This is cutadapt 2.10 with Python 3.6.7 Command line parameters: -j 2 -a AGATCGGAAGAGC -A AGATCGGAAGAGC -q 20 -m 36 -O 3 -o fastq/merge.sampleB_1.fastq.gz -p fastq/merge.sampleB_2.fastq.gz sampleB_1.fastq.gz sampleB_2.fastq.gz Processing reads on 2 cores in paired-end mode ... Finished in 1.08 s (27 us/read; 2.26 M reads/minute). === Summary === Total read pairs processed: 40,685 Read 1 with adapter: 1,699 (4.2%) Read 2 with adapter: 474 (1.2%) Pairs written (passing filters): 40,675 (100.0%) Total basepairs processed: 10,171,250 bp Read 1: 5,085,625 bp Read 2: 5,085,625 bp Quality-trimmed: 1,139,180 bp (11.2%) Read 1: 569,590 bp Read 2: 569,590 bp Total written (filtered): 9,008,333 bp (88.6%) Read 1: 4,502,154 bp Read 2: 4,506,179 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1699 times No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.8% C: 0.5% G: 22.8% T: 37.8% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 988 635.7 0 988 4 344 158.9 0 344 5 18 39.7 0 18 6 7 9.9 0 7 7 10 2.5 0 10 8 17 0.6 0 17 9 15 0.2 0 13 2 10 13 0.0 1 10 3 11 14 0.0 1 14 12 15 0.0 1 14 1 13 12 0.0 1 9 3 14 11 0.0 1 11 15 7 0.0 1 7 16 10 0.0 1 9 1 17 10 0.0 1 10 18 12 0.0 1 12 19 4 0.0 1 4 20 6 0.0 1 6 21 11 0.0 1 11 22 6 0.0 1 5 1 23 6 0.0 1 6 24 7 0.0 1 7 25 10 0.0 1 10 26 7 0.0 1 7 27 3 0.0 1 3 28 5 0.0 1 5 29 8 0.0 1 8 30 6 0.0 1 6 31 9 0.0 1 9 32 9 0.0 1 9 33 6 0.0 1 6 34 4 0.0 1 4 35 5 0.0 1 5 36 4 0.0 1 4 37 3 0.0 1 3 38 4 0.0 1 4 39 6 0.0 1 6 40 5 0.0 1 5 41 4 0.0 1 4 42 1 0.0 1 1 43 6 0.0 1 6 44 1 0.0 1 1 45 4 0.0 1 4 46 2 0.0 1 2 47 4 0.0 1 4 48 2 0.0 1 2 49 3 0.0 1 3 50 1 0.0 1 1 51 2 0.0 1 2 52 2 0.0 1 2 53 2 0.0 1 2 54 1 0.0 1 1 55 3 0.0 1 3 57 3 0.0 1 3 59 1 0.0 1 1 62 2 0.0 1 2 63 1 0.0 1 1 64 1 0.0 1 1 65 1 0.0 1 1 67 2 0.0 1 2 69 1 0.0 1 1 72 1 0.0 1 1 73 1 0.0 1 1 77 2 0.0 1 2 78 1 0.0 1 1 81 1 0.0 1 1 83 1 0.0 1 1 84 1 0.0 1 1 85 1 0.0 1 1 87 1 0.0 1 1 96 1 0.0 1 1 111 1 0.0 1 1 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 474 times No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 50.4% C: 18.6% G: 0.2% T: 30.6% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 3 84 635.7 0 84 4 30 158.9 0 30 5 17 39.7 0 17 6 7 9.9 0 7 7 9 2.5 0 9 8 15 0.6 0 15 9 14 0.2 0 14 10 11 0.0 1 10 1 11 14 0.0 1 12 2 12 15 0.0 1 12 3 13 12 0.0 1 12 14 11 0.0 1 11 15 7 0.0 1 6 1 16 10 0.0 1 10 17 10 0.0 1 9 1 18 12 0.0 1 12 19 4 0.0 1 4 20 6 0.0 1 6 21 11 0.0 1 11 22 6 0.0 1 6 23 6 0.0 1 6 24 7 0.0 1 6 1 25 10 0.0 1 10 26 7 0.0 1 7 27 3 0.0 1 3 28 5 0.0 1 5 29 8 0.0 1 8 30 6 0.0 1 6 31 9 0.0 1 9 32 9 0.0 1 9 33 6 0.0 1 6 34 4 0.0 1 4 35 5 0.0 1 5 36 4 0.0 1 4 37 3 0.0 1 3 38 4 0.0 1 4 39 6 0.0 1 6 40 5 0.0 1 5 41 4 0.0 1 4 42 1 0.0 1 1 43 6 0.0 1 6 44 1 0.0 1 1 45 4 0.0 1 4 46 2 0.0 1 2 47 4 0.0 1 4 48 2 0.0 1 2 49 3 0.0 1 3 50 1 0.0 1 1 51 2 0.0 1 2 52 2 0.0 1 2 53 2 0.0 1 2 54 1 0.0 1 1 55 3 0.0 1 3 57 3 0.0 1 3 59 1 0.0 1 1 62 2 0.0 1 2 63 1 0.0 1 1 64 1 0.0 1 1 65 1 0.0 1 1 67 2 0.0 1 2 69 1 0.0 1 1 72 1 0.0 1 1 73 1 0.0 1 1 77 2 0.0 1 2 78 1 0.0 1 1 81 1 0.0 1 1 83 1 0.0 1 1 84 1 0.0 1 1 85 1 0.0 1 1 87 1 0.0 1 1 96 1 0.0 1 1 111 1 0.0 1 1