SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_3_S1_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_3_S1_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 2762.35 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 88,647,204 Reads with adapters: 26,645,742 (30.1%) Reads written (passing filters): 88,647,204 (100.0%) Total basepairs processed: 10,523,694,906 bp Quality-trimmed: 26,883,431 bp (0.3%) Total written (filtered): 10,460,917,173 bp (99.4%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 26645742 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 30.4% C: 14.0% G: 28.0% T: 27.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20652933 22161801.0 0 20652933 2 4097086 5540450.2 0 4097086 3 1547786 1385112.6 0 1547786 4 282239 346278.1 0 282239 5 39236 86569.5 0 39236 6 8539 21642.4 0 8539 7 1092 5410.6 0 1092 8 618 1352.6 0 618 9 875 338.2 0 141 734 10 940 84.5 1 17 923 11 328 21.1 1 0 328 12 145 5.3 1 1 144 13 79 5.3 1 0 79 14 95 5.3 1 0 95 15 96 5.3 1 2 94 16 141 5.3 1 0 141 17 205 5.3 1 2 203 18 143 5.3 1 0 143 19 136 5.3 1 1 135 20 188 5.3 1 3 185 21 182 5.3 1 1 181 22 149 5.3 1 0 149 23 109 5.3 1 0 109 24 121 5.3 1 1 120 25 119 5.3 1 0 119 26 136 5.3 1 0 136 27 163 5.3 1 2 161 28 123 5.3 1 0 123 29 166 5.3 1 1 165 30 130 5.3 1 0 130 31 129 5.3 1 0 129 32 144 5.3 1 2 142 33 139 5.3 1 0 139 34 129 5.3 1 2 127 35 136 5.3 1 2 134 36 148 5.3 1 5 143 37 151 5.3 1 1 150 38 125 5.3 1 0 125 39 106 5.3 1 3 103 40 132 5.3 1 0 132 41 130 5.3 1 2 128 42 116 5.3 1 1 115 43 163 5.3 1 0 163 44 137 5.3 1 0 137 45 133 5.3 1 2 131 46 116 5.3 1 2 114 47 134 5.3 1 1 133 48 119 5.3 1 1 118 49 130 5.3 1 0 130 50 129 5.3 1 0 129 51 158 5.3 1 0 158 52 132 5.3 1 1 131 53 109 5.3 1 1 108 54 103 5.3 1 0 103 55 119 5.3 1 1 118 56 98 5.3 1 0 98 57 128 5.3 1 1 127 58 120 5.3 1 0 120 59 106 5.3 1 0 106 60 106 5.3 1 3 103 61 121 5.3 1 2 119 62 94 5.3 1 0 94 63 113 5.3 1 0 113 64 106 5.3 1 1 105 65 146 5.3 1 2 144 66 116 5.3 1 0 116 67 124 5.3 1 3 121 68 99 5.3 1 1 98 69 87 5.3 1 0 87 70 103 5.3 1 1 102 71 117 5.3 1 1 116 72 117 5.3 1 1 116 73 96 5.3 1 1 95 74 98 5.3 1 0 98 75 100 5.3 1 0 100 76 83 5.3 1 0 83 77 81 5.3 1 0 81 78 91 5.3 1 0 91 79 105 5.3 1 4 101 80 95 5.3 1 0 95 81 105 5.3 1 2 103 82 135 5.3 1 2 133 83 110 5.3 1 1 109 84 107 5.3 1 3 104 85 92 5.3 1 0 92 86 92 5.3 1 1 91 87 88 5.3 1 2 86 88 87 5.3 1 0 87 89 91 5.3 1 0 91 90 101 5.3 1 0 101 91 86 5.3 1 0 86 92 65 5.3 1 0 65 93 88 5.3 1 0 88 94 105 5.3 1 1 104 95 79 5.3 1 1 78 96 84 5.3 1 0 84 97 94 5.3 1 1 93 98 81 5.3 1 0 81 99 69 5.3 1 0 69 100 91 5.3 1 0 91 101 74 5.3 1 1 73 102 66 5.3 1 0 66 103 83 5.3 1 0 83 104 65 5.3 1 0 65 105 111 5.3 1 0 111 106 82 5.3 1 0 82 107 95 5.3 1 0 95 108 88 5.3 1 0 88 109 103 5.3 1 0 103 110 81 5.3 1 2 79 111 80 5.3 1 0 80 112 77 5.3 1 2 75 113 92 5.3 1 3 89 114 87 5.3 1 1 86 115 78 5.3 1 0 78 116 86 5.3 1 0 86 117 99 5.3 1 0 99 118 73 5.3 1 1 72 119 93 5.3 1 0 93 120 85 5.3 1 1 84 121 71 5.3 1 0 71 122 83 5.3 1 1 82 123 60 5.3 1 0 60 124 95 5.3 1 1 94 125 62 5.3 1 1 61 126 58 5.3 1 0 58 127 59 5.3 1 0 59 128 77 5.3 1 2 75 129 81 5.3 1 0 81 130 88 5.3 1 0 88 131 80 5.3 1 1 79 132 77 5.3 1 0 77 133 80 5.3 1 3 77 134 59 5.3 1 1 58 135 56 5.3 1 0 56 136 80 5.3 1 0 80 137 65 5.3 1 0 65 138 64 5.3 1 2 62 139 94 5.3 1 0 94 140 63 5.3 1 0 63 141 100 5.3 1 0 100 142 65 5.3 1 0 65 143 59 5.3 1 0 59 144 81 5.3 1 1 80 145 74 5.3 1 0 74 146 50 5.3 1 0 50 147 27 5.3 1 0 27 148 23 5.3 1 0 23 149 12 5.3 1 0 12 150 14 5.3 1 0 14 151 22 5.3 1 0 22 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz ============================================= 88647204 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 88647204 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 696909 (0.79%)