SUMMARISING RUN PARAMETERS ========================== Input filename: SRR10065370_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Python version: could not detect Number of cores used for trimming: 2 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 641). 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 2 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR10065370_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1643.162 s (22.293 µs/read; 2.69 M reads/minute). === Summary === Total reads processed: 73,706,359 Reads with adapters: 36,371,564 (49.3%) Reads written (passing filters): 73,706,359 (100.0%) Total basepairs processed: 11,055,953,850 bp Quality-trimmed: 75,479,888 bp (0.7%) Total written (filtered): 10,941,265,242 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36371564 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.7% C: 16.8% G: 0.3% T: 31.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 36182939 18426589.8 0 36182939 2 38091 4606647.4 0 38091 3 32325 1151661.9 0 32325 4 13462 287915.5 0 13462 5 6248 71978.9 0 6248 6 4379 17994.7 0 4379 7 4381 4498.7 0 4381 8 3753 1124.7 0 3753 9 3569 281.2 0 3563 6 10 4134 70.3 1 3767 367 11 3510 17.6 1 3084 426 12 3675 4.4 1 3340 335 13 2939 1.1 1 2669 270 14 3899 1.1 1 3564 335 15 2211 1.1 1 2010 201 16 2625 1.1 1 2410 215 17 2980 1.1 1 2734 246 18 1735 1.1 1 1616 119 19 2767 1.1 1 2562 205 20 1919 1.1 1 1771 148 21 1795 1.1 1 1644 151 22 1948 1.1 1 1799 149 23 1907 1.1 1 1748 159 24 2812 1.1 1 2527 285 25 1453 1.1 1 1311 142 26 1467 1.1 1 1323 144 27 1426 1.1 1 1275 151 28 1868 1.1 1 1672 196 29 1205 1.1 1 1045 160 30 2056 1.1 1 1832 224 31 718 1.1 1 624 94 32 1636 1.1 1 1479 157 33 1102 1.1 1 985 117 34 956 1.1 1 823 133 35 1212 1.1 1 1102 110 36 1024 1.1 1 899 125 37 821 1.1 1 723 98 38 824 1.1 1 718 106 39 958 1.1 1 852 106 40 856 1.1 1 733 123 41 846 1.1 1 735 111 42 1015 1.1 1 858 157 43 584 1.1 1 514 70 44 867 1.1 1 760 107 45 672 1.1 1 566 106 46 609 1.1 1 530 79 47 746 1.1 1 641 105 48 599 1.1 1 480 119 49 598 1.1 1 486 112 50 566 1.1 1 458 108 51 508 1.1 1 413 95 52 448 1.1 1 380 68 53 525 1.1 1 448 77 54 656 1.1 1 549 107 55 360 1.1 1 307 53 56 426 1.1 1 347 79 57 814 1.1 1 663 151 58 340 1.1 1 273 67 59 263 1.1 1 212 51 60 416 1.1 1 342 74 61 335 1.1 1 277 58 62 320 1.1 1 259 61 63 1004 1.1 1 801 203 64 190 1.1 1 146 44 65 230 1.1 1 172 58 66 162 1.1 1 115 47 67 311 1.1 1 251 60 68 280 1.1 1 206 74 69 236 1.1 1 176 60 70 253 1.1 1 189 64 71 251 1.1 1 179 72 72 294 1.1 1 216 78 73 309 1.1 1 222 87 74 382 1.1 1 294 88 75 489 1.1 1 349 140 76 1454 1.1 1 1283 171 77 520 1.1 1 432 88 78 254 1.1 1 171 83 79 159 1.1 1 104 55 80 130 1.1 1 81 49 81 118 1.1 1 75 43 82 111 1.1 1 58 53 83 95 1.1 1 58 37 84 106 1.1 1 61 45 85 77 1.1 1 46 31 86 90 1.1 1 52 38 87 87 1.1 1 57 30 88 74 1.1 1 42 32 89 76 1.1 1 40 36 90 84 1.1 1 41 43 91 59 1.1 1 29 30 92 86 1.1 1 44 42 93 62 1.1 1 28 34 94 76 1.1 1 32 44 95 74 1.1 1 32 42 96 61 1.1 1 38 23 97 50 1.1 1 21 29 98 59 1.1 1 32 27 99 41 1.1 1 20 21 100 55 1.1 1 34 21 101 42 1.1 1 23 19 102 38 1.1 1 18 20 103 48 1.1 1 27 21 104 41 1.1 1 22 19 105 35 1.1 1 22 13 106 41 1.1 1 22 19 107 29 1.1 1 14 15 108 45 1.1 1 21 24 109 31 1.1 1 17 14 110 41 1.1 1 22 19 111 35 1.1 1 14 21 112 35 1.1 1 16 19 113 28 1.1 1 23 5 114 29 1.1 1 19 10 115 32 1.1 1 22 10 116 28 1.1 1 16 12 117 35 1.1 1 20 15 118 30 1.1 1 14 16 119 38 1.1 1 23 15 120 29 1.1 1 19 10 121 30 1.1 1 15 15 122 25 1.1 1 15 10 123 24 1.1 1 12 12 124 19 1.1 1 12 7 125 19 1.1 1 9 10 126 19 1.1 1 10 9 127 16 1.1 1 9 7 128 13 1.1 1 5 8 129 10 1.1 1 5 5 130 14 1.1 1 8 6 131 8 1.1 1 3 5 132 7 1.1 1 4 3 133 9 1.1 1 2 7 134 6 1.1 1 4 2 135 7 1.1 1 6 1 136 10 1.1 1 5 5 137 2 1.1 1 0 2 138 2 1.1 1 0 2 139 1 1.1 1 0 1 140 1 1.1 1 1 141 2 1.1 1 2 142 1 1.1 1 0 1 143 3 1.1 1 1 2 144 1 1.1 1 0 1 145 1 1.1 1 1 146 2 1.1 1 1 1 147 1 1.1 1 0 1 149 7 1.1 1 0 7 150 47 1.1 1 6 41 RUN STATISTICS FOR INPUT FILE: SRR10065370_2.fastq.gz ============================================= 73706359 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 73706359 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 32428 (0.04%)