SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308508_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: 145236). 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 ERR12308508_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1163.795 s (19.948 µs/read; 3.01 M reads/minute). === Summary === Total reads processed: 58,342,110 Reads with adapters: 33,219,890 (56.9%) Reads written (passing filters): 58,342,110 (100.0%) Total basepairs processed: 8,809,658,610 bp Quality-trimmed: 52,758,727 bp (0.6%) Total written (filtered): 8,358,491,218 bp (94.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 33219890 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.8% C: 18.6% G: 1.9% T: 29.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 21600650 14585527.5 0 21600650 2 540132 3646381.9 0 540132 3 322797 911595.5 0 322797 4 227201 227898.9 0 227201 5 242826 56974.7 0 242826 6 216804 14243.7 0 216804 7 217766 3560.9 0 217766 8 255788 890.2 0 255788 9 137312 222.6 0 136876 436 10 229008 55.6 1 200735 28273 11 194714 13.9 1 173402 21312 12 211817 3.5 1 175257 36560 13 209928 0.9 1 172114 37814 14 243727 0.9 1 197062 46665 15 172871 0.9 1 143322 29549 16 196067 0.9 1 162479 33588 17 257742 0.9 1 215178 42564 18 130868 0.9 1 108136 22732 19 260007 0.9 1 213442 46565 20 200574 0.9 1 167380 33194 21 115019 0.9 1 96302 18717 22 187333 0.9 1 155475 31858 23 186132 0.9 1 154175 31957 24 260688 0.9 1 213734 46954 25 213872 0.9 1 179543 34329 26 130438 0.9 1 108579 21859 27 118238 0.9 1 98883 19355 28 193412 0.9 1 163287 30125 29 148096 0.9 1 125875 22221 30 172502 0.9 1 144320 28182 31 161045 0.9 1 135671 25374 32 172185 0.9 1 143866 28319 33 162436 0.9 1 136896 25540 34 164072 0.9 1 138359 25713 35 168252 0.9 1 145003 23249 36 159665 0.9 1 137136 22529 37 116893 0.9 1 100019 16874 38 151885 0.9 1 129679 22206 39 166502 0.9 1 142621 23881 40 124030 0.9 1 106824 17206 41 133479 0.9 1 114934 18545 42 151750 0.9 1 130895 20855 43 113990 0.9 1 98189 15801 44 134867 0.9 1 115228 19639 45 140227 0.9 1 120652 19575 46 118478 0.9 1 102321 16157 47 127355 0.9 1 110541 16814 48 115855 0.9 1 100634 15221 49 115388 0.9 1 100172 15216 50 113171 0.9 1 98638 14533 51 106846 0.9 1 93404 13442 52 108036 0.9 1 94447 13589 53 105316 0.9 1 92231 13085 54 126295 0.9 1 111201 15094 55 75187 0.9 1 66196 8991 56 100166 0.9 1 87624 12542 57 132252 0.9 1 116027 16225 58 68213 0.9 1 59678 8535 59 77019 0.9 1 68565 8454 60 99208 0.9 1 87771 11437 61 89036 0.9 1 79239 9797 62 66192 0.9 1 58842 7350 63 144504 0.9 1 129442 15062 64 64848 0.9 1 57344 7504 65 49267 0.9 1 43954 5313 66 48197 0.9 1 43115 5082 67 79776 0.9 1 71945 7831 68 69427 0.9 1 62501 6926 69 57971 0.9 1 52371 5600 70 64412 0.9 1 58460 5952 71 58171 0.9 1 52903 5268 72 58345 0.9 1 53018 5327 73 74499 0.9 1 68065 6434 74 52086 0.9 1 47445 4641 75 52477 0.9 1 47997 4480 76 29573 0.9 1 26876 2697 77 30301 0.9 1 27524 2777 78 32811 0.9 1 29947 2864 79 31987 0.9 1 29274 2713 80 31462 0.9 1 28781 2681 81 29875 0.9 1 27330 2545 82 28642 0.9 1 26250 2392 83 28002 0.9 1 25703 2299 84 26098 0.9 1 24032 2066 85 24954 0.9 1 22952 2002 86 23265 0.9 1 21439 1826 87 20790 0.9 1 19178 1612 88 19610 0.9 1 18134 1476 89 18995 0.9 1 17608 1387 90 18192 0.9 1 16909 1283 91 16569 0.9 1 15304 1265 92 15491 0.9 1 14458 1033 93 14466 0.9 1 13426 1040 94 12933 0.9 1 12040 893 95 12018 0.9 1 11126 892 96 11315 0.9 1 10501 814 97 10246 0.9 1 9521 725 98 9915 0.9 1 9250 665 99 9221 0.9 1 8600 621 100 8646 0.9 1 8110 536 101 7569 0.9 1 7031 538 102 6738 0.9 1 6305 433 103 6144 0.9 1 5706 438 104 5257 0.9 1 4905 352 105 5022 0.9 1 4668 354 106 4387 0.9 1 4117 270 107 4018 0.9 1 3733 285 108 3539 0.9 1 3322 217 109 3137 0.9 1 2930 207 110 2769 0.9 1 2607 162 111 2458 0.9 1 2292 166 112 2157 0.9 1 2028 129 113 1848 0.9 1 1732 116 114 1587 0.9 1 1472 115 115 1444 0.9 1 1344 100 116 1196 0.9 1 1099 97 117 1082 0.9 1 1008 74 118 881 0.9 1 816 65 119 851 0.9 1 778 73 120 2020 0.9 1 1894 126 121 1595 0.9 1 1536 59 122 583 0.9 1 542 41 123 453 0.9 1 403 50 124 403 0.9 1 360 43 125 355 0.9 1 310 45 126 307 0.9 1 269 38 127 254 0.9 1 214 40 128 210 0.9 1 183 27 129 233 0.9 1 205 28 130 157 0.9 1 147 10 131 196 0.9 1 179 17 132 117 0.9 1 103 14 133 182 0.9 1 159 23 134 123 0.9 1 110 13 135 165 0.9 1 145 20 136 119 0.9 1 109 10 137 121 0.9 1 109 12 138 88 0.9 1 71 17 139 123 0.9 1 106 17 140 80 0.9 1 74 6 141 88 0.9 1 76 12 142 61 0.9 1 44 17 143 59 0.9 1 49 10 144 33 0.9 1 20 13 145 65 0.9 1 45 20 146 29 0.9 1 17 12 147 49 0.9 1 28 21 148 36 0.9 1 30 6 149 68 0.9 1 54 14 150 41 0.9 1 26 15 151 416 0.9 1 92 324 RUN STATISTICS FOR INPUT FILE: ERR12308508_1.fastq.gz ============================================= 58342110 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 58342110 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 76840 (0.13%)