No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) Path to Cutadapt set as: 'cutadapt' (default) Cutadapt seems to be working fine (tested command 'cutadapt --version') AUTO-DETECTING ADAPTER TYPE =========================== Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> zr2096_10_s1_R1_val_1.fq.gz <<) Found perfect matches for the following adapter sequences: Adapter type Count Sequence Sequences analysed Percentage Illumina 0 AGATCGGAAGAGC 1000000 0.00 smallRNA 0 TGGAATTCTCGG 1000000 0.00 Nextera 0 CTGTCTCTTATA 1000000 0.00 Unable to auto-detect most prominent adapter from the first specified file (count Illumina: 0, count smallRNA: 0) Defaulting to Illumina universal adapter ( AGATCGGAAGAGC ). Specify -a SEQUENCE to avoid this behavior). Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_10_s1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_10_s1_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_10_s1_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_10_s1_R1_val_1.fq.gz <<< 10000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_10_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 317.85 s (18 us/read; 3.31 M reads/minute). === Summary === Total reads processed: 17,535,871 Reads with adapters: 9,111,482 (52.0%) Reads written (passing filters): 17,535,871 (100.0%) Total basepairs processed: 1,343,649,791 bp Quality-trimmed: 2,371,417 bp (0.2%) Total written (filtered): 1,330,382,298 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9111482 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 41.8% C: 11.4% G: 10.5% T: 36.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7880131 4383967.8 0 7880131 2 916137 1095991.9 0 916137 3 254812 273998.0 0 254812 4 37063 68499.5 0 37063 5 4077 17124.9 0 4077 6 3562 4281.2 0 3562 7 985 1070.3 0 985 8 459 267.6 0 459 9 691 66.9 0 233 458 10 969 16.7 1 224 745 11 1142 4.2 1 141 1001 12 585 1.0 1 118 467 13 696 0.3 1 0 696 14 1021 0.3 1 0 1021 15 1963 0.3 1 0 1963 16 3493 0.3 1 0 3493 17 2845 0.3 1 0 2845 18 175 0.3 1 0 175 19 51 0.3 1 0 51 20 27 0.3 1 0 27 21 31 0.3 1 0 31 22 27 0.3 1 0 27 23 25 0.3 1 0 25 24 21 0.3 1 0 21 25 32 0.3 1 0 32 26 28 0.3 1 0 28 27 18 0.3 1 0 18 28 27 0.3 1 0 27 29 16 0.3 1 0 16 30 21 0.3 1 0 21 31 27 0.3 1 0 27 32 16 0.3 1 0 16 33 18 0.3 1 0 18 34 12 0.3 1 0 12 35 16 0.3 1 0 16 36 13 0.3 1 0 13 37 14 0.3 1 0 14 38 15 0.3 1 0 15 39 11 0.3 1 0 11 40 9 0.3 1 0 9 41 19 0.3 1 0 19 42 14 0.3 1 0 14 43 8 0.3 1 0 8 44 14 0.3 1 0 14 45 9 0.3 1 0 9 46 7 0.3 1 0 7 47 13 0.3 1 0 13 48 13 0.3 1 0 13 49 10 0.3 1 0 10 50 13 0.3 1 0 13 51 11 0.3 1 0 11 52 9 0.3 1 0 9 53 9 0.3 1 0 9 54 9 0.3 1 0 9 55 3 0.3 1 0 3 56 6 0.3 1 0 6 57 2 0.3 1 0 2 58 4 0.3 1 0 4 59 4 0.3 1 0 4 60 2 0.3 1 0 2 61 5 0.3 1 0 5 62 4 0.3 1 0 4 63 3 0.3 1 0 3 64 3 0.3 1 0 3 65 2 0.3 1 0 2 66 2 0.3 1 0 2 67 1 0.3 1 0 1 68 1 0.3 1 0 1 70 1 0.3 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_10_s1_R1_val_1.fq.gz ============================================= 17535871 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_10_s1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_10_s1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_10_s1_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_10_s1_R2_val_2.fq.gz <<< 10000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_10_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 295.53 s (17 us/read; 3.56 M reads/minute). === Summary === Total reads processed: 17,535,871 Reads with adapters: 6,542,882 (37.3%) Reads written (passing filters): 17,535,871 (100.0%) Total basepairs processed: 1,350,521,498 bp Quality-trimmed: 912,488 bp (0.1%) Total written (filtered): 1,342,409,660 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 6542882 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.4% C: 13.3% G: 3.4% T: 35.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 6191324 4383967.8 0 6191324 2 241739 1095991.9 0 241739 3 77178 273998.0 0 77178 4 15391 68499.5 0 15391 5 1837 17124.9 0 1837 6 1007 4281.2 0 1007 7 241 1070.3 0 241 8 131 267.6 0 131 9 645 66.9 0 536 109 10 421 16.7 1 45 376 11 857 4.2 1 212 645 12 557 1.0 1 69 488 13 1000 0.3 1 0 1000 14 1719 0.3 1 0 1719 15 2629 0.3 1 0 2629 16 3361 0.3 1 0 3361 17 2147 0.3 1 0 2147 18 185 0.3 1 0 185 19 36 0.3 1 0 36 20 19 0.3 1 0 19 21 20 0.3 1 0 20 22 25 0.3 1 0 25 23 20 0.3 1 0 20 24 25 0.3 1 0 25 25 25 0.3 1 0 25 26 17 0.3 1 0 17 27 15 0.3 1 0 15 28 29 0.3 1 0 29 29 15 0.3 1 0 15 30 18 0.3 1 0 18 31 24 0.3 1 0 24 32 14 0.3 1 0 14 33 7 0.3 1 0 7 34 10 0.3 1 0 10 35 8 0.3 1 0 8 36 6 0.3 1 0 6 37 6 0.3 1 0 6 38 2 0.3 1 0 2 39 12 0.3 1 0 12 40 12 0.3 1 0 12 41 10 0.3 1 0 10 42 9 0.3 1 0 9 43 11 0.3 1 0 11 44 9 0.3 1 0 9 45 15 0.3 1 0 15 46 10 0.3 1 0 10 47 6 0.3 1 0 6 48 8 0.3 1 0 8 49 8 0.3 1 0 8 50 8 0.3 1 0 8 51 9 0.3 1 0 9 52 3 0.3 1 0 3 53 4 0.3 1 0 4 54 3 0.3 1 0 3 55 3 0.3 1 0 3 56 3 0.3 1 0 3 57 4 0.3 1 0 4 58 2 0.3 1 0 2 59 3 0.3 1 0 3 60 3 0.3 1 0 3 61 3 0.3 1 0 3 62 1 0.3 1 0 1 63 1 0.3 1 0 1 64 3 0.3 1 0 3 65 1 0.3 1 0 1 66 1 0.3 1 0 1 68 2 0.3 1 0 2 69 1 0.3 1 0 1 70 1 0.3 1 0 1 72 1 0.3 1 0 1 73 1 0.3 1 0 1 74 1 0.3 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_10_s1_R2_val_2.fq.gz ============================================= 17535871 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_10_s1_R1_val_1_trimmed.fq.gz and zr2096_10_s1_R2_val_2_trimmed.fq.gz file_1: zr2096_10_s1_R1_val_1_trimmed.fq.gz, file_2: zr2096_10_s1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_10_s1_R1_val_1_trimmed.fq.gz and zr2096_10_s1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_10_s1_R1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_10_s1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 17535871 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 69974 (0.40%) >>> Now running FastQC on the validated data zr2096_10_s1_R1_val_1_val_1.fq.gz<<< Started analysis of zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 5% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 10% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 15% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 20% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 25% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 30% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 35% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 40% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 45% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 50% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 55% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 60% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 65% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 70% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 75% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 80% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 85% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 90% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz Approx 95% complete for zr2096_10_s1_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_10_s1_R2_val_2_val_2.fq.gz<<< Started analysis of zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 5% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 10% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 15% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 20% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 25% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 30% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 35% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 40% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 45% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 50% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 55% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 60% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 65% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 70% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 75% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 80% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 85% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 90% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Approx 95% complete for zr2096_10_s1_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr2096_10_s1_R1_val_1_trimmed.fq.gz and zr2096_10_s1_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_1_s1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_1_s1_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_1_s1_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_1_s1_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_1_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 500.73 s (17 us/read; 3.45 M reads/minute). === Summary === Total reads processed: 28,769,621 Reads with adapters: 13,951,269 (48.5%) Reads written (passing filters): 28,769,621 (100.0%) Total basepairs processed: 2,212,297,559 bp Quality-trimmed: 2,801,564 bp (0.1%) Total written (filtered): 2,192,471,144 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13951269 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 42.6% C: 12.9% G: 11.2% T: 33.