SUMMARISING RUN PARAMETERS ========================== Input filename: SRR10065368_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: 634). 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 SRR10065368_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1243.534 s (18.848 µs/read; 3.18 M reads/minute). === Summary === Total reads processed: 65,976,313 Reads with adapters: 32,256,970 (48.9%) Reads written (passing filters): 65,976,313 (100.0%) Total basepairs processed: 9,896,446,950 bp Quality-trimmed: 67,151,738 bp (0.7%) Total written (filtered): 9,794,824,177 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 32256970 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.5% C: 16.7% G: 0.3% T: 31.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 32104033 16494078.2 0 32104033 2 29420 4123519.6 0 29420 3 24851 1030879.9 0 24851 4 10050 257720.0 0 10050 5 5298 64430.0 0 5298 6 3939 16107.5 0 3939 7 4023 4026.9 0 4023 8 3576 1006.7 0 3576 9 3170 251.7 0 3166 4 10 3806 62.9 1 3506 300 11 3064 15.7 1 2746 318 12 3230 3.9 1 2977 253 13 2712 1.0 1 2530 182 14 3381 1.0 1 3124 257 15 1957 1.0 1 1834 123 16 2260 1.0 1 2128 132 17 2632 1.0 1 2466 166 18 1615 1.0 1 1517 98 19 2208 1.0 1 2055 153 20 1938 1.0 1 1831 107 21 1502 1.0 1 1416 86 22 1716 1.0 1 1601 115 23 1667 1.0 1 1563 104 24 2491 1.0 1 2275 216 25 1243 1.0 1 1145 98 26 1264 1.0 1 1152 112 27 1192 1.0 1 1073 119 28 1527 1.0 1 1389 138 29 1032 1.0 1 936 96 30 1713 1.0 1 1566 147 31 760 1.0 1 711 49 32 1370 1.0 1 1259 111 33 877 1.0 1 773 104 34 1041 1.0 1 958 83 35 754 1.0 1 676 78 36 823 1.0 1 729 94 37 761 1.0 1 689 72 38 766 1.0 1 676 90 39 723 1.0 1 680 43 40 803 1.0 1 718 85 41 614 1.0 1 551 63 42 713 1.0 1 641 72 43 545 1.0 1 504 41 44 598 1.0 1 547 51 45 632 1.0 1 570 62 46 446 1.0 1 385 61 47 655 1.0 1 566 89 48 463 1.0 1 395 68 49 527 1.0 1 465 62 50 465 1.0 1 411 54 51 462 1.0 1 407 55 52 424 1.0 1 354 70 53 380 1.0 1 321 59 54 544 1.0 1 460 84 55 242 1.0 1 209 33 56 353 1.0 1 301 52 57 601 1.0 1 526 75 58 246 1.0 1 205 41 59 202 1.0 1 168 34 60 301 1.0 1 266 35 61 231 1.0 1 195 36 62 250 1.0 1 190 60 63 694 1.0 1 553 141 64 136 1.0 1 106 30 65 150 1.0 1 117 33 66 113 1.0 1 88 25 67 204 1.0 1 172 32 68 204 1.0 1 162 42 69 193 1.0 1 162 31 70 168 1.0 1 128 40 71 187 1.0 1 147 40 72 200 1.0 1 151 49 73 209 1.0 1 157 52 74 199 1.0 1 135 64 75 336 1.0 1 245 91 76 836 1.0 1 740 96 77 306 1.0 1 237 69 78 151 1.0 1 108 43 79 97 1.0 1 62 35 80 84 1.0 1 50 34 81 56 1.0 1 36 20 82 56 1.0 1 35 21 83 52 1.0 1 26 26 84 55 1.0 1 29 26 85 52 1.0 1 33 19 86 44 1.0 1 23 21 87 49 1.0 1 33 16 88 47 1.0 1 18 29 89 49 1.0 1 31 18 90 44 1.0 1 22 22 91 41 1.0 1 24 17 92 48 1.0 1 26 22 93 42 1.0 1 22 20 94 38 1.0 1 23 15 95 35 1.0 1 19 16 96 34 1.0 1 19 15 97 31 1.0 1 17 14 98 41 1.0 1 23 18 99 16 1.0 1 13 3 100 31 1.0 1 19 12 101 39 1.0 1 19 20 102 25 1.0 1 9 16 103 26 1.0 1 17 9 104 22 1.0 1 19 3 105 25 1.0 1 13 12 106 18 1.0 1 9 9 107 23 1.0 1 7 16 108 22 1.0 1 9 13 109 17 1.0 1 5 12 110 22 1.0 1 12 10 111 19 1.0 1 7 12 112 14 1.0 1 7 7 113 12 1.0 1 5 7 114 12 1.0 1 5 7 115 20 1.0 1 9 11 116 25 1.0 1 15 10 117 19 1.0 1 11 8 118 14 1.0 1 8 6 119 15 1.0 1 9 6 120 16 1.0 1 11 5 121 17 1.0 1 9 8 122 14 1.0 1 7 7 123 14 1.0 1 9 5 124 11 1.0 1 4 7 125 7 1.0 1 5 2 126 11 1.0 1 6 5 127 3 1.0 1 2 1 128 14 1.0 1 5 9 129 6 1.0 1 3 3 130 7 1.0 1 4 3 131 8 1.0 1 4 4 132 7 1.0 1 1 6 133 2 1.0 1 2 134 1 1.0 1 1 135 2 1.0 1 1 1 136 3 1.0 1 2 1 137 2 1.0 1 2 138 2 1.0 1 2 139 1 1.0 1 0 1 142 2 1.0 1 2 143 1 1.0 1 1 144 1 1.0 1 1 147 2 1.0 1 0 2 148 2 1.0 1 0 2 149 2 1.0 1 1 1 150 13 1.0 1 0 13 RUN STATISTICS FOR INPUT FILE: SRR10065368_2.fastq.gz ============================================= 65976313 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 65976313 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 33882 (0.05%)