SUMMARISING RUN PARAMETERS ========================== Input filename: SRR18245595_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: 45998). 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 SRR18245595_2.fastq.gz Processing single-end reads on 1 core ... Finished in 4198.066 s (51.912 µs/read; 1.16 M reads/minute). === Summary === Total reads processed: 80,869,598 Reads with adapters: 42,502,879 (52.6%) Reads written (passing filters): 80,869,598 (100.0%) Total basepairs processed: 12,130,439,700 bp Quality-trimmed: 29,123,747 bp (0.2%) Total written (filtered): 11,896,494,947 bp (98.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 42502879 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.9% C: 19.8% G: 0.4% T: 30.7% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 36834854 20217399.5 0 36834854 2 240934 5054349.9 0 240934 3 224912 1263587.5 0 224912 4 204125 315896.9 0 204125 5 190372 78974.2 0 190372 6 162061 19743.6 0 162061 7 167636 4935.9 0 167636 8 178390 1234.0 0 178390 9 118564 308.5 0 117985 579 10 157250 77.1 1 141889 15361 11 148484 19.3 1 132202 16282 12 148532 4.8 1 132703 15829 13 134570 1.2 1 121823 12747 14 141140 1.2 1 126033 15107 15 122226 1.2 1 110151 12075 16 125078 1.2 1 112030 13048 17 138484 1.2 1 125111 13373 18 92764 1.2 1 83292 9472 19 139481 1.2 1 126359 13122 20 98477 1.2 1 89507 8970 21 84682 1.2 1 76029 8653 22 96212 1.2 1 87483 8729 23 92550 1.2 1 84536 8014 24 115709 1.2 1 105055 10654 25 98450 1.2 1 90504 7946 26 65048 1.2 1 59119 5929 27 65329 1.2 1 59247 6082 28 79155 1.2 1 73261 5894 29 69326 1.2 1 63257 6069 30 75299 1.2 1 69447 5852 31 61967 1.2 1 57153 4814 32 65425 1.2 1 60288 5137 33 64937 1.2 1 59577 5360 34 71667 1.2 1 65675 5992 35 55516 1.2 1 50998 4518 36 49476 1.2 1 44836 4640 37 69716 1.2 1 65249 4467 38 45116 1.2 1 41585 3531 39 52668 1.2 1 48705 3963 40 54743 1.2 1 50761 3982 41 26169 1.2 1 23108 3061 42 49790 1.2 1 46679 3111 43 36619 1.2 1 32888 3731 44 106952 1.2 1 101574 5378 45 44301 1.2 1 41108 3193 46 15206 1.2 1 13378 1828 47 43732 1.2 1 41699 2033 48 17168 1.2 1 15841 1327 49 20191 1.2 1 18590 1601 50 15904 1.2 1 14955 949 51 16384 1.2 1 15108 1276 52 11574 1.2 1 10785 789 53 22990 1.2 1 21761 1229 54 31722 1.2 1 30355 1367 55 16273 1.2 1 15096 1177 56 22666 1.2 1 21313 1353 57 37344 1.2 1 35865 1479 58 17798 1.2 1 16654 1144 59 16196 1.2 1 15217 979 60 28762 1.2 1 27510 1252 61 19137 1.2 1 18255 882 62 11808 1.2 1 10992 816 63 27335 1.2 1 26057 1278 64 34164 1.2 1 32907 1257 65 19849 1.2 1 18973 876 66 20707 1.2 1 19730 977 67 22562 1.2 1 21879 683 68 10011 1.2 1 9445 566 69 12632 1.2 1 12099 533 70 14532 1.2 1 14023 509 71 7515 1.2 1 7132 383 72 4658 1.2 1 4386 272 73 4109 1.2 1 3855 254 74 4430 1.2 1 4164 266 75 4997 1.2 1 4703 294 76 6990 1.2 1 6619 371 77 7180 1.2 1 6756 424 78 8137 1.2 1 7739 398 79 8750 1.2 1 8333 417 80 8893 1.2 1 8479 414 81 9011 1.2 1 8575 436 82 9311 1.2 1 8857 454 83 10956 1.2 1 10471 485 84 9962 1.2 1 9468 494 85 9966 1.2 1 9503 463 86 9116 1.2 1 8671 445 87 8381 1.2 1 7968 413 88 8125 1.2 1 7755 370 89 7617 1.2 1 7241 376 90 7778 1.2 1 7426 352 91 7376 1.2 1 7068 308 92 7278 1.2 1 6962 316 93 7102 1.2 1 6776 326 94 6863 1.2 1 6580 283 95 6729 1.2 1 6451 278 96 6771 1.2 1 6477 294 97 6955 1.2 1 6667 288 98 6822 1.2 1 6553 269 99 6758 1.2 1 6476 282 100 6869 1.2 1 6599 270 101 6205 1.2 1 5946 259 102 5930 1.2 1 5714 216 103 5910 1.2 1 5662 248 104 5710 1.2 1 5472 238 105 5801 1.2 1 5562 239 106 5897 1.2 1 5627 270 107 5780 1.2 1 5557 223 108 5734 1.2 1 5533 201 109 5642 1.2 1 5425 217 110 5366 1.2 1 5120 246 111 5315 1.2 1 5103 212 112 5253 1.2 1 5036 217 113 5324 1.2 1 5123 201 114 5406 1.2 1 5157 249 115 5284 1.2 1 5080 204 116 5268 1.2 1 5051 217 117 5349 1.2 1 5110 239 118 5506 1.2 1 5234 272 119 5565 1.2 1 5261 304 120 5476 1.2 1 5104 372 121 5346 1.2 1 4967 379 122 5650 1.2 1 5104 546 123 5849 1.2 1 5171 678 124 5702 1.2 1 4824 878 125 5959 1.2 1 4813 1146 126 5684 1.2 1 4364 1320 127 5601 1.2 1 4037 1564 128 5856 1.2 1 3977 1879 129 6134 1.2 1 4077 2057 130 5922 1.2 1 3492 2430 131 6160 1.2 1 3323 2837 132 6232 1.2 1 3015 3217 133 6703 1.2 1 2944 3759 134 6365 1.2 1 2507 3858 135 6128 1.2 1 2237 3891 136 5439 1.2 1 1931 3508 137 4274 1.2 1 1713 2561 138 3416 1.2 1 1725 1691 139 2837 1.2 1 1619 1218 140 2544 1.2 1 1545 999 141 2676 1.2 1 1996 680 142 1999 1.2 1 1534 465 143 2218 1.2 1 1790 428 144 2686 1.2 1 2205 481 145 3408 1.2 1 2761 647 146 1913 1.2 1 1462 451 147 442 1.2 1 284 158 148 5529 1.2 1 4788 741 149 2076 1.2 1 1710 366 150 43202 1.2 1 38134 5068 RUN STATISTICS FOR INPUT FILE: SRR18245595_2.fastq.gz ============================================= 80869598 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 80869598 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 141263 (0.17%)