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12089535 7192405.2 0 12089535 2 1366413 1798101.3 0 1366413 3 377788 449525.3 0 377788 4 51322 112381.3 0 51322 5 4482 28095.3 0 4482 6 10125 7023.8 0 10125 7 3455 1756.0 0 3455 8 1181 439.0 0 1181 9 903 109.7 0 371 532 10 2019 27.4 1 681 1338 11 1542 6.9 1 335 1207 12 2428 1.7 1 467 1961 13 2643 0.4 1 0 2643 14 3692 0.4 1 0 3692 15 7146 0.4 1 0 7146 16 12849 0.4 1 0 12849 17 10577 0.4 1 0 10577 18 787 0.4 1 0 787 19 185 0.4 1 0 185 20 80 0.4 1 0 80 21 78 0.4 1 0 78 22 76 0.4 1 0 76 23 96 0.4 1 0 96 24 110 0.4 1 0 110 25 116 0.4 1 0 116 26 112 0.4 1 0 112 27 98 0.4 1 0 98 28 82 0.4 1 0 82 29 66 0.4 1 0 66 30 97 0.4 1 0 97 31 78 0.4 1 0 78 32 63 0.4 1 0 63 33 64 0.4 1 0 64 34 72 0.4 1 0 72 35 61 0.4 1 0 61 36 48 0.4 1 0 48 37 56 0.4 1 0 56 38 62 0.4 1 0 62 39 48 0.4 1 0 48 40 43 0.4 1 0 43 41 44 0.4 1 0 44 42 39 0.4 1 0 39 43 23 0.4 1 0 23 44 37 0.4 1 0 37 45 36 0.4 1 0 36 46 29 0.4 1 0 29 47 35 0.4 1 0 35 48 34 0.4 1 0 34 49 23 0.4 1 0 23 50 28 0.4 1 0 28 51 25 0.4 1 0 25 52 27 0.4 1 0 27 53 25 0.4 1 0 25 54 18 0.4 1 0 18 55 14 0.4 1 0 14 56 18 0.4 1 0 18 57 16 0.4 1 0 16 58 15 0.4 1 0 15 59 9 0.4 1 0 9 60 8 0.4 1 0 8 61 11 0.4 1 0 11 62 10 0.4 1 0 10 63 10 0.4 1 0 10 64 11 0.4 1 0 11 65 6 0.4 1 0 6 66 10 0.4 1 0 10 67 9 0.4 1 0 9 68 6 0.4 1 0 6 69 4 0.4 1 0 4 70 5 0.4 1 0 5 71 4 0.4 1 0 4 72 1 0.4 1 0 1 74 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_1_s1_R1_val_1.fq.gz ============================================= 28769621 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_1_s1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_1_s1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_1_s1_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_1_s1_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_1_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 480.94 s (17 us/read; 3.59 M reads/minute). === Summary === Total reads processed: 28,769,621 Reads with adapters: 10,183,601 (35.4%) Reads written (passing filters): 28,769,621 (100.0%) Total basepairs processed: 2,217,133,462 bp Quality-trimmed: 1,521,478 bp (0.1%) Total written (filtered): 2,204,094,879 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10183601 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 49.2% C: 14.7% G: 3.1% T: 33.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9628778 7192405.2 0 9628778 2 380148 1798101.3 0 380148 3 102398 449525.3 0 102398 4 19858 112381.3 0 19858 5 2661 28095.3 0 2661 6 3026 7023.8 0 3026 7 510 1756.0 0 510 8 316 439.0 0 316 9 1755 109.7 0 1284 471 10 1357 27.4 1 209 1148 11 1730 6.9 1 583 1147 12 1831 1.7 1 285 1546 13 3378 0.4 1 0 3378 14 6036 0.4 1 0 6036 15 9260 0.4 1 0 9260 16 11525 0.4 1 0 11525 17 6626 0.4 1 0 6626 18 634 0.4 1 0 634 19 133 0.4 1 0 133 20 81 0.4 1 0 81 21 52 0.4 1 0 52 22 88 0.4 1 0 88 23 74 0.4 1 0 74 24 96 0.4 1 0 96 25 104 0.4 1 0 104 26 86 0.4 1 0 86 27 72 0.4 1 0 72 28 66 0.4 1 0 66 29 70 0.4 1 0 70 30 58 0.4 1 0 58 31 57 0.4 1 0 57 32 56 0.4 1 0 56 33 61 0.4 1 0 61 34 39 0.4 1 0 39 35 25 0.4 1 0 25 36 39 0.4 1 0 39 37 29 0.4 1 0 29 38 24 0.4 1 0 24 39 35 0.4 1 0 35 40 22 0.4 1 0 22 41 40 0.4 1 0 40 42 28 0.4 1 0 28 43 24 0.4 1 0 24 44 28 0.4 1 0 28 45 22 0.4 1 0 22 46 25 0.4 1 0 25 47 16 0.4 1 0 16 48 17 0.4 1 0 17 49 10 0.4 1 0 10 50 19 0.4 1 0 19 51 10 0.4 1 0 10 52 14 0.4 1 0 14 53 19 0.4 1 0 19 54 17 0.4 1 0 17 55 12 0.4 1 0 12 56 10 0.4 1 0 10 57 8 0.4 1 0 8 58 6 0.4 1 0 6 59 6 0.4 1 0 6 60 8 0.4 1 0 8 61 8 0.4 1 0 8 62 12 0.4 1 0 12 63 5 0.4 1 0 5 64 5 0.4 1 0 5 65 3 0.4 1 0 3 66 6 0.4 1 0 6 67 6 0.4 1 0 6 68 5 0.4 1 0 5 69 5 0.4 1 0 5 70 5 0.4 1 0 5 71 3 0.4 1 0 3 72 3 0.4 1 0 3 74 2 0.4 1 0 2 RUN STATISTICS FOR INPUT FILE: zr2096_1_s1_R2_val_2.fq.gz ============================================= 28769621 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_1_s1_R1_val_1_trimmed.fq.gz and zr2096_1_s1_R2_val_2_trimmed.fq.gz file_1: zr2096_1_s1_R1_val_1_trimmed.fq.gz, file_2: zr2096_1_s1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_1_s1_R1_val_1_trimmed.fq.gz and zr2096_1_s1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_1_s1_R1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_1_s1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 28769621 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 116452 (0.40%) >>> Now running FastQC on the validated data zr2096_1_s1_R1_val_1_val_1.fq.gz<<< Started analysis of zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 5% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 10% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 15% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 20% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 25% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 30% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 35% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 40% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 45% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 50% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 55% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 60% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 65% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 70% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 75% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 80% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 85% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 90% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz Approx 95% complete for zr2096_1_s1_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_1_s1_R2_val_2_val_2.fq.gz<<< Started analysis of zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 5% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 10% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 15% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 20% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 25% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 30% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 35% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 40% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 45% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 50% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 55% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 60% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 65% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 70% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 75% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 80% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 85% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 90% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Approx 95% complete for zr2096_1_s1_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr2096_1_s1_R1_val_1_trimmed.fq.gz and zr2096_1_s1_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_2_s1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_2_s1_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_2_s1_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_2_s1_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_2_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 532.93 s (17 us/read; 3.44 M reads/minute). === Summary === Total reads processed: 30,577,202 Reads with adapters: 14,512,994 (47.5%) Reads written (passing filters): 30,577,202 (100.0%) Total basepairs processed: 2,204,631,142 bp Quality-trimmed: 2,199,144 bp (0.1%) Total written (filtered): 2,184,012,404 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14512994 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.6% C: 13.6% G: 12.5% T: 34.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12090258 7644300.5 0 12090258 2 1838068 1911075.1 0 1838068 3 449466 477768.8 0 449466 4 55948 119442.2 0 55948 5 5611 29860.5 0 5611 6 6664 7465.1 0 6664 7 3531 1866.3 0 3531 8 1562 466.6 0 1562 9 1300 116.6 0 485 815 10 2850 29.2 1 987 1863 11 2115 7.3 1 390 1725 12 2366 1.8 1 604 1762 13 3473 0.5 1 0 3473 14 5213 0.5 1 0 5213 15 9651 0.5 1 0 9651 16 17434 0.5 1 0 17434 17 13784 0.5 1 0 13784 18 1000 0.5 1 0 1000 19 229 0.5 1 0 229 20 101 0.5 1 0 101 21 117 0.5 1 0 117 22 113 0.5 1 0 113 23 85 0.5 1 0 85 24 99 0.5 1 0 99 25 112 0.5 1 0 112 26 124 0.5 1 0 124 27 106 0.5 1 0 106 28 97 0.5 1 0 97 29 82 0.5 1 0 82 30 108 0.5 1 0 108 31 73 0.5 1 0 73 32 92 0.5 1 0 92 33 87 0.5 1 0 87 34 79 0.5 1 0 79 35 62 0.5 1 0 62 36 46 0.5 1 0 46 37 53 0.5 1 0 53 38 50 0.5 1 0 50 39 41 0.5 1 0 41 40 43 0.5 1 0 43 41 47 0.5 1 0 47 42 53 0.5 1 0 53 43 51 0.5 1 0 51 44 53 0.5 1 0 53 45 48 0.5 1 0 48 46 36 0.5 1 0 36 47 34 0.5 1 0 34 48 34 0.5 1 0 34 49 29 0.5 1 0 29 50 31 0.5 1 0 31 51 32 0.5 1 0 32 52 34 0.5 1 0 34 53 22 0.5 1 0 22 54 19 0.5 1 0 19 55 20 0.5 1 0 20 56 23 0.5 1 0 23 57 11 0.5 1 0 11 58 16 0.5 1 0 16 59 18 0.5 1 0 18 60 9 0.5 1 0 9 61 18 0.5 1 0 18 62 10 0.5 1 0 10 63 6 0.5 1 0 6 64 5 0.5 1 0 5 65 11 0.5 1 0 11 66 7 0.5 1 0 7 67 8 0.5 1 0 8 68 1 0.5 1 0 1 69 2 0.5 1 0 2 70 5 0.5 1 0 5 71 3 0.5 1 0 3 72 1 0.5 1 0 1 73 1 0.5 1 0 1 74 2 0.5 1 0 2 75 1 0.5 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_2_s1_R1_val_1.fq.gz ============================================= 30577202 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_2_s1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_2_s1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_2_s1_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_2_s1_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_2_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 496.66 s (16 us/read; 3.69 M reads/minute). === Summary === Total reads processed: 30,577,202 Reads with adapters: 10,310,937 (33.7%) Reads written (passing filters): 30,577,202 (100.0%) Total basepairs processed: 2,210,198,514 bp Quality-trimmed: 1,435,870 bp (0.1%) Total written (filtered): 2,196,492,805 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10310937 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.0% C: 16.0% G: 4.3% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9512775 7644300.5 0 9512775 2 538390 1911075.1 0 538390 3 156475 477768.8 0 156475 4 26348 119442.2 0 26348 5 2581 29860.5 0 2581 6 3032 7465.1 0 3032 7 734 1866.3 0 734 8 400 466.6 0 400 9 2281 116.6 0 1872 409 10 1990 29.2 1 280 