SUMMARISING RUN PARAMETERS ========================== Input filename: SRR546472_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: 13521). 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 SRR546472_2.fastq.gz Processing single-end reads on 1 core ... Finished in 2107.461 s (30.826 µs/read; 1.95 M reads/minute). === Summary === Total reads processed: 68,365,315 Reads with adapters: 34,718,811 (50.8%) Reads written (passing filters): 68,365,315 (100.0%) Total basepairs processed: 6,152,878,350 bp Quality-trimmed: 126,461,476 bp (2.1%) Total written (filtered): 5,966,221,925 bp (97.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 34718811 times Minimum overlap: 1 No. of allowed errors: 1-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.8% C: 17.6% G: 0.3% T: 29.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 33364066 17091328.8 0 33364066 2 53235 4272832.2 0 53235 3 54237 1068208.0 0 54237 4 52511 267052.0 0 52511 5 59369 66763.0 0 59369 6 37490 16690.8 0 37490 7 34692 4172.7 0 34692 8 41813 1043.2 0 41813 9 46650 260.8 0 46517 133 10 37126 65.2 1 36552 574 11 40525 16.3 1 39530 995 12 34552 4.1 1 33895 657 13 36764 1.0 1 35864 900 14 33221 1.0 1 32527 694 15 35733 1.0 1 34704 1029 16 39293 1.0 1 38122 1171 17 33444 1.0 1 32611 833 18 35748 1.0 1 34766 982 19 31791 1.0 1 31017 774 20 35063 1.0 1 33935 1128 21 39042 1.0 1 37801 1241 22 31727 1.0 1 30978 749 23 27769 1.0 1 27133 636 24 26856 1.0 1 26270 586 25 27521 1.0 1 26782 739 26 30190 1.0 1 29277 913 27 30295 1.0 1 29462 833 28 25271 1.0 1 24649 622 29 27763 1.0 1 27027 736 30 22485 1.0 1 22026 459 31 20330 1.0 1 19940 390 32 19151 1.0 1 18739 412 33 19352 1.0 1 18891 461 34 19582 1.0 1 19144 438 35 16682 1.0 1 16306 376 36 17138 1.0 1 16745 393 37 16842 1.0 1 16418 424 38 16338 1.0 1 15902 436 39 17017 1.0 1 16518 499 40 18196 1.0 1 17739 457 41 12662 1.0 1 12394 268 42 10806 1.0 1 10555 251 43 12641 1.0 1 12350 291 44 10066 1.0 1 9865 201 45 8067 1.0 1 7918 149 46 7109 1.0 1 6983 126 47 6846 1.0 1 6723 123 48 5485 1.0 1 5381 104 49 5166 1.0 1 5044 122 50 5589 1.0 1 5500 89 51 3713 1.0 1 3646 67 52 3358 1.0 1 3284 74 53 3020 1.0 1 2967 53 54 2708 1.0 1 2650 58 55 2018 1.0 1 1980 38 56 1796 1.0 1 1748 48 57 1483 1.0 1 1449 34 58 1466 1.0 1 1437 29 59 965 1.0 1 948 17 60 891 1.0 1 870 21 61 1129 1.0 1 1095 34 62 780 1.0 1 757 23 63 1332 1.0 1 1285 47 64 2407 1.0 1 2381 26 65 306 1.0 1 295 11 66 89 1.0 1 85 4 67 6 1.0 1 6 69 1 1.0 1 1 70 4 1.0 1 3 1 71 29 1.0 1 26 3 73 1 1.0 1 0 1 76 2 1.0 1 2 RUN STATISTICS FOR INPUT FILE: SRR546472_2.fastq.gz ============================================= 68365315 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 68365315 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 762103 (1.11%)