SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245604_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: 87149). 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 SRR18245604_2.fastq.gz Processing single-end reads on 1 core ... Finished in 3908.092 s (45.344 µs/read; 1.32 M reads/minute). === Summary === Total reads processed: 86,188,301 Reads with adapters: 48,414,995 (56.2%) Reads written (passing filters): 86,188,301 (100.0%) Total basepairs processed: 12,928,245,150 bp Quality-trimmed: 45,977,100 bp (0.4%) Total written (filtered): 12,498,423,226 bp (96.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 48414995 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.8% C: 18.2% G: 0.4% T: 32.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 38239336 21547075.2 0 38239336 2 340319 5386768.8 0 340319 3 331551 1346692.2 0 331551 4 297900 336673.1 0 297900 5 282078 84168.3 0 282078 6 240244 21042.1 0 240244 7 238213 5260.5 0 238213 8 253054 1315.1 0 253054 9 206454 328.8 0 205645 809 10 238366 82.2 1 219497 18869 11 225724 20.5 1 202951 22773 12 231883 5.1 1 208718 23165 13 207978 1.3 1 188595 19383 14 218593 1.3 1 196959 21634 15 193425 1.3 1 176134 17291 16 198700 1.3 1 179167 19533 17 212743 1.3 1 193765 18978 18 157394 1.3 1 143320 14074 19 193930 1.3 1 177181 16749 20 186835 1.3 1 171048 15787 21 150700 1.3 1 136070 14630 22 161524 1.3 1 148168 13356 23 153046 1.3 1 141145 11901 24 173566 1.3 1 159100 14466 25 167555 1.3 1 155540 12015 26 119991 1.3 1 109764 10227 27 128258 1.3 1 116523 11735 28 136192 1.3 1 126980 9212 29 124174 1.3 1 113913 10261 30 129111 1.3 1 119852 9259 31 115525 1.3 1 107168 8357 32 116459 1.3 1 108549 7910 33 128094 1.3 1 118560 9534 34 105534 1.3 1 96559 8975 35 103047 1.3 1 95399 7648 36 109162 1.3 1 102146 7016 37 94368 1.3 1 87644 6724 38 93610 1.3 1 86946 6664 39 97716 1.3 1 90782 6934 40 83930 1.3 1 77962 5968 41 87424 1.3 1 81549 5875 42 113904 1.3 1 106912 6992 43 64069 1.3 1 58570 5499 44 134690 1.3 1 127668 7022 45 104390 1.3 1 97617 6773 46 64128 1.3 1 57500 6628 47 143527 1.3 1 138492 5035 48 27098 1.3 1 24221 2877 49 73669 1.3 1 68948 4721 50 27016 1.3 1 25001 2015 51 44088 1.3 1 41105 2983 52 29709 1.3 1 27384 2325 53 60154 1.3 1 56845 3309 54 94332 1.3 1 90361 3971 55 27639 1.3 1 25217 2422 56 63614 1.3 1 58728 4886 57 216119 1.3 1 209990 6129 58 38153 1.3 1 35354 2799 59 20663 1.3 1 18187 2476 60 127442 1.3 1 123170 4272 61 23712 1.3 1 22214 1498 62 19247 1.3 1 16995 2252 63 113462 1.3 1 108776 4686 64 131042 1.3 1 127628 3414 65 14705 1.3 1 13356 1349 66 31439 1.3 1 29772 1667 67 20156 1.3 1 19229 927 68 14003 1.3 1 12896 1107 69 21559 1.3 1 20351 1208 70 31921 1.3 1 30610 1311 71 14079 1.3 1 13159 920 72 13310 1.3 1 12453 857 73 16573 1.3 1 15638 935 74 18219 1.3 1 17179 1040 75 26388 1.3 1 25040 1348 76 32253 1.3 1 30872 1381 77 26866 1.3 1 25580 1286 78 30166 1.3 1 28951 1215 79 30634 1.3 1 29253 1381 80 31112 1.3 1 29785 1327 81 31304 1.3 1 29970 1334 82 31475 1.3 1 29994 1481 83 35925 1.3 1 34375 1550 84 31986 1.3 1 30561 1425 85 32086 1.3 1 30712 1374 86 30287 1.3 1 28953 1334 87 27642 1.3 1 26403 1239 88 27599 1.3 1 26410 1189 89 26081 1.3 1 24920 1161 90 25730 1.3 1 24672 1058 91 24282 1.3 1 23294 988 92 24445 1.3 1 23360 1085 93 23553 1.3 1 22519 1034 94 23067 1.3 1 22150 917 95 22640 1.3 1 21628 1012 96 21864 1.3 1 20855 1009 97 22423 1.3 1 21496 927 98 23096 1.3 1 22155 941 99 22075 1.3 1 21182 893 100 21519 1.3 1 20649 870 101 19823 1.3 1 19025 798 102 18793 1.3 1 17968 825 103 18039 1.3 1 17244 795 104 17223 1.3 1 16460 763 105 17075 1.3 1 16369 706 106 16863 1.3 1 16141 722 107 16032 1.3 1 15327 705 108 15604 1.3 1 14916 688 109 15072 1.3 1 14424 648 110 14749 1.3 1 14096 653 111 14034 1.3 1 13396 638 112 13412 1.3 1 12814 598 113 13288 1.3 1 12721 567 114 13278 1.3 1 12673 605 115 13241 1.3 1 12671 570 116 12909 1.3 1 12311 598 117 12539 1.3 1 12002 537 118 11950 1.3 1 11413 537 119 11735 1.3 1 11185 550 120 11174 1.3 1 10588 586 121 10556 1.3 1 9948 608 122 10216 1.3 1 9537 679 123 10281 1.3 1 9456 825 124 9633 1.3 1 8580 1053 125 9491 1.3 1 8321 1170 126 9147 1.3 1 7749 1398 127 8757 1.3 1 7224 1533 128 8265 1.3 1 6680 1585 129 7859 1.3 1 6102 1757 130 7088 1.3 1 5515 1573 131 6742 1.3 1 5268 1474 132 6242 1.3 1 4858 1384 133 5639 1.3 1 4197 1442 134 5152 1.3 1 3707 1445 135 4575 1.3 1 3189 1386 136 4031 1.3 1 2737 1294 137 3663 1.3 1 2705 958 138 3310 1.3 1 2616 694 139 3198 1.3 1 2609 589 140 3166 1.3 1 2697 469 141 3766 1.3 1 3295 471 142 3069 1.3 1 2681 388 143 2721 1.3 1 2363 358 144 4113 1.3 1 3541 572 145 5164 1.3 1 4345 819 146 2460 1.3 1 2023 437 147 283 1.3 1 196 87 148 1843 1.3 1 1404 439 149 863 1.3 1 658 205 150 18834 1.3 1 15948 2886 RUN STATISTICS FOR INPUT FILE: SRR18245604_2.fastq.gz ============================================= 86188301 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 86188301 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 107348 (0.12%)