SUMMARISING RUN PARAMETERS ========================== Input filename: SRR10065369_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: 589). 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 SRR10065369_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1421.751 s (20.257 µs/read; 2.96 M reads/minute). === Summary === Total reads processed: 70,186,712 Reads with adapters: 34,346,354 (48.9%) Reads written (passing filters): 70,186,712 (100.0%) Total basepairs processed: 10,528,006,800 bp Quality-trimmed: 76,044,626 bp (0.7%) Total written (filtered): 10,415,207,532 bp (98.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 34346354 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.3% C: 16.7% G: 0.3% T: 31.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 34176838 17546678.0 0 34176838 2 34507 4386669.5 0 34507 3 29609 1096667.4 0 29609 4 12598 274166.8 0 12598 5 5780 68541.7 0 5780 6 4041 17135.4 0 4041 7 4148 4283.9 0 4148 8 3488 1071.0 0 3488 9 3216 267.7 0 3211 5 10 3718 66.9 1 3401 317 11 3157 16.7 1 2785 372 12 3409 4.2 1 3127 282 13 2736 1.0 1 2520 216 14 3407 1.0 1 3114 293 15 2022 1.0 1 1883 139 16 2343 1.0 1 2135 208 17 2787 1.0 1 2608 179 18 1542 1.0 1 1434 108 19 2391 1.0 1 2235 156 20 1731 1.0 1 1610 121 21 1594 1.0 1 1468 126 22 1726 1.0 1 1615 111 23 1683 1.0 1 1562 121 24 2580 1.0 1 2364 216 25 1413 1.0 1 1287 126 26 1225 1.0 1 1099 126 27 1160 1.0 1 1036 124 28 1538 1.0 1 1388 150 29 1095 1.0 1 961 134 30 1637 1.0 1 1508 129 31 795 1.0 1 711 84 32 1313 1.0 1 1184 129 33 999 1.0 1 909 90 34 1062 1.0 1 952 110 35 987 1.0 1 843 144 36 873 1.0 1 785 88 37 855 1.0 1 739 116 38 910 1.0 1 823 87 39 815 1.0 1 708 107 40 827 1.0 1 705 122 41 755 1.0 1 675 80 42 1085 1.0 1 963 122 43 408 1.0 1 371 37 44 793 1.0 1 720 73 45 558 1.0 1 478 80 46 482 1.0 1 406 76 47 687 1.0 1 606 81 48 533 1.0 1 453 80 49 471 1.0 1 409 62 50 496 1.0 1 429 67 51 411 1.0 1 334 77 52 423 1.0 1 355 68 53 411 1.0 1 351 60 54 595 1.0 1 505 90 55 273 1.0 1 224 49 56 367 1.0 1 307 60 57 678 1.0 1 568 110 58 274 1.0 1 224 50 59 255 1.0 1 215 40 60 354 1.0 1 292 62 61 279 1.0 1 231 48 62 247 1.0 1 206 41 63 828 1.0 1 679 149 64 164 1.0 1 120 44 65 142 1.0 1 102 40 66 119 1.0 1 84 35 67 231 1.0 1 179 52 68 224 1.0 1 164 60 69 227 1.0 1 175 52 70 202 1.0 1 156 46 71 224 1.0 1 174 50 72 203 1.0 1 148 55 73 206 1.0 1 151 55 74 281 1.0 1 215 66 75 404 1.0 1 280 124 76 951 1.0 1 821 130 77 345 1.0 1 264 81 78 188 1.0 1 122 66 79 131 1.0 1 83 48 80 99 1.0 1 56 43 81 76 1.0 1 45 31 82 86 1.0 1 47 39 83 68 1.0 1 39 29 84 74 1.0 1 41 33 85 58 1.0 1 35 23 86 73 1.0 1 38 35 87 57 1.0 1 31 26 88 68 1.0 1 36 32 89 53 1.0 1 28 25 90 59 1.0 1 29 30 91 45 1.0 1 17 28 92 59 1.0 1 33 26 93 51 1.0 1 23 28 94 43 1.0 1 25 18 95 41 1.0 1 19 22 96 44 1.0 1 16 28 97 44 1.0 1 22 22 98 41 1.0 1 21 20 99 36 1.0 1 16 20 100 38 1.0 1 16 22 101 34 1.0 1 17 17 102 37 1.0 1 19 18 103 28 1.0 1 18 10 104 34 1.0 1 20 14 105 20 1.0 1 9 11 106 25 1.0 1 15 10 107 30 1.0 1 16 14 108 29 1.0 1 14 15 109 27 1.0 1 12 15 110 21 1.0 1 13 8 111 12 1.0 1 6 6 112 18 1.0 1 8 10 113 22 1.0 1 11 11 114 24 1.0 1 12 12 115 26 1.0 1 14 12 116 19 1.0 1 10 9 117 14 1.0 1 7 7 118 18 1.0 1 15 3 119 19 1.0 1 18 1 120 20 1.0 1 12 8 121 17 1.0 1 9 8 122 16 1.0 1 9 7 123 16 1.0 1 6 10 124 11 1.0 1 8 3 125 13 1.0 1 4 9 126 19 1.0 1 9 10 127 9 1.0 1 3 6 128 14 1.0 1 6 8 129 12 1.0 1 4 8 130 11 1.0 1 7 4 131 11 1.0 1 6 5 132 9 1.0 1 3 6 133 5 1.0 1 5 134 7 1.0 1 5 2 135 1 1.0 1 1 136 5 1.0 1 3 2 137 4 1.0 1 2 2 138 2 1.0 1 1 1 141 1 1.0 1 1 143 1 1.0 1 0 1 145 1 1.0 1 0 1 148 2 1.0 1 1 1 149 2 1.0 1 0 2 150 15 1.0 1 1 14 RUN STATISTICS FOR INPUT FILE: SRR10065369_2.fastq.gz ============================================= 70186712 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 70186712 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 35364 (0.05%)