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 (>> Library_Geoduck_MG_1_S3_L002_R1_001_val_1_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). gzip: stdout: Broken pipe Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_1_S3_L002_R1_001_val_1_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 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 Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2647.70 s (32 us/read; 1.88 M reads/minute). === Summary === Total reads processed: 82,999,052 Reads with adapters: 41,700,384 (50.2%) Reads written (passing filters): 82,999,052 (100.0%) Total basepairs processed: 10,399,588,050 bp Quality-trimmed: 7,072,599 bp (0.1%) Total written (filtered): 10,336,922,292 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 41700384 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.4% C: 21.5% G: 15.5% T: 24.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 31152549 20749763.0 0 31152549 2 8123960 5187440.8 0 8123960 3 2136355 1296860.2 0 2136355 4 178787 324215.0 0 178787 5 72465 81053.8 0 72465 6 17460 20263.4 0 17460 7 3839 5065.9 0 3839 8 543 1266.5 0 543 9 2556 316.6 0 214 2342 10 3325 79.2 1 82 3243 11 1240 19.8 1 14 1226 12 328 4.9 1 5 323 13 96 1.2 1 0 96 14 52 1.2 1 3 49 15 87 1.2 1 2 85 16 62 1.2 1 1 61 17 92 1.2 1 0 92 18 53 1.2 1 0 53 19 63 1.2 1 1 62 20 72 1.2 1 0 72 21 72 1.2 1 0 72 22 74 1.2 1 0 74 23 52 1.2 1 0 52 24 73 1.2 1 0 73 25 73 1.2 1 0 73 26 36 1.2 1 0 36 27 63 1.2 1 0 63 28 60 1.2 1 2 58 29 86 1.2 1 0 86 30 68 1.2 1 1 67 31 92 1.2 1 0 92 32 48 1.2 1 0 48 33 71 1.2 1 0 71 34 61 1.2 1 0 61 35 74 1.2 1 0 74 36 55 1.2 1 0 55 37 57 1.2 1 0 57 38 51 1.2 1 0 51 39 58 1.2 1 0 58 40 71 1.2 1 4 67 41 55 1.2 1 1 54 42 49 1.2 1 1 48 43 66 1.2 1 2 64 44 46 1.2 1 1 45 45 73 1.2 1 0 73 46 59 1.2 1 1 58 47 44 1.2 1 0 44 48 69 1.2 1 0 69 49 54 1.2 1 1 53 50 70 1.2 1 1 69 51 56 1.2 1 0 56 52 54 1.2 1 1 53 53 37 1.2 1 0 37 54 52 1.2 1 0 52 55 53 1.2 1 1 52 56 55 1.2 1 0 55 57 63 1.2 1 2 61 58 62 1.2 1 0 62 59 43 1.2 1 0 43 60 66 1.2 1 0 66 61 56 1.2 1 0 56 62 76 1.2 1 0 76 63 47 1.2 1 0 47 64 59 1.2 1 0 59 65 85 1.2 1 0 85 66 47 1.2 1 0 47 67 45 1.2 1 0 45 68 44 1.2 1 0 44 69 58 1.2 1 0 58 70 66 1.2 1 0 66 71 46 1.2 1 0 46 72 50 1.2 1 1 49 73 47 1.2 1 0 47 74 33 1.2 1 0 33 75 51 1.2 1 0 51 76 27 1.2 1 0 27 77 44 1.2 1 0 44 78 55 1.2 1 0 55 79 68 1.2 1 0 68 80 45 1.2 1 1 44 81 39 1.2 1 0 39 82 69 1.2 1 0 69 83 47 1.2 1 1 46 84 72 1.2 1 0 72 85 78 1.2 1 0 78 86 57 1.2 1 0 57 87 62 1.2 1 0 62 88 53 1.2 1 0 53 89 45 1.2 1 0 45 90 52 1.2 1 0 52 91 74 1.2 1 0 74 92 55 1.2 1 0 55 93 52 1.2 1 0 52 94 51 1.2 1 0 51 95 43 1.2 1 0 43 96 71 1.2 1 0 71 97 58 1.2 1 0 58 98 31 1.2 1 0 31 99 60 1.2 1 0 60 100 51 1.2 1 0 51 101 47 1.2 1 0 47 102 36 1.2 1 0 36 103 51 1.2 1 0 51 104 62 1.2 1 0 62 105 53 1.2 1 0 53 106 34 1.2 1 0 34 107 65 1.2 1 1 64 108 55 1.2 1 0 55 109 39 1.2 1 0 39 110 40 1.2 1 0 40 111 50 1.2 1 0 50 112 48 1.2 1 0 48 113 38 1.2 1 0 38 114 55 1.2 1 0 55 115 47 1.2 1 0 47 116 68 1.2 1 1 67 117 53 1.2 1 0 53 118 41 1.2 1 0 41 119 49 1.2 1 0 49 120 31 1.2 1 0 31 121 47 1.2 1 0 47 122 45 1.2 1 0 45 123 52 1.2 1 0 52 124 24 1.2 1 0 24 125 49 1.2 1 0 49 126 43 1.2 1 0 43 127 46 1.2 1 0 46 128 59 1.2 1 0 59 129 41 1.2 1 0 41 130 47 1.2 1 0 47 131 50 1.2 1 0 50 132 48 1.2 1 0 48 133 58 1.2 1 0 58 134 40 1.2 1 0 40 135 46 1.2 1 0 46 136 35 1.2 1 0 35 137 34 1.2 1 0 34 138 38 1.2 1 0 38 139 15 1.2 1 0 15 140 21 1.2 1 0 21 141 10 1.2 1 0 10 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz ============================================= 82999052 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_1_S3_L002_R2_001_val_2_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 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 Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2757.68 s (33 us/read; 1.81 M reads/minute). === Summary === Total reads processed: 82,999,052 Reads with adapters: 29,185,201 (35.2%) Reads written (passing filters): 82,999,052 (100.0%) Total basepairs processed: 10,052,257,721 bp Quality-trimmed: 27,927,865 bp (0.3%) Total written (filtered): 9,990,844,321 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29185201 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.9% C: 22.1% G: 6.6% T: 24.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 26290758 20749763.0 0 26290758 2 2135097 5187440.8 0 2135097 3 581764 1296860.2 0 581764 4 158432 324215.0 0 158432 5 5056 81053.8 0 5056 6 4203 20263.4 0 4203 7 1024 5065.9 0 1024 8 176 1266.5 0 176 9 798 316.6 0 196 602 10 852 79.2 1 12 840 11 345 19.8 1 1 344 12 109 4.9 1 0 109 13 59 1.2 1 0 59 14 56 1.2 1 0 56 15 48 1.2 1 0 48 16 51 1.2 1 0 51 17 63 1.2 1 0 63 18 63 1.2 1 1 62 19 71 1.2 1 0 71 20 56 1.2 1 0 56 21 52 1.2 1 2 50 22 54 1.2 1 1 53 23 84 1.2 1 2 82 24 53 1.2 1 2 51 25 74 1.2 1 0 74 26 84 1.2 1 0 84 27 51 1.2 1 0 51 28 78 1.2 1 0 78 29 54 1.2 1 0 54 30 53 1.2 1 0 53 31 47 1.2 1 0 47 32 50 1.2 1 1 49 33 55 1.2 1 0 55 34 70 1.2 1 1 69 35 45 1.2 1 0 45 36 42 1.2 1 0 42 37 65 1.2 1 0 65 38 61 1.2 1 0 61 39 54 1.2 1 0 54 40 76 1.2 1 0 76 41 61 1.2 1 0 61 42 45 1.2 1 0 45 43 44 1.2 1 0 44 44 67 1.2 1 0 67 45 67 1.2 1 0 67 46 73 1.2 1 1 72 47 59 1.2 1 1 58 48 64 1.2 1 0 64 49 40 1.2 1 0 40 50 58 1.2 1 0 58 51 63 1.2 1 0 63 52 44 1.2 1 1 43 53 57 1.2 1 0 