SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_2_S4_L002_R2_001_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: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 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_02/20181211_metagenomics_trimmed_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a GATCGTCGGACT Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2870.62 s (35 us/read; 1.72 M reads/minute). === Summary === Total reads processed: 82,206,331 Reads with adapters: 25,143,341 (30.6%) Reads written (passing filters): 82,206,331 (100.0%) Total basepairs processed: 10,653,232,429 bp Quality-trimmed: 30,779,948 bp (0.3%) Total written (filtered): 10,588,614,497 bp (99.4%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 25143341 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 30.1% C: 14.9% G: 28.2% T: 26.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19313397 20551582.8 0 19313397 2 4142191 5137895.7 0 4142191 3 1428582 1284473.9 0 1428582 4 198307 321118.5 0 198307 5 36414 80279.6 0 36414 6 8949 20069.9 0 8949 7 950 5017.5 0 950 8 639 1254.4 0 639 9 748 313.6 0 130 618 10 789 78.4 1 8 781 11 219 19.6 1 2 217 12 76 4.9 1 0 76 13 75 4.9 1 0 75 14 84 4.9 1 0 84 15 82 4.9 1 1 81 16 107 4.9 1 0 107 17 121 4.9 1 1 120 18 119 4.9 1 0 119 19 125 4.9 1 1 124 20 123 4.9 1 2 121 21 132 4.9 1 1 131 22 135 4.9 1 0 135 23 92 4.9 1 1 91 24 96 4.9 1 0 96 25 93 4.9 1 0 93 26 112 4.9 1 1 111 27 112 4.9 1 3 109 28 112 4.9 1 1 111 29 111 4.9 1 1 110 30 109 4.9 1 0 109 31 96 4.9 1 1 95 32 116 4.9 1 0 116 33 111 4.9 1 3 108 34 121 4.9 1 0 121 35 102 4.9 1 1 101 36 108 4.9 1 0 108 37 106 4.9 1 0 106 38 104 4.9 1 0 104 39 128 4.9 1 0 128 40 93 4.9 1 1 92 41 80 4.9 1 0 80 42 91 4.9 1 0 91 43 114 4.9 1 0 114 44 91 4.9 1 0 91 45 97 4.9 1 0 97 46 96 4.9 1 0 96 47 119 4.9 1 0 119 48 96 4.9 1 0 96 49 96 4.9 1 0 96 50 124 4.9 1 0 124 51 107 4.9 1 1 106 52 115 4.9 1 1 114 53 89 4.9 1 1 88 54 83 4.9 1 0 83 55 113 4.9 1 0 113 56 89 4.9 1 0 89 57 106 4.9 1 1 105 58 108 4.9 1 0 108 59 95 4.9 1 1 94 60 124 4.9 1 0 124 61 84 4.9 1 0 84 62 104 4.9 1 0 104 63 78 4.9 1 0 78 64 107 4.9 1 0 107 65 159 4.9 1 0 159 66 93 4.9 1 1 92 67 85 4.9 1 0 85 68 102 4.9 1 3 99 69 97 4.9 1 1 96 70 99 4.9 1 2 97 71 83 4.9 1 1 82 72 89 4.9 1 0 89 73 99 4.9 1 0 99 74 90 4.9 1 1 89 75 74 4.9 1 1 73 76 89 4.9 1 0 89 77 85 4.9 1 0 85 78 100 4.9 1 3 97 79 83 4.9 1 0 83 80 120 4.9 1 0 120 81 86 4.9 1 0 86 82 68 4.9 1 2 66 83 85 4.9 1 1 84 84 94 4.9 1 0 94 85 62 4.9 1 0 62 86 91 4.9 1 2 89 87 81 4.9 1 0 81 88 76 4.9 1 0 76 89 87 4.9 1 1 86 90 86 4.9 1 2 84 91 72 4.9 1 0 72 92 80 4.9 1 1 79 93 87 4.9 1 1 86 94 67 4.9 1 0 67 95 68 4.9 1 0 68 96 81 4.9 1 0 81 97 60 4.9 1 0 60 98 98 4.9 1 3 95 99 103 4.9 1 1 102 100 92 4.9 1 1 91 101 92 4.9 1 0 92 102 88 4.9 1 0 88 103 78 4.9 1 0 78 104 80 4.9 1 1 79 105 78 4.9 1 0 78 106 82 4.9 1 0 82 107 78 4.9 1 0 78 108 88 4.9 1 0 88 109 66 4.9 1 0 66 110 72 4.9 1 0 72 111 77 4.9 1 1 76 112 65 4.9 1 0 65 113 74 4.9 1 1 73 114 90 4.9 1 0 90 115 106 4.9 1 0 106 116 56 4.9 1 0 56 117 70 4.9 1 0 70 118 72 4.9 1 0 72 119 83 4.9 1 0 83 120 67 4.9 1 0 67 121 49 4.9 1 0 49 122 60 4.9 1 0 60 123 60 4.9 1 0 60 124 100 4.9 1 0 100 125 92 4.9 1 2 90 126 51 4.9 1 1 50 127 62 4.9 1 0 62 128 70 4.9 1 0 70 129 50 4.9 1 0 50 130 69 4.9 1 0 69 131 71 4.9 1 0 71 132 84 4.9 1 0 84 133 73 4.9 1 0 73 134 70 4.9 1 0 70 135 78 4.9 1 1 77 136 70 4.9 1 1 69 137 58 4.9 1 2 56 138 66 4.9 1 2 64 139 81 4.9 1 0 81 140 74 4.9 1 0 74 141 76 4.9 1 0 76 142 67 4.9 1 0 67 143 112 4.9 1 1 111 144 77 4.9 1 0 77 145 67 4.9 1 0 67 146 34 4.9 1 0 34 147 23 4.9 1 0 23 148 17 4.9 1 0 17 149 22 4.9 1 0 22 150 19 4.9 1 0 19 151 14 4.9 1 0 14 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz ============================================= 82206331 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 82206331 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 290422 (0.35%)