SUMMARISING RUN PARAMETERS ========================== Input filename: SRR546473_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: 10729). 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 SRR546473_1.fastq.gz Processing single-end reads on 1 core ... Finished in 2332.336 s (29.588 µs/read; 2.03 M reads/minute). === Summary === Total reads processed: 78,826,347 Reads with adapters: 29,948,664 (38.0%) Reads written (passing filters): 78,826,347 (100.0%) Total basepairs processed: 7,094,371,230 bp Quality-trimmed: 125,745,119 bp (1.8%) Total written (filtered): 6,905,323,856 bp (97.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29948664 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.8% C: 0.1% G: 14.3% T: 47.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22562512 19706586.8 0 22562512 2 4079086 4926646.7 0 4079086 3 1378825 1231661.7 0 1378825 4 652017 307915.4 0 652017 5 56819 76978.9 0 56819 6 50367 19244.7 0 50367 7 49553 4811.2 0 49553 8 45791 1202.8 0 45791 9 53117 300.7 0 52192 925 10 50397 75.2 1 48258 2139 11 48405 18.8 1 47235 1170 12 39470 4.7 1 38577 893 13 40005 1.2 1 39019 986 14 39037 1.2 1 37928 1109 15 45724 1.2 1 44609 1115 16 36305 1.2 1 35157 1148 17 48558 1.2 1 47358 1200 18 38300 1.2 1 37265 1035 19 42080 1.2 1 41094 986 20 34684 1.2 1 33831 853 21 33763 1.2 1 32944 819 22 35171 1.2 1 34344 827 23 30196 1.2 1 29434 762 24 33650 1.2 1 32876 774 25 27336 1.2 1 26527 809 26 40646 1.2 1 39687 959 27 32250 1.2 1 31507 743 28 25003 1.2 1 24438 565 29 21816 1.2 1 21268 548 30 26465 1.2 1 25881 584 31 22102 1.2 1 21599 503 32 19722 1.2 1 19271 451 33 20195 1.2 1 19723 472 34 19430 1.2 1 18976 454 35 18258 1.2 1 17698 560 36 28729 1.2 1 28001 728 37 23825 1.2 1 23222 603 38 19751 1.2 1 19286 465 39 15903 1.2 1 15567 336 40 4705 1.2 1 4535 170 41 7368 1.2 1 7178 190 42 7272 1.2 1 7015 257 43 5388 1.2 1 5253 135 44 3787 1.2 1 3643 144 45 5949 1.2 1 5771 178 46 5013 1.2 1 4873 140 47 3321 1.2 1 3222 99 48 2822 1.2 1 2745 77 49 3354 1.2 1 3260 94 50 2751 1.2 1 2684 67 51 1859 1.2 1 1804 55 52 2016 1.2 1 1959 57 53 1821 1.2 1 1770 51 54 2341 1.2 1 2316 25 55 1155 1.2 1 1126 29 56 1018 1.2 1 995 23 57 266 1.2 1 259 7 58 318 1.2 1 304 14 59 218 1.2 1 212 6 60 329 1.2 1 322 7 61 54 1.2 1 53 1 62 33 1.2 1 27 6 63 40 1.2 1 38 2 64 45 1.2 1 44 1 65 57 1.2 1 55 2 66 55 1.2 1 53 2 67 19 1.2 1 17 2 68 2 1.2 1 2 69 2 1.2 1 0 2 70 1 1.2 1 1 71 3 1.2 1 3 76 1 1.2 1 1 79 2 1.2 1 0 2 80 1 1.2 1 0 1 82 1 1.2 1 0 1 83 3 1.2 1 1 2 84 1 1.2 1 0 1 85 2 1.2 1 0 2 87 1 1.2 1 0 1 88 1 1.2 1 0 1 89 1 1.2 1 0 1 90 5 1.2 1 0 5 RUN STATISTICS FOR INPUT FILE: SRR546473_1.fastq.gz ============================================= 78826347 sequences processed in total