57 54 34 1.2 1 0 34 55 55 1.2 1 0 55 56 72 1.2 1 0 72 57 51 1.2 1 0 51 58 52 1.2 1 0 52 59 46 1.2 1 0 46 60 51 1.2 1 0 51 61 62 1.2 1 3 59 62 64 1.2 1 0 64 63 66 1.2 1 0 66 64 44 1.2 1 2 42 65 51 1.2 1 0 51 66 65 1.2 1 0 65 67 62 1.2 1 0 62 68 66 1.2 1 0 66 69 60 1.2 1 0 60 70 68 1.2 1 0 68 71 53 1.2 1 0 53 72 69 1.2 1 0 69 73 54 1.2 1 0 54 74 52 1.2 1 0 52 75 67 1.2 1 0 67 76 39 1.2 1 0 39 77 54 1.2 1 0 54 78 61 1.2 1 0 61 79 42 1.2 1 0 42 80 45 1.2 1 0 45 81 49 1.2 1 0 49 82 67 1.2 1 0 67 83 85 1.2 1 0 85 84 55 1.2 1 0 55 85 45 1.2 1 0 45 86 44 1.2 1 0 44 87 49 1.2 1 0 49 88 60 1.2 1 0 60 89 67 1.2 1 0 67 90 53 1.2 1 0 53 91 47 1.2 1 0 47 92 44 1.2 1 0 44 93 45 1.2 1 0 45 94 56 1.2 1 0 56 95 53 1.2 1 1 52 96 69 1.2 1 0 69 97 43 1.2 1 0 43 98 40 1.2 1 0 40 99 67 1.2 1 0 67 100 44 1.2 1 0 44 101 44 1.2 1 0 44 102 45 1.2 1 0 45 103 60 1.2 1 0 60 104 63 1.2 1 0 63 105 35 1.2 1 0 35 106 51 1.2 1 0 51 107 46 1.2 1 0 46 108 32 1.2 1 0 32 109 47 1.2 1 0 47 110 34 1.2 1 0 34 111 44 1.2 1 0 44 112 36 1.2 1 0 36 113 54 1.2 1 0 54 114 36 1.2 1 0 36 115 50 1.2 1 0 50 116 49 1.2 1 0 49 117 46 1.2 1 0 46 118 55 1.2 1 0 55 119 32 1.2 1 0 32 120 41 1.2 1 0 41 121 34 1.2 1 0 34 122 58 1.2 1 0 58 123 36 1.2 1 0 36 124 47 1.2 1 0 47 125 35 1.2 1 0 35 126 33 1.2 1 0 33 127 32 1.2 1 0 32 128 46 1.2 1 0 46 129 42 1.2 1 0 42 130 43 1.2 1 0 43 131 57 1.2 1 0 57 132 32 1.2 1 0 32 133 33 1.2 1 0 33 134 40 1.2 1 0 40 135 23 1.2 1 0 23 136 23 1.2 1 0 23 137 19 1.2 1 0 19 138 9 1.2 1 0 9 139 19 1.2 1 0 19 140 26 1.2 1 0 26 141 2 1.2 1 0 2 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz ============================================= 82999052 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 82999052 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1380605 (1.66%) >>> Now running FastQC on the validated data Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_2_S4_L002_R1_001_val_1_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 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 Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2533.76 s (31 us/read; 1.94 M reads/minute). === Summary === Total reads processed: 81,915,909 Reads with adapters: 43,086,020 (52.6%) Reads written (passing filters): 81,915,909 (100.0%) Total basepairs processed: 10,082,741,867 bp Quality-trimmed: 6,642,171 bp (0.1%) Total written (filtered): 10,019,067,706 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43086020 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.1% C: 20.7% G: 14.6% T: 25.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 32531578 20478977.2 0 32531578 2 7993009 5119744.3 0 7993009 3 2259950 1279936.1 0 2259950 4 196255 319984.0 0 196255 5 75854 79996.0 0 75854 6 13495 19999.0 0 13495 7 2651 4999.8 0 2651 8 474 1249.9 0 474 9 2451 312.5 0 148 2303 10 3328 78.1 1 45 3283 11 1135 19.5 1 8 1127 12 289 4.9 1 1 288 13 58 1.2 1 0 58 14 40 1.2 1 0 40 15 51 1.2 1 0 51 16 38 1.2 1 1 37 17 42 1.2 1 0 42 18 63 1.2 1 0 63 19 54 1.2 1 0 54 20 41 1.2 1 1 40 21 63 1.2 1 0 63 22 57 1.2 1 0 57 23 69 1.2 1 1 68 24 60 1.2 1 0 60 25 55 1.2 1 0 55 26 55 1.2 1 0 55 27 51 1.2 1 0 51 28 46 1.2 1 0 46 29 74 1.2 1 0 74 30 40 1.2 1 0 40 31 45 1.2 1 0 45 32 49 1.2 1 0 49 33 50 1.2 1 0 50 34 45 1.2 1 0 45 35 66 1.2 1 0 66 36 43 1.2 1 0 43 37 51 1.2 1 0 51 38 49 1.2 1 0 49 39 55 1.2 1 0 55 40 53 1.2 1 0 53 41 47 1.2 1 0 47 42 38 1.2 1 0 38 43 36 1.2 1 0 36 44 47 1.2 1 1 46 45 80 1.2 1 0 80 46 46 1.2 1 0 46 47 53 1.2 1 0 53 48 41 1.2 1 0 41 49 69 1.2 1 0 69 50 31 1.2 1 0 31 51 47 1.2 1 0 47 52 51 1.2 1 0 51 53 41 1.2 1 0 41 54 49 1.2 1 0 49 55 37 1.2 1 0 37 56 25 1.2 1 0 25 57 50 1.2 1 0 50 58 30 1.2 1 0 30 59 41 1.2 1 0 41 60 45 1.2 1 0 45 61 39 1.2 1 0 39 62 45 1.2 1 0 45 63 52 1.2 1 0 52 64 32 1.2 1 0 32 65 49 1.2 1 0 49 66 42 1.2 1 0 42 67 32 1.2 1 0 32 68 34 1.2 1 0 34 69 60 1.2 1 2 58 70 49 1.2 1 0 49 71 63 1.2 1 0 63 72 47 1.2 1 0 47 73 33 1.2 1 0 33 74 36 1.2 1 0 36 75 39 1.2 1 0 39 76 48 1.2 1 0 48 77 41 1.2 1 0 41 78 42 1.2 1 0 42 79 65 1.2 1 0 65 80 38 1.2 1 0 38 81 20 1.2 1 0 20 82 56 1.2 1 0 56 83 39 1.2 1 0 39 84 38 1.2 1 0 38 85 57 1.2 1 0 57 86 46 1.2 1 0 46 87 54 1.2 1 0 54 88 37 1.2 1 0 37 89 18 1.2 1 0 18 90 44 1.2 1 0 44 91 50 1.2 1 0 50 92 47 1.2 1 0 47 93 67 1.2 1 0 67 94 40 1.2 1 1 39 95 46 1.2 1 0 46 96 57 1.2 1 1 56 97 39 1.2 1 0 39 98 20 1.2 1 0 20 99 41 1.2 1 0 41 100 28 1.2 1 0 28 101 31 1.2 1 0 31 102 52 1.2 1 0 52 103 54 1.2 1 2 52 104 46 1.2 1 1 45 105 60 1.2 1 0 60 106 25 1.2 1 0 25 107 43 1.2 1 0 43 108 28 1.2 1 0 28 109 35 1.2 1 0 35 110 29 1.2 1 0 29 111 44 1.2 1 0 44 112 37 1.2 1 0 37 113 41 1.2 1 0 41 114 46 1.2 1 0 46 115 42 1.2 1 1 41 116 34 1.2 1 2 32 117 47 1.2 1 0 47 118 58 1.2 1 0 58 119 50 1.2 1 0 50 120 51 1.2 1 0 51 121 37 1.2 1 0 37 122 30 1.2 1 0 30 123 30 1.2 1 0 30 124 22 1.2 1 0 22 125 24 1.2 1 0 24 126 39 1.2 1 0 39 127 32 1.2 1 0 32 128 30 1.2 1 0 30 129 41 1.2 1 0 41 130 29 1.2 1 0 29 131 33 1.2 1 0 33 132 30 1.2 1 0 30 133 38 1.2 1 0 38 134 20 1.2 1 0 20 135 35 1.2 1 0 35 136 25 1.2 1 0 25 137 29 1.2 1 0 29 138 27 1.2 1 0 27 139 18 1.2 1 0 18 140 24 1.2 1 0 24 141 8 1.2 1 0 8 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz ============================================= 81915909 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_2_S4_L002_R2_001_val_2_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 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 Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2663.59 s (33 us/read; 1.85 M reads/minute). === Summary === Total reads processed: 81,915,909 Reads with adapters: 29,570,997 (36.1%) Reads written (passing filters): 81,915,909 (100.0%) Total basepairs processed: 9,760,961,319 bp Quality-trimmed: 23,808,476 bp (0.2%) Total written (filtered): 9,703,465,118 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29570997 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.6% C: 21.2% G: 5.8% T: 25.