,854,062 (100.0%) Total basepairs processed: 11,588,810,446 bp Quality-trimmed: 156,554,748 bp (1.4%) Total written (filtered): 11,139,728,147 bp (96.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 22682130 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.6% C: 32.8% G: 30.3% T: 11.2% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 9155382 20463515.5 0 9155382 2 4697338 5115878.9 0 4697338 3 825915 1278969.7 0 825915 4 91821 319742.4 0 91821 5 31485 79935.6 0 31485 6 8363 19983.9 0 8363 7 5206 4996.0 0 5206 8 2837 1249.0 0 2837 9 14144 312.2 0 10058 4086 10 8627 78.1 1 4597 4030 11 13694 19.5 1 6445 7249 12 19509 4.9 1 10568 8941 13 9485 1.2 1 3617 5868 14 15333 1.2 1 6766 8567 15 22280 1.2 1 10753 11527 16 21227 1.2 1 10224 11003 17 32513 1.2 1 19540 12973 18 42430 1.2 1 23769 18661 19 165630 1.2 1 125932 39698 20 61212 1.2 1 45624 15588 21 24137 1.2 1 13887 10250 22 30148 1.2 1 16383 13765 23 53671 1.2 1 30269 23402 24 582378 1.2 1 519190 63188 25 211182 1.2 1 178726 32456 26 249513 1.2 1 218315 31198 27 1461814 1.2 1 1398848 62966 28 185466 1.2 1 165995 19471 29 593088 1.2 1 567384 25704 30 117215 1.2 1 108426 8789 31 68665 1.2 1 59970 8695 32 337956 1.2 1 319623 18333 33 151570 1.2 1 133685 17885 34 882989 1.2 1 848047 34942 35 191689 1.2 1 173865 17824 36 543076 1.2 1 517105 25971 37 64015 1.2 1 56049 7966 38 99692 1.2 1 93967 5725 39 29781 1.2 1 25454 4327 40 122794 1.2 1 111418 11376 41 260809 1.2 1 245402 15407 42 47946 1.2 1 41621 6325 43 50939 1.2 1 45358 5581 44 42994 1.2 1 35375 7619 45 137271 1.2 1 127822 9449 46 43724 1.2 1 39497 4227 47 29562 1.2 1 26175 3387 48 6494 1.2 1 5204 1290 49 27743 1.2 1 24967 2776 50 79166 1.2 1 74539 4627 51 21148 1.2 1 17994 3154 52 46489 1.2 1 43578 2911 53 39311 1.2 1 36222 3089 54 17661 1.2 1 15240 2421 55 51330 1.2 1 48651 2679 56 17623 1.2 1 15741 1882 57 21239 1.2 1 19485 1754 58 21729 1.2 1 19906 1823 59 42440 1.2 1 39540 2900 60 23378 1.2 1 21434 1944 61 17653 1.2 1 15630 2023 62 36174 1.2 1 34220 1954 63 12302 1.2 1 10805 1497 64 21500 1.2 1 20116 1384 65 12392 1.2 1 11291 1101 66 12692 1.2 1 11470 1222 67 15062 1.2 1 13881 1181 68 23358 1.2 1 22049 1309 69 18029 1.2 1 16793 1236 70 10804 1.2 1 9873 931 71 19570 1.2 1 18634 936 72 10514 1.2 1 9659 855 73 10764 1.2 1 10058 706 74 12789 1.2 1 12116 673 75 12267 1.2 1 11731 536 76 5026 1.2 1 4707 319 77 1361 1.2 1 1141 220 78 1717 1.2 1 1506 211 79 3127 1.2 1 2831 296 80 3965 1.2 1 3664 301 81 4425 1.2 1 4149 276 82 4230 1.2 1 3917 313 83 4282 1.2 1 3943 339 84 4067 1.2 1 3762 305 85 3841 1.2 1 3540 301 86 3440 1.2 1 3166 274 87 3119 1.2 1 2874 245 88 2974 1.2 1 2731 243 89 2675 1.2 1 2462 213 90 2566 1.2 1 2334 232 91 2389 1.2 1 2207 182 92 2299 1.2 1 2091 208 93 2068 1.2 1 1885 183 94 2071 1.2 1 1866 205 95 1907 1.2 1 1768 139 96 1827 1.2 1 1702 125 97 1739 1.2 1 1574 165 98 1547 1.2 1 1413 134 99 1514 1.2 1 1355 159 100 1481 1.2 1 1345 136 101 1305 1.2 1 1184 121 102 1349 1.2 1 1138 211 103 1087 1.2 1 983 104 104 1062 1.2 1 944 118 105 1074 1.2 1 941 133 106 936 1.2 1 824 112 107 1030 1.2 1 903 127 108 930 1.2 1 805 125 109 963 1.2 1 831 132 110 718 1.2 1 643 75 111 722 1.2 1 636 86 112 717 1.2 1 586 131 113 669 1.2 1 554 115 114 681 1.2 1 598 83 115 627 1.2 1 552 75 116 678 1.2 1 612 66 117 671 1.2 1 565 106 118 776 1.2 1 636 140 119 681 1.2 1 601 80 120 663 1.2 1 557 106 121 706 1.2 1 599 107 122 692 1.2 1 596 96 123 695 1.2 1 604 91 124 717 1.2 1 639 78 125 841 1.2 1 724 117 126 939 1.2 1 823 116 127 1028 1.2 1 924 104 128 1115 1.2 1 998 117 129 1327 1.2 1 1175 152 130 1429 1.2 1 1294 135 131 1523 1.2 1 1387 136 132 1706 1.2 1 1561 145 133 1936 1.2 1 1767 169 134 2394 1.2 1 2246 148 135 2529 1.2 1 2367 162 136 2550 1.2 1 2387 163 137 3192 1.2 1 2978 214 138 3385 1.2 1 3142 243 139 3147 1.2 1 2952 195 140 3924 1.2 1 3683 241 141 5785 1.2 1 5408 377 142 3018 1.2 1 2797 221 143 3389 1.2 1 3173 216 144 3889 1.2 1 3663 226 145 4517 1.2 1 4252 265 146 6947 1.2 1 6570 377 147 7928 1.2 1 7473 455 148 2209 1.2 1 2002 207 149 337 1.2 1 132 205 150 1204 1.2 1 702 502 RUN STATISTICS FOR INPUT FILE: DE-5_trimmed_2.fastq.gz ============================================= 81854062 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 81854062 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 986474 (1.21%)