1710 11 2737 7.3 1 1038 1699 12 2694 1.8 1 424 2270 13 5326 0.5 1 0 5326 14 9353 0.5 1 0 9353 15 14674 0.5 1 0 14674 16 17913 0.5 1 0 17913 17 10146 0.5 1 0 10146 18 1035 0.5 1 0 1035 19 201 0.5 1 0 201 20 113 0.5 1 0 113 21 73 0.5 1 0 73 22 101 0.5 1 0 101 23 102 0.5 1 0 102 24 98 0.5 1 0 98 25 114 0.5 1 0 114 26 95 0.5 1 0 95 27 76 0.5 1 0 76 28 70 0.5 1 0 70 29 80 0.5 1 0 80 30 79 0.5 1 0 79 31 71 0.5 1 0 71 32 56 0.5 1 0 56 33 49 0.5 1 0 49 34 52 0.5 1 0 52 35 48 0.5 1 0 48 36 29 0.5 1 0 29 37 32 0.5 1 0 32 38 28 0.5 1 0 28 39 34 0.5 1 0 34 40 24 0.5 1 0 24 41 25 0.5 1 0 25 42 30 0.5 1 0 30 43 28 0.5 1 0 28 44 25 0.5 1 0 25 45 25 0.5 1 0 25 46 19 0.5 1 0 19 47 17 0.5 1 0 17 48 19 0.5 1 0 19 49 27 0.5 1 0 27 50 22 0.5 1 0 22 51 15 0.5 1 0 15 52 18 0.5 1 0 18 53 8 0.5 1 0 8 54 15 0.5 1 0 15 55 15 0.5 1 0 15 56 11 0.5 1 0 11 57 5 0.5 1 0 5 58 13 0.5 1 0 13 59 12 0.5 1 0 12 60 10 0.5 1 0 10 61 10 0.5 1 0 10 62 8 0.5 1 0 8 63 8 0.5 1 0 8 64 6 0.5 1 0 6 65 6 0.5 1 0 6 66 4 0.5 1 0 4 67 4 0.5 1 0 4 68 4 0.5 1 0 4 69 8 0.5 1 0 8 70 5 0.5 1 0 5 71 2 0.5 1 0 2 72 3 0.5 1 0 3 75 1 0.5 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_2_s1_R2_val_2.fq.gz ============================================= 30577202 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_2_s1_R1_val_1_trimmed.fq.gz and zr2096_2_s1_R2_val_2_trimmed.fq.gz file_1: zr2096_2_s1_R1_val_1_trimmed.fq.gz, file_2: zr2096_2_s1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_2_s1_R1_val_1_trimmed.fq.gz and zr2096_2_s1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_2_s1_R1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_2_s1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 30577202 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 173241 (0.57%) >>> Now running FastQC on the validated data zr2096_2_s1_R1_val_1_val_1.fq.gz<<< Started analysis of zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 5% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 10% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 15% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 20% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 25% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 30% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 35% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 40% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 45% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 50% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 55% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 60% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 65% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 70% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 75% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 80% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 85% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 90% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz Approx 95% complete for zr2096_2_s1_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_2_s1_R2_val_2_val_2.fq.gz<<< Started analysis of zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 5% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 10% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 15% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 20% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 25% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 30% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 35% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 40% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 45% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 50% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 55% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 60% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 65% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 70% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 75% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 80% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 85% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 90% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Approx 95% complete for zr2096_2_s1_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr2096_2_s1_R1_val_1_trimmed.fq.gz and zr2096_2_s1_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_3_s1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_3_s1_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_3_s1_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_3_s1_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_3_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 528.55 s (18 us/read; 3.37 M reads/minute). === Summary === Total reads processed: 29,717,035 Reads with adapters: 14,839,892 (49.9%) Reads written (passing filters): 29,717,035 (100.0%) Total basepairs processed: 2,250,213,060 bp Quality-trimmed: 2,201,183 bp (0.1%) Total written (filtered): 2,229,749,103 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14839892 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.5% C: 12.3% G: 11.2% T: 35.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12643021 7429258.8 0 12643021 2 1660557 1857314.7 0 1660557 3 416913 464328.7 0 416913 4 58121 116082.2 0 58121 5 4835 29020.5 0 4835 6 6188 7255.1 0 6188 7 2776 1813.8 0 2776 8 1330 453.4 0 1330 9 1563 113.4 0 393 1170 10 2379 28.3 1 708 1671 11 1616 7.1 1 335 1281 12 1802 1.8 1 402 1400 13 2639 0.4 1 0 2639 14 3753 0.4 1 0 3753 15 7039 0.4 1 0 7039 16 12740 0.4 1 0 12740 17 9851 0.4 1 0 9851 18 734 0.4 1 0 734 19 155 0.4 1 0 155 20 91 0.4 1 0 91 21 77 0.4 1 0 77 22 66 0.4 1 0 66 23 65 0.4 1 0 65 24 65 0.4 1 0 65 25 101 0.4 1 0 101 26 85 0.4 1 0 85 27 69 0.4 1 0 69 28 74 0.4 1 0 74 29 69 0.4 1 0 69 30 59 0.4 1 0 59 31 65 0.4 1 0 65 32 68 0.4 1 0 68 33 59 0.4 1 0 59 34 50 0.4 1 0 50 35 39 0.4 1 0 39 36 38 0.4 1 0 38 37 33 0.4 1 0 33 38 38 0.4 1 0 38 39 33 0.4 1 0 33 40 36 0.4 1 0 36 41 27 0.4 1 0 27 42 39 0.4 1 0 39 43 33 0.4 1 0 33 44 45 0.4 1 0 45 45 46 0.4 1 0 46 46 40 0.4 1 0 40 47 34 0.4 1 0 34 48 23 0.4 1 0 23 49 27 0.4 1 0 27 50 27 0.4 1 0 27 51 33 0.4 1 0 33 52 22 0.4 1 0 22 53 23 0.4 1 0 23 54 16 0.4 1 0 16 55 16 0.4 1 0 16 56 8 0.4 1 0 8 57 11 0.4 1 0 11 58 16 0.4 1 0 16 59 11 0.4 1 0 11 60 10 0.4 1 0 10 61 12 0.4 1 0 12 62 9 0.4 1 0 9 63 15 0.4 1 0 15 64 13 0.4 1 0 13 65 10 0.4 1 0 10 66 8 0.4 1 0 8 67 4 0.4 1 0 4 68 4 0.4 1 0 4 69 3 0.4 1 0 3 70 3 0.4 1 0 3 71 3 0.4 1 0 3 72 5 0.4 1 0 5 73 4 0.4 1 0 4 RUN STATISTICS FOR INPUT FILE: zr2096_3_s1_R1_val_1.fq.gz ============================================= 29717035 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_3_s1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_3_s1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_3_s1_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_3_s1_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_3_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 496.55 s (17 us/read; 3.59 M reads/minute). === Summary === Total reads processed: 29,717,035 Reads with adapters: 10,542,555 (35.5%) Reads written (passing filters): 29,717,035 (100.0%) Total basepairs processed: 2,255,215,984 bp Quality-trimmed: 1,235,022 bp (0.1%) Total written (filtered): 2,241,832,027 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10542555 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 14.2% G: 3.9% T: 36.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9855419 7429258.8 0 9855419 2 463577 1857314.7 0 463577 3 138213 464328.7 0 138213 4 25485 116082.2 0 25485 5 2509 29020.5 0 2509 6 2493 7255.1 0 2493 7 651 1813.8 0 651 8 331 453.4 0 331 9 1829 113.4 0 1488 341 10 1617 28.3 1 217 1400 11 2230 7.1 1 796 1434 12 2140 1.8 1 323 1817 13 4051 0.4 1 0 4051 14 7268 0.4 1 0 7268 15 11032 0.4 1 0 11032 16 13856 0.4 1 0 13856 17 7626 0.4 1 0 7626 18 721 0.4 1 0 721 19 128 0.4 1 0 128 20 85 0.4 1 0 85 21 72 0.4 1 0 72 22 65 0.4 1 0 65 23 74 0.4 1 0 74 24 90 0.4 1 0 90 25 53 0.4 1 0 53 26 79 0.4 1 0 79 27 55 0.4 1 0 55 28 61 0.4 1 0 61 29 56 0.4 1 0 56 30 65 0.4 1 0 65 31 67 0.4 1 0 67 32 44 0.4 1 0 44 33 31 0.4 1 0 31 34 30 0.4 1 0 30 35 23 0.4 1 0 23 36 26 0.4 1 0 26 37 23 0.4 1 0 23 38 26 0.4 1 0 26 39 21 0.4 1 0 21 40 19 0.4 1 0 19 41 16 0.4 1 0 16 42 16 0.4 1 0 16 43 29 0.4 1 0 29 44 14 0.4 1 0 14 45 20 0.4 1 0 20 46 20 0.4 1 0 20 47 5 0.4 1 0 5 48 15 0.4 1 0 15 49 12 0.4 1 0 12 50 17 0.4 1 0 17 51 7 0.4 1 0 7 52 10 0.4 1 0 10 53 6 0.4 1 0 6 54 9 0.4 1 0 9 55 12 0.4 1 0 12 56 9 0.4 1 0 9 57 12 0.4 1 0 12 58 9 0.4 1 0 9 59 9 0.4 1 0 9 60 8 0.4 1 0 8 61 10 0.4 1 0 10 62 11 0.4 1 0 11 63 7 0.4 1 0 7 64 7 0.4 1 0 7 65 7 0.4 1 0 7 66 5 0.4 1 0 5 67 5 0.4 1 0 5 68 3 0.4 1 0 3 69 2 0.4 1 0 2 72 1 0.4 1 0 1 73 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_3_s1_R2_val_2.fq.gz ============================================= 29717035 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_3_s1_R1_val_1_trimmed.fq.gz and zr2096_3_s1_R2_val_2_trimmed.fq.gz file_1: zr2096_3_s1_R1_val_1_trimmed.fq.gz, file_2: zr2096_3_s1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_3_s1_R1_val_1_trimmed.fq.gz and zr2096_3_s1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_3_s1_R1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_3_s1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 29717035 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 116679 (0.39%) >>> Now running FastQC on the validated data zr2096_3_s1_R1_val_1_val_1.fq.gz<<< Started analysis of zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 5% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 10% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 15% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 20% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 25% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 30% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 35% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 40% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 45% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 50% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 55% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 60% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 65% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 70% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 75% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 80% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 85% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 90% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz Approx 95% complete for zr2096_3_s1_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_3_s1_R2_val_2_val_2.fq.gz<<< Started analysis of zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 5% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 10% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 15% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 20% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 25% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 30% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 35% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 40% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 45% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 50% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 55% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 60% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 65% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 70% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 75% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 80% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 85% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 90% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Approx 95% complete for zr2096_3_s1_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr2096_3_s1_R1_val_1_trimmed.fq.gz and zr2096_3_s1_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_4_s1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_4_s1_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_4_s1_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_4_s1_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_4_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 417.84 s (17 us/read; 3.47 M reads/minute). === Summary === Total reads processed: 24,165,270 Reads with adapters: 11,921,202 (49.3%) Reads written (passing filters): 24,165,270 (100.0%) Total basepairs processed: 1,774,487,009 bp Quality-trimmed: 1,789,083 bp (0.1%) Total written (filtered): 1,757,760,454 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11921202 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.8% C: 13.1% G: 11.6% T: 35.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10000118 6041317.5 0 10000118 2 1454355 1510329.4 0 1454355 3 364623 377582.3 0 364623 4 47308 94395.6 0 47308 5 4199 23598.9 0 4199 6 4181 5899.7 0 4181 7 2065 1474.9 0 2065 8 1141 368.7 0 1141 9 1051 92.2 0 320 731 10 2190 23.0 1 754 1436 11 1658 5.8 1 353 1305 12 1643 1.4 1 373 1270 13 2312 0.4 1 0 2312 14 3590 0.4 1 0 3590 15 6778 0.4 1 0 6778 16 12199 0.4 1 0 12199 17 9365 0.4 1 0 9365 18 689 0.4 1 0 689 19 130 0.4 1 0 130 20 87 0.4 1 0 87 21 72 0.4 1 0 72 22 68 0.4 1 0 68 23 56 0.4 1 0 56 24 73 0.4 1 0 73 25 94 0.4 1 0 94 26 79 0.4 1 0 79 27 67 0.4 1 0 67 28 61 0.4 1 0 61 29 55 0.4 1 0 55 30 64 0.4 1 0 64 31 61 0.4 1 0 61 32 51 0.4 1 0 51 33 45 0.4 1 0 45 34 31 0.4 1 0 31 35 31 0.4 1 0 31 36 43 0.4 1 0 43 37 38 0.4 1 0 38 38 27 0.4 1 0 27 39 27 0.4 1 0 27 40 31 0.4 1 0 31 41 34 0.4 1 0 34 42 37 0.4 1 0 37 43 16 0.4 1 0 16 44 24 0.4 1 0 24 45 32 0.4 1 0 32 46 25 0.4 1 0 25 47 22 0.4 1 0 22 48 25 0.4 1 0 25 49 18 0.4 1 0 18 50 13 0.4 1 0 13 51 20 0.4 1 0 20 52 21 0.4 1 0 21 53 14 0.4 1 0 14 54 11 0.4 1 0 11 55 14 0.4 1 0 14 56 15 0.4 1 0 15 57 12 0.4 1 0 12 58 11 0.4 1 0 11 59 9 0.4 1 0 9 60 8 0.4 1 0 8 61 8 0.4 1 0 8 62 10 0.4 1 0 10 63 9 0.4 1 0 9 64 10 0.4 1 0 10 65 6 0.4 1 0 6 66 1 0.4 1 0 1 67 5 0.4 1 0 5 68 3 0.4 1 0 3 69 1 0.4 1 0 1 70 3 0.4 1 0 3 71 4 0.4 1 0 4 72 3 0.4 1 0 3 73 1 0.4 1 0 1 74 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_4_s1_R1_val_1.fq.gz ============================================= 24165270 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_4_s1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_4_s1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_4_s1_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_4_s1_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_4_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 397.43 s (16 us/read; 3.65 M reads/minute). === Summary === Total reads processed: 24,165,270 Reads with adapters: 8,490,982 (35.1%) Reads written (passing filters): 24,165,270 (100.0%) Total basepairs processed: 1,778,167,602 bp Quality-trimmed: 1,046,692 bp (0.1%) Total written (filtered): 1,767,000,593 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8490982 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.2% C: 15.3% G: 4.1% T: 35.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7857531 6041317.5 0 7857531 2 418598 1510329.4 0 418598 3 126135 377582.3 0 126135 4 21522 94395.6 0 21522 5 2047 23598.9 0 2047 6 2472 5899.7 0 2472 7 578 1474.9 0 578 8 347 368.7 0 347 9 2202 92.2 0 1819 383 10 1780 23.0 1 270 1510 11 2485 5.8 1 880 1605 12 2667 1.4 1 440 2227 13 4671 0.4 1 0 4671 14 8700 0.4 1 0 8700 15 13182 0.4 1 0 13182 16 15593 0.4 1 0 15593 17 7996 0.4 1 0 7996 18 843 0.4 1 0 843 19 175 0.4 1 0 175 20 90 0.4 1 0 90 21 79 0.4 1 0 79 22 69 0.4 1 0 69 23 78 0.4 1 0 78 24 76 0.4 1 0 76 25 81 0.4 1 0 81 26 66 0.4 1 0 66 27 74 0.4 1 0 74 28 58 0.4 1 0 58 29 54 0.4 1 0 54 30 63 0.4 1 0 63 31 46 0.4 1 0 46 32 57 0.4 1 0 57 33 44 0.4 1 0 44 34 41 0.4 1 0 41 35 26 0.4 1 0 26 36 28 0.4 1 0 28 37 28 0.4 1 0 28 38 26 0.4 1 0 26 39 18 0.4 1 0 18 40 31 0.4 1 0 31 41 25 0.4 1 0 25 42 23 0.4 1 0 23 43 24 0.4 1 0 24 44 16 0.4 1 0 16 45 16 0.4 1 0 16 46 18 0.4 1 0 18 47 15 0.4 1 0 15 48 13 0.4 1 0 13 49 7 0.4 1 0 7 50 17 0.4 1 0 17 51 14 0.4 1 0 14 52 9 0.4 1 0 9 53 10 0.4 1 0 10 54 12 0.4 1 0 12 55 13 0.4 1 0 13 56 5 0.4 1 0 5 57 9 0.4 1 0 9 58 7 0.4 1 0 7 59 6 0.4 1 0 6 60 11 0.4 1 0 11 61 11 0.4 1 0 11 62 4 0.4 1 0 4 63 4 0.4 1 0 4 64 8 0.4 1 0 8 65 1 0.4 1 0 1 66 6 0.4 1 0 6 67 3 0.4 1 0 3 68 5 0.4 1 0 5 69 5 0.4 1 0 5 70 1 0.4 1 0 1 71 4 0.4 1 0 4 72 3 0.4 1 0 3 RUN STATISTICS FOR INPUT FILE: zr2096_4_s1_R2_val_2.fq.gz ============================================= 24165270 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_4_s1_R1_val_1_trimmed.fq.gz and zr2096_4_s1_R2_val_2_trimmed.fq.gz file_1: zr2096_4_s1_R1_val_1_trimmed.fq.gz, file_2: zr2096_4_s1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_4_s1_R1_val_1_trimmed.fq.gz and zr2096_4_s1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_4_s1_R1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_4_s1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 24165270 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 134660 (0.56%) >>> Now running FastQC on the validated data zr2096_4_s1_R1_val_1_val_1.fq.gz<<< Started analysis of zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 5% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 10% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 15% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 20% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 25% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 30% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 35% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 40% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 45% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 50% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 55% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 60% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 65% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 70% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 75% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 80% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 85% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 90% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz Approx 95% complete for zr2096_4_s1_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_4_s1_R2_val_2_val_2.fq.gz<<< Started analysis of zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 5% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 10% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 15% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 20% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 25% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 30% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 35% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 40% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 45% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 50% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 55% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 60% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 65% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 70% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 75% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 80% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 85% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 90% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Approx 95% complete for zr2096_4_s1_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr2096_4_s1_R1_val_1_trimmed.fq.gz and zr2096_4_s1_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_5_s1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_5_s1_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_5_s1_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_5_s1_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_5_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 558.78 s (18 us/read; 3.40 M reads/minute). === Summary === Total reads processed: 31,629,718 Reads with adapters: 15,896,587 (50.3%) Reads written (passing filters): 31,629,718 (100.0%) Total basepairs processed: 2,404,730,852 bp Quality-trimmed: 2,548,776 bp (0.1%) Total written (filtered): 2,383,094,134 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15896587 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.4% C: 11.8% G: 10.9% T: 36.