SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245583_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: 109052). 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 SRR18245583_2.fastq.gz Processing single-end reads on 1 core ... Finished in 5157.467 s (58.514 µs/read; 1.03 M reads/minute). === Summary === Total reads processed: 88,140,600 Reads with adapters: 50,651,176 (57.5%) Reads written (passing filters): 88,140,600 (100.0%) Total basepairs processed: 13,221,090,000 bp Quality-trimmed: 42,030,046 bp (0.3%) Total written (filtered): 12,696,459,137 bp (96.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 50651176 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.3% C: 19.0% G: 0.5% T: 33.0% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 37390083 22035150.0 0 37390083 2 434651 5508787.5 0 434651 3 426251 1377196.9 0 426251 4 388546 344299.2 0 388546 5 371464 86074.8 0 371464 6 318512 21518.7 0 318512 7 319627 5379.7 0 319627 8 344094 1344.9 0 344094 9 266484 336.2 0 265352 1132 10 320579 84.1 1 294151 26428 11 304942 21.0 1 273756 31186 12 311773 5.3 1 279510 32263 13 282303 1.3 1 255009 27294 14 297660 1.3 1 267286 30374 15 260119 1.3 1 235546 24573 16 270215 1.3 1 243073 27142 17 293159 1.3 1 265562 27597 18 211665 1.3 1 191927 19738 19 265894 1.3 1 241703 24191 20 254152 1.3 1 231764 22388 21 205281 1.3 1 184328 20953 22 218839 1.3 1 200058 18781 23 210286 1.3 1 193109 17177 24 238873 1.3 1 217954 20919 25 230618 1.3 1 212825 17793 26 164225 1.3 1 149903 14322 27 175409 1.3 1 158739 16670 28 187290 1.3 1 173858 13432 29 168529 1.3 1 154141 14388 30 175331 1.3 1 162104 13227 31 157438 1.3 1 145230 12208 32 157218 1.3 1 145860 11358 33 175415 1.3 1 161812 13603 34 141707 1.3 1 129078 12629 35 139176 1.3 1 128121 11055 36 146975 1.3 1 136793 10182 37 127537 1.3 1 118303 9234 38 124871 1.3 1 115643 9228 39 132376 1.3 1 122600 9776 40 107514 1.3 1 99188 8326 41 115492 1.3 1 107335 8157 42 155769 1.3 1 146094 9675 43 76768 1.3 1 69544 7224 44 182382 1.3 1 171859 10523 45 126515 1.3 1 117543 8972 46 80060 1.3 1 71323 8737 47 180321 1.3 1 173283 7038 48 34206 1.3 1 30456 3750 49 91848 1.3 1 85801 6047 50 33324 1.3 1 30805 2519 51 53841 1.3 1 49877 3964 52 34975 1.3 1 31942 3033 53 73448 1.3 1 69195 4253 54 114090 1.3 1 108892 5198 55 32655 1.3 1 29586 3069 56 75284 1.3 1 69155 6129 57 244755 1.3 1 237023 7732 58 44641 1.3 1 41070 3571 59 23740 1.3 1 20831 2909 60 144234 1.3 1 138855 5379 61 27771 1.3 1 25827 1944 62 21771 1.3 1 19177 2594 63 124839 1.3 1 119264 5575 64 146066 1.3 1 141762 4304 65 16729 1.3 1 15113 1616 66 35718 1.3 1 33797 1921 67 22014 1.3 1 20898 1116 68 14940 1.3 1 13714 1226 69 23495 1.3 1 22036 1459 70 35092 1.3 1 33550 1542 71 15026 1.3 1 14057 969 72 14060 1.3 1 13083 977 73 17045 1.3 1 16018 1027 74 18259 1.3 1 17116 1143 75 25618 1.3 1 24220 1398 76 28917 1.3 1 27381 1536 77 27778 1.3 1 26242 1536 78 31012 1.3 1 29536 1476 79 31828 1.3 1 30259 1569 80 32209 1.3 1 30641 1568 81 32190 1.3 1 30632 1558 82 33104 1.3 1 31323 1781 83 39454 1.3 1 37657 1797 84 34272 1.3 1 32532 1740 85 35145 1.3 1 33591 1554 86 31712 1.3 1 30154 1558 87 28995 1.3 1 27589 1406 88 28106 1.3 1 26757 1349 89 26419 1.3 1 25150 1269 90 26467 1.3 1 25307 1160 91 25443 1.3 1 24282 1161 92 25115 1.3 1 24038 1077 93 24772 1.3 1 23678 1094 94 23829 1.3 1 22788 1041 95 23585 1.3 1 22542 1043 96 23433 1.3 1 22377 1056 97 24062 1.3 1 23045 1017 98 24552 1.3 1 23594 958 99 23954 1.3 1 23000 954 100 23431 1.3 1 22450 981 101 21358 1.3 1 20504 854 102 20493 1.3 1 19592 901 103 20180 1.3 1 19324 856 104 19895 1.3 1 19108 787 105 20409 1.3 1 19602 807 106 19940 1.3 1 19143 797 107 19705 1.3 1 18862 843 108 19794 1.3 1 19035 759 109 19013 1.3 1 18256 757 110 18989 1.3 1 18264 725 111 18944 1.3 1 18261 683 112 19220 1.3 1 18497 723 113 19041 1.3 1 18305 736 114 18764 1.3 1 18055 709 115 18189 1.3 1 17530 659 116 18356 1.3 1 17650 706 117 17741 1.3 1 17011 730 118 17917 1.3 1 17210 707 119 17614 1.3 1 16872 742 120 17090 1.3 1 16283 807 121 16588 1.3 1 15839 749 122 16343 1.3 1 15428 915 123 17286 1.3 1 16247 1039 124 16174 1.3 1 15070 1104 125 15944 1.3 1 14636 1308 126 15114 1.3 1 13594 1520 127 14165 1.3 1 12485 1680 128 13782 1.3 1 11817 1965 129 13390 1.3 1 11068 2322 130 12613 1.3 1 9906 2707 131 13012 1.3 1 9586 3426 132 12638 1.3 1 8652 3986 133 12551 1.3 1 8031 4520 134 11857 1.3 1 6998 4859 135 10822 1.3 1 6079 4743 136 9425 1.3 1 5132 4293 137 8077 1.3 1 4874 3203 138 7218 1.3 1 5126 2092 139 6464 1.3 1 4836 1628 140 6375 1.3 1 5036 1339 141 7227 1.3 1 6166 1061 142 5644 1.3 1 4843 801 143 5686 1.3 1 4841 845 144 7773 1.3 1 6625 1148 145 9945 1.3 1 8313 1632 146 4965 1.3 1 3991 974 147 661 1.3 1 459 202 148 7191 1.3 1 5862 1329 149 3075 1.3 1 2471 604 150 62863 1.3 1 53385 9478 RUN STATISTICS FOR INPUT FILE: SRR18245583_2.fastq.gz ============================================= 88140600 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 88140600 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 246986 (0.28%)