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.sampleA_1.fastq.gz -p fastq/merge.sampleA_2.fastq.gz sampleA_1.fastq.gz sampleA_2.fastq.gz Processing reads on 2 cores in paired-end mode ... Finished in 1.15 s (28 us/read; 2.13 M reads/minute). === Summary === Total read pairs processed: 40,685 Read 1 with adapter: 1,767 (4.3%) Read 2 with adapter: 454 (1.1%) Pairs written (passing filters): 40,672 (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): 9,008,246 bp (88.6%) Read 1: 4,501,940 bp Read 2: 4,506,306 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 1767 times No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.3% C: 0.3% G: 23.9% T: 37.4% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 3 986 635.7 0 986 4 426 158.9 0 426 5 20 39.7 0 20 6 18 9.9 0 18 7 17 2.5 0 17 8 7 0.6 0 7 9 14 0.2 0 13 1 10 11 0.0 1 9 2 11 8 0.0 1 8 12 10 0.0 1 10 13 14 0.0 1 13 1 14 17 0.0 1 15 2 15 7 0.0 1 6 1 16 15 0.0 1 14 1 17 7 0.0 1 7 18 8 0.0 1 8 19 10 0.0 1 10 20 4 0.0 1 3 1 21 9 0.0 1 8 1 22 3 0.0 1 3 23 10 0.0 1 9 1 24 12 0.0 1 12 25 5 0.0 1 5 26 3 0.0 1 3 27 5 0.0 1 5 28 6 0.0 1 6 29 8 0.0 1 8 30 5 0.0 1 4 1 31 6 0.0 1 6 32 2 0.0 1 1 1 33 4 0.0 1 4 34 2 0.0 1 2 35 1 0.0 1 1 36 2 0.0 1 2 37 4 0.0 1 4 38 5 0.0 1 5 39 4 0.0 1 4 40 3 0.0 1 3 41 2 0.0 1 2 42 2 0.0 1 2 43 3 0.0 1 3 44 4 0.0 1 4 45 4 0.0 1 4 46 2 0.0 1 2 47 5 0.0 1 5 48 1 0.0 1 1 49 1 0.0 1 1 52 1 0.0 1 1 53 4 0.0 1 4 54 2 0.0 1 2 56 1 0.0 1 1 57 1 0.0 1 1 58 4 0.0 1 4 59 3 0.0 1 3 60 2 0.0 1 2 61 1 0.0 1 1 62 2 0.0 1 2 65 1 0.0 1 1 66 3 0.0 1 3 67 1 0.0 1 1 68 1 0.0 1 1 70 2 0.0 1 2 73 1 0.0 1 1 74 2 0.0 1 2 78 1 0.0 1 1 80 1 0.0 1 1 82 1 0.0 1 1 84 1 0.0 1 1 85 1 0.0 1 1 86 1 0.0 1 1 91 1 0.0 1 1 92 1 0.0 1 1 97 1 0.0 1 1 99 1 0.0 1 1 101 1 0.0 1 1 111 2 0.0 1 2 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 454 times No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.9% C: 19.6% G: 0.2% T: 30.8% none/other: 0.4% Overview of removed sequences length count expect max.err error counts 3 75 635.7 0 75 4 30 158.9 0 30 5 19 39.7 0 19 6 18 9.9 0 18 7 16 2.5 0 16 8 7 0.6 0 7 9 11 0.2 0 11 10 10 0.0 1 9 1 11 8 0.0 1 8 12 10 0.0 1 10 13 14 0.0 1 11 3 14 17 0.0 1 17 15 7 0.0 1 6 1 16 15 0.0 1 14 1 17 7 0.0 1 7 18 8 0.0 1 8 19 10 0.0 1 9 1 20 4 0.0 1 4 21 9 0.0 1 9 22 3 0.0 1 3 23 10 0.0 1 10 24 12 0.0 1 12 25 5 0.0 1 5 26 3 0.0 1 3 27 5 0.0 1 5 28 6 0.0 1 6 29 8 0.0 1 7 1 30 5 0.0 1 5 31 6 0.0 1 6 32 2 0.0 1 2 33 4 0.0 1 4 34 2 0.0 1 2 35 1 0.0 1 1 36 2 0.0 1 2 37 4 0.0 1 4 38 5 0.0 1 5 39 4 0.0 1 4 40 3 0.0 1 3 41 2 0.0 1 2 42 2 0.0 1 2 43 3 0.0 1 3 44 4 0.0 1 4 45 4 0.0 1 4 46 2 0.0 1 2 47 5 0.0 1 5 48 1 0.0 1 1 49 1 0.0 1 1 52 1 0.0 1 1 53 4 0.0 1 4 54 2 0.0 1 2 56 1 0.0 1 1 57 1 0.0 1 1 58 4 0.0 1 4 59 3 0.0 1 3 60 2 0.0 1 2 61 1 0.0 1 1 62 2 0.0 1 2 65 1 0.0 1 1 66 3 0.0 1 3 67 1 0.0 1 1 68 1 0.0 1 1 70 2 0.0 1 2 73 1 0.0 1 1 74 2 0.0 1 2 78 1 0.0 1 1 80 1 0.0 1 1 82 1 0.0 1 1 84 1 0.0 1 1 85 1 0.0 1 1 86 1 0.0 1 1 91 1 0.0 1 1 92 1 0.0 1 1 97 1 0.0 1 1 99 1 0.0 1 1 101 1 0.0 1 1 111 2 0.0 1 2