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13584485 7907429.5 0 13584485 2 1763666 1976857.4 0 1763666 3 449266 494214.3 0 449266 4 66342 123553.6 0 66342 5 6358 30888.4 0 6358 6 5668 7722.1 0 5668 7 2600 1930.5 0 2600 8 1104 482.6 0 1104 9 911 120.7 0 268 643 10 1305 30.2 1 278 1027 11 942 7.5 1 120 822 12 675 1.9 1 117 558 13 874 0.5 1 0 874 14 1154 0.5 1 0 1154 15 2172 0.5 1 0 2172 16 4142 0.5 1 0 4142 17 3621 0.5 1 0 3621 18 238 0.5 1 0 238 19 64 0.5 1 0 64 20 38 0.5 1 0 38 21 22 0.5 1 0 22 22 35 0.5 1 0 35 23 32 0.5 1 0 32 24 30 0.5 1 0 30 25 35 0.5 1 0 35 26 40 0.5 1 0 40 27 32 0.5 1 0 32 28 37 0.5 1 0 37 29 30 0.5 1 0 30 30 29 0.5 1 0 29 31 28 0.5 1 0 28 32 33 0.5 1 0 33 33 33 0.5 1 0 33 34 25 0.5 1 0 25 35 24 0.5 1 0 24 36 30 0.5 1 0 30 37 21 0.5 1 0 21 38 28 0.5 1 0 28 39 26 0.5 1 0 26 40 25 0.5 1 0 25 41 23 0.5 1 0 23 42 30 0.5 1 0 30 43 25 0.5 1 0 25 44 27 0.5 1 0 27 45 21 0.5 1 0 21 46 14 0.5 1 0 14 47 23 0.5 1 0 23 48 18 0.5 1 0 18 49 22 0.5 1 0 22 50 17 0.5 1 0 17 51 17 0.5 1 0 17 52 12 0.5 1 0 12 53 15 0.5 1 0 15 54 10 0.5 1 0 10 55 14 0.5 1 0 14 56 10 0.5 1 0 10 57 8 0.5 1 0 8 58 8 0.5 1 0 8 59 13 0.5 1 0 13 60 6 0.5 1 0 6 61 5 0.5 1 0 5 62 3 0.5 1 0 3 63 2 0.5 1 0 2 64 6 0.5 1 0 6 65 2 0.5 1 0 2 66 7 0.5 1 0 7 67 1 0.5 1 0 1 68 2 0.5 1 0 2 69 2 0.5 1 0 2 70 1 0.5 1 0 1 71 2 0.5 1 0 2 73 1 0.5 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_5_s1_R1_val_1.fq.gz ============================================= 31629718 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_5_s1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_5_s1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_5_s1_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_5_s1_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_5_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 528.23 s (17 us/read; 3.59 M reads/minute). === Summary === Total reads processed: 31,629,718 Reads with adapters: 11,310,341 (35.8%) Reads written (passing filters): 31,629,718 (100.0%) Total basepairs processed: 2,408,754,938 bp Quality-trimmed: 1,286,497 bp (0.1%) Total written (filtered): 2,394,990,512 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11310341 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 13.8% G: 3.6% T: 36.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10652114 7907429.5 0 10652114 2 466681 1976857.4 0 466681 3 137131 494214.3 0 137131 4 27002 123553.6 0 27002 5 2290 30888.4 0 2290 6 2170 7722.1 0 2170 7 466 1930.5 0 466 8 186 482.6 0 186 9 915 120.7 0 777 138 10 688 30.2 1 75 613 11 989 7.5 1 255 734 12 879 1.9 1 101 778 13 1466 0.5 1 0 1466 14 2820 0.5 1 0 2820 15 4385 0.5 1 0 4385 16 5573 0.5 1 0 5573 17 3358 0.5 1 0 3358 18 332 0.5 1 0 332 19 55 0.5 1 0 55 20 35 0.5 1 0 35 21 30 0.5 1 0 30 22 31 0.5 1 0 31 23 31 0.5 1 0 31 24 42 0.5 1 0 42 25 43 0.5 1 0 43 26 27 0.5 1 0 27 27 23 0.5 1 0 23 28 36 0.5 1 0 36 29 35 0.5 1 0 35 30 26 0.5 1 0 26 31 26 0.5 1 0 26 32 26 0.5 1 0 26 33 26 0.5 1 0 26 34 21 0.5 1 0 21 35 26 0.5 1 0 26 36 17 0.5 1 0 17 37 31 0.5 1 0 31 38 17 0.5 1 0 17 39 18 0.5 1 0 18 40 25 0.5 1 0 25 41 18 0.5 1 0 18 42 16 0.5 1 0 16 43 8 0.5 1 0 8 44 22 0.5 1 0 22 45 18 0.5 1 0 18 46 12 0.5 1 0 12 47 16 0.5 1 0 16 48 12 0.5 1 0 12 49 14 0.5 1 0 14 50 12 0.5 1 0 12 51 12 0.5 1 0 12 52 6 0.5 1 0 6 53 15 0.5 1 0 15 54 4 0.5 1 0 4 55 5 0.5 1 0 5 56 1 0.5 1 0 1 57 12 0.5 1 0 12 58 7 0.5 1 0 7 59 6 0.5 1 0 6 60 4 0.5 1 0 4 61 3 0.5 1 0 3 62 3 0.5 1 0 3 63 7 0.5 1 0 7 64 1 0.5 1 0 1 65 4 0.5 1 0 4 66 1 0.5 1 0 1 67 3 0.5 1 0 3 68 1 0.5 1 0 1 69 2 0.5 1 0 2 70 1 0.5 1 0 1 71 1 0.5 1 0 1 72 1 0.5 1 0 1 73 1 0.5 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_5_s1_R2_val_2.fq.gz ============================================= 31629718 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_5_s1_R1_val_1_trimmed.fq.gz and zr2096_5_s1_R2_val_2_trimmed.fq.gz file_1: zr2096_5_s1_R1_val_1_trimmed.fq.gz, file_2: zr2096_5_s1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_5_s1_R1_val_1_trimmed.fq.gz and zr2096_5_s1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_5_s1_R1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_5_s1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 31629718 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 84829 (0.27%) >>> Now running FastQC on the validated data zr2096_5_s1_R1_val_1_val_1.fq.gz<<< Started analysis of zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 5% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 10% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 15% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 20% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 25% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 30% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 35% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 40% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 45% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 50% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 55% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 60% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 65% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 70% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 75% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 80% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 85% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 90% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz Approx 95% complete for zr2096_5_s1_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_5_s1_R2_val_2_val_2.fq.gz<<< Started analysis of zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 5% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 10% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 15% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 20% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 25% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 30% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 35% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 40% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 45% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 50% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 55% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 60% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 65% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 70% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 75% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 80% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 85% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 90% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Approx 95% complete for zr2096_5_s1_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr2096_5_s1_R1_val_1_trimmed.fq.gz and zr2096_5_s1_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_6_s1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_6_s1_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_6_s1_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_6_s1_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_6_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 425.86 s (18 us/read; 3.39 M reads/minute). === Summary === Total reads processed: 24,080,119 Reads with adapters: 11,885,324 (49.4%) Reads written (passing filters): 24,080,119 (100.0%) Total basepairs processed: 1,778,574,588 bp Quality-trimmed: 1,878,979 bp (0.1%) Total written (filtered): 1,761,896,293 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11885324 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.5% C: 12.0% G: 11.9% T: 36.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9952709 6020029.8 0 9952709 2 1470198 1505007.4 0 1470198 3 366956 376251.9 0 366956 4 48963 94063.0 0 48963 5 4202 23515.7 0 4202 6 4623 5878.9 0 4623 7 2246 1469.7 0 2246 8 1172 367.4 0 1172 9 981 91.9 0 286 695 10 1850 23.0 1 561 1289 11 1284 5.7 1 245 1039 12 1260 1.4 1 285 975 13 1829 0.4 1 0 1829 14 2752 0.4 1 0 2752 15 5214 0.4 1 0 5214 16 9578 0.4 1 0 9578 17 7522 0.4 1 0 7522 18 536 0.4 1 0 536 19 118 0.4 1 0 118 20 59 0.4 1 0 59 21 50 0.4 1 0 50 22 53 0.4 1 0 53 23 46 0.4 1 0 46 24 83 0.4 1 0 83 25 68 0.4 1 0 68 26 62 0.4 1 0 62 27 51 0.4 1 0 51 28 48 0.4 1 0 48 29 59 0.4 1 0 59 30 39 0.4 1 0 39 31 60 0.4 1 0 60 32 54 0.4 1 0 54 33 45 0.4 1 0 45 34 27 0.4 1 0 27 35 30 0.4 1 0 30 36 29 0.4 1 0 29 37 30 0.4 1 0 30 38 19 0.4 1 0 19 39 30 0.4 1 0 30 40 33 0.4 1 0 33 41 24 0.4 1 0 24 42 35 0.4 1 0 35 43 25 0.4 1 0 25 44 27 0.4 1 0 27 45 26 0.4 1 0 26 46 21 0.4 1 0 21 47 12 0.4 1 0 12 48 18 0.4 1 0 18 49 10 0.4 1 0 10 50 16 0.4 1 0 16 51 16 0.4 1 0 16 52 13 0.4 1 0 13 53 8 0.4 1 0 8 54 11 0.4 1 0 11 55 14 0.4 1 0 14 56 10 0.4 1 0 10 57 7 0.4 1 0 7 58 4 0.4 1 0 4 59 10 0.4 1 0 10 60 10 0.4 1 0 10 61 7 0.4 1 0 7 62 3 0.4 1 0 3 63 4 0.4 1 0 4 64 6 0.4 1 0 6 65 2 0.4 1 0 2 66 1 0.4 1 0 1 67 3 0.4 1 0 3 68 6 0.4 1 0 6 69 3 0.4 1 0 3 70 1 0.4 1 0 1 71 1 0.4 1 0 1 72 2 0.4 1 0 2 RUN STATISTICS FOR INPUT FILE: zr2096_6_s1_R1_val_1.fq.gz ============================================= 24080119 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_6_s1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_6_s1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_6_s1_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_6_s1_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_6_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 395.47 s (16 us/read; 3.65 M reads/minute). === Summary === Total reads processed: 24,080,119 Reads with adapters: 8,546,733 (35.5%) Reads written (passing filters): 24,080,119 (100.0%) Total basepairs processed: 1,782,249,619 bp Quality-trimmed: 1,044,332 bp (0.1%) Total written (filtered): 1,771,289,577 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8546733 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.6% C: 14.7% G: 3.9% T: 35.