SUMMARISING RUN PARAMETERS ========================== Input filename: SRR10065366_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: 465). Second best hit was Nextera (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 SRR10065366_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1726.927 s (21.192 µs/read; 2.83 M reads/minute). === Summary === Total reads processed: 81,490,382 Reads with adapters: 39,258,927 (48.2%) Reads written (passing filters): 81,490,382 (100.0%) Total basepairs processed: 12,223,557,300 bp Quality-trimmed: 97,368,418 bp (0.8%) Total written (filtered): 12,084,745,665 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 39258927 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.0% C: 16.7% G: 0.3% T: 32.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 39092345 20372595.5 0 39092345 2 40098 5093148.9 0 40098 3 31518 1273287.2 0 31518 4 12130 318321.8 0 12130 5 5336 79580.5 0 5336 6 3564 19895.1 0 3564 7 3616 4973.8 0 3616 8 3223 1243.4 0 3223 9 2849 310.9 0 2840 9 10 3455 77.7 1 3197 258 11 2696 19.4 1 2375 321 12 3070 4.9 1 2811 259 13 2371 1.2 1 2162 209 14 3159 1.2 1 2889 270 15 1807 1.2 1 1655 152 16 2040 1.2 1 1877 163 17 2485 1.2 1 2300 185 18 1436 1.2 1 1333 103 19 2164 1.2 1 2031 133 20 1565 1.2 1 1455 110 21 1256 1.2 1 1163 93 22 1626 1.2 1 1521 105 23 1480 1.2 1 1364 116 24 2192 1.2 1 2029 163 25 1172 1.2 1 1045 127 26 1222 1.2 1 1095 127 27 1068 1.2 1 934 134 28 1363 1.2 1 1217 146 29 1008 1.2 1 909 99 30 1469 1.2 1 1305 164 31 664 1.2 1 592 72 32 1087 1.2 1 970 117 33 952 1.2 1 845 107 34 940 1.2 1 851 89 35 731 1.2 1 654 77 36 870 1.2 1 787 83 37 739 1.2 1 660 79 38 861 1.2 1 747 114 39 518 1.2 1 466 52 40 651 1.2 1 572 79 41 589 1.2 1 524 65 42 788 1.2 1 695 93 43 477 1.2 1 418 59 44 659 1.2 1 577 82 45 532 1.2 1 453 79 46 439 1.2 1 377 62 47 583 1.2 1 518 65 48 433 1.2 1 357 76 49 424 1.2 1 368 56 50 438 1.2 1 380 58 51 387 1.2 1 341 46 52 361 1.2 1 296 65 53 377 1.2 1 320 57 54 568 1.2 1 457 111 55 217 1.2 1 186 31 56 375 1.2 1 302 73 57 636 1.2 1 509 127 58 243 1.2 1 196 47 59 252 1.2 1 203 49 60 292 1.2 1 253 39 61 221 1.2 1 178 43 62 245 1.2 1 186 59 63 784 1.2 1 649 135 64 154 1.2 1 120 34 65 157 1.2 1 119 38 66 101 1.2 1 74 27 67 218 1.2 1 173 45 68 205 1.2 1 160 45 69 190 1.2 1 150 40 70 204 1.2 1 162 42 71 181 1.2 1 131 50 72 172 1.2 1 128 44 73 209 1.2 1 160 49 74 276 1.2 1 201 75 75 374 1.2 1 279 95 76 984 1.2 1 868 116 77 391 1.2 1 314 77 78 161 1.2 1 119 42 79 97 1.2 1 59 38 80 87 1.2 1 50 37 81 56 1.2 1 30 26 82 80 1.2 1 46 34 83 63 1.2 1 30 33 84 58 1.2 1 32 26 85 65 1.2 1 39 26 86 59 1.2 1 32 27 87 57 1.2 1 32 25 88 63 1.2 1 30 33 89 44 1.2 1 25 19 90 50 1.2 1 26 24 91 39 1.2 1 27 12 92 42 1.2 1 27 15 93 48 1.2 1 30 18 94 40 1.2 1 17 23 95 34 1.2 1 21 13 96 32 1.2 1 19 13 97 31 1.2 1 18 13 98 29 1.2 1 18 11 99 38 1.2 1 22 16 100 30 1.2 1 15 15 101 17 1.2 1 8 9 102 28 1.2 1 19 9 103 46 1.2 1 29 17 104 24 1.2 1 13 11 105 22 1.2 1 11 11 106 22 1.2 1 15 7 107 24 1.2 1 16 8 108 26 1.2 1 9 17 109 23 1.2 1 12 11 110 18 1.2 1 9 9 111 23 1.2 1 17 6 112 28 1.2 1 17 11 113 20 1.2 1 9 11 114 25 1.2 1 12 13 115 21 1.2 1 15 6 116 21 1.2 1 15 6 117 24 1.2 1 16 8 118 21 1.2 1 11 10 119 14 1.2 1 9 5 120 19 1.2 1 7 12 121 27 1.2 1 18 9 122 16 1.2 1 8 8 123 16 1.2 1 6 10 124 14 1.2 1 10 4 125 11 1.2 1 8 3 126 18 1.2 1 10 8 127 11 1.2 1 7 4 128 18 1.2 1 12 6 129 5 1.2 1 4 1 130 12 1.2 1 8 4 131 8 1.2 1 4 4 132 7 1.2 1 3 4 133 9 1.2 1 5 4 134 4 1.2 1 3 1 135 4 1.2 1 4 136 2 1.2 1 1 1 140 2 1.2 1 2 141 1 1.2 1 1 142 1 1.2 1 1 143 2 1.2 1 1 1 145 1 1.2 1 1 148 1 1.2 1 1 149 2 1.2 1 1 1 150 34 1.2 1 6 28 RUN STATISTICS FOR INPUT FILE: SRR10065366_2.fastq.gz ============================================= 81490382 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 81490382 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 48290 (0.06%)