SUMMARISING RUN PARAMETERS ========================== Input filename: ERR13913470_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: 18467). 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 ERR13913470_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1805.599 s (20.393 µs/read; 2.94 M reads/minute). === Summary === Total reads processed: 88,538,712 Reads with adapters: 45,426,154 (51.3%) Reads written (passing filters): 88,538,712 (100.0%) Total basepairs processed: 13,280,806,800 bp Quality-trimmed: 51,762,828 bp (0.4%) Total written (filtered): 13,128,750,998 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 45426154 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.6% C: 17.2% G: 0.3% T: 29.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 43186283 22134678.0 0 43186283 2 98937 5533669.5 0 98937 3 94578 1383417.4 0 94578 4 69772 345854.3 0 69772 5 62856 86463.6 0 62856 6 55011 21615.9 0 55011 7 57068 5404.0 0 57068 8 60698 1351.0 0 60698 9 46719 337.7 0 46702 17 10 55794 84.4 1 52404 3390 11 53117 21.1 1 49259 3858 12 53250 5.3 1 40467 12783 13 50073 1.3 1 37775 12298 14 54583 1.3 1 40936 13647 15 45436 1.3 1 34187 11249 16 47379 1.3 1 35654 11725 17 59093 1.3 1 44749 14344 18 33806 1.3 1 25584 8222 19 60078 1.3 1 46125 13953 20 39028 1.3 1 29305 9723 21 33604 1.3 1 25559 8045 22 41984 1.3 1 31870 10114 23 40742 1.3 1 31136 9606 24 55111 1.3 1 42197 12914 25 46682 1.3 1 35431 11251 26 27211 1.3 1 20841 6370 27 27689 1.3 1 21416 6273 28 38496 1.3 1 29855 8641 29 32232 1.3 1 24970 7262 30 38807 1.3 1 30370 8437 31 28424 1.3 1 22013 6411 32 36762 1.3 1 28914 7848 33 31227 1.3 1 24246 6981 34 26911 1.3 1 21046 5865 35 29412 1.3 1 23271 6141 36 27488 1.3 1 21559 5929 37 28703 1.3 1 22766 5937 38 25304 1.3 1 20006 5298 39 29229 1.3 1 23378 5851 40 28266 1.3 1 22105 6161 41 19063 1.3 1 15334 3729 42 21098 1.3 1 16719 4379 43 21968 1.3 1 17539 4429 44 21965 1.3 1 17647 4318 45 19550 1.3 1 15562 3988 46 19729 1.3 1 15923 3806 47 19566 1.3 1 15632 3934 48 18808 1.3 1 15027 3781 49 17221 1.3 1 13976 3245 50 16143 1.3 1 12961 3182 51 16815 1.3 1 13470 3345 52 15042 1.3 1 12151 2891 53 14597 1.3 1 11686 2911 54 14149 1.3 1 11453 2696 55 12838 1.3 1 10510 2328 56 13784 1.3 1 11258 2526 57 11059 1.3 1 9048 2011 58 11571 1.3 1 9470 2101 59 14048 1.3 1 11596 2452 60 8292 1.3 1 6738 1554 61 9516 1.3 1 7801 1715 62 10292 1.3 1 8558 1734 63 8769 1.3 1 7180 1589 64 7940 1.3 1 6584 1356 65 14013 1.3 1 11667 2346 66 5894 1.3 1 4822 1072 67 5053 1.3 1 4121 932 68 5337 1.3 1 4435 902 69 7117 1.3 1 5962 1155 70 6709 1.3 1 5612 1097 71 5287 1.3 1 4423 864 72 5422 1.3 1 4503 919 73 5047 1.3 1 4170 877 74 4601 1.3 1 3845 756 75 5807 1.3 1 4792 1015 76 4099 1.3 1 3399 700 77 3198 1.3 1 2627 571 78 964 1.3 1 776 188 79 1961 1.3 1 1658 303 80 2250 1.3 1 1907 343 81 2199 1.3 1 1869 330 82 1957 1.3 1 1628 329 83 1817 1.3 1 1497 320 84 1621 1.3 1 1359 262 85 1465 1.3 1 1196 269 86 1306 1.3 1 1054 252 87 1121 1.3 1 938 183 88 1028 1.3 1 835 193 89 879 1.3 1 709 170 90 828 1.3 1 676 152 91 687 1.3 1 556 131 92 640 1.3 1 506 134 93 538 1.3 1 410 128 94 424 1.3 1 317 107 95 433 1.3 1 321 112 96 319 1.3 1 227 92 97 348 1.3 1 246 102 98 271 1.3 1 194 77 99 244 1.3 1 154 90 100 235 1.3 1 159 76 101 232 1.3 1 146 86 102 197 1.3 1 120 77 103 170 1.3 1 105 65 104 138 1.3 1 92 46 105 148 1.3 1 91 57 106 150 1.3 1 90 60 107 128 1.3 1 76 52 108 149 1.3 1 87 62 109 115 1.3 1 69 46 110 107 1.3 1 64 43 111 98 1.3 1 55 43 112 115 1.3 1 62 53 113 102 1.3 1 57 45 114 92 1.3 1 64 28 115 86 1.3 1 45 41 116 95 1.3 1 59 36 117 94 1.3 1 65 29 118 86 1.3 1 55 31 119 78 1.3 1 38 40 120 81 1.3 1 48 33 121 71 1.3 1 43 28 122 82 1.3 1 50 32 123 80 1.3 1 46 34 124 68 1.3 1 39 29 125 53 1.3 1 38 15 126 62 1.3 1 42 20 127 55 1.3 1 25 30 128 51 1.3 1 34 17 129 49 1.3 1 28 21 130 49 1.3 1 36 13 131 36 1.3 1 22 14 132 27 1.3 1 19 8 133 37 1.3 1 25 12 134 23 1.3 1 19 4 135 15 1.3 1 11 4 136 27 1.3 1 21 6 137 11 1.3 1 7 4 138 18 1.3 1 14 4 139 12 1.3 1 7 5 140 17 1.3 1 8 9 141 7 1.3 1 4 3 142 3 1.3 1 1 2 143 4 1.3 1 2 2 144 7 1.3 1 3 4 145 8 1.3 1 4 4 146 4 1.3 1 3 1 147 11 1.3 1 6 5 148 6 1.3 1 4 2 149 7 1.3 1 4 3 150 8 1.3 1 2 6 RUN STATISTICS FOR INPUT FILE: ERR13913470_2.fastq.gz ============================================= 88538712 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 88538712 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 16915 (0.02%)