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 7935438 6020029.8 0 7935438 2 414461 1505007.4 0 414461 3 127936 376251.9 0 127936 4 20586 94063.0 0 20586 5 2037 23515.7 0 2037 6 2157 5878.9 0 2157 7 484 1469.7 0 484 8 249 367.4 0 249 9 1575 91.9 0 1326 249 10 1311 23.0 1 166 1145 11 1791 5.7 1 614 1177 12 1769 1.4 1 251 1518 13 3146 0.4 1 0 3146 14 5998 0.4 1 0 5998 15 8811 0.4 1 0 8811 16 10983 0.4 1 0 10983 17 6124 0.4 1 0 6124 18 598 0.4 1 0 598 19 104 0.4 1 0 104 20 55 0.4 1 0 55 21 50 0.4 1 0 50 22 64 0.4 1 0 64 23 63 0.4 1 0 63 24 55 0.4 1 0 55 25 68 0.4 1 0 68 26 62 0.4 1 0 62 27 53 0.4 1 0 53 28 49 0.4 1 0 49 29 55 0.4 1 0 55 30 55 0.4 1 0 55 31 60 0.4 1 0 60 32 33 0.4 1 0 33 33 37 0.4 1 0 37 34 30 0.4 1 0 30 35 23 0.4 1 0 23 36 21 0.4 1 0 21 37 13 0.4 1 0 13 38 21 0.4 1 0 21 39 25 0.4 1 0 25 40 15 0.4 1 0 15 41 16 0.4 1 0 16 42 27 0.4 1 0 27 43 14 0.4 1 0 14 44 15 0.4 1 0 15 45 21 0.4 1 0 21 46 15 0.4 1 0 15 47 12 0.4 1 0 12 48 5 0.4 1 0 5 49 19 0.4 1 0 19 50 7 0.4 1 0 7 51 7 0.4 1 0 7 52 15 0.4 1 0 15 53 8 0.4 1 0 8 54 8 0.4 1 0 8 55 5 0.4 1 0 5 56 6 0.4 1 0 6 57 6 0.4 1 0 6 58 9 0.4 1 0 9 59 9 0.4 1 0 9 60 4 0.4 1 0 4 61 2 0.4 1 0 2 62 5 0.4 1 0 5 63 10 0.4 1 0 10 64 4 0.4 1 0 4 65 6 0.4 1 0 6 66 4 0.4 1 0 4 67 2 0.4 1 0 2 68 2 0.4 1 0 2 69 1 0.4 1 0 1 70 1 0.4 1 0 1 71 1 0.4 1 0 1 72 2 0.4 1 0 2 RUN STATISTICS FOR INPUT FILE: zr2096_6_s1_R2_val_2.fq.gz ============================================= 24080119 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_6_s1_R1_val_1_trimmed.fq.gz and zr2096_6_s1_R2_val_2_trimmed.fq.gz file_1: zr2096_6_s1_R1_val_1_trimmed.fq.gz, file_2: zr2096_6_s1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_6_s1_R1_val_1_trimmed.fq.gz and zr2096_6_s1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_6_s1_R1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_6_s1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 24080119 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 116633 (0.48%) >>> Now running FastQC on the validated data zr2096_6_s1_R1_val_1_val_1.fq.gz<<< Started analysis of zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 5% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 10% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 15% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 20% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 25% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 30% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 35% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 40% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 45% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 50% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 55% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 60% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 65% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 70% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 75% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 80% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 85% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 90% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz Approx 95% complete for zr2096_6_s1_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_6_s1_R2_val_2_val_2.fq.gz<<< Started analysis of zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 5% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 10% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 15% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 20% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 25% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 30% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 35% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 40% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 45% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 50% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 55% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 60% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 65% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 70% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 75% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 80% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 85% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 90% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Approx 95% complete for zr2096_6_s1_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr2096_6_s1_R1_val_1_trimmed.fq.gz and zr2096_6_s1_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_7_s1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_7_s1_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_7_s1_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_7_s1_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_7_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 522.24 s (18 us/read; 3.38 M reads/minute). === Summary === Total reads processed: 29,396,171 Reads with adapters: 15,322,123 (52.1%) Reads written (passing filters): 29,396,171 (100.0%) Total basepairs processed: 2,268,807,805 bp Quality-trimmed: 2,405,652 bp (0.1%) Total written (filtered): 2,247,866,315 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15322123 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 41.3% C: 11.6% G: 10.4% T: 36.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13174202 7349042.8 0 13174202 2 1613069 1837260.7 0 1613069 3 425181 459315.2 0 425181 4 62087 114828.8 0 62087 5 5314 28707.2 0 5314 6 5442 7176.8 0 5442 7 2228 1794.2 0 2228 8 984 448.5 0 984 9 1235 112.1 0 317 918 10 1797 28.0 1 515 1282 11 1428 7.0 1 242 1186 12 1333 1.8 1 315 1018 13 1950 0.4 1 0 1950 14 2578 0.4 1 0 2578 15 4886 0.4 1 0 4886 16 8947 0.4 1 0 8947 17 7389 0.4 1 0 7389 18 518 0.4 1 0 518 19 92 0.4 1 0 92 20 71 0.4 1 0 71 21 42 0.4 1 0 42 22 61 0.4 1 0 61 23 65 0.4 1 0 65 24 54 0.4 1 0 54 25 62 0.4 1 0 62 26 65 0.4 1 0 65 27 37 0.4 1 0 37 28 40 0.4 1 0 40 29 31 0.4 1 0 31 30 35 0.4 1 0 35 31 50 0.4 1 0 50 32 46 0.4 1 0 46 33 39 0.4 1 0 39 34 48 0.4 1 0 48 35 40 0.4 1 0 40 36 36 0.4 1 0 36 37 35 0.4 1 0 35 38 33 0.4 1 0 33 39 30 0.4 1 0 30 40 35 0.4 1 0 35 41 24 0.4 1 0 24 42 25 0.4 1 0 25 43 28 0.4 1 0 28 44 24 0.4 1 0 24 45 36 0.4 1 0 36 46 31 0.4 1 0 31 47 33 0.4 1 0 33 48 18 0.4 1 0 18 49 23 0.4 1 0 23 50 27 0.4 1 0 27 51 24 0.4 1 0 24 52 21 0.4 1 0 21 53 22 0.4 1 0 22 54 9 0.4 1 0 9 55 23 0.4 1 0 23 56 20 0.4 1 0 20 57 16 0.4 1 0 16 58 15 0.4 1 0 15 59 8 0.4 1 0 8 60 11 0.4 1 0 11 61 14 0.4 1 0 14 62 4 0.4 1 0 4 63 13 0.4 1 0 13 64 6 0.4 1 0 6 65 6 0.4 1 0 6 66 3 0.4 1 0 3 67 5 0.4 1 0 5 68 3 0.4 1 0 3 69 6 0.4 1 0 6 70 2 0.4 1 0 2 71 3 0.4 1 0 3 72 4 0.4 1 0 4 74 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_7_s1_R1_val_1.fq.gz ============================================= 29396171 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_7_s1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_7_s1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_7_s1_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_7_s1_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_7_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 487.24 s (17 us/read; 3.62 M reads/minute). === Summary === Total reads processed: 29,396,171 Reads with adapters: 10,758,286 (36.6%) Reads written (passing filters): 29,396,171 (100.0%) Total basepairs processed: 2,277,104,260 bp Quality-trimmed: 1,105,332 bp (0.0%) Total written (filtered): 2,263,946,009 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10758286 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.0% C: 13.7% G: 3.4% T: 36.