SUMMARISING RUN PARAMETERS ========================== Input filename: DE-7_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: 2268). Second best hit was smallRNA (count: 23) 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-7_trimmed_2.fastq.gz Processing single-end reads on 8 cores ... Finished in 306.302 s (4.361 µs/read; 13.76 M reads/minute). === Summary === Total reads processed: 70,236,818 Reads with adapters: 19,157,508 (27.3%) Reads written (passing filters): 70,236,818 (100.0%) Total basepairs processed: 9,951,871,780 bp Quality-trimmed: 130,291,579 bp (1.3%) Total written (filtered): 9,574,901,144 bp (96.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 19157508 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 25.2% C: 33.4% G: 30.3% T: 11.0% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 7652651 17559204.5 0 7652651 2 4076650 4389801.1 0 4076650 3 690211 1097450.3 0 690211 4 77709 274362.6 0 77709 5 27104 68590.6 0 27104 6 7407 17147.7 0 7407 7 4784 4286.9 0 4784 8 2378 1071.7 0 2378 9 11835 267.9 0 8237 3598 10 7276 67.0 1 3837 3439 11 11618 16.7 1 5585 6033 12 16839 4.2 1 9122 7717 13 7660 1.0 1 2954 4706 14 13080 1.0 1 5743 7337 15 18707 1.0 1 8963 9744 16 17313 1.0 1 8303 9010 17 27302 1.0 1 16393 10909 18 35474 1.0 1 19678 15796 19 138616 1.0 1 105308 33308 20 51548 1.0 1 38462 13086 21 20168 1.0 1 11399 8769 22 25293 1.0 1 13549 11744 23 45197 1.0 1 25502 19695 24 506523 1.0 1 451668 54855 25 185296 1.0 1 156810 28486 26 213003 1.0 1 186372 26631 27 1240485 1.0 1 1186617 53868 28 154906 1.0 1 138412 16494 29 480126 1.0 1 459204 20922 30 99223 1.0 1 91708 7515 31 58521 1.0 1 51041 7480 32 286598 1.0 1 270648 15950 33 124790 1.0 1 109419 15371 34 738387 1.0 1 709037 29350 35 164543 1.0 1 149407 15136 36 446762 1.0 1 425157 21605 37 53803 1.0 1 47197 6606 38 79904 1.0 1 75006 4898 39 25330 1.0 1 21733 3597 40 99366 1.0 1 90021 9345 41 212722 1.0 1 200005 12717 42 37771 1.0 1 32747 5024 43 42023 1.0 1 37302 4721 44 35658 1.0 1 29173 6485 45 114586 1.0 1 106526 8060 46 34757 1.0 1 31184 3573 47 25687 1.0 1 22696 2991 48 5500 1.0 1 4450 1050 49 22584 1.0 1 20225 2359 50 65818 1.0 1 62005 3813 51 18120 1.0 1 15280 2840 52 38340 1.0 1 35840 2500 53 32274 1.0 1 29770 2504 54 15221 1.0 1 13168 2053 55 44517 1.0 1 42219 2298 56 15193 1.0 1 13567 1626 57 18234 1.0 1 16605 1629 58 18679 1.0 1 17024 1655 59 39103 1.0 1 36495 2608 60 20632 1.0 1 18938 1694 61 15221 1.0 1 13442 1779 62 29361 1.0 1 27741 1620 63 9383 1.0 1 8117 1266 64 19053 1.0 1 17802 1251 65 9994 1.0 1 9021 973 66 10997 1.0 1 9983 1014 67 13218 1.0 1 12111 1107 68 20680 1.0 1 19443 1237 69 15956 1.0 1 14848 1108 70 10040 1.0 1 9145 895 71 17047 1.0 1 16209 838 72 9426 1.0 1 8656 770 73 9651 1.0 1 8994 657 74 11609 1.0 1 11042 567 75 10956 1.0 1 10487 469 76 4452 1.0 1 4159 293 77 1245 1.0 1 1055 190 78 1611 1.0 1 1410 201 79 2925 1.0 1 2673 252 80 3869 1.0 1 3608 261 81 4129 1.0 1 3860 269 82 4035 1.0 1 3719 316 83 3821 1.0 1 3508 313 84 3602 1.0 1 3326 276 85 3390 1.0 1 3124 266 86 3101 1.0 1 2876 225 87 2820 1.0 1 2622 198 88 2765 1.0 1 2554 211 89 2601 1.0 1 2400 201 90 2369 1.0 1 2145 224 91 2233 1.0 1 2055 178 92 2119 1.0 1 1933 186 93 2049 1.0 1 1875 174 94 1869 1.0 1 1706 163 95 1682 1.0 1 1567 115 96 1603 1.0 1 1488 115 97 1518 1.0 1 1395 123 98 1368 1.0 1 1267 101 99 1362 1.0 1 1237 125 100 1280 1.0 1 1174 106 101 1232 1.0 1 1119 113 102 1186 1.0 1 1019 167 103 1060 1.0 1 980 80 104 1015 1.0 1 893 122 105 922 1.0 1 826 96 106 884 1.0 1 799 85 107 865 1.0 1 780 85 108 781 1.0 1 704 77 109 815 1.0 1 710 105 110 736 1.0 1 651 85 111 630 1.0 1 567 63 112 681 1.0 1 582 99 113 593 1.0 1 526 67 114 605 1.0 1 540 65 115 581 1.0 1 510 71 116 591 1.0 1 534 57 117 604 1.0 1 537 67 118 711 1.0 1 594 117 119 612 1.0 1 516 96 120 613 1.0 1 544 69 121 680 1.0 1 595 85 122 705 1.0 1 625 80 123 714 1.0 1 612 102 124 816 1.0 1 718 98 125 893 1.0 1 808 85 126 970 1.0 1 869 101 127 1071 1.0 1 970 101 128 1182 1.0 1 1074 108 129 1457 1.0 1 1288 169 130 1529 1.0 1 1370 159 131 1679 1.0 1 1523 156 132 1889 1.0 1 1725 164 133 2075 1.0 1 1921 154 134 2520 1.0 1 2379 141 135 2691 1.0 1 2515 176 136 2755 1.0 1 2577 178 137 3233 1.0 1 3051 182 138 3291 1.0 1 3085 206 139 3006 1.0 1 2820 186 140 3423 1.0 1 3179 244 141 4712 1.0 1 4416 296 142 2313 1.0 1 2152 161 143 2463 1.0 1 2301 162 144 2865 1.0 1 2695 170 145 3230 1.0 1 3069 161 146 4407 1.0 1 4166 241 147 5071 1.0 1 4727 344 148 1172 1.0 1 1047 125 149 206 1.0 1 65 141 150 558 1.0 1 278 280 RUN STATISTICS FOR INPUT FILE: DE-7_trimmed_2.fastq.gz ============================================= 70236818 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 70236818 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 588094 (0.84%)