SUMMARISING RUN PARAMETERS ========================== Input filename: DE-1_trimmed_1.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: 2209). Second best hit was smallRNA (count: 26) 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-1_trimmed_1.fastq.gz Processing single-end reads on 8 cores ... Finished in 387.953 s (4.310 µs/read; 13.92 M reads/minute). === Summary === Total reads processed: 90,005,528 Reads with adapters: 17,742,138 (19.7%) Reads written (passing filters): 90,005,528 (100.0%) Total basepairs processed: 12,270,812,127 bp Quality-trimmed: 81,820,996 bp (0.7%) Total written (filtered): 12,005,562,212 bp (97.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 17742138 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.5% C: 33.9% G: 17.9% T: 12.3% none/other: 5.4% Overview of removed sequences length count expect max.err error counts 1 10321087 22501382.0 0 10321087 2 5094168 5625345.5 0 5094168 3 739609 1406336.4 0 739609 4 105282 351584.1 0 105282 5 43251 87896.0 0 43251 6 6636 21974.0 0 6636 7 2948 5493.5 0 2948 8 304 1373.4 0 304 9 5328 343.3 0 2361 2967 10 1360 85.8 1 356 1004 11 5146 21.5 1 449 4697 12 6705 5.4 1 226 6479 13 1709 1.3 1 585 1124 14 10258 1.3 1 432 9826 15 3262 1.3 1 648 2614 16 8324 1.3 1 1125 7199 17 9100 1.3 1 1372 7728 18 6725 1.3 1 1353 5372 19 8992 1.3 1 2065 6927 20 8507 1.3 1 2073 6434 21 12725 1.3 1 3784 8941 22 8291 1.3 1 2526 5765 23 5608 1.3 1 1792 3816 24 8898 1.3 1 3314 5584 25 7701 1.3 1 2887 4814 26 9848 1.3 1 4138 5710 27 23010 1.3 1 9993 13017 28 8680 1.3 1 2507 6173 29 8621 1.3 1 3490 5131 30 7088 1.3 1 3642 3446 31 15485 1.3 1 8470 7015 32 6199 1.3 1 2255 3944 33 19922 1.3 1 10597 9325 34 4348 1.3 1 1285 3063 35 12193 1.3 1 6220 5973 36 14078 1.3 1 7650 6428 37 5678 1.3 1 2071 3607 38 11719 1.3 1 5864 5855 39 8526 1.3 1 4134 4392 40 9783 1.3 1 4969 4814 41 15569 1.3 1 8069 7500 42 4335 1.3 1 1697 2638 43 13183 1.3 1 6667 6516 44 4640 1.3 1 2376 2264 45 8778 1.3 1 4769 4009 46 8040 1.3 1 4229 3811 47 7521 1.3 1 4134 3387 48 8535 1.3 1 4477 4058 49 8325 1.3 1 4341 3984 50 8162 1.3 1 4218 3944 51 8013 1.3 1 4129 3884 52 7870 1.3 1 4085 3785 53 7647 1.3 1 3861 3786 54 7139 1.3 1 3621 3518 55 7122 1.3 1 3598 3524 56 6763 1.3 1 3288 3475 57 6897 1.3 1 3316 3581 58 6531 1.3 1 3308 3223 59 5767 1.3 1 2825 2942 60 4654 1.3 1 2366 2288 61 3899 1.3 1 2047 1852 62 3251 1.3 1 1662 1589 63 2621 1.3 1 1342 1279 64 2189 1.3 1 1132 1057 65 1835 1.3 1 988 847 66 1630 1.3 1 835 795 67 1663 1.3 1 876 787 68 1677 1.3 1 883 794 69 1739 1.3 1 898 841 70 1799 1.3 1 917 882 71 1743 1.3 1 879 864 72 1658 1.3 1 851 807 73 1494 1.3 1 760 734 74 1473 1.3 1 730 743 75 1328 1.3 1 675 653 76 1234 1.3 1 592 642 77 1153 1.3 1 545 608 78 1010 1.3 1 491 519 79 970 1.3 1 456 514 80 992 1.3 1 410 582 81 967 1.3 1 367 600 82 951 1.3 1 374 577 83 832 1.3 1 299 533 84 750 1.3 1 307 443 85 644 1.3 1 251 393 86 591 1.3 1 211 380 87 556 1.3 1 206 350 88 546 1.3 1 160 386 89 603 1.3 1 251 352 90 513 1.3 1 327 186 91 516 1.3 1 310 206 92 406 1.3 1 269 137 93 383 1.3 1 244 139 94 348 1.3 1 216 132 95 330 1.3 1 203 127 96 311 1.3 1 178 133 97 293 1.3 1 161 132 98 259 1.3 1 163 96 99 228 1.3 1 132 96 100 255 1.3 1 153 102 101 191 1.3 1 115 76 102 208 1.3 1 105 103 103 157 1.3 1 86 71 104 152 1.3 1 70 82 105 145 1.3 1 59 86 106 101 1.3 1 32 69 107 85 1.3 1 25 60 108 111 1.3 1 24 87 109 95 1.3 1 16 79 110 83 1.3 1 17 66 111 72 1.3 1 20 52 112 63 1.3 1 19 44 113 77 1.3 1 12 65 114 78 1.3 1 25 53 115 62 1.3 1 6 56 116 79 1.3 1 15 64 117 87 1.3 1 22 65 118 93 1.3 1 12 81 119 62 1.3 1 8 54 120 82 1.3 1 10 72 121 75 1.3 1 8 67 122 74 1.3 1 5 69 123 75 1.3 1 10 65 124 55 1.3 1 13 42 125 61 1.3 1 9 52 126 52 1.3 1 17 35 127 69 1.3 1 12 57 128 94 1.3 1 8 86 129 91 1.3 1 28 63 130 84 1.3 1 18 66 131 92 1.3 1 17 75 132 89 1.3 1 37 52 133 121 1.3 1 24 97 134 128 1.3 1 36 92 135 130 1.3 1 37 93 136 124 1.3 1 32 92 137 123 1.3 1 34 89 138 125 1.3 1 45 80 139 165 1.3 1 46 119 140 213 1.3 1 83 130 141 290 1.3 1 115 175 142 179 1.3 1 55 124 143 199 1.3 1 62 137 144 287 1.3 1 85 202 145 292 1.3 1 76 216 146 389 1.3 1 117 272 147 734 1.3 1 186 548 148 604 1.3 1 58 546 149 10077 1.3 1 5 10072 150 926731 1.3 1 24 926707 RUN STATISTICS FOR INPUT FILE: DE-1_trimmed_1.fastq.gz ============================================= 90005528 sequences processed in total