SUMMARISING RUN PARAMETERS ========================== Input filename: SRR10065372_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: 514). 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 SRR10065372_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1468.737 s (19.608 µs/read; 3.06 M reads/minute). === Summary === Total reads processed: 74,905,667 Reads with adapters: 36,045,407 (48.1%) Reads written (passing filters): 74,905,667 (100.0%) Total basepairs processed: 11,235,850,050 bp Quality-trimmed: 139,216,732 bp (1.2%) Total written (filtered): 11,058,309,931 bp (98.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36045407 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.6% C: 16.3% G: 0.4% T: 32.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 35859121 18726416.8 0 35859121 2 49207 4681604.2 0 49207 3 44768 1170401.0 0 44768 4 15134 292600.3 0 15134 5 5973 73150.1 0 5973 6 3271 18287.5 0 3271 7 2578 4571.9 0 2578 8 2682 1143.0 0 2682 9 2737 285.7 0 2728 9 10 2513 71.4 1 2362 151 11 2715 17.9 1 2454 261 12 2414 4.5 1 2264 150 13 2344 1.1 1 2205 139 14 2305 1.1 1 2175 130 15 1777 1.1 1 1682 95 16 1968 1.1 1 1852 116 17 1634 1.1 1 1537 97 18 1454 1.1 1 1382 72 19 1571 1.1 1 1496 75 20 1494 1.1 1 1398 96 21 1492 1.1 1 1359 133 22 1406 1.1 1 1325 81 23 1252 1.1 1 1186 66 24 1226 1.1 1 1158 68 25 1170 1.1 1 1085 85 26 1124 1.1 1 1030 94 27 1090 1.1 1 968 122 28 1074 1.1 1 997 77 29 1157 1.1 1 1035 122 30 1130 1.1 1 1041 89 31 797 1.1 1 734 63 32 801 1.1 1 744 57 33 875 1.1 1 800 75 34 852 1.1 1 777 75 35 742 1.1 1 669 73 36 741 1.1 1 670 71 37 764 1.1 1 683 81 38 710 1.1 1 641 69 39 606 1.1 1 543 63 40 645 1.1 1 573 72 41 608 1.1 1 537 71 42 595 1.1 1 538 57 43 537 1.1 1 483 54 44 517 1.1 1 478 39 45 504 1.1 1 455 49 46 528 1.1 1 466 62 47 439 1.1 1 403 36 48 475 1.1 1 420 55 49 458 1.1 1 395 63 50 445 1.1 1 384 61 51 456 1.1 1 395 61 52 384 1.1 1 316 68 53 406 1.1 1 360 46 54 383 1.1 1 337 46 55 361 1.1 1 315 46 56 373 1.1 1 333 40 57 328 1.1 1 299 29 58 295 1.1 1 251 44 59 326 1.1 1 276 50 60 287 1.1 1 259 28 61 311 1.1 1 264 47 62 305 1.1 1 257 48 63 367 1.1 1 299 68 64 943 1.1 1 891 52 65 351 1.1 1 310 41 66 189 1.1 1 153 36 67 243 1.1 1 181 62 68 205 1.1 1 160 45 69 229 1.1 1 174 55 70 222 1.1 1 178 44 71 242 1.1 1 185 57 72 211 1.1 1 157 54 73 241 1.1 1 181 60 74 224 1.1 1 160 64 75 335 1.1 1 255 80 76 1206 1.1 1 1051 155 77 464 1.1 1 392 72 78 154 1.1 1 115 39 79 108 1.1 1 71 37 80 98 1.1 1 75 23 81 98 1.1 1 64 34 82 100 1.1 1 63 37 83 103 1.1 1 71 32 84 101 1.1 1 65 36 85 94 1.1 1 75 19 86 100 1.1 1 71 29 87 90 1.1 1 57 33 88 83 1.1 1 54 29 89 101 1.1 1 63 38 90 87 1.1 1 60 27 91 70 1.1 1 45 25 92 77 1.1 1 48 29 93 77 1.1 1 46 31 94 63 1.1 1 43 20 95 69 1.1 1 41 28 96 69 1.1 1 47 22 97 58 1.1 1 46 12 98 55 1.1 1 42 13 99 73 1.1 1 46 27 100 61 1.1 1 33 28 101 62 1.1 1 37 25 102 65 1.1 1 38 27 103 53 1.1 1 39 14 104 47 1.1 1 29 18 105 48 1.1 1 29 19 106 56 1.1 1 37 19 107 49 1.1 1 35 14 108 41 1.1 1 26 15 109 39 1.1 1 28 11 110 34 1.1 1 24 10 111 40 1.1 1 27 13 112 32 1.1 1 20 12 113 50 1.1 1 40 10 114 47 1.1 1 30 17 115 35 1.1 1 22 13 116 31 1.1 1 22 9 117 32 1.1 1 22 10 118 32 1.1 1 20 12 119 22 1.1 1 13 9 120 32 1.1 1 17 15 121 33 1.1 1 21 12 122 18 1.1 1 11 7 123 20 1.1 1 9 11 124 31 1.1 1 21 10 125 16 1.1 1 10 6 126 20 1.1 1 11 9 127 17 1.1 1 11 6 128 14 1.1 1 11 3 129 12 1.1 1 5 7 130 12 1.1 1 7 5 131 10 1.1 1 6 4 132 4 1.1 1 4 133 4 1.1 1 2 2 134 1 1.1 1 1 135 3 1.1 1 1 2 136 3 1.1 1 2 1 137 1 1.1 1 0 1 138 1 1.1 1 1 141 1 1.1 1 0 1 144 1 1.1 1 0 1 146 1 1.1 1 0 1 147 2 1.1 1 0 2 149 2 1.1 1 0 2 150 37 1.1 1 1 36 RUN STATISTICS FOR INPUT FILE: SRR10065372_2.fastq.gz ============================================= 74905667 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 74905667 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 83917 (0.11%)