SUMMARISING RUN PARAMETERS ========================== Input filename: ERR10684017_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: 84293). 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 ERR10684017_1.fastq.gz Processing single-end reads on 2 cores ... Finished in 1579.390 s (18.206 µs/read; 3.30 M reads/minute). === Summary === Total reads processed: 86,749,190 Reads with adapters: 48,308,611 (55.7%) Reads written (passing filters): 86,749,190 (100.0%) Total basepairs processed: 13,099,127,690 bp Quality-trimmed: 62,479,984 bp (0.5%) Total written (filtered): 12,660,378,874 bp (96.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 48308611 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 51.0% C: 18.4% G: 1.0% T: 29.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 37740570 21687297.5 0 37740570 2 597482 5421824.4 0 597482 3 292724 1355456.1 0 292724 4 228089 338864.0 0 228089 5 234468 84716.0 0 234468 6 210420 21179.0 0 210420 7 205620 5294.8 0 205620 8 254099 1323.7 0 254099 9 148075 330.9 0 147455 620 10 212584 82.7 1 192635 19949 11 182449 20.7 1 163046 19403 12 208421 5.2 1 179002 29419 13 194596 1.3 1 168305 26291 14 239681 1.3 1 206415 33266 15 152840 1.3 1 131731 21109 16 186417 1.3 1 160999 25418 17 253826 1.3 1 221208 32618 18 113266 1.3 1 97556 15710 19 250558 1.3 1 217021 33537 20 173676 1.3 1 152128 21548 21 102416 1.3 1 88453 13963 22 165073 1.3 1 143508 21565 23 166966 1.3 1 145370 21596 24 225407 1.3 1 195952 29455 25 191899 1.3 1 168838 23061 26 133806 1.3 1 117077 16729 27 103035 1.3 1 89443 13592 28 186256 1.3 1 165392 20864 29 113678 1.3 1 99281 14397 30 181946 1.3 1 161814 20132 31 104986 1.3 1 92331 12655 32 156146 1.3 1 138716 17430 33 135724 1.3 1 120181 15543 34 120496 1.3 1 105853 14643 35 164594 1.3 1 145514 19080 36 145017 1.3 1 131047 13970 37 68228 1.3 1 60555 7673 38 128583 1.3 1 114332 14251 39 161626 1.3 1 143975 17651 40 118535 1.3 1 106009 12526 41 79482 1.3 1 70822 8660 42 120930 1.3 1 108528 12402 43 99590 1.3 1 89159 10431 44 105302 1.3 1 94775 10527 45 114241 1.3 1 102286 11955 46 108295 1.3 1 97416 10879 47 98666 1.3 1 89506 9160 48 90413 1.3 1 81354 9059 49 101240 1.3 1 91037 10203 50 88463 1.3 1 80664 7799 51 84421 1.3 1 76722 7699 52 86597 1.3 1 78787 7810 53 85406 1.3 1 77559 7847 54 102860 1.3 1 93817 9043 55 60219 1.3 1 54835 5384 56 81317 1.3 1 73923 7394 57 116988 1.3 1 106719 10269 58 52192 1.3 1 47151 5041 59 57702 1.3 1 52640 5062 60 86162 1.3 1 78701 7461 61 71252 1.3 1 65372 5880 62 51253 1.3 1 46528 4725 63 129304 1.3 1 119625 9679 64 50998 1.3 1 46593 4405 65 40094 1.3 1 36830 3264 66 38570 1.3 1 35365 3205 67 65420 1.3 1 60870 4550 68 55871 1.3 1 51289 4582 69 50176 1.3 1 46350 3826 70 57150 1.3 1 53005 4145 71 53355 1.3 1 49462 3893 72 51960 1.3 1 48062 3898 73 67545 1.3 1 62827 4718 74 40483 1.3 1 37574 2909 75 38174 1.3 1 35615 2559 76 27824 1.3 1 25738 2086 77 28551 1.3 1 26432 2119 78 30475 1.3 1 28330 2145 79 29634 1.3 1 27580 2054 80 29246 1.3 1 27248 1998 81 28944 1.3 1 27006 1938 82 28083 1.3 1 26148 1935 83 28460 1.3 1 26528 1932 84 26815 1.3 1 25063 1752 85 26550 1.3 1 24810 1740 86 24649 1.3 1 23116 1533 87 22948 1.3 1 21425 1523 88 21857 1.3 1 20465 1392 89 20898 1.3 1 19578 1320 90 20943 1.3 1 19675 1268 91 18965 1.3 1 17828 1137 92 18245 1.3 1 17123 1122 93 17714 1.3 1 16673 1041 94 15847 1.3 1 14922 925 95 15144 1.3 1 14280 864 96 14575 1.3 1 13708 867 97 13806 1.3 1 12953 853 98 13372 1.3 1 12706 666 99 12953 1.3 1 12256 697 100 12344 1.3 1 11646 698 101 10713 1.3 1 10119 594 102 9686 1.3 1 9161 525 103 9196 1.3 1 8671 525 104 8406 1.3 1 7974 432 105 7808 1.3 1 7379 429 106 7123 1.3 1 6762 361 107 6623 1.3 1 6279 344 108 6007 1.3 1 5692 315 109 5634 1.3 1 5363 271 110 4842 1.3 1 4593 249 111 4635 1.3 1 4441 194 112 4156 1.3 1 3971 185 113 3542 1.3 1 3370 172 114 3121 1.3 1 2952 169 115 2659 1.3 1 2533 126 116 2271 1.3 1 2178 93 117 2181 1.3 1 2061 120 118 1775 1.3 1 1701 74 119 1687 1.3 1 1598 89 120 13123 1.3 1 12584 539 121 2048 1.3 1 1957 91 122 941 1.3 1 893 48 123 809 1.3 1 773 36 124 581 1.3 1 539 42 125 439 1.3 1 410 29 126 351 1.3 1 328 23 127 262 1.3 1 244 18 128 205 1.3 1 186 19 129 250 1.3 1 236 14 130 178 1.3 1 166 12 131 147 1.3 1 129 18 132 160 1.3 1 140 20 133 140 1.3 1 122 18 134 101 1.3 1 96 5 135 138 1.3 1 128 10 136 90 1.3 1 81 9 137 135 1.3 1 122 13 138 83 1.3 1 66 17 139 118 1.3 1 105 13 140 89 1.3 1 71 18 141 119 1.3 1 102 17 142 77 1.3 1 57 20 143 56 1.3 1 46 10 144 69 1.3 1 46 23 145 80 1.3 1 71 9 146 69 1.3 1 54 15 147 72 1.3 1 55 17 148 55 1.3 1 42 13 149 66 1.3 1 51 15 150 57 1.3 1 29 28 151 227 1.3 1 171 56 RUN STATISTICS FOR INPUT FILE: ERR10684017_1.fastq.gz ============================================= 86749190 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 86749190 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 93499 (0.11%)