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 26805812 20478977.2 0 26805812 2 1987373 5119744.3 0 1987373 3 594076 1279936.1 0 594076 4 168388 319984.0 0 168388 5 4152 79996.0 0 4152 6 2916 19999.0 0 2916 7 783 4999.8 0 783 8 136 1249.9 0 136 9 659 312.5 0 168 491 10 801 78.1 1 8 793 11 313 19.5 1 6 307 12 110 4.9 1 2 108 13 48 1.2 1 0 48 14 42 1.2 1 0 42 15 35 1.2 1 0 35 16 46 1.2 1 0 46 17 38 1.2 1 0 38 18 43 1.2 1 0 43 19 58 1.2 1 0 58 20 62 1.2 1 0 62 21 50 1.2 1 0 50 22 52 1.2 1 0 52 23 54 1.2 1 0 54 24 55 1.2 1 0 55 25 72 1.2 1 0 72 26 63 1.2 1 0 63 27 48 1.2 1 1 47 28 73 1.2 1 0 73 29 42 1.2 1 0 42 30 40 1.2 1 0 40 31 42 1.2 1 0 42 32 49 1.2 1 0 49 33 43 1.2 1 1 42 34 47 1.2 1 0 47 35 38 1.2 1 1 37 36 55 1.2 1 0 55 37 34 1.2 1 0 34 38 61 1.2 1 1 60 39 52 1.2 1 0 52 40 43 1.2 1 1 42 41 46 1.2 1 0 46 42 40 1.2 1 0 40 43 55 1.2 1 0 55 44 43 1.2 1 0 43 45 47 1.2 1 0 47 46 48 1.2 1 0 48 47 52 1.2 1 0 52 48 45 1.2 1 0 45 49 62 1.2 1 0 62 50 46 1.2 1 0 46 51 46 1.2 1 1 45 52 47 1.2 1 0 47 53 47 1.2 1 0 47 54 31 1.2 1 0 31 55 50 1.2 1 0 50 56 68 1.2 1 0 68 57 34 1.2 1 0 34 58 47 1.2 1 0 47 59 38 1.2 1 0 38 60 50 1.2 1 0 50 61 57 1.2 1 1 56 62 53 1.2 1 0 53 63 69 1.2 1 0 69 64 39 1.2 1 0 39 65 46 1.2 1 0 46 66 45 1.2 1 0 45 67 53 1.2 1 1 52 68 41 1.2 1 1 40 69 23 1.2 1 0 23 70 59 1.2 1 0 59 71 49 1.2 1 0 49 72 40 1.2 1 0 40 73 41 1.2 1 0 41 74 45 1.2 1 0 45 75 37 1.2 1 0 37 76 35 1.2 1 0 35 77 55 1.2 1 0 55 78 42 1.2 1 0 42 79 38 1.2 1 0 38 80 44 1.2 1 0 44 81 36 1.2 1 0 36 82 48 1.2 1 0 48 83 56 1.2 1 0 56 84 40 1.2 1 1 39 85 32 1.2 1 0 32 86 49 1.2 1 0 49 87 43 1.2 1 0 43 88 42 1.2 1 0 42 89 52 1.2 1 0 52 90 39 1.2 1 0 39 91 49 1.2 1 0 49 92 51 1.2 1 0 51 93 42 1.2 1 1 41 94 58 1.2 1 0 58 95 38 1.2 1 0 38 96 53 1.2 1 0 53 97 41 1.2 1 0 41 98 19 1.2 1 0 19 99 54 1.2 1 0 54 100 44 1.2 1 0 44 101 39 1.2 1 0 39 102 48 1.2 1 0 48 103 59 1.2 1 0 59 104 42 1.2 1 0 42 105 30 1.2 1 2 28 106 57 1.2 1 0 57 107 36 1.2 1 0 36 108 28 1.2 1 0 28 109 40 1.2 1 0 40 110 40 1.2 1 0 40 111 29 1.2 1 0 29 112 36 1.2 1 0 36 113 42 1.2 1 0 42 114 32 1.2 1 0 32 115 57 1.2 1 0 57 116 48 1.2 1 0 48 117 38 1.2 1 0 38 118 25 1.2 1 0 25 119 28 1.2 1 0 28 120 34 1.2 1 0 34 121 28 1.2 1 0 28 122 52 1.2 1 0 52 123 21 1.2 1 0 21 124 41 1.2 1 0 41 125 23 1.2 1 0 23 126 31 1.2 1 0 31 127 20 1.2 1 0 20 128 61 1.2 1 0 61 129 46 1.2 1 0 46 130 30 1.2 1 0 30 131 43 1.2 1 0 43 132 25 1.2 1 0 25 133 15 1.2 1 0 15 134 28 1.2 1 0 28 135 27 1.2 1 0 27 136 23 1.2 1 0 23 137 19 1.2 1 0 19 138 7 1.2 1 0 7 139 9 1.2 1 0 9 140 6 1.2 1 0 6 141 11 1.2 1 0 11 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz ============================================= 81915909 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 81915909 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1771719 (2.16%) >>> Now running FastQC on the validated data Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_3_S1_L002_R1_001_val_1_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 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 Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2440.19 s (28 us/read; 2.16 M reads/minute). === Summary === Total reads processed: 87,950,295 Reads with adapters: 43,354,347 (49.3%) Reads written (passing filters): 87,950,295 (100.0%) Total basepairs processed: 9,821,337,199 bp Quality-trimmed: 7,779,520 bp (0.1%) Total written (filtered): 9,755,934,901 bp (99.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 43354347 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.0% C: 21.4% G: 14.8% T: 25.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 32474107 21987573.8 0 32474107 2 8337730 5496893.4 0 8337730 3 2230881 1374223.4 0 2230881 4 175628 343555.8 0 175628 5 104322 85889.0 0 104322 6 13872 21472.2 0 13872 7 2929 5368.1 0 2929 8 554 1342.0 0 554 9 2956 335.5 0 202 2754 10 4757 83.9 1 98 4659 11 1287 21.0 1 6 1281 12 222 5.2 1 0 222 13 69 1.3 1 0 69 14 47 1.3 1 0 47 15 62 1.3 1 0 62 16 38 1.3 1 0 38 17 54 1.3 1 0 54 18 60 1.3 1 0 60 19 58 1.3 1 1 57 20 63 1.3 1 0 63 21 45 1.3 1 0 45 22 59 1.3 1 0 59 23 48 1.3 1 0 48 24 53 1.3 1 0 53 25 65 1.3 1 0 65 26 38 1.3 1 0 38 27 28 1.3 1 0 28 28 43 1.3 1 1 42 29 67 1.3 1 0 67 30 42 1.3 1 0 42 31 42 1.3 1 0 42 32 31 1.3 1 0 31 33 46 1.3 1 0 46 34 57 1.3 1 0 57 35 47 1.3 1 0 47 36 60 1.3 1 0 60 37 49 1.3 1 0 49 38 47 1.3 1 0 47 39 40 1.3 1 0 40 40 59 1.3 1 0 59 41 48 1.3 1 0 48 42 38 1.3 1 0 38 43 46 1.3 1 0 46 44 39 1.3 1 0 39 45 77 1.3 1 0 77 46 40 1.3 1 0 40 47 37 1.3 1 0 37 48 59 1.3 1 0 59 49 54 1.3 1 0 54 50 49 1.3 1 1 48 51 49 1.3 1 0 49 52 41 1.3 1 0 41 53 35 1.3 1 0 35 54 40 1.3 1 0 40 55 39 1.3 1 0 39 56 28 1.3 1 1 27 57 42 1.3 1 0 42 58 49 1.3 1 0 49 59 45 1.3 