SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308516_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: 104216). 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 ERR12308516_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1062.218 s (16.211 µs/read; 3.70 M reads/minute). === Summary === Total reads processed: 65,523,131 Reads with adapters: 31,304,936 (47.8%) Reads written (passing filters): 65,523,131 (100.0%) Total basepairs processed: 9,893,992,781 bp Quality-trimmed: 36,419,222 bp (0.4%) Total written (filtered): 9,557,310,604 bp (96.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 31304936 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.3% C: 1.0% G: 16.1% T: 45.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17632586 16380782.8 0 17632586 2 2972651 4095195.7 0 2972651 3 1341426 1023798.9 0 1341426 4 623838 255949.7 0 623838 5 231124 63987.4 0 231124 6 202791 15996.9 0 202791 7 195435 3999.2 0 195435 8 218368 999.8 0 218368 9 190991 250.0 0 189968 1023 10 201514 62.5 1 186764 14750 11 215626 15.6 1 193564 22062 12 219115 3.9 1 200223 18892 13 188605 1.0 1 174620 13985 14 198099 1.0 1 177992 20107 15 201272 1.0 1 185882 15390 16 191102 1.0 1 171171 19931 17 214498 1.0 1 191398 23100 18 241525 1.0 1 225707 15818 19 113388 1.0 1 105593 7795 20 178315 1.0 1 165409 12906 21 189348 1.0 1 175485 13863 22 155982 1.0 1 145603 10379 23 186066 1.0 1 171966 14100 24 170400 1.0 1 152383 18017 25 170789 1.0 1 159568 11221 26 143715 1.0 1 135299 8416 27 170005 1.0 1 158091 11914 28 157870 1.0 1 148420 9450 29 156510 1.0 1 143267 13243 30 191814 1.0 1 181183 10631 31 90618 1.0 1 85408 5210 32 145971 1.0 1 137586 8385 33 136482 1.0 1 126010 10472 34 156155 1.0 1 145023 11132 35 110760 1.0 1 104742 6018 36 137968 1.0 1 129765 8203 37 122814 1.0 1 117280 5534 38 118330 1.0 1 108629 9701 39 128547 1.0 1 120753 7794 40 105453 1.0 1 100925 4528 41 124292 1.0 1 116855 7437 42 150922 1.0 1 141968 8954 43 107578 1.0 1 95461 12117 44 75661 1.0 1 69993 5668 45 175021 1.0 1 166486 8535 46 32072 1.0 1 28869 3203 47 109971 1.0 1 101031 8940 48 526193 1.0 1 507660 18533 49 90460 1.0 1 85803 4657 50 87323 1.0 1 83453 3870 51 98565 1.0 1 95034 3531 52 54789 1.0 1 52694 2095 53 30343 1.0 1 28528 1815 54 144391 1.0 1 140987 3404 55 23900 1.0 1 22840 1060 56 10611 1.0 1 9803 808 57 39551 1.0 1 38553 998 58 5654 1.0 1 5194 460 59 11616 1.0 1 11064 552 60 10272 1.0 1 9783 489 61 5565 1.0 1 4956 609 62 47423 1.0 1 46068 1355 63 31226 1.0 1 30563 663 64 6318 1.0 1 5931 387 65 9152 1.0 1 8447 705 66 39775 1.0 1 38712 1063 67 14921 1.0 1 14193 728 68 32473 1.0 1 31213 1260 69 35546 1.0 1 33891 1655 70 63014 1.0 1 60881 2133 71 17384 1.0 1 16499 885 72 3326 1.0 1 3012 314 73 7376 1.0 1 7022 354 74 16126 1.0 1 15473 653 75 21218 1.0 1 20382 836 76 22654 1.0 1 21773 881 77 22040 1.0 1 21099 941 78 20968 1.0 1 20169 799 79 19965 1.0 1 19170 795 80 18838 1.0 1 18020 818 81 17608 1.0 1 16944 664 82 16169 1.0 1 15547 622 83 15344 1.0 1 14695 649 84 14335 1.0 1 13689 646 85 13140 1.0 1 12652 488 86 12107 1.0 1 11639 468 87 11148 1.0 1 10710 438 88 10148 1.0 1 9729 419 89 9639 1.0 1 9237 402 90 8949 1.0 1 8601 348 91 8454 1.0 1 8127 327 92 7496 1.0 1 7221 275 93 6886 1.0 1 6620 266 94 6481 1.0 1 6251 230 95 5982 1.0 1 5732 250 96 5346 1.0 1 5151 195 97 5077 1.0 1 4860 217 98 4486 1.0 1 4300 186 99 4252 1.0 1 4074 178 100 3810 1.0 1 3662 148 101 3407 1.0 1 3253 154 102 3211 1.0 1 3086 125 103 2820 1.0 1 2694 126 104 2584 1.0 1 2484 100 105 2353 1.0 1 2237 116 106 2006 1.0 1 1924 82 107 1837 1.0 1 1774 63 108 1623 1.0 1 1536 87 109 1491 1.0 1 1425 66 110 1226 1.0 1 1144 82 111 1133 1.0 1 1075 58 112 964 1.0 1 902 62 113 832 1.0 1 792 40 114 699 1.0 1 665 34 115 611 1.0 1 570 41 116 476 1.0 1 444 32 117 403 1.0 1 373 30 118 371 1.0 1 350 21 119 324 1.0 1 303 21 120 346 1.0 1 314 32 121 275 1.0 1 250 25 122 188 1.0 1 158 30 123 172 1.0 1 147 25 124 135 1.0 1 112 23 125 140 1.0 1 117 23 126 110 1.0 1 92 18 127 120 1.0 1 92 28 128 77 1.0 1 61 16 129 66 1.0 1 56 10 130 67 1.0 1 59 8 131 90 1.0 1 78 12 132 45 1.0 1 36 9 133 71 1.0 1 57 14 134 50 1.0 1 38 12 135 47 1.0 1 44 3 136 43 1.0 1 38 5 137 61 1.0 1 53 8 138 45 1.0 1 28 17 139 50 1.0 1 41 9 140 49 1.0 1 28 21 141 32 1.0 1 25 7 142 28 1.0 1 17 11 143 46 1.0 1 30 16 144 27 1.0 1 17 10 145 36 1.0 1 14 22 146 28 1.0 1 16 12 147 41 1.0 1 25 16 148 36 1.0 1 20 16 149 50 1.0 1 33 17 150 35 1.0 1 12 23 151 4743 1.0 1 21 4722 RUN STATISTICS FOR INPUT FILE: ERR12308516_1.fastq.gz ============================================= 65523131 sequences processed in total