SUMMARISING RUN PARAMETERS ========================== Input filename: ERR12308527_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: 131605). 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 ERR12308527_2.fastq.gz Processing single-end reads on 2 cores ... Finished in 1265.220 s (17.742 µs/read; 3.38 M reads/minute). === Summary === Total reads processed: 71,310,492 Reads with adapters: 39,554,731 (55.5%) Reads written (passing filters): 71,310,492 (100.0%) Total basepairs processed: 10,767,884,292 bp Quality-trimmed: 62,775,426 bp (0.6%) Total written (filtered): 10,288,758,507 bp (95.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 39554731 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.2% C: 19.5% G: 2.8% T: 28.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 26033984 17827623.0 0 26033984 2 831896 4456905.8 0 831896 3 452955 1114226.4 0 452955 4 301500 278556.6 0 301500 5 322095 69639.2 0 322095 6 285005 17409.8 0 285005 7 270216 4352.4 0 270216 8 329650 1088.1 0 329650 9 193116 272.0 0 192546 570 10 289691 68.0 1 257665 32026 11 255211 17.0 1 227888 27323 12 274998 4.3 1 237307 37691 13 269861 1.1 1 232676 37185 14 286153 1.1 1 243565 42588 15 227212 1.1 1 198008 29204 16 271072 1.1 1 234334 36738 17 269122 1.1 1 234640 34482 18 215966 1.1 1 188829 27137 19 265808 1.1 1 228199 37609 20 282597 1.1 1 246565 36032 21 176116 1.1 1 153810 22306 22 232000 1.1 1 201614 30386 23 228223 1.1 1 197918 30305 24 276569 1.1 1 237470 39099 25 261374 1.1 1 229256 32118 26 176203 1.1 1 153146 23057 27 174709 1.1 1 152254 22455 28 224376 1.1 1 198326 26050 29 186206 1.1 1 164954 21252 30 204823 1.1 1 179606 25217 31 193967 1.1 1 170737 23230 32 200578 1.1 1 175571 25007 33 190097 1.1 1 167075 23022 34 189930 1.1 1 168399 21531 35 183156 1.1 1 164081 19075 36 170241 1.1 1 152504 17737 37 165004 1.1 1 146662 18342 38 191093 1.1 1 170596 20497 39 146290 1.1 1 129367 16923 40 156780 1.1 1 140379 16401 41 154831 1.1 1 138746 16085 42 166078 1.1 1 149111 16967 43 127193 1.1 1 113987 13206 44 143939 1.1 1 128439 15500 45 150837 1.1 1 135049 15788 46 130843 1.1 1 116516 14327 47 131387 1.1 1 118632 12755 48 122698 1.1 1 110543 12155 49 123147 1.1 1 110714 12433 50 116841 1.1 1 105808 11033 51 111785 1.1 1 101286 10499 52 112200 1.1 1 101402 10798 53 105924 1.1 1 96313 9611 54 118616 1.1 1 107825 10791 55 82164 1.1 1 74974 7190 56 99049 1.1 1 89805 9244 57 124377 1.1 1 112563 11814 58 66634 1.1 1 60338 6296 59 76410 1.1 1 69978 6432 60 91414 1.1 1 83644 7770 61 84014 1.1 1 76945 7069 62 64903 1.1 1 59364 5539 63 125261 1.1 1 115356 9905 64 59248 1.1 1 54165 5083 65 46448 1.1 1 42634 3814 66 43704 1.1 1 40035 3669 67 68719 1.1 1 63827 4892 68 60850 1.1 1 56193 4657 69 50167 1.1 1 46515 3652 70 54284 1.1 1 50557 3727 71 49691 1.1 1 46122 3569 72 48973 1.1 1 45427 3546 73 62541 1.1 1 58481 4060 74 43975 1.1 1 40895 3080 75 42760 1.1 1 39943 2817 76 22883 1.1 1 21226 1657 77 23854 1.1 1 22167 1687 78 25626 1.1 1 23957 1669 79 24578 1.1 1 22939 1639 80 24300 1.1 1 22735 1565 81 23068 1.1 1 21588 1480 82 21554 1.1 1 20177 1377 83 21085 1.1 1 19738 1347 84 19769 1.1 1 18505 1264 85 18570 1.1 1 17350 1220 86 17223 1.1 1 16122 1101 87 15534 1.1 1 14576 958 88 14339 1.1 1 13436 903 89 13486 1.1 1 12642 844 90 12947 1.1 1 12215 732 91 11673 1.1 1 10950 723 92 11130 1.1 1 10443 687 93 10480 1.1 1 9828 652 94 9262 1.1 1 8648 614 95 8648 1.1 1 8114 534 96 8132 1.1 1 7654 478 97 7267 1.1 1 6835 432 98 7043 1.1 1 6624 419 99 6508 1.1 1 6145 363 100 6035 1.1 1 5650 385 101 5286 1.1 1 4940 346 102 4545 1.1 1 4234 311 103 4293 1.1 1 4064 229 104 3780 1.1 1 3550 230 105 3473 1.1 1 3283 190 106 3275 1.1 1 3066 209 107 2952 1.1 1 2755 197 108 2563 1.1 1 2394 169 109 2353 1.1 1 2203 150 110 2080 1.1 1 1945 135 111 1878 1.1 1 1748 130 112 1767 1.1 1 1653 114 113 1562 1.1 1 1437 125 114 1402 1.1 1 1300 102 115 1137 1.1 1 1056 81 116 1041 1.1 1 963 78 117 937 1.1 1 865 72 118 789 1.1 1 732 57 119 745 1.1 1 665 80 120 928 1.1 1 866 62 121 676 1.1 1 602 74 122 485 1.1 1 430 55 123 418 1.1 1 359 59 124 374 1.1 1 327 47 125 304 1.1 1 255 49 126 318 1.1 1 258 60 127 266 1.1 1 222 44 128 198 1.1 1 155 43 129 187 1.1 1 158 29 130 156 1.1 1 136 20 131 164 1.1 1 135 29 132 127 1.1 1 105 22 133 121 1.1 1 99 22 134 121 1.1 1 100 21 135 119 1.1 1 101 18 136 84 1.1 1 70 14 137 77 1.1 1 57 20 138 84 1.1 1 58 26 139 86 1.1 1 70 16 140 59 1.1 1 45 14 141 62 1.1 1 53 9 142 38 1.1 1 25 13 143 55 1.1 1 39 16 144 53 1.1 1 31 22 145 41 1.1 1 22 19 146 46 1.1 1 27 19 147 49 1.1 1 30 19 148 43 1.1 1 29 14 149 71 1.1 1 49 22 150 35 1.1 1 17 18 151 286 1.1 1 64 222 RUN STATISTICS FOR INPUT FILE: ERR12308527_2.fastq.gz ============================================= 71310492 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 71310492 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 62106 (0.09%)