1 0 45 60 28 1.3 1 0 28 61 36 1.3 1 0 36 62 49 1.3 1 0 49 63 32 1.3 1 0 32 64 47 1.3 1 1 46 65 32 1.3 1 1 31 66 49 1.3 1 0 49 67 43 1.3 1 0 43 68 33 1.3 1 0 33 69 38 1.3 1 0 38 70 38 1.3 1 1 37 71 44 1.3 1 0 44 72 44 1.3 1 0 44 73 31 1.3 1 0 31 74 37 1.3 1 0 37 75 33 1.3 1 1 32 76 43 1.3 1 0 43 77 50 1.3 1 0 50 78 24 1.3 1 0 24 79 23 1.3 1 0 23 80 27 1.3 1 0 27 81 30 1.3 1 0 30 82 35 1.3 1 1 34 83 50 1.3 1 1 49 84 34 1.3 1 0 34 85 37 1.3 1 0 37 86 46 1.3 1 0 46 87 43 1.3 1 0 43 88 23 1.3 1 0 23 89 41 1.3 1 0 41 90 35 1.3 1 0 35 91 45 1.3 1 0 45 92 29 1.3 1 0 29 93 41 1.3 1 0 41 94 24 1.3 1 0 24 95 38 1.3 1 0 38 96 36 1.3 1 0 36 97 41 1.3 1 0 41 98 35 1.3 1 0 35 99 34 1.3 1 0 34 100 37 1.3 1 0 37 101 28 1.3 1 0 28 102 24 1.3 1 0 24 103 47 1.3 1 0 47 104 32 1.3 1 2 30 105 48 1.3 1 0 48 106 39 1.3 1 0 39 107 35 1.3 1 0 35 108 24 1.3 1 0 24 109 31 1.3 1 0 31 110 31 1.3 1 0 31 111 39 1.3 1 0 39 112 42 1.3 1 0 42 113 52 1.3 1 0 52 114 33 1.3 1 0 33 115 35 1.3 1 0 35 116 47 1.3 1 0 47 117 34 1.3 1 0 34 118 44 1.3 1 0 44 119 22 1.3 1 0 22 120 24 1.3 1 0 24 121 22 1.3 1 0 22 122 24 1.3 1 0 24 123 43 1.3 1 0 43 124 33 1.3 1 0 33 125 31 1.3 1 0 31 126 42 1.3 1 0 42 127 31 1.3 1 0 31 128 20 1.3 1 0 20 129 33 1.3 1 0 33 130 26 1.3 1 0 26 131 28 1.3 1 0 28 132 54 1.3 1 0 54 133 31 1.3 1 0 31 134 34 1.3 1 0 34 135 29 1.3 1 0 29 136 24 1.3 1 0 24 137 45 1.3 1 0 45 138 26 1.3 1 0 26 139 18 1.3 1 0 18 140 6 1.3 1 0 6 141 4 1.3 1 0 4 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz ============================================= 87950295 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_3_S1_L002_R2_001_val_2_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 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 Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2520.42 s (29 us/read; 2.09 M reads/minute). === Summary === Total reads processed: 87,950,295 Reads with adapters: 29,237,966 (33.2%) Reads written (passing filters): 87,950,295 (100.0%) Total basepairs processed: 9,561,681,685 bp Quality-trimmed: 21,909,122 bp (0.2%) Total written (filtered): 9,506,058,038 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29237966 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.3% C: 21.8% G: 6.4% T: 25.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 26193220 21987573.8 0 26193220 2 2136185 5496893.4 0 2136185 3 723830 1374223.4 0 723830 4 168923 343555.8 0 168923 5 4279 85889.0 0 4279 6 3286 21472.2 0 3286 7 990 5368.1 0 990 8 191 1342.0 0 191 9 902 335.5 0 238 664 10 882 83.9 1 9 873 11 318 21.0 1 1 317 12 111 5.2 1 0 111 13 60 1.3 1 0 60 14 48 1.3 1 0 48 15 47 1.3 1 2 45 16 45 1.3 1 0 45 17 47 1.3 1 0 47 18 36 1.3 1 0 36 19 60 1.3 1 0 60 20 63 1.3 1 0 63 21 37 1.3 1 0 37 22 46 1.3 1 0 46 23 60 1.3 1 0 60 24 54 1.3 1 0 54 25 46 1.3 1 0 46 26 52 1.3 1 0 52 27 46 1.3 1 0 46 28 57 1.3 1 1 56 29 44 1.3 1 0 44 30 53 1.3 1 0 53 31 43 1.3 1 0 43 32 53 1.3 1 0 53 33 44 1.3 1 0 44 34 51 1.3 1 0 51 35 38 1.3 1 0 38 36 63 1.3 1 0 63 37 65 1.3 1 0 65 38 55 1.3 1 0 55 39 50 1.3 1 0 50 40 31 1.3 1 0 31 41 48 1.3 1 0 48 42 49 1.3 1 0 49 43 39 1.3 1 0 39 44 46 1.3 1 0 46 45 57 1.3 1 0 57 46 55 1.3 1 0 55 47 33 1.3 1 0 33 48 43 1.3 1 0 43 49 26 1.3 1 0 26 50 41 1.3 1 0 41 51 44 1.3 1 0 44 52 37 1.3 1 0 37 53 51 1.3 1 0 51 54 24 1.3 1 0 24 55 45 1.3 1 0 45 56 42 1.3 1 0 42 57 35 1.3 1 0 35 58 29 1.3 1 0 29 59 43 1.3 1 1 42 60 57 1.3 1 0 57 61 42 1.3 1 0 42 62 42 1.3 1 0 42 63 37 1.3 1 0 37 64 46 1.3 1 2 44 65 43 1.3 1 0 43 66 26 1.3 1 0 26 67 35 1.3 1 0 35 68 46 1.3 1 0 46 69 41 1.3 1 0 41 70 38 1.3 1 0 38 71 60 1.3 1 0 60 72 49 1.3 1 0 49 73 24 1.3 1 0 24 74 50 1.3 1 0 50 75 39 1.3 1 0 39 76 37 1.3 1 0 37 77 49 1.3 1 0 49 78 40 1.3 1 0 40 79 32 1.3 1 1 31 80 30 1.3 1 0 30 81 29 1.3 1 0 29 82 38 1.3 1 0 38 83 33 1.3 1 0 33 84 41 1.3 1 0 41 85 37 1.3 1 0 37 86 42 1.3 1 1 41 87 37 1.3 1 0 37 88 35 1.3 1 1 34 89 31 1.3 1 0 31 90 36 1.3 1 0 36 91 42 1.3 1 0 42 92 33 1.3 1 0 33 93 29 1.3 1 2 27 94 28 1.3 1 0 28 95 36 1.3 1 0 36 96 33 1.3 1 0 33 97 36 1.3 1 0 36 98 30 1.3 1 0 30 99 27 1.3 1 0 27 100 28 1.3 1 0 28 101 39 1.3 1 0 39 102 34 1.3 1 0 34 103 45 1.3 1 0 45 104 46 1.3 1 0 46 105 31 1.3 1 0 31 106 27 1.3 1 0 27 107 30 1.3 1 0 30 108 32 1.3 1 0 32 109 36 1.3 1 0 36 110 20 1.3 1 0 20 111 25 1.3 1 0 25 112 30 1.3 1 0 30 113 24 1.3 1 0 24 114 39 1.3 1 0 39 115 36 1.3 1 0 36 116 35 1.3 1 0 35 117 28 1.3 1 0 28 118 27 1.3 1 0 27 119 32 1.3 1 0 32 120 20 1.3 1 0 20 121 24 1.3 1 0 24 122 39 1.3 1 0 39 123 22 1.3 1 0 22 124 23 1.3 1 0 23 125 29 1.3 1 0 29 126 21 1.3 1 0 21 127 49 1.3 1 0 49 128 32 1.3 1 0 32 129 20 1.3 1 0 20 130 30 1.3 1 0 30 131 26 1.3 1 0 26 132 23 1.3 1 0 23 133 19 1.3 1 0 19 134 21 1.3 1 0 21 135 25 1.3 1 0 25 136 26 1.3 1 0 26 137 19 1.3 1 0 19 138 19 1.3 1 0 19 139 10 1.3 1 0 10 140 7 1.3 1 0 7 141 4 1.3 1 0 4 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz ============================================= 87950295 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 87950295 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 4216708 (4.79%) >>> Now running FastQC on the validated data Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_5_S6_L002_R1_001_val_1_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 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 Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2228.49 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 71,733,777 Reads with adapters: 39,189,986 (54.6%) Reads written (passing filters): 71,733,777 (100.0%) Total basepairs processed: 8,977,160,164 bp Quality-trimmed: 5,550,572 bp (0.1%) Total written (filtered): 8,920,153,289 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 39189986 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.8% C: 20.1% G: 13.9% T: 26.