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10149728 7349042.8 0 10149728 2 415524 1837260.7 0 415524 3 125897 459315.2 0 125897 4 25485 114828.8 0 25485 5 2188 28707.2 0 2188 6 2123 7176.8 0 2123 7 480 1794.2 0 480 8 239 448.5 0 239 9 1166 112.1 0 956 210 10 1018 28.0 1 117 901 11 1422 7.0 1 539 883 12 1403 1.8 1 183 1220 13 2531 0.4 1 0 2531 14 4759 0.4 1 0 4759 15 7190 0.4 1 0 7190 16 9467 0.4 1 0 9467 17 5914 0.4 1 0 5914 18 505 0.4 1 0 505 19 93 0.4 1 0 93 20 53 0.4 1 0 53 21 53 0.4 1 0 53 22 49 0.4 1 0 49 23 49 0.4 1 0 49 24 53 0.4 1 0 53 25 58 0.4 1 0 58 26 46 0.4 1 0 46 27 46 0.4 1 0 46 28 47 0.4 1 0 47 29 38 0.4 1 0 38 30 45 0.4 1 0 45 31 62 0.4 1 0 62 32 37 0.4 1 0 37 33 31 0.4 1 0 31 34 30 0.4 1 0 30 35 28 0.4 1 0 28 36 25 0.4 1 0 25 37 17 0.4 1 0 17 38 20 0.4 1 0 20 39 19 0.4 1 0 19 40 17 0.4 1 0 17 41 13 0.4 1 0 13 42 25 0.4 1 0 25 43 16 0.4 1 0 16 44 20 0.4 1 0 20 45 23 0.4 1 0 23 46 15 0.4 1 0 15 47 18 0.4 1 0 18 48 15 0.4 1 0 15 49 22 0.4 1 0 22 50 8 0.4 1 0 8 51 12 0.4 1 0 12 52 11 0.4 1 0 11 53 11 0.4 1 0 11 54 12 0.4 1 0 12 55 9 0.4 1 0 9 56 16 0.4 1 0 16 57 12 0.4 1 0 12 58 11 0.4 1 0 11 59 10 0.4 1 0 10 60 7 0.4 1 0 7 61 6 0.4 1 0 6 62 3 0.4 1 0 3 63 7 0.4 1 0 7 64 9 0.4 1 0 9 65 3 0.4 1 0 3 66 1 0.4 1 0 1 67 2 0.4 1 0 2 68 3 0.4 1 0 3 69 1 0.4 1 0 1 71 3 0.4 1 0 3 72 3 0.4 1 0 3 73 2 0.4 1 0 2 74 1 0.4 1 0 1 75 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_7_s1_R2_val_2.fq.gz ============================================= 29396171 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_7_s1_R1_val_1_trimmed.fq.gz and zr2096_7_s1_R2_val_2_trimmed.fq.gz file_1: zr2096_7_s1_R1_val_1_trimmed.fq.gz, file_2: zr2096_7_s1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_7_s1_R1_val_1_trimmed.fq.gz and zr2096_7_s1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_7_s1_R1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_7_s1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 29396171 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 85493 (0.29%) >>> Now running FastQC on the validated data zr2096_7_s1_R1_val_1_val_1.fq.gz<<< Started analysis of zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 5% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 10% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 15% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 20% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 25% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 30% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 35% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 40% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 45% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 50% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 55% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 60% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 65% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 70% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 75% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 80% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 85% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 90% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz Approx 95% complete for zr2096_7_s1_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_7_s1_R2_val_2_val_2.fq.gz<<< Started analysis of zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 5% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 10% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 15% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 20% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 25% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 30% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 35% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 40% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 45% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 50% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 55% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 60% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 65% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 70% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 75% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 80% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 85% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 90% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Approx 95% complete for zr2096_7_s1_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr2096_7_s1_R1_val_1_trimmed.fq.gz and zr2096_7_s1_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_8_s1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_8_s1_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_8_s1_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_8_s1_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_8_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 526.12 s (18 us/read; 3.38 M reads/minute). === Summary === Total reads processed: 29,619,538 Reads with adapters: 14,917,969 (50.4%) Reads written (passing filters): 29,619,538 (100.0%) Total basepairs processed: 2,260,916,887 bp Quality-trimmed: 2,375,264 bp (0.1%) Total written (filtered): 2,240,385,329 bp (99.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14917969 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.7% C: 12.0% G: 10.9% T: 36.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12734623 7404884.5 0 12734623 2 1654721 1851221.1 0 1654721 3 418088 462805.3 0 418088 4 64100 115701.3 0 64100 5 4898 28925.3 0 4898 6 4825 7231.3 0 4825 7 2422 1807.8 0 2422 8 1107 452.0 0 1107 9 929 113.0 0 268 661 10 1732 28.2 1 456 1276 11 1240 7.1 1 221 1019 12 1335 1.8 1 341 994 13 1850 0.4 1 0 1850 14 2618 0.4 1 0 2618 15 4918 0.4 1 0 4918 16 9233 0.4 1 0 9233 17 7451 0.4 1 0 7451 18 443 0.4 1 0 443 19 97 0.4 1 0 97 20 57 0.4 1 0 57 21 50 0.4 1 0 50 22 42 0.4 1 0 42 23 53 0.4 1 0 53 24 55 0.4 1 0 55 25 57 0.4 1 0 57 26 65 0.4 1 0 65 27 56 0.4 1 0 56 28 44 0.4 1 0 44 29 44 0.4 1 0 44 30 44 0.4 1 0 44 31 39 0.4 1 0 39 32 38 0.4 1 0 38 33 38 0.4 1 0 38 34 38 0.4 1 0 38 35 38 0.4 1 0 38 36 30 0.4 1 0 30 37 30 0.4 1 0 30 38 31 0.4 1 0 31 39 22 0.4 1 0 22 40 29 0.4 1 0 29 41 27 0.4 1 0 27 42 20 0.4 1 0 20 43 29 0.4 1 0 29 44 26 0.4 1 0 26 45 28 0.4 1 0 28 46 23 0.4 1 0 23 47 19 0.4 1 0 19 48 32 0.4 1 0 32 49 27 0.4 1 0 27 50 17 0.4 1 0 17 51 12 0.4 1 0 12 52 12 0.4 1 0 12 53 11 0.4 1 0 11 54 15 0.4 1 0 15 55 9 0.4 1 0 9 56 14 0.4 1 0 14 57 10 0.4 1 0 10 58 20 0.4 1 0 20 59 13 0.4 1 0 13 60 10 0.4 1 0 10 61 6 0.4 1 0 6 62 7 0.4 1 0 7 63 18 0.4 1 0 18 64 4 0.4 1 0 4 65 6 0.4 1 0 6 66 5 0.4 1 0 5 67 3 0.4 1 0 3 68 5 0.4 1 0 5 69 1 0.4 1 0 1 70 3 0.4 1 0 3 71 4 0.4 1 0 4 72 2 0.4 1 0 2 74 1 0.4 1 0 1 RUN STATISTICS FOR INPUT FILE: zr2096_8_s1_R1_val_1.fq.gz ============================================= 29619538 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_8_s1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_8_s1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_8_s1_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_8_s1_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_8_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 498.04 s (17 us/read; 3.57 M reads/minute). === Summary === Total reads processed: 29,619,538 Reads with adapters: 10,646,858 (35.9%) Reads written (passing filters): 29,619,538 (100.0%) Total basepairs processed: 2,266,654,553 bp Quality-trimmed: 1,200,478 bp (0.1%) Total written (filtered): 2,253,454,035 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10646858 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.1% C: 14.5% G: 3.5% T: 35.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10020563 7404884.5 0 10020563 2 428579 1851221.1 0 428579 3 127057 462805.3 0 127057 4 25733 115701.3 0 25733 5 2192 28925.3 0 2192 6 2101 7231.3 0 2101 7 447 1807.8 0 447 8 226 452.0 0 226 9 1258 113.0 0 1038 220 10 1006 28.2 1 132 874 11 1561 7.1 1 579 982 12 1584 1.8 1 213 1371 13 2970 0.4 1 0 2970 14 5029 0.4 1 0 5029 15 8015 0.4 1 0 8015 16 10482 0.4 1 0 10482 17 6434 0.4 1 0 6434 18 502 0.4 1 0 502 19 89 0.4 1 0 89 20 69 0.4 1 0 69 21 33 0.4 1 0 33 22 35 0.4 1 0 35 23 53 0.4 1 0 53 24 55 0.4 1 0 55 25 51 0.4 1 0 51 26 43 0.4 1 0 43 27 39 0.4 1 0 39 28 34 0.4 1 0 34 29 42 0.4 1 0 42 30 42 0.4 1 0 42 31 41 0.4 1 0 41 32 48 0.4 1 0 48 33 37 0.4 1 0 37 34 25 0.4 1 0 25 35 21 0.4 1 0 21 36 24 0.4 1 0 24 37 14 0.4 1 0 14 38 20 0.4 1 0 20 39 15 0.4 1 0 15 40 18 0.4 1 0 18 41 15 0.4 1 0 15 42 14 0.4 1 0 14 43 23 0.4 1 0 23 44 15 0.4 1 0 15 45 14 0.4 1 0 14 46 15 0.4 1 0 15 47 11 0.4 1 0 11 48 19 0.4 1 0 19 49 12 0.4 1 0 12 50 21 0.4 1 0 21 51 13 0.4 1 0 13 52 6 0.4 1 0 6 53 4 0.4 1 0 4 54 11 0.4 1 0 11 55 8 0.4 1 0 8 56 6 0.4 1 0 6 57 8 0.4 1 0 8 58 13 0.4 1 0 13 59 5 0.4 1 0 5 60 7 0.4 1 0 7 61 3 0.4 1 0 3 62 3 0.4 1 0 3 63 4 0.4 1 0 4 64 2 0.4 1 0 2 65 3 0.4 1 0 3 66 1 0.4 1 0 1 67 4 0.4 1 0 4 68 2 0.4 1 0 2 69 1 0.4 1 0 1 70 3 0.4 1 0 3 72 3 0.4 1 0 3 73 2 0.4 1 0 2 RUN STATISTICS FOR INPUT FILE: zr2096_8_s1_R2_val_2.fq.gz ============================================= 29619538 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_8_s1_R1_val_1_trimmed.fq.gz and zr2096_8_s1_R2_val_2_trimmed.fq.gz file_1: zr2096_8_s1_R1_val_1_trimmed.fq.gz, file_2: zr2096_8_s1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_8_s1_R1_val_1_trimmed.fq.gz and zr2096_8_s1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_8_s1_R1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_8_s1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 29619538 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 93858 (0.32%) >>> Now running FastQC on the validated data zr2096_8_s1_R1_val_1_val_1.fq.gz<<< Started analysis of zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 5% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 10% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 15% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 20% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 25% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 30% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 35% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 40% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 45% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 50% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 55% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 60% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 65% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 70% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 75% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 80% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 85% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 90% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz Approx 95% complete for zr2096_8_s1_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_8_s1_R2_val_2_val_2.fq.gz<<< Started analysis of zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 5% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 10% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 15% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 20% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 25% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 30% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 35% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 40% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 45% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 50% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 55% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 60% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 65% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 70% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 75% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 80% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 85% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 90% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Approx 95% complete for zr2096_8_s1_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr2096_8_s1_R1_val_1_trimmed.fq.gz and zr2096_8_s1_R2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_9_s1_R1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_9_s1_R1_val_1.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_9_s1_R1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_9_s1_R1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_9_s1_R1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 568.18 s (18 us/read; 3.39 M reads/minute). === Summary === Total reads processed: 32,090,732 Reads with adapters: 16,247,494 (50.6%) Reads written (passing filters): 32,090,732 (100.0%) Total basepairs processed: 2,422,296,960 bp Quality-trimmed: 5,121,841 bp (0.2%) Total written (filtered): 2,397,514,901 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16247494 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.6% C: 11.2% G: 11.0% T: 37.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13951064 8022683.0 0 13951064 2 1714451 2005670.8 0 1714451 3 463830 501417.7 0 463830 4 67603 125354.4 0 67603 5 6836 31338.6 0 6836 6 7175 7834.7 0 7175 7 2246 1958.7 0 2246 8 1054 489.7 0 1054 9 1330 122.4 0 441 889 10 1773 30.6 1 343 1430 11 2274 7.7 1 300 1974 12 1304 1.9 1 261 1043 13 1582 0.5 1 0 1582 14 2362 0.5 1 0 2362 15 4762 0.5 1 0 4762 16 8728 0.5 1 0 8728 17 7514 0.5 1 0 7514 18 361 0.5 1 0 361 19 60 0.5 1 0 60 20 28 0.5 1 0 28 21 36 0.5 1 0 36 22 32 0.5 1 0 32 23 27 0.5 1 0 27 24 22 0.5 1 0 22 25 42 0.5 1 0 42 26 42 0.5 1 0 42 27 40 0.5 1 0 40 28 35 0.5 1 0 35 29 35 0.5 1 0 35 30 34 0.5 1 0 34 31 46 0.5 1 0 46 32 30 0.5 1 0 30 33 33 0.5 1 0 33 34 18 0.5 1 0 18 35 31 0.5 1 0 31 36 26 0.5 1 0 26 37 42 0.5 1 0 42 38 22 0.5 1 0 22 39 25 0.5 1 0 25 40 33 0.5 1 0 33 41 25 0.5 1 0 25 42 21 0.5 1 0 21 43 36 0.5 1 0 36 44 23 0.5 1 0 23 45 30 0.5 1 0 30 46 27 0.5 1 0 27 47 25 0.5 1 0 25 48 25 0.5 1 0 25 49 26 0.5 1 0 26 50 20 0.5 1 0 20 51 16 0.5 1 0 16 52 23 0.5 1 0 23 53 18 0.5 1 0 18 54 9 0.5 1 0 9 55 14 0.5 1 0 14 56 13 0.5 1 0 13 57 15 0.5 1 0 15 58 15 0.5 1 0 15 59 16 0.5 1 0 16 60 11 0.5 1 0 11 61 16 0.5 1 0 16 62 11 0.5 1 0 11 63 16 0.5 1 0 16 64 12 0.5 1 0 12 65 11 0.5 1 0 11 66 8 0.5 1 0 8 67 6 0.5 1 0 6 68 6 0.5 1 0 6 69 3 0.5 1 0 3 70 5 0.5 1 0 5 71 2 0.5 1 0 2 72 2 0.5 1 0 2 RUN STATISTICS FOR INPUT FILE: zr2096_9_s1_R1_val_1.fq.gz ============================================= 32090732 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/zr2096_9_s1_R2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: zr2096_9_s1_R2_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; default (inconclusive auto-detection)) 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 All Read 1 sequences will be trimmed by 2 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir ~/Downloads/20180410_trimgalore_trim14bp5prim_2bp3prime_Cvirginica_MBD/20180410_fastqc_trimgalore_14bp5prime_2bp3prime_Cvirginica_MBD --threads 18' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to zr2096_9_s1_R2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file zr2096_9_s1_R2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC zr2096_9_s1_R2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 533.88 s (17 us/read; 3.61 M reads/minute). === Summary === Total reads processed: 32,090,732 Reads with adapters: 12,065,165 (37.6%) Reads written (passing filters): 32,090,732 (100.0%) Total basepairs processed: 2,435,867,609 bp Quality-trimmed: 1,897,278 bp (0.1%) Total written (filtered): 2,420,389,815 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12065165 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.3% C: 14.5% G: 3.3% T: 34.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11369976 8022683.0 0 11369976 2 480206 2005670.8 0 480206 3 135922 501417.7 0 135922 4 26588 125354.4 0 26588 5 3510 31338.6 0 3510 6 1945 7834.7 0 1945 7 456 1958.7 0 456 8 286 489.7 0 286 9 1414 122.4 0 1191 223 10 1205 30.6 1 159 1046 11 2243 7.7 1 628 1615 12 1796 1.9 1 276 1520 13 3224 0.5 1 0 3224 14 6064 0.5 1 0 6064 15 9139 0.5 1 0 9139 16 12213 0.5 1 0 12213 17 7453 0.5 1 0 7453 18 550 0.5 1 0 550 19 63 0.5 1 0 63 20 39 0.5 1 0 39 21 37 0.5 1 0 37 22 20 0.5 1 0 20 23 32 0.5 1 0 32 24 34 0.5 1 0 34 25 44 0.5 1 0 44 26 30 0.5 1 0 30 27 25 0.5 1 0 25 28 46 0.5 1 0 46 29 32 0.5 1 0 32 30 43 0.5 1 0 43 31 37 0.5 1 0 37 32 42 0.5 1 0 42 33 24 0.5 1 0 24 34 23 0.5 1 0 23 35 19 0.5 1 0 19 36 16 0.5 1 0 16 37 9 0.5 1 0 9 38 17 0.5 1 0 17 39 17 0.5 1 0 17 40 14 0.5 1 0 14 41 22 0.5 1 0 22 42 17 0.5 1 0 17 43 15 0.5 1 0 15 44 20 0.5 1 0 20 45 13 0.5 1 0 13 46 19 0.5 1 0 19 47 16 0.5 1 0 16 48 17 0.5 1 0 17 49 12 0.5 1 0 12 50 12 0.5 1 0 12 51 10 0.5 1 0 10 52 15 0.5 1 0 15 53 8 0.5 1 0 8 54 12 0.5 1 0 12 55 10 0.5 1 0 10 56 11 0.5 1 0 11 57 8 0.5 1 0 8 58 13 0.5 1 0 13 59 4 0.5 1 0 4 60 3 0.5 1 0 3 61 6 0.5 1 0 6 62 9 0.5 1 0 9 63 7 0.5 1 0 7 64 5 0.5 1 0 5 65 7 0.5 1 0 7 66 6 0.5 1 0 6 67 1 0.5 1 0 1 68 5 0.5 1 0 5 70 5 0.5 1 0 5 71 1 0.5 1 0 1 72 1 0.5 1 0 1 73 2 0.5 1 0 2 RUN STATISTICS FOR INPUT FILE: zr2096_9_s1_R2_val_2.fq.gz ============================================= 32090732 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files zr2096_9_s1_R1_val_1_trimmed.fq.gz and zr2096_9_s1_R2_val_2_trimmed.fq.gz file_1: zr2096_9_s1_R1_val_1_trimmed.fq.gz, file_2: zr2096_9_s1_R2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: zr2096_9_s1_R1_val_1_trimmed.fq.gz and zr2096_9_s1_R2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to zr2096_9_s1_R1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to zr2096_9_s1_R2_val_2_val_2.fq.gz Total number of sequences analysed: 32090732 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 199437 (0.62%) >>> Now running FastQC on the validated data zr2096_9_s1_R1_val_1_val_1.fq.gz<<< Started analysis of zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 5% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 10% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 15% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 20% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 25% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 30% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 35% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 40% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 45% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 50% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 55% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 60% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 65% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 70% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 75% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 80% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 85% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 90% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz Approx 95% complete for zr2096_9_s1_R1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data zr2096_9_s1_R2_val_2_val_2.fq.gz<<< Started analysis of zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 5% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 10% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 15% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 20% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 25% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 30% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 35% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 40% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 45% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 50% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 55% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 60% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 65% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 70% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 75% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 80% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 85% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 90% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Approx 95% complete for zr2096_9_s1_R2_val_2_val_2.fq.gz Deleting both intermediate output files zr2096_9_s1_R1_val_1_trimmed.fq.gz and zr2096_9_s1_R2_val_2_trimmed.fq.gz 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