SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308506_1.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: 118336). 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 ERR12308506_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1748.857 s (19.146 µs/read; 3.13 M reads/minute). === Summary === Total reads processed: 91,343,928 Reads with adapters: 51,324,287 (56.2%) Reads written (passing filters): 91,343,928 (100.0%) Total basepairs processed: 13,792,933,128 bp Quality-trimmed: 77,963,697 bp (0.6%) Total written (filtered): 13,235,723,961 bp (96.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 51324287 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.1% C: 21.0% G: 2.9% T: 27.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 34579254 22835982.0 0 34579254 2 1066065 5708995.5 0 1066065 3 647453 1427248.9 0 647453 4 464449 356812.2 0 464449 5 472310 89203.1 0 472310 6 416917 22300.8 0 416917 7 391976 5575.2 0 391976 8 474162 1393.8 0 474162 9 267349 348.4 0 266496 853 10 397824 87.1 1 355643 42181 11 357254 21.8 1 321395 35859 12 384249 5.4 1 329341 54908 13 373992 1.4 1 320490 53502 14 434713 1.4 1 367013 67700 15 298045 1.4 1 258289 39756 16 355104 1.4 1 305160 49944 17 418675 1.4 1 363294 55381 18 255381 1.4 1 220791 34590 19 366517 1.4 1 311867 54650 20 364444 1.4 1 316340 48104 21 201486 1.4 1 174549 26937 22 287722 1.4 1 247940 39782 23 283703 1.4 1 243372 40331 24 332985 1.4 1 282752 50233 25 326514 1.4 1 283356 43158 26 221555 1.4 1 190530 31025 27 236977 1.4 1 204543 32434 28 277201 1.4 1 242566 34635 29 231859 1.4 1 203362 28497 30 244242 1.4 1 211814 32428 31 221692 1.4 1 192380 29312 32 220923 1.4 1 191080 29843 33 219816 1.4 1 189775 30041 34 201574 1.4 1 177478 24096 35 203182 1.4 1 178963 24219 36 216366 1.4 1 189357 27009 37 215785 1.4 1 191141 24644 38 187284 1.4 1 166686 20598 39 151454 1.4 1 133132 18322 40 182197 1.4 1 161329 20868 41 154506 1.4 1 137108 17398 42 167938 1.4 1 148421 19517 43 146294 1.4 1 129311 16983 44 151242 1.4 1 132762 18480 45 157402 1.4 1 138662 18740 46 143777 1.4 1 126916 16861 47 136117 1.4 1 121295 14822 48 130403 1.4 1 115940 14463 49 132863 1.4 1 117910 14953 50 122929 1.4 1 110291 12638 51 115081 1.4 1 103069 12012 52 115263 1.4 1 102669 12594 53 108261 1.4 1 97172 11089 54 121525 1.4 1 109508 12017 55 83132 1.4 1 74902 8230 56 101717 1.4 1 90951 10766 57 129078 1.4 1 115527 13551 58 68642 1.4 1 61394 7248 59 79881 1.4 1 72591 7290 60 97209 1.4 1 87664 9545 61 86191 1.4 1 78055 8136 62 65039 1.4 1 58802 6237 63 130044 1.4 1 118585 11459 64 59116 1.4 1 53308 5808 65 46266 1.4 1 42048 4218 66 44654 1.4 1 40513 4141 67 70702 1.4 1 64938 5764 68 61567 1.4 1 56284 5283 69 51848 1.4 1 47466 4382 70 56650 1.4 1 52193 4457 71 51154 1.4 1 47130 4024 72 50050 1.4 1 45978 4072 73 62922 1.4 1 58206 4716 74 44359 1.4 1 40902 3457 75 44561 1.4 1 41398 3163 76 26537 1.4 1 24445 2092 77 24490 1.4 1 22524 1966 78 26253 1.4 1 24237 2016 79 25407 1.4 1 23489 1918 80 25228 1.4 1 23339 1889 81 24006 1.4 1 22243 1763 82 22748 1.4 1 21043 1705 83 22104 1.4 1 20485 1619 84 20826 1.4 1 19257 1569 85 20218 1.4 1 18696 1522 86 18044 1.4 1 16776 1268 87 16784 1.4 1 15614 1170 88 15333 1.4 1 14228 1105 89 15050 1.4 1 14057 993 90 13929 1.4 1 13046 883 91 12796 1.4 1 11909 887 92 12242 1.4 1 11486 756 93 11545 1.4 1 10781 764 94 10237 1.4 1 9538 699 95 9935 1.4 1 9289 646 96 9032 1.4 1 8440 592 97 8631 1.4 1 8040 591 98 8431 1.4 1 7846 585 99 7760 1.4 1 7202 558 100 7590 1.4 1 7117 473 101 6474 1.4 1 5987 487 102 5820 1.4 1 5412 408 103 5193 1.4 1 4887 306 104 4727 1.4 1 4454 273 105 4504 1.4 1 4185 319 106 4030 1.4 1 3757 273 107 3738 1.4 1 3472 266 108 3589 1.4 1 3369 220 109 3172 1.4 1 2955 217 110 2837 1.4 1 2620 217 111 2753 1.4 1 2571 182 112 2503 1.4 1 2355 148 113 2282 1.4 1 2123 159 114 1990 1.4 1 1834 156 115 1793 1.4 1 1657 136 116 1479 1.4 1 1353 126 117 1313 1.4 1 1206 107 118 1223 1.4 1 1123 100 119 1127 1.4 1 1031 96 120 2177 1.4 1 2060 117 121 1378 1.4 1 1283 95 122 752 1.4 1 668 84 123 650 1.4 1 559 91 124 509 1.4 1 448 61 125 473 1.4 1 408 65 126 355 1.4 1 303 52 127 311 1.4 1 244 67 128 296 1.4 1 243 53 129 252 1.4 1 217 35 130 186 1.4 1 163 23 131 173 1.4 1 146 27 132 150 1.4 1 129 21 133 150 1.4 1 134 16 134 115 1.4 1 94 21 135 110 1.4 1 93 17 136 88 1.4 1 72 16 137 119 1.4 1 92 27 138 66 1.4 1 51 15 139 76 1.4 1 61 15 140 68 1.4 1 49 19 141 104 1.4 1 73 31 142 49 1.4 1 36 13 143 53 1.4 1 36 17 144 62 1.4 1 36 26 145 75 1.4 1 60 15 146 65 1.4 1 43 22 147 58 1.4 1 46 12 148 64 1.4 1 40 24 149 79 1.4 1 53 26 150 62 1.4 1 29 33 151 426 1.4 1 95 331 RUN STATISTICS FOR INPUT FILE: ERR12308506_1.fastq.gz ============================================= 91343928 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 91343928 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 82662 (0.09%)