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 29988597 17933444.2 0 29988597 2 6858970 4483361.1 0 6858970 3 2069436 1120840.3 0 2069436 4 184402 280210.1 0 184402 5 64402 70052.5 0 64402 6 10720 17513.1 0 10720 7 2103 4378.3 0 2103 8 386 1094.6 0 386 9 2129 273.6 0 152 1977 10 2889 68.4 1 34 2855 11 959 17.1 1 4 955 12 247 4.3 1 0 247 13 53 1.1 1 0 53 14 32 1.1 1 0 32 15 34 1.1 1 0 34 16 29 1.1 1 0 29 17 29 1.1 1 0 29 18 52 1.1 1 2 50 19 42 1.1 1 0 42 20 51 1.1 1 0 51 21 74 1.1 1 0 74 22 54 1.1 1 0 54 23 70 1.1 1 0 70 24 51 1.1 1 0 51 25 46 1.1 1 0 46 26 38 1.1 1 0 38 27 41 1.1 1 0 41 28 43 1.1 1 0 43 29 83 1.1 1 0 83 30 31 1.1 1 0 31 31 41 1.1 1 0 41 32 39 1.1 1 0 39 33 33 1.1 1 0 33 34 51 1.1 1 0 51 35 55 1.1 1 0 55 36 28 1.1 1 0 28 37 31 1.1 1 0 31 38 38 1.1 1 0 38 39 34 1.1 1 0 34 40 29 1.1 1 0 29 41 40 1.1 1 0 40 42 32 1.1 1 0 32 43 32 1.1 1 0 32 44 23 1.1 1 0 23 45 70 1.1 1 0 70 46 35 1.1 1 0 35 47 49 1.1 1 0 49 48 37 1.1 1 0 37 49 73 1.1 1 0 73 50 29 1.1 1 0 29 51 21 1.1 1 0 21 52 33 1.1 1 0 33 53 40 1.1 1 0 40 54 26 1.1 1 0 26 55 47 1.1 1 0 47 56 43 1.1 1 0 43 57 43 1.1 1 0 43 58 40 1.1 1 0 40 59 33 1.1 1 1 32 60 42 1.1 1 0 42 61 24 1.1 1 0 24 62 39 1.1 1 0 39 63 40 1.1 1 0 40 64 34 1.1 1 0 34 65 50 1.1 1 0 50 66 25 1.1 1 0 25 67 30 1.1 1 0 30 68 22 1.1 1 0 22 69 45 1.1 1 0 45 70 49 1.1 1 0 49 71 41 1.1 1 0 41 72 57 1.1 1 0 57 73 34 1.1 1 0 34 74 19 1.1 1 0 19 75 41 1.1 1 0 41 76 39 1.1 1 0 39 77 36 1.1 1 2 34 78 41 1.1 1 0 41 79 54 1.1 1 0 54 80 65 1.1 1 0 65 81 18 1.1 1 0 18 82 43 1.1 1 2 41 83 33 1.1 1 0 33 84 33 1.1 1 0 33 85 41 1.1 1 0 41 86 46 1.1 1 0 46 87 44 1.1 1 0 44 88 44 1.1 1 0 44 89 27 1.1 1 0 27 90 30 1.1 1 0 30 91 38 1.1 1 0 38 92 31 1.1 1 0 31 93 61 1.1 1 0 61 94 40 1.1 1 0 40 95 28 1.1 1 0 28 96 46 1.1 1 0 46 97 38 1.1 1 0 38 98 18 1.1 1 0 18 99 40 1.1 1 0 40 100 35 1.1 1 1 34 101 29 1.1 1 0 29 102 42 1.1 1 0 42 103 24 1.1 1 0 24 104 34 1.1 1 0 34 105 48 1.1 1 0 48 106 16 1.1 1 0 16 107 45 1.1 1 0 45 108 35 1.1 1 0 35 109 30 1.1 1 0 30 110 18 1.1 1 0 18 111 43 1.1 1 0 43 112 32 1.1 1 0 32 113 44 1.1 1 0 44 114 29 1.1 1 0 29 115 32 1.1 1 0 32 116 35 1.1 1 0 35 117 29 1.1 1 0 29 118 35 1.1 1 0 35 119 56 1.1 1 0 56 120 27 1.1 1 0 27 121 26 1.1 1 0 26 122 25 1.1 1 0 25 123 48 1.1 1 0 48 124 18 1.1 1 0 18 125 18 1.1 1 0 18 126 23 1.1 1 0 23 127 23 1.1 1 0 23 128 37 1.1 1 0 37 129 35 1.1 1 0 35 130 12 1.1 1 0 12 131 32 1.1 1 0 32 132 22 1.1 1 0 22 133 14 1.1 1 0 14 134 21 1.1 1 0 21 135 46 1.1 1 0 46 136 28 1.1 1 0 28 137 20 1.1 1 0 20 138 28 1.1 1 0 28 139 10 1.1 1 0 10 140 28 1.1 1 0 28 141 10 1.1 1 0 10 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz ============================================= 71733777 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_5_S6_L002_R2_001_val_2_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 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 Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2350.16 s (33 us/read; 1.83 M reads/minute). === Summary === Total reads processed: 71,733,777 Reads with adapters: 26,952,904 (37.6%) Reads written (passing filters): 71,733,777 (100.0%) Total basepairs processed: 8,728,992,125 bp Quality-trimmed: 19,201,281 bp (0.2%) Total written (filtered): 8,679,330,386 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 26952904 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.5% C: 20.6% G: 5.1% T: 25.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24590621 17933444.2 0 24590621 2 1716070 4483361.1 0 1716070 3 476291 1120840.3 0 476291 4 157132 280210.1 0 157132 5 3490 70052.5 0 3490 6 2281 17513.1 0 2281 7 598 4378.3 0 598 8 114 1094.6 0 114 9 559 273.6 0 141 418 10 703 68.4 1 12 691 11 238 17.1 1 0 238 12 85 4.3 1 0 85 13 43 1.1 1 0 43 14 42 1.1 1 0 42 15 36 1.1 1 0 36 16 34 1.1 1 0 34 17 41 1.1 1 0 41 18 69 1.1 1 0 69 19 50 1.1 1 0 50 20 35 1.1 1 0 35 21 53 1.1 1 0 53 22 47 1.1 1 1 46 23 59 1.1 1 0 59 24 40 1.1 1 1 39 25 55 1.1 1 0 55 26 48 1.1 1 0 48 27 34 1.1 1 0 34 28 70 1.1 1 0 70 29 46 1.1 1 0 46 30 46 1.1 1 0 46 31 33 1.1 1 0 33 32 47 1.1 1 1 46 33 37 1.1 1 0 37 34 50 1.1 1 0 50 35 64 1.1 1 1 63 36 37 1.1 1 0 37 37 32 1.1 1 0 32 38 43 1.1 1 0 43 39 54 1.1 1 0 54 40 60 1.1 1 0 60 41 46 1.1 1 0 46 42 39 1.1 1 0 39 43 65 1.1 1 0 65 44 28 1.1 1 0 28 45 40 1.1 1 0 40 46 44 1.1 1 0 44 47 44 1.1 1 0 44 48 34 1.1 1 0 34 49 55 1.1 1 0 55 50 45 1.1 1 0 45 51 50 1.1 1 0 50 52 27 1.1 1 0 27 53 47 1.1 1 0 47 54 25 1.1 1 0 25 55 38 1.1 1 0 38 56 49 1.1 1 0 49 57 40 1.1 1 1 39 58 26 1.1 1 0 26 59 42 1.1 1 0 42 60 37 1.1 1 0 37 61 35 1.1 1 0 35 62 37 1.1 1 0 37 63 49 1.1 1 0 49 64 49 1.1 1 0 49 65 31 1.1 1 0 31 66 30 1.1 1 0 30 67 25 1.1 1 0 25 68 38 1.1 1 0 38 69 22 1.1 1 0 22 70 48 1.1 1 0 48 71 52 1.1 1 0 52 72 37 1.1 1 0 37 73 50 1.1 1 0 50 74 37 1.1 1 0 37 75 34 1.1 1 0 34 76 33 1.1 1 0 33 77 33 1.1 1 0 33 78 