SUMMARISING RUN PARAMETERS ========================== Input filename: SRR546471_1.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: 21296). 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 SRR546471_1.fastq.gz Processing single-end reads on 1 core ... Finished in 2087.188 s (29.480 µs/read; 2.04 M reads/minute). === Summary === Total reads processed: 70,799,691 Reads with adapters: 27,283,386 (38.5%) Reads written (passing filters): 70,799,691 (100.0%) Total basepairs processed: 6,371,972,190 bp Quality-trimmed: 119,364,311 bp (1.9%) Total written (filtered): 6,176,114,101 bp (96.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 27283386 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.4% C: 0.2% G: 15.5% T: 46.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19533223 17699922.8 0 19533223 2 3775345 4424980.7 0 3775345 3 1303572 1106245.2 0 1303572 4 627302 276561.3 0 627302 5 83291 69140.3 0 83291 6 71928 17285.1 0 71928 7 72012 4321.3 0 72012 8 68179 1080.3 0 68179 9 82302 270.1 0 81252 1050 10 75148 67.5 1 72711 2437 11 73054 16.9 1 71416 1638 12 59201 4.2 1 57784 1417 13 60262 1.1 1 58782 1480 14 59284 1.1 1 57512 1772 15 69356 1.1 1 67650 1706 16 56063 1.1 1 54244 1819 17 77227 1.1 1 75308 1919 18 59030 1.1 1 57435 1595 19 67617 1.1 1 65844 1773 20 54516 1.1 1 53169 1347 21 54177 1.1 1 52886 1291 22 57517 1.1 1 56255 1262 23 48891 1.1 1 47665 1226 24 54333 1.1 1 53112 1221 25 45972 1.1 1 44589 1383 26 70166 1.1 1 68681 1485 27 55337 1.1 1 54135 1202 28 40788 1.1 1 39882 906 29 36826 1.1 1 35913 913 30 45771 1.1 1 44844 927 31 37307 1.1 1 36458 849 32 34206 1.1 1 33474 732 33 33739 1.1 1 32998 741 34 33739 1.1 1 33067 672 35 31599 1.1 1 30704 895 36 51677 1.1 1 50709 968 37 41269 1.1 1 40419 850 38 36921 1.1 1 36237 684 39 29211 1.1 1 28781 430 40 9031 1.1 1 8770 261 41 13397 1.1 1 13088 309 42 12679 1.1 1 12452 227 43 9520 1.1 1 9346 174 44 6815 1.1 1 6615 200 45 10770 1.1 1 10546 224 46 8989 1.1 1 8816 173 47 5822 1.1 1 5696 126 48 5086 1.1 1 4955 131 49 6253 1.1 1 6126 127 50 4886 1.1 1 4803 83 51 3532 1.1 1 3461 71 52 3501 1.1 1 3424 77 53 3419 1.1 1 3327 92 54 4465 1.1 1 4404 61 55 2395 1.1 1 2336 59 56 2096 1.1 1 2065 31 57 478 1.1 1 453 25 58 690 1.1 1 671 19 59 496 1.1 1 469 27 60 800 1.1 1 784 16 61 161 1.1 1 159 2 62 84 1.1 1 76 8 63 124 1.1 1 118 6 64 117 1.1 1 109 8 65 163 1.1 1 155 8 66 169 1.1 1 159 10 67 54 1.1 1 50 4 68 4 1.1 1 1 3 69 5 1.1 1 1 4 70 5 1.1 1 0 5 71 3 1.1 1 1 2 72 2 1.1 1 0 2 74 1 1.1 1 0 1 76 1 1.1 1 0 1 80 1 1.1 1 0 1 83 3 1.1 1 0 3 84 1 1.1 1 0 1 85 2 1.1 1 0 2 87 2 1.1 1 0 2 88 3 1.1 1 0 3 89 3 1.1 1 0 3 RUN STATISTICS FOR INPUT FILE: SRR546471_1.fastq.gz ============================================= 70799691 sequences processed in total