SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_1_S3_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_1_S3_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 2965.08 s (36 us/read; 1.68 M reads/minute). === Summary === Total reads processed: 83,250,751 Reads with adapters: 28,068,498 (33.7%) Reads written (passing filters): 83,250,751 (100.0%) Total basepairs processed: 10,958,582,398 bp Quality-trimmed: 31,766,281 bp (0.3%) Total written (filtered): 10,889,697,750 bp (99.4%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 28068498 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 27.6% C: 18.7% G: 29.7% T: 24.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22263643 20812687.8 0 22263643 2 4175157 5203171.9 0 4175157 3 1340361 1300793.0 0 1340361 4 201062 325198.2 0 201062 5 54039 81299.6 0 54039 6 11455 20324.9 0 11455 7 1296 5081.2 0 1296 8 1359 1270.3 0 1359 9 1154 317.6 0 275 879 10 1086 79.4 1 12 1074 11 379 19.8 1 1 378 12 125 5.0 1 0 125 13 117 5.0 1 1 116 14 123 5.0 1 3 120 15 120 5.0 1 3 117 16 147 5.0 1 0 147 17 187 5.0 1 1 186 18 170 5.0 1 3 167 19 136 5.0 1 1 135 20 133 5.0 1 1 132 21 176 5.0 1 2 174 22 180 5.0 1 0 180 23 124 5.0 1 1 123 24 131 5.0 1 1 130 25 157 5.0 1 1 156 26 134 5.0 1 0 134 27 174 5.0 1 0 174 28 154 5.0 1 1 153 29 201 5.0 1 3 198 30 133 5.0 1 1 132 31 133 5.0 1 2 131 32 150 5.0 1 0 150 33 130 5.0 1 0 130 34 139 5.0 1 0 139 35 137 5.0 1 2 135 36 153 5.0 1 1 152 37 155 5.0 1 1 154 38 152 5.0 1 1 151 39 163 5.0 1 2 161 40 142 5.0 1 4 138 41 160 5.0 1 2 158 42 150 5.0 1 4 146 43 138 5.0 1 2 136 44 154 5.0 1 2 152 45 110 5.0 1 2 108 46 129 5.0 1 3 126 47 166 5.0 1 1 165 48 149 5.0 1 0 149 49 145 5.0 1 0 145 50 150 5.0 1 2 148 51 148 5.0 1 1 147 52 158 5.0 1 2 156 53 140 5.0 1 1 139 54 159 5.0 1 1 158 55 137 5.0 1 3 134 56 154 5.0 1 3 151 57 152 5.0 1 2 150 58 133 5.0 1 3 130 59 137 5.0 1 3 134 60 167 5.0 1 1 166 61 148 5.0 1 0 148 62 149 5.0 1 0 149 63 108 5.0 1 1 107 64 142 5.0 1 0 142 65 179 5.0 1 0 179 66 137 5.0 1 1 136 67 146 5.0 1 0 146 68 123 5.0 1 1 122 69 174 5.0 1 0 174 70 133 5.0 1 0 133 71 127 5.0 1 1 126 72 116 5.0 1 0 116 73 132 5.0 1 0 132 74 133 5.0 1 0 133 75 159 5.0 1 1 158 76 149 5.0 1 3 146 77 146 5.0 1 0 146 78 122 5.0 1 3 119 79 128 5.0 1 0 128 80 136 5.0 1 0 136 81 131 5.0 1 2 129 82 130 5.0 1 0 130 83 127 5.0 1 0 127 84 149 5.0 1 0 149 85 136 5.0 1 2 134 86 111 5.0 1 3 108 87 158 5.0 1 0 158 88 139 5.0 1 0 139 89 119 5.0 1 3 116 90 122 5.0 1 0 122 91 160 5.0 1 3 157 92 128 5.0 1 3 125 93 107 5.0 1 2 105 94 112 5.0 1 1 111 95 122 5.0 1 0 122 96 145 5.0 1 1 144 97 99 5.0 1 1 98 98 123 5.0 1 0 123 99 114 5.0 1 1 113 100 96 5.0 1 0 96 101 111 5.0 1 0 111 102 132 5.0 1 2 130 103 120 5.0 1 3 117 104 133 5.0 1 0 133 105 119 5.0 1 0 119 106 126 5.0 1 1 125 107 101 5.0 1 1 100 108 104 5.0 1 1 103 109 124 5.0 1 0 124 110 110 5.0 1 0 110 111 125 5.0 1 0 125 112 86 5.0 1 0 86 113 119 5.0 1 1 118 114 136 5.0 1 0 136 115 133 5.0 1 0 133 116 118 5.0 1 0 118 117 104 5.0 1 2 102 118 104 5.0 1 0 104 119 121 5.0 1 0 121 120 129 5.0 1 5 124 121 83 5.0 1 1 82 122 103 5.0 1 2 101 123 113 5.0 1 3 110 124 160 5.0 1 2 158 125 104 5.0 1 1 103 126 102 5.0 1 0 102 127 94 5.0 1 0 94 128 109 5.0 1 0 109 129 119 5.0 1 0 119 130 83 5.0 1 0 83 131 102 5.0 1 0 102 132 118 5.0 1 0 118 133 94 5.0 1 0 94 134 82 5.0 1 2 80 135 111 5.0 1 4 107 136 86 5.0 1 0 86 137 85 5.0 1 1 84 138 70 5.0 1 0 70 139 88 5.0 1 0 88 140 85 5.0 1 0 85 141 102 5.0 1 0 102 142 77 5.0 1 2 75 143 107 5.0 1 0 107 144 100 5.0 1 1 99 145 107 5.0 1 0 107 146 42 5.0 1 0 42 147 19 5.0 1 0 19 148 25 5.0 1 0 25 149 16 5.0 1 0 16 150 20 5.0 1 0 20 151 19 5.0 1 0 19 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz ============================================= 83250751 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 83250751 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 251699 (0.30%)