23 1.1 1 0 23 79 45 1.1 1 0 45 80 49 1.1 1 0 49 81 34 1.1 1 0 34 82 21 1.1 1 0 21 83 28 1.1 1 0 28 84 35 1.1 1 0 35 85 21 1.1 1 0 21 86 46 1.1 1 0 46 87 40 1.1 1 0 40 88 28 1.1 1 0 28 89 29 1.1 1 0 29 90 46 1.1 1 0 46 91 47 1.1 1 0 47 92 29 1.1 1 0 29 93 47 1.1 1 0 47 94 31 1.1 1 0 31 95 27 1.1 1 0 27 96 37 1.1 1 0 37 97 46 1.1 1 0 46 98 19 1.1 1 0 19 99 29 1.1 1 0 29 100 36 1.1 1 0 36 101 32 1.1 1 0 32 102 41 1.1 1 0 41 103 49 1.1 1 0 49 104 28 1.1 1 0 28 105 30 1.1 1 0 30 106 46 1.1 1 0 46 107 33 1.1 1 0 33 108 33 1.1 1 0 33 109 35 1.1 1 0 35 110 19 1.1 1 0 19 111 22 1.1 1 0 22 112 30 1.1 1 0 30 113 38 1.1 1 0 38 114 39 1.1 1 0 39 115 40 1.1 1 0 40 116 35 1.1 1 0 35 117 22 1.1 1 0 22 118 27 1.1 1 0 27 119 31 1.1 1 0 31 120 23 1.1 1 0 23 121 31 1.1 1 0 31 122 50 1.1 1 0 50 123 27 1.1 1 0 27 124 24 1.1 1 0 24 125 39 1.1 1 0 39 126 22 1.1 1 0 22 127 22 1.1 1 0 22 128 30 1.1 1 0 30 129 38 1.1 1 0 38 130 16 1.1 1 0 16 131 35 1.1 1 0 35 132 34 1.1 1 0 34 133 14 1.1 1 0 14 134 22 1.1 1 0 22 135 19 1.1 1 0 19 136 20 1.1 1 0 20 137 14 1.1 1 0 14 138 11 1.1 1 0 11 139 17 1.1 1 0 17 140 12 1.1 1 0 12 141 13 1.1 1 0 13 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz ============================================= 71733777 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 71733777 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1178612 (1.64%) >>> Now running FastQC on the validated data Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_6_S5_L002_R1_001_val_1_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 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 Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2284.51 s (31 us/read; 1.92 M reads/minute). === Summary === Total reads processed: 73,192,078 Reads with adapters: 38,909,941 (53.2%) Reads written (passing filters): 73,192,078 (100.0%) Total basepairs processed: 9,070,248,848 bp Quality-trimmed: 5,447,904 bp (0.1%) Total written (filtered): 9,013,153,573 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 38909941 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.5% C: 20.6% G: 14.2% T: 25.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 29294615 18298019.5 0 29294615 2 7281849 4574504.9 0 7281849 3 2053808 1143626.2 0 2053808 4 177566 285906.6 0 177566 5 73954 71476.6 0 73954 6 13089 17869.2 0 13089 7 2757 4467.3 0 2757 8 380 1116.8 0 380 9 2284 279.2 0 194 2090 10 2964 69.8 1 61 2903 11 1037 17.5 1 6 1031 12 241 4.4 1 2 239 13 45 1.1 1 0 45 14 45 1.1 1 0 45 15 47 1.1 1 0 47 16 49 1.1 1 0 49 17 39 1.1 1 0 39 18 54 1.1 1 0 54 19 44 1.1 1 1 43 20 57 1.1 1 0 57 21 61 1.1 1 0 61 22 67 1.1 1 1 66 23 60 1.1 1 0 60 24 53 1.1 1 0 53 25 52 1.1 1 0 52 26 33 1.1 1 0 33 27 45 1.1 1 0 45 28 44 1.1 1 0 44 29 100 1.1 1 0 100 30 38 1.1 1 0 38 31 42 1.1 1 0 42 32 62 1.1 1 0 62 33 51 1.1 1 0 51 34 46 1.1 1 0 46 35 69 1.1 1 0 69 36 38 1.1 1 0 38 37 48 1.1 1 0 48 38 38 1.1 1 0 38 39 53 1.1 1 0 53 40 41 1.1 1 0 41 41 59 1.1 1 3 56 42 44 1.1 1 0 44 43 42 1.1 1 0 42 44 43 1.1 1 0 43 45 84 1.1 1 0 84 46 19 1.1 1 0 19 47 33 1.1 1 0 33 48 46 1.1 1 0 46 49 79 1.1 1 0 79 50 43 1.1 1 0 43 51 48 1.1 1 0 48 52 42 1.1 1 0 42 53 24 1.1 1 0 24 54 47 1.1 1 0 47 55 39 1.1 1 0 39 56 31 1.1 1 0 31 57 53 1.1 1 0 53 58 38 1.1 1 0 38 59 44 1.1 1 0 44 60 61 1.1 1 0 61 61 45 1.1 1 0 45 62 51 1.1 1 0 51 63 31 1.1 1 0 31 64 34 1.1 1 0 34 65 61 1.1 1 0 61 66 48 1.1 1 0 48 67 37 1.1 1 0 37 68 42 1.1 1 0 42 69 35 1.1 1 0 35 70 55 1.1 1 0 55 71 41 1.1 1 0 41 72 62 1.1 1 0 62 73 53 1.1 1 0 53 74 29 1.1 1 0 29 75 37 1.1 1 0 37 76 46 1.1 1 0 46 77 48 1.1 1 0 48 78 49 1.1 1 0 49 79 47 1.1 1 0 47 80 19 1.1 1 0 19 81 20 1.1 1 0 20 82 43 1.1 1 0 43 83 42 1.1 1 1 41 84 41 1.1 1 0 41 85 33 1.1 1 0 33 86 62 1.1 1 0 62 87 46 1.1 1 0 46 88 42 1.1 1 0 42 89 39 1.1 1 0 39 90 51 1.1 1 0 51 91 34 1.1 1 0 34 92 44 1.1 1 0 44 93 41 1.1 1 0 41 94 29 1.1 1 0 29 95 29 1.1 1 0 29 96 72 1.1 1 0 72 97 42 1.1 1 0 42 98 34 1.1 1 0 34 99 40 1.1 1 0 40 100 20 1.1 1 0 20 101 62 1.1 1 0 62 102 26 1.1 1 0 26 103 37 1.1 1 0 37 104 29 1.1 1 0 29 105 68 1.1 1 0 68 106 23 1.1 1 0 23 107 52 1.1 1 0 52 108 35 1.1 1 0 35 109 34 1.1 1 0 34 110 24 1.1 1 0 24 111 42 1.1 1 0 42 112 28 1.1 1 0 28 113 39 1.1 1 0 39 114 42 1.1 1 0 42 115 51 1.1 1 0 51 116 43 1.1 1 0 43 117 28 1.1 1 0 28 118 42 1.1 1 0 42 119 30 1.1 1 0 30 120 24 1.1 1 0 24 121 31 1.1 1 0 31 122 32 1.1 1 0 32 123 40 1.1 1 0 40 124 42 1.1 1 0 42 125 22 1.1 1 0 22 126 34 1.1 1 0 34 127 37 1.1 1 0 37 128 28 1.1 1 0 28 129 34 1.1 1 0 34 130 45 1.1 1 0 45 131 38 1.1 1 0 38 132 38 1.1 1 0 38 133 28 1.1 1 0 28 134 12 1.1 1 0 12 135 38 1.1 1 0 38 136 31 1.1 1 0 31 137 29 1.1 1 0 29 138 24 1.1 1 0 24 139 23 1.1 1 0 23 140 13 1.1 1 0 13 141 5 1.1 1 0 5 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz ============================================= 73192078 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_6_S5_L002_R2_001_val_2_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 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 Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2398.35 s (33 us/read; 1.83 M reads/minute). === Summary === Total reads processed: 73,192,078 Reads with adapters: 26,780,011 (36.6%) Reads written (passing filters): 73,192,078 (100.0%) Total basepairs processed: 8,814,341,687 bp Quality-trimmed: 19,241,904 bp (0.2%) Total written (filtered): 8,764,670,030 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 26780011 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.0% C: 21.3% G: 5.2% T: 25.