This is cutadapt 2.3 with Python 3.7.3 Command line parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cutIL_NP_MseI_1.fq.gz -p /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cutIL_NP_MseI_2.fq.gz /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//raw/NP_MseI/NP_MseI_R1.fastq.gz /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//raw/NP_MseI/NP_MseI_R2.fastq.gz -m 8 Processing reads on 1 core in paired-end mode ... Finished in 0.17 s (63 us/read; 0.95 M reads/minute). === Summary === Total read pairs processed: 2,650 Read 1 with adapter: 67 (2.5%) Read 2 with adapter: 49 (1.8%) Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 2,650 (100.0%) Total basepairs processed: 530,000 bp Read 1: 265,000 bp Read 2: 265,000 bp Total written (filtered): 528,095 bp (99.6%) Read 1: 263,890 bp Read 2: 264,205 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; Type: regular 3'; Length: 34; Trimmed: 67 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-34 bp: 3 Bases preceding removed adapters: A: 10.4% C: 7.5% G: 19.4% T: 62.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 21 41.4 0 21 4 1 10.4 0 1 5 1 2.6 0 1 6 9 0.6 0 9 7 1 0.2 0 1 9 4 0.0 0 2 2 10 1 0.0 1 1 13 1 0.0 1 1 15 1 0.0 1 1 16 1 0.0 1 0 1 17 1 0.0 1 1 20 1 0.0 2 1 21 2 0.0 2 2 26 2 0.0 2 2 31 1 0.0 3 1 33 3 0.0 3 3 37 9 0.0 3 6 3 38 4 0.0 3 2 2 45 1 0.0 3 0 1 48 2 0.0 3 2 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT; Type: regular 3'; Length: 58; Trimmed: 49 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50-58 bp: 5 Bases preceding removed adapters: A: 12.2% C: 12.2% G: 12.2% T: 63.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 8 41.4 0 8 4 5 10.4 0 5 6 9 0.6 0 9 7 1 0.2 0 1 9 3 0.0 0 1 2 10 1 0.0 1 1 13 1 0.0 1 1 15 1 0.0 1 0 1 16 1 0.0 1 0 1 17 1 0.0 1 1 20 1 0.0 2 1 21 2 0.0 2 2 26 1 0.0 2 1 31 1 0.0 3 1 33 3 0.0 3 1 2 37 6 0.0 3 0 0 0 6 38 4 0.0 3 0 0 2 1 1 This is cutadapt 2.3 with Python 3.7.3 Command line parameters: -g pr_plasmid1=TGACTATGGTTGCAAGAGACGAAGCTTCGTCTCAGTCTTAA -y {name} -g pr_plasmid2=ATGTTCTCCTCATG -y {name} -G pr_plasmid1=TGACTATGGTTGCAAGAGACGAAGCTTCGTCTCAGTCTTAA -y {name} -G pr_plasmid2=ATGTTCTCCTCATG -y {name} -o /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cut_barc_praimers_cutIL_NP_MseI_1.fq.gz -p /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cut_barc_praimers_cutIL_NP_MseI_2.fq.gz /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cutIL_NP_MseI_1.fq.gz /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cutIL_NP_MseI_2.fq.gz --overlap 20 Processing reads on 1 core in paired-end mode ... Finished in 0.20 s (75 us/read; 0.80 M reads/minute). === Summary === Total read pairs processed: 2,650 Read 1 with adapter: 1,378 (52.0%) Read 2 with adapter: 2,018 (76.2%) Pairs written (passing filters): 2,650 (100.0%) Total basepairs processed: 528,095 bp Read 1: 263,890 bp Read 2: 264,205 bp Total written (filtered): 442,957 bp (83.9%) Read 1: 207,015 bp Read 2: 235,942 bp === First read: Adapter pr_plasmid1 === Sequence: TGACTATGGTTGCAAGAGACGAAGCTTCGTCTCAGTCTTAA; Type: regular 5'; Length: 41; Trimmed: 1378 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-41 bp: 4 Overview of removed sequences length count expect max.err error counts 38 5 0.0 3 0 0 0 0 5 39 20 0.0 3 0 0 0 18 2 40 3 0.0 4 0 0 2 0 1 41 1143 0.0 4 1028 99 9 5 2 42 2 0.0 4 0 2 43 192 0.0 4 0 0 171 10 11 44 3 0.0 4 0 0 0 3 45 10 0.0 4 0 0 0 0 10 === First read: Adapter pr_plasmid2 === Sequence: ATGTTCTCCTCATG; Type: regular 5'; Length: 14; Trimmed: 0 times. === Second read: Adapter pr_plasmid1 === Sequence: TGACTATGGTTGCAAGAGACGAAGCTTCGTCTCAGTCTTAA; Type: regular 5'; Length: 41; Trimmed: 0 times. === Second read: Adapter pr_plasmid2 === Sequence: ATGTTCTCCTCATG; Type: regular 5'; Length: 14; Trimmed: 2018 times. No. of allowed errors: 0-9 bp: 0; 10-14 bp: 1 Overview of removed sequences length count expect max.err error counts 13 7 0.0 1 0 7 14 1993 0.0 1 1914 79 15 18 0.0 1 0 18 This is cutadapt 2.3 with Python 3.7.3 Command line parameters: -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -A AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT -o /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cutIL_NP_Tru9I_1.fq.gz -p /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cutIL_NP_Tru9I_2.fq.gz /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//raw/NP_Tru9I/NP_Tru9I_R1.fastq.gz /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//raw/NP_Tru9I/NP_Tru9I_R2.fastq.gz -m 8 Processing reads on 1 core in paired-end mode ... Finished in 0.14 s (65 us/read; 0.92 M reads/minute). === Summary === Total read pairs processed: 2,128 Read 1 with adapter: 56 (2.6%) Read 2 with adapter: 38 (1.8%) Pairs that were too short: 0 (0.0%) Pairs written (passing filters): 2,128 (100.0%) Total basepairs processed: 425,600 bp Read 1: 212,800 bp Read 2: 212,800 bp Total written (filtered): 424,485 bp (99.7%) Read 1: 212,182 bp Read 2: 212,303 bp === First read: Adapter 1 === Sequence: AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC; Type: regular 3'; Length: 34; Trimmed: 56 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-34 bp: 3 Bases preceding removed adapters: A: 3.6% C: 7.1% G: 66.1% T: 23.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 17 33.2 0 17 4 2 8.3 0 2 5 2 2.1 0 2 6 2 0.5 0 2 8 1 0.0 0 1 9 2 0.0 0 2 10 1 0.0 1 1 11 16 0.0 1 13 3 12 1 0.0 1 1 14 1 0.0 1 1 15 2 0.0 1 2 16 1 0.0 1 1 17 1 0.0 1 1 20 2 0.0 2 2 32 1 0.0 3 1 37 2 0.0 3 2 38 1 0.0 3 1 52 1 0.0 3 1 === Second read: Adapter 2 === Sequence: AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCCGTATCATT; Type: regular 3'; Length: 58; Trimmed: 38 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-49 bp: 4; 50-58 bp: 5 Bases preceding removed adapters: A: 21.1% C: 52.6% G: 5.3% T: 21.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 3 2 33.2 0 2 4 2 8.3 0 2 5 2 2.1 0 2 6 2 0.5 0 2 8 1 0.0 0 1 9 1 0.0 0 0 1 10 1 0.0 1 0 1 11 16 0.0 1 12 4 12 1 0.0 1 1 14 1 0.0 1 1 15 1 0.0 1 1 16 1 0.0 1 1 17 1 0.0 1 0 1 20 2 0.0 2 2 32 1 0.0 3 0 0 0 1 37 2 0.0 3 0 0 0 2 38 1 0.0 3 0 0 0 1 This is cutadapt 2.3 with Python 3.7.3 Command line parameters: -g pr_plasmid1=TGACTATGGTTGCAAGAGACGAAGCTTCGTCTCAGTCTTAA -y {name} -g pr_plasmid2=ATGTTCTCCTCATG -y {name} -G pr_plasmid1=TGACTATGGTTGCAAGAGACGAAGCTTCGTCTCAGTCTTAA -y {name} -G pr_plasmid2=ATGTTCTCCTCATG -y {name} -o /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cut_barc_praimers_cutIL_NP_Tru9I_1.fq.gz -p /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cut_barc_praimers_cutIL_NP_Tru9I_2.fq.gz /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cutIL_NP_Tru9I_1.fq.gz /mnt/scratch/ws/psbelokopytova/202301211721polina/4c_plasmid/2022-11-22//cutadapt/cutIL_NP_Tru9I_2.fq.gz --overlap 20 Processing reads on 1 core in paired-end mode ... Finished in 0.18 s (84 us/read; 0.71 M reads/minute). === Summary === Total read pairs processed: 2,128 Read 1 with adapter: 1,048 (49.2%) Read 2 with adapter: 1,549 (72.8%) Pairs written (passing filters): 2,128 (100.0%) Total basepairs processed: 424,485 bp Read 1: 212,182 bp Read 2: 212,303 bp Total written (filtered): 359,753 bp (84.8%) Read 1: 169,130 bp Read 2: 190,623 bp === First read: Adapter pr_plasmid1 === Sequence: TGACTATGGTTGCAAGAGACGAAGCTTCGTCTCAGTCTTAA; Type: regular 5'; Length: 41; Trimmed: 1048 times. No. of allowed errors: 0-9 bp: 0; 10-19 bp: 1; 20-29 bp: 2; 30-39 bp: 3; 40-41 bp: 4 Overview of removed sequences length count expect max.err error counts 38 13 0.0 3 0 0 0 7 6 39 18 0.0 3 0 0 0 1 17 40 23 0.0 4 0 6 4 12 1 41 913 0.0 4 814 87 7 4 1 42 3 0.0 4 0 0 0 0 3 43 56 0.0 4 0 0 56 44 21 0.0 4 0 0 0 21 45 1 0.0 4 0 0 0 0 1 === First read: Adapter pr_plasmid2 === Sequence: ATGTTCTCCTCATG; Type: regular 5'; Length: 14; Trimmed: 0 times. === Second read: Adapter pr_plasmid1 === Sequence: TGACTATGGTTGCAAGAGACGAAGCTTCGTCTCAGTCTTAA; Type: regular 5'; Length: 41; Trimmed: 0 times. === Second read: Adapter pr_plasmid2 === Sequence: ATGTTCTCCTCATG; Type: regular 5'; Length: 14; Trimmed: 1549 times. No. of allowed errors: 0-9 bp: 0; 10-14 bp: 1 Overview of removed sequences length count expect max.err error counts 13 6 0.0 1 0 6 14 1543 0.0 1 1501 42