SUMMARISING RUN PARAMETERS ========================== Input filename: SRR10065374_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: 665). Second best hit was smallRNA (count: 1) 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 SRR10065374_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1464.312 s (19.133 µs/read; 3.14 M reads/minute). === Summary === Total reads processed: 76,534,362 Reads with adapters: 36,181,070 (47.3%) Reads written (passing filters): 76,534,362 (100.0%) Total basepairs processed: 11,480,154,300 bp Quality-trimmed: 95,728,069 bp (0.8%) Total written (filtered): 11,345,550,108 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36181070 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.4% C: 16.5% G: 0.3% T: 32.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 35985965 19133590.5 0 35985965 2 40549 4783397.6 0 40549 3 32762 1195849.4 0 32762 4 14744 298962.4 0 14744 5 6914 74740.6 0 6914 6 5076 18685.1 0 5076 7 5196 4671.3 0 5196 8 4250 1167.8 0 4250 9 3729 292.0 0 3720 9 10 4587 73.0 1 4232 355 11 3455 18.2 1 3110 345 12 4162 4.6 1 3800 362 13 3197 1.1 1 2931 266 14 4191 1.1 1 3831 360 15 2384 1.1 1 2194 190 16 2762 1.1 1 2570 192 17 3232 1.1 1 2966 266 18 1829 1.1 1 1709 120 19 2837 1.1 1 2628 209 20 1892 1.1 1 1741 151 21 1701 1.1 1 1585 116 22 2034 1.1 1 1859 175 23 1966 1.1 1 1815 151 24 2669 1.1 1 2397 272 25 1569 1.1 1 1427 142 26 1573 1.1 1 1444 129 27 1524 1.1 1 1380 144 28 1861 1.1 1 1662 199 29 1279 1.1 1 1131 148 30 1866 1.1 1 1681 185 31 878 1.1 1 788 90 32 1420 1.1 1 1294 126 33 1014 1.1 1 918 96 34 1269 1.1 1 1145 124 35 1133 1.1 1 1013 120 36 1025 1.1 1 904 121 37 876 1.1 1 768 108 38 970 1.1 1 819 151 39 980 1.1 1 840 140 40 773 1.1 1 668 105 41 783 1.1 1 690 93 42 878 1.1 1 769 109 43 547 1.1 1 486 61 44 734 1.1 1 646 88 45 679 1.1 1 578 101 46 584 1.1 1 505 79 47 696 1.1 1 601 95 48 539 1.1 1 437 102 49 542 1.1 1 465 77 50 502 1.1 1 419 83 51 451 1.1 1 387 64 52 476 1.1 1 394 82 53 477 1.1 1 400 77 54 609 1.1 1 480 129 55 284 1.1 1 238 46 56 381 1.1 1 321 60 57 719 1.1 1 599 120 58 263 1.1 1 206 57 59 256 1.1 1 215 41 60 322 1.1 1 262 60 61 296 1.1 1 237 59 62 269 1.1 1 213 56 63 850 1.1 1 682 168 64 153 1.1 1 103 50 65 156 1.1 1 119 37 66 134 1.1 1 101 33 67 258 1.1 1 214 44 68 204 1.1 1 137 67 69 199 1.1 1 151 48 70 198 1.1 1 160 38 71 239 1.1 1 184 55 72 214 1.1 1 167 47 73 289 1.1 1 230 59 74 337 1.1 1 251 86 75 445 1.1 1 329 116 76 1163 1.1 1 1034 129 77 390 1.1 1 316 74 78 171 1.1 1 124 47 79 131 1.1 1 87 44 80 107 1.1 1 67 40 81 88 1.1 1 50 38 82 85 1.1 1 43 42 83 86 1.1 1 42 44 84 91 1.1 1 51 40 85 77 1.1 1 44 33 86 75 1.1 1 38 37 87 61 1.1 1 32 29 88 65 1.1 1 33 32 89 59 1.1 1 35 24 90 61 1.1 1 34 27 91 59 1.1 1 25 34 92 64 1.1 1 28 36 93 60 1.1 1 35 25 94 55 1.1 1 27 28 95 43 1.1 1 26 17 96 53 1.1 1 30 23 97 44 1.1 1 28 16 98 42 1.1 1 25 17 99 42 1.1 1 23 19 100 32 1.1 1 20 12 101 27 1.1 1 15 12 102 38 1.1 1 24 14 103 31 1.1 1 16 15 104 44 1.1 1 25 19 105 36 1.1 1 22 14 106 29 1.1 1 19 10 107 30 1.1 1 17 13 108 28 1.1 1 16 12 109 26 1.1 1 15 11 110 27 1.1 1 16 11 111 29 1.1 1 13 16 112 22 1.1 1 18 4 113 31 1.1 1 20 11 114 29 1.1 1 12 17 115 29 1.1 1 21 8 116 31 1.1 1 18 13 117 18 1.1 1 11 7 118 24 1.1 1 15 9 119 24 1.1 1 15 9 120 23 1.1 1 9 14 121 16 1.1 1 6 10 122 23 1.1 1 12 11 123 15 1.1 1 7 8 124 12 1.1 1 8 4 125 17 1.1 1 10 7 126 16 1.1 1 8 8 127 10 1.1 1 5 5 128 15 1.1 1 4 11 129 14 1.1 1 10 4 130 7 1.1 1 5 2 131 7 1.1 1 5 2 132 7 1.1 1 2 5 133 9 1.1 1 5 4 134 5 1.1 1 3 2 135 4 1.1 1 1 3 136 6 1.1 1 4 2 137 3 1.1 1 3 139 2 1.1 1 1 1 142 1 1.1 1 0 1 143 2 1.1 1 0 2 146 1 1.1 1 0 1 148 3 1.1 1 0 3 149 6 1.1 1 1 5 150 33 1.1 1 3 30 RUN STATISTICS FOR INPUT FILE: SRR10065374_2.fastq.gz ============================================= 76534362 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 76534362 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 43582 (0.06%)