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24336596 18298019.5 0 24336596 2 1776956 4574504.9 0 1776956 3 497249 1143626.2 0 497249 4 154272 285906.6 0 154272 5 4282 71476.6 0 4282 6 2808 17869.2 0 2808 7 676 4467.3 0 676 8 109 1116.8 0 109 9 654 279.2 0 195 459 10 751 69.8 1 8 743 11 306 17.5 1 3 303 12 123 4.4 1 0 123 13 34 1.1 1 0 34 14 57 1.1 1 0 57 15 40 1.1 1 1 39 16 35 1.1 1 1 34 17 49 1.1 1 1 48 18 56 1.1 1 0 56 19 59 1.1 1 0 59 20 43 1.1 1 0 43 21 49 1.1 1 0 49 22 65 1.1 1 0 65 23 46 1.1 1 0 46 24 41 1.1 1 0 41 25 62 1.1 1 0 62 26 64 1.1 1 0 64 27 46 1.1 1 0 46 28 95 1.1 1 0 95 29 25 1.1 1 0 25 30 53 1.1 1 0 53 31 34 1.1 1 0 34 32 39 1.1 1 0 39 33 54 1.1 1 1 53 34 41 1.1 1 1 40 35 62 1.1 1 0 62 36 39 1.1 1 0 39 37 37 1.1 1 0 37 38 55 1.1 1 0 55 39 56 1.1 1 0 56 40 40 1.1 1 0 40 41 51 1.1 1 0 51 42 30 1.1 1 0 30 43 54 1.1 1 0 54 44 38 1.1 1 0 38 45 55 1.1 1 0 55 46 72 1.1 1 0 72 47 52 1.1 1 0 52 48 32 1.1 1 0 32 49 42 1.1 1 0 42 50 42 1.1 1 0 42 51 41 1.1 1 0 41 52 30 1.1 1 1 29 53 32 1.1 1 2 30 54 32 1.1 1 0 32 55 29 1.1 1 0 29 56 45 1.1 1 0 45 57 27 1.1 1 0 27 58 33 1.1 1 0 33 59 34 1.1 1 1 33 60 47 1.1 1 0 47 61 74 1.1 1 0 74 62 46 1.1 1 0 46 63 55 1.1 1 2 53 64 37 1.1 1 0 37 65 31 1.1 1 0 31 66 59 1.1 1 0 59 67 42 1.1 1 0 42 68 38 1.1 1 0 38 69 42 1.1 1 0 42 70 53 1.1 1 0 53 71 61 1.1 1 0 61 72 73 1.1 1 0 73 73 47 1.1 1 0 47 74 43 1.1 1 0 43 75 34 1.1 1 0 34 76 32 1.1 1 0 32 77 39 1.1 1 0 39 78 53 1.1 1 0 53 79 37 1.1 1 0 37 80 50 1.1 1 0 50 81 34 1.1 1 0 34 82 35 1.1 1 0 35 83 38 1.1 1 0 38 84 35 1.1 1 0 35 85 42 1.1 1 0 42 86 35 1.1 1 1 34 87 36 1.1 1 0 36 88 38 1.1 1 0 38 89 51 1.1 1 0 51 90 40 1.1 1 0 40 91 44 1.1 1 0 44 92 35 1.1 1 0 35 93 37 1.1 1 0 37 94 65 1.1 1 0 65 95 53 1.1 1 0 53 96 41 1.1 1 0 41 97 44 1.1 1 0 44 98 39 1.1 1 0 39 99 40 1.1 1 0 40 100 35 1.1 1 0 35 101 32 1.1 1 0 32 102 41 1.1 1 0 41 103 68 1.1 1 0 68 104 56 1.1 1 0 56 105 18 1.1 1 0 18 106 42 1.1 1 0 42 107 42 1.1 1 0 42 108 25 1.1 1 0 25 109 29 1.1 1 0 29 110 25 1.1 1 0 25 111 31 1.1 1 0 31 112 35 1.1 1 0 35 113 39 1.1 1 0 39 114 29 1.1 1 0 29 115 34 1.1 1 0 34 116 48 1.1 1 0 48 117 39 1.1 1 0 39 118 27 1.1 1 0 27 119 26 1.1 1 0 26 120 38 1.1 1 0 38 121 34 1.1 1 3 31 122 32 1.1 1 0 32 123 27 1.1 1 0 27 124 33 1.1 1 0 33 125 18 1.1 1 0 18 126 37 1.1 1 0 37 127 44 1.1 1 0 44 128 43 1.1 1 0 43 129 21 1.1 1 0 21 130 33 1.1 1 0 33 131 31 1.1 1 0 31 132 29 1.1 1 0 29 133 27 1.1 1 0 27 134 27 1.1 1 0 27 135 25 1.1 1 0 25 136 17 1.1 1 0 17 137 22 1.1 1 0 22 138 16 1.1 1 0 16 139 17 1.1 1 0 17 140 6 1.1 1 0 6 141 9 1.1 1 0 9 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz ============================================= 73192078 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 73192078 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1330834 (1.82%) >>> Now running FastQC on the validated data Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_7_S2_L002_R1_001_val_1_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 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 Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2698.58 s (31 us/read; 1.95 M reads/minute). === Summary === Total reads processed: 87,796,904 Reads with adapters: 46,651,194 (53.1%) Reads written (passing filters): 87,796,904 (100.0%) Total basepairs processed: 10,805,650,041 bp Quality-trimmed: 6,308,354 bp (0.1%) Total written (filtered): 10,737,578,830 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46651194 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.8% C: 20.3% G: 14.1% T: 25.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 35252729 21949226.0 0 35252729 2 8581491 5487306.5 0 8581491 3 2476883 1371826.6 0 2476883 4 218934 342956.7 0 218934 5 89680 85739.2 0 89680 6 14438 21434.8 0 14438 7 3010 5358.7 0 3010 8 485 1339.7 0 485 9 2660 334.9 0 174 2486 10 3700 83.7 1 62 3638 11 1225 20.9 1 15 1210 12 279 5.2 1 1 278 13 62 1.3 1 0 62 14 51 1.3 1 0 51 15 48 1.3 1 0 48 16 34 1.3 1 0 34 17 48 1.3 1 0 48 18 55 1.3 1 0 55 19 45 1.3 1 0 45 20 52 1.3 1 0 52 21 72 1.3 1 0 72 22 89 1.3 1 0 89 23 54 1.3 1 0 54 24 41 1.3 1 0 41 25 35 1.3 1 0 35 26 42 1.3 1 0 42 27 57 1.3 1 0 57 28 43 1.3 1 0 43 29 82 1.3 1 0 82 30 62 1.3 1 0 62 31 48 1.3 1 0 48 32 61 1.3 1 0 61 33 44 1.3 1 0 44 34 60 1.3 1 0 60 35 57 1.3 1 0 57 36 61 1.3 1 0 61 37 47 1.3 1 1 46 38 52 1.3 1 0 52 39 52 1.3 1 0 52 40 54 1.3 1 1 53 41 42 1.3 1 0 42 42 43 1.3 1 0 43 43 31 1.3 1 2 29 44 55 1.3 1 0 55 45 70 1.3 1 0 70 46 33 1.3 1 0 33 47 48 1.3 1 0 48 48 55 1.3 1 2 53 49 53 1.3 1 0 53 50 49 1.3 1 0 49 51 27 1.3 1 0 27 52 50 1.3 1 0 50 53 38 1.3 1 0 38 54 40 1.3 1 0 40 55 51 1.3 1 0 51 56 36 1.3 1 0 36 57 40 1.3 1 0 40 58 56 1.3 1 1 55 59 47 1.3 1 0 47 60 28 1.3 1 0 28 61 39 1.3 1 0 39 62 71 1.3 1 3 68 63 56 1.3 1 0 56 64 55 1.3 1 0 55 65 50 1.3 1 0 50 66 31 1.3 1 0 31 67 35 1.3 1 0 35 68 48 1.3 1 0 48 69 45 1.3 1 0 45 70 48 1.3 1 0 48 71 50 1.3 1 0 50 72 61 1.3 1 0 61 73 57 1.3 1 0 57 74 19 1.3 1 0 19 75 61 1.3 1 0 61 76 56 1.3 1 2 54 77 48 1.3 1 0 48 78 36 1.3 1 0 36 79 65 1.3 1 0 65 80 36 1.3 1 0 36 81 32 1.3 1 0 32 82 52 1.3 1 0 52 83 34 1.3 1 