SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245601_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: 186959). 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 1 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC SRR18245601_2.fastq.gz Processing single-end reads on 1 core ... Finished in 3619.899 s (41.425 µs/read; 1.45 M reads/minute). === Summary === Total reads processed: 87,384,726 Reads with adapters: 52,914,299 (60.6%) Reads written (passing filters): 87,384,726 (100.0%) Total basepairs processed: 13,107,708,900 bp Quality-trimmed: 53,020,706 bp (0.4%) Total written (filtered): 11,660,337,331 bp (89.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 52914299 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.0% C: 17.3% G: 1.1% T: 32.6% none/other: 3.0% Overview of removed sequences length count expect max.err error counts 1 33989141 21846181.5 0 33989141 2 283119 5461545.4 0 283119 3 264686 1365386.3 0 264686 4 237932 341346.6 0 237932 5 233944 85336.6 0 233944 6 196002 21334.2 0 196002 7 198633 5333.5 0 198633 8 219028 1333.4 0 219028 9 164023 333.3 0 163131 892 10 207354 83.3 1 185153 22201 11 201526 20.8 1 174760 26766 12 205642 5.2 1 179609 26033 13 190558 1.3 1 168108 22450 14 201805 1.3 1 176645 25160 15 177771 1.3 1 157323 20448 16 190390 1.3 1 166618 23772 17 205611 1.3 1 182640 22971 18 150227 1.3 1 133161 17066 19 195904 1.3 1 174464 21440 20 187396 1.3 1 167199 20197 21 151396 1.3 1 132085 19311 22 166177 1.3 1 148569 17608 23 160403 1.3 1 144306 16097 24 189699 1.3 1 169828 19871 25 184527 1.3 1 166901 17626 26 129236 1.3 1 115354 13882 27 141093 1.3 1 124429 16664 28 155339 1.3 1 141962 13377 29 144081 1.3 1 127847 16234 30 150855 1.3 1 136917 13938 31 136963 1.3 1 123870 13093 32 139620 1.3 1 127524 12096 33 159566 1.3 1 144838 14728 34 131163 1.3 1 116169 14994 35 133324 1.3 1 120332 12992 36 139493 1.3 1 127752 11741 37 124338 1.3 1 113376 10962 38 124237 1.3 1 112908 11329 39 135874 1.3 1 123376 12498 40 112582 1.3 1 102060 10522 41 121257 1.3 1 111083 10174 42 169096 1.3 1 156670 12426 43 85264 1.3 1 75432 9832 44 215394 1.3 1 201139 14255 45 149959 1.3 1 137025 12934 46 94781 1.3 1 81786 12995 47 217581 1.3 1 207156 10425 48 43234 1.3 1 37274 5960 49 109122 1.3 1 99666 9456 50 39833 1.3 1 36057 3776 51 70744 1.3 1 64093 6651 52 44010 1.3 1 39361 4649 53 94533 1.3 1 88043 6490 54 150998 1.3 1 142988 8010 55 47188 1.3 1 41928 5260 56 104927 1.3 1 94905 10022 57 375612 1.3 1 361780 13832 58 72178 1.3 1 65308 6870 59 36191 1.3 1 31284 4907 60 232787 1.3 1 223026 9761 61 43555 1.3 1 39992 3563 62 35677 1.3 1 30903 4774 63 208295 1.3 1 197591 10704 64 255848 1.3 1 247705 8143 65 30106 1.3 1 26832 3274 66 67379 1.3 1 63238 4141 67 40771 1.3 1 38466 2305 68 27553 1.3 1 24754 2799 69 45162 1.3 1 42082 3080 70 70057 1.3 1 66403 3654 71 30178 1.3 1 27751 2427 72 28615 1.3 1 26226 2389 73 37130 1.3 1 34256 2874 74 44645 1.3 1 40786 3859 75 75210 1.3 1 69234 5976 76 91669 1.3 1 85394 6275 77 66785 1.3 1 61741 5044 78 71484 1.3 1 67202 4282 79 73882 1.3 1 69499 4383 80 76915 1.3 1 72659 4256 81 78861 1.3 1 74239 4622 82 85827 1.3 1 79954 5873 83 112426 1.3 1 106340 6086 84 98278 1.3 1 92153 6125 85 104245 1.3 1 98542 5703 86 91595 1.3 1 86382 5213 87 82637 1.3 1 77624 5013 88 80431 1.3 1 75579 4852 89 76037 1.3 1 72027 4010 90 77501 1.3 1 73808 3693 91 76426 1.3 1 72832 3594 92 76990 1.3 1 73395 3595 93 77390 1.3 1 73882 3508 94 76663 1.3 1 73045 3618 95 77012 1.3 1 73373 3639 96 76973 1.3 1 73412 3561 97 82021 1.3 1 78415 3606 98 86652 1.3 1 83184 3468 99 87598 1.3 1 83995 3603 100 86974 1.3 1 83537 3437 101 82955 1.3 1 79527 3428 102 81435 1.3 1 77982 3453 103 81415 1.3 1 78128 3287 104 81364 1.3 1 78139 3225 105 84239 1.3 1 81056 3183 106 85768 1.3 1 82567 3201 107 87002 1.3 1 83643 3359 108 87079 1.3 1 83756 3323 109 85749 1.3 1 82319 3430 110 86339 1.3 1 82868 3471 111 87983 1.3 1 84566 3417 112 88469 1.3 1 84994 3475 113 91831 1.3 1 88263 3568 114 93890 1.3 1 90289 3601 115 95308 1.3 1 91710 3598 116 100527 1.3 1 96779 3748 117 101868 1.3 1 98066 3802 118 105481 1.3 1 101344 4137 119 106253 1.3 1 101928 4325 120 106170 1.3 1 101228 4942 121 106377 1.3 1 101472 4905 122 106305 1.3 1 101283 5022 123 116017 1.3 1 110050 5967 124 111111 1.3 1 105102 6009 125 112241 1.3 1 105142 7099 126 110159 1.3 1 101941 8218 127 105971 1.3 1 96117 9854 128 109015 1.3 1 95552 13463 129 118655 1.3 1 98289 20366 130 120249 1.3 1 90228 30021 131 136889 1.3 1 89387 47502 132 149177 1.3 1 84452 64725 133 161989 1.3 1 81983 80006 134 157296 1.3 1 75703 81593 135 151712 1.3 1 69247 82465 136 139009 1.3 1 62011 76998 137 117584 1.3 1 60754 56830 138 105914 1.3 1 65657 40257 139 93192 1.3 1 63396 29796 140 87545 1.3 1 64600 22945 141 97031 1.3 1 81073 15958 142 75503 1.3 1 65362 10141 143 82791 1.3 1 72570 10221 144 102976 1.3 1 89528 13448 145 122776 1.3 1 104937 17839 146 64408 1.3 1 51969 12439 147 12961 1.3 1 9012 3949 148 140702 1.3 1 119801 20901 149 69644 1.3 1 57566 12078 150 1509175 1.3 1 1349851 159324 RUN STATISTICS FOR INPUT FILE: SRR18245601_2.fastq.gz ============================================= 87384726 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 87384726 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 3977530 (4.55%)