SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245585_2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.10 Cutadapt version: 4.2 Number of cores used for trimming: 1 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 101592). 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 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR18245585_2.fastq.gz Processing single-end reads on 1 core ... Finished in 5762.873 s (70.232 µs/read; 0.85 M reads/minute). === Summary === Total reads processed: 82,055,348 Reads with adapters: 46,528,259 (56.7%) Reads written (passing filters): 82,055,348 (100.0%) Total basepairs processed: 12,308,302,200 bp Quality-trimmed: 45,217,977 bp (0.4%) Total written (filtered): 11,815,070,210 bp (96.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46528259 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.4% C: 18.2% G: 0.4% T: 32.9% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 35565899 20513837.0 0 35565899 2 305463 5128459.2 0 305463 3 304501 1282114.8 0 304501 4 269564 320528.7 0 269564 5 264948 80132.2 0 264948 6 215680 20033.0 0 215680 7 221576 5008.3 0 221576 8 242235 1252.1 0 242235 9 187203 313.0 0 186405 798 10 221100 78.3 1 204306 16794 11 218428 19.6 1 195858 22570 12 219630 4.9 1 199206 20424 13 201295 1.2 1 184126 17169 14 207102 1.2 1 188395 18707 15 188420 1.2 1 172090 16330 16 196862 1.2 1 177940 18922 17 204334 1.2 1 187694 16640 18 158792 1.2 1 145798 12994 19 192080 1.2 1 175839 16241 20 183888 1.2 1 169180 14708 21 154955 1.2 1 139515 15440 22 162857 1.2 1 150601 12256 23 155047 1.2 1 144099 10948 24 179821 1.2 1 165590 14231 25 176980 1.2 1 164779 12201 26 120367 1.2 1 109834 10533 27 134582 1.2 1 122095 12487 28 142446 1.2 1 133322 9124 29 135979 1.2 1 124532 11447 30 137912 1.2 1 127941 9971 31 125675 1.2 1 116430 9245 32 125982 1.2 1 117659 8323 33 137913 1.2 1 127916 9997 34 118723 1.2 1 107360 11363 35 117818 1.2 1 108958 8860 36 119328 1.2 1 112262 7066 37 107629 1.2 1 100088 7541 38 108569 1.2 1 100777 7792 39 112482 1.2 1 104457 8025 40 100891 1.2 1 94290 6601 41 101567 1.2 1 95456 6111 42 137492 1.2 1 130291 7201 43 71713 1.2 1 65152 6561 44 176500 1.2 1 168544 7956 45 123518 1.2 1 115789 7729 46 78552 1.2 1 70145 8407 47 173277 1.2 1 168160 5117 48 31002 1.2 1 27027 3975 49 88505 1.2 1 82461 6044 50 31077 1.2 1 28701 2376 51 54548 1.2 1 50443 4105 52 35669 1.2 1 32763 2906 53 73141 1.2 1 69515 3626 54 116542 1.2 1 112360 4182 55 33079 1.2 1 29896 3183 56 78614 1.2 1 72353 6261 57 285738 1.2 1 278686 7052 58 47585 1.2 1 43648 3937 59 25300 1.2 1 22101 3199 60 160401 1.2 1 155586 4815 61 27973 1.2 1 26100 1873 62 23303 1.2 1 20414 2889 63 134392 1.2 1 128765 5627 64 185913 1.2 1 181888 4025 65 20414 1.2 1 18351 2063 66 39133 1.2 1 36927 2206 67 23074 1.2 1 21913 1161 68 17135 1.2 1 15405 1730 69 24827 1.2 1 23332 1495 70 39150 1.2 1 37409 1741 71 17142 1.2 1 15885 1257 72 16282 1.2 1 14986 1296 73 21044 1.2 1 19629 1415 74 23636 1.2 1 21996 1640 75 35105 1.2 1 33004 2101 76 42525 1.2 1 40085 2440 77 35920 1.2 1 33881 2039 78 38891 1.2 1 37192 1699 79 39338 1.2 1 37598 1740 80 39728 1.2 1 38022 1706 81 39851 1.2 1 38150 1701 82 41115 1.2 1 39244 1871 83 46397 1.2 1 44362 2035 84 43694 1.2 1 41694 2000 85 47736 1.2 1 45666 2070 86 41015 1.2 1 39227 1788 87 36935 1.2 1 35335 1600 88 35663 1.2 1 34138 1525 89 33650 1.2 1 32232 1418 90 33950 1.2 1 32681 1269 91 32502 1.2 1 31251 1251 92 31708 1.2 1 30550 1158 93 31694 1.2 1 30464 1230 94 30156 1.2 1 28900 1256 95 29657 1.2 1 28499 1158 96 28532 1.2 1 27434 1098 97 28400 1.2 1 27253 1147 98 29041 1.2 1 27929 1112 99 29151 1.2 1 28112 1039 100 29382 1.2 1 28318 1064 101 26133 1.2 1 25173 960 102 24445 1.2 1 23476 969 103 23462 1.2 1 22498 964 104 22233 1.2 1 21282 951 105 22317 1.2 1 21455 862 106 21834 1.2 1 20967 867 107 21070 1.2 1 20266 804 108 21027 1.2 1 20281 746 109 19616 1.2 1 18891 725 110 19260 1.2 1 18484 776 111 18029 1.2 1 17277 752 112 17575 1.2 1 16890 685 113 17486 1.2 1 16787 699 114 16830 1.2 1 16131 699 115 16770 1.2 1 16130 640 116 16407 1.2 1 15722 685 117 16355 1.2 1 15696 659 118 16272 1.2 1 15594 678 119 15564 1.2 1 14901 663 120 14855 1.2 1 14174 681 121 14185 1.2 1 13487 698 122 13000 1.2 1 12241 759 123 13032 1.2 1 12181 851 124 12117 1.2 1 11100 1017 125 12223 1.2 1 11043 1180 126 11534 1.2 1 10154 1380 127 10567 1.2 1 9062 1505 128 10342 1.2 1 8663 1679 129 9697 1.2 1 7974 1723 130 8736 1.2 1 7083 1653 131 8354 1.2 1 6563 1791 132 7718 1.2 1 5889 1829 133 7251 1.2 1 5361 1890 134 6415 1.2 1 4456 1959 135 5882 1.2 1 4018 1864 136 4910 1.2 1 3240 1670 137 4323 1.2 1 3111 1212 138 4111 1.2 1 3256 855 139 3740 1.2 1 3011 729 140 3720 1.2 1 3154 566 141 4330 1.2 1 3820 510 142 3558 1.2 1 3135 423 143 3442 1.2 1 2983 459 144 4993 1.2 1 4425 568 145 6044 1.2 1 5154 890 146 2861 1.2 1 2354 507 147 302 1.2 1 207 95 148 2825 1.2 1 2193 632 149 1187 1.2 1 923 264 150 25390 1.2 1 21786 3604 RUN STATISTICS FOR INPUT FILE: SRR18245585_2.fastq.gz ============================================= 82055348 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 82055348 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 134130 (0.16%)