0 34 84 51 1.3 1 0 51 85 80 1.3 1 0 80 86 60 1.3 1 0 60 87 62 1.3 1 0 62 88 31 1.3 1 0 31 89 41 1.3 1 0 41 90 37 1.3 1 0 37 91 33 1.3 1 0 33 92 37 1.3 1 0 37 93 36 1.3 1 0 36 94 26 1.3 1 0 26 95 24 1.3 1 0 24 96 54 1.3 1 0 54 97 48 1.3 1 0 48 98 34 1.3 1 0 34 99 48 1.3 1 0 48 100 41 1.3 1 0 41 101 45 1.3 1 0 45 102 35 1.3 1 0 35 103 32 1.3 1 0 32 104 42 1.3 1 0 42 105 48 1.3 1 0 48 106 40 1.3 1 0 40 107 57 1.3 1 0 57 108 53 1.3 1 0 53 109 33 1.3 1 0 33 110 23 1.3 1 0 23 111 39 1.3 1 0 39 112 60 1.3 1 0 60 113 58 1.3 1 0 58 114 47 1.3 1 0 47 115 27 1.3 1 0 27 116 51 1.3 1 0 51 117 28 1.3 1 0 28 118 20 1.3 1 0 20 119 35 1.3 1 0 35 120 22 1.3 1 0 22 121 47 1.3 1 0 47 122 33 1.3 1 0 33 123 55 1.3 1 0 55 124 24 1.3 1 0 24 125 17 1.3 1 0 17 126 46 1.3 1 0 46 127 33 1.3 1 0 33 128 45 1.3 1 0 45 129 30 1.3 1 0 30 130 46 1.3 1 0 46 131 44 1.3 1 0 44 132 46 1.3 1 0 46 133 30 1.3 1 0 30 134 16 1.3 1 0 16 135 43 1.3 1 0 43 136 23 1.3 1 0 23 137 30 1.3 1 0 30 138 23 1.3 1 0 23 139 6 1.3 1 0 6 140 13 1.3 1 0 13 141 7 1.3 1 0 7 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz ============================================= 87796904 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_7_S2_L002_R2_001_val_2_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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_03/20181211_metagenomics_trimmed_fastqc --threads 16' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 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 Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2844.06 s (32 us/read; 1.85 M reads/minute). === Summary === Total reads processed: 87,796,904 Reads with adapters: 32,159,143 (36.6%) Reads written (passing filters): 87,796,904 (100.0%) Total basepairs processed: 10,520,390,091 bp Quality-trimmed: 21,808,749 bp (0.2%) Total written (filtered): 10,462,140,160 bp (99.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 32159143 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.4% C: 20.9% G: 5.1% T: 25.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 29258517 21949226.0 0 29258517 2 2105430 5487306.5 0 2105430 3 590395 1371826.6 0 590395 4 188733 342956.7 0 188733 5 4513 85739.2 0 4513 6 3281 21434.8 0 3281 7 804 5358.7 0 804 8 140 1339.7 0 140 9 687 334.9 0 212 475 10 782 83.7 1 14 768 11 315 20.9 1 1 314 12 118 5.2 1 0 118 13 32 1.3 1 0 32 14 55 1.3 1 0 55 15 38 1.3 1 0 38 16 42 1.3 1 0 42 17 35 1.3 1 0 35 18 67 1.3 1 0 67 19 58 1.3 1 0 58 20 57 1.3 1 0 57 21 47 1.3 1 0 47 22 62 1.3 1 0 62 23 72 1.3 1 0 72 24 59 1.3 1 2 57 25 79 1.3 1 0 79 26 54 1.3 1 0 54 27 42 1.3 1 0 42 28 55 1.3 1 0 55 29 44 1.3 1 0 44 30 47 1.3 1 1 46 31 44 1.3 1 0 44 32 41 1.3 1 0 41 33 60 1.3 1 0 60 34 54 1.3 1 0 54 35 48 1.3 1 0 48 36 59 1.3 1 0 59 37 55 1.3 1 0 55 38 57 1.3 1 0 57 39 64 1.3 1 0 64 40 39 1.3 1 0 39 41 57 1.3 1 0 57 42 43 1.3 1 0 43 43 54 1.3 1 0 54 44 48 1.3 1 0 48 45 41 1.3 1 0 41 46 53 1.3 1 0 53 47 35 1.3 1 0 35 48 54 1.3 1 0 54 49 42 1.3 1 0 42 50 92 1.3 1 0 92 51 49 1.3 1 0 49 52 52 1.3 1 0 52 53 65 1.3 1 0 65 54 36 1.3 1 0 36 55 46 1.3 1 0 46 56 50 1.3 1 0 50 57 38 1.3 1 1 37 58 32 1.3 1 0 32 59 42 1.3 1 0 42 60 41 1.3 1 0 41 61 50 1.3 1 0 50 62 38 1.3 1 0 38 63 52 1.3 1 0 52 64 41 1.3 1 0 41 65 34 1.3 1 0 34 66 38 1.3 1 0 38 67 36 1.3 1 0 36 68 51 1.3 1 0 51 69 40 1.3 1 0 40 70 42 1.3 1 0 42 71 51 1.3 1 0 51 72 47 1.3 1 0 47 73 39 1.3 1 0 39 74 41 1.3 1 0 41 75 41 1.3 1 0 41 76 41 1.3 1 0 41 77 40 1.3 1 0 40 78 45 1.3 1 1 44 79 34 1.3 1 0 34 80 41 1.3 1 0 41 81 42 1.3 1 0 42 82 43 1.3 1 0 43 83 53 1.3 1 0 53 84 46 1.3 1 0 46 85 29 1.3 1 1 28 86 50 1.3 1 0 50 87 42 1.3 1 0 42 88 46 1.3 1 0 46 89 44 1.3 1 0 44 90 23 1.3 1 0 23 91 50 1.3 1 1 49 92 28 1.3 1 0 28 93 33 1.3 1 0 33 94 68 1.3 1 0 68 95 47 1.3 1 0 47 96 30 1.3 1 0 30 97 48 1.3 1 0 48 98 57 1.3 1 0 57 99 49 1.3 1 0 49 100 37 1.3 1 0 37 101 27 1.3 1 0 27 102 33 1.3 1 0 33 103 48 1.3 1 0 48 104 47 1.3 1 0 47 105 30 1.3 1 0 30 106 33 1.3 1 0 33 107 36 1.3 1 0 36 108 47 1.3 1 0 47 109 46 1.3 1 0 46 110 17 1.3 1 0 17 111 30 1.3 1 0 30 112 30 1.3 1 0 30 113 47 1.3 1 0 47 114 39 1.3 1 0 39 115 41 1.3 1 0 41 116 54 1.3 1 0 54 117 27 1.3 1 0 27 118 32 1.3 1 0 32 119 27 1.3 1 0 27 120 46 1.3 1 0 46 121 28 1.3 1 0 28 122 44 1.3 1 0 44 123 27 1.3 1 0 27 124 37 1.3 1 0 37 125 25 1.3 1 0 25 126 25 1.3 1 0 25 127 30 1.3 1 0 30 128 34 1.3 1 3 31 129 43 1.3 1 0 43 130 33 1.3 1 0 33 131 36 1.3 1 0 36 132 25 1.3 1 0 25 133 19 1.3 1 0 19 134 13 1.3 1 0 13 135 34 1.3 1 0 34 136 36 1.3 1 0 36 137 15 1.3 1 0 15 138 11 1.3 1 0 11 139 18 1.3 1 0 18 140 3 1.3 1 0 3 141 12 1.3 1 0 12 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz ============================================= 87796904 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2.fq.gz Total number of sequences analysed: 87796904 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1630281 (1.86%) >>> Now running FastQC on the validated data Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 10% complete for 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complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1_trimmed.fq.gz and Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2_trimmed.fq.gz ==================================================================================================== gzip: stdout: Broken pipe