SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_7_S2_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_7_S2_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 3080.97 s (35 us/read; 1.71 M reads/minute). === Summary === Total reads processed: 88,036,439 Reads with adapters: 26,382,081 (30.0%) Reads written (passing filters): 88,036,439 (100.0%) Total basepairs processed: 11,468,192,237 bp Quality-trimmed: 27,232,414 bp (0.2%) Total written (filtered): 11,405,183,000 bp (99.5%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 26382081 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 31.3% C: 13.7% G: 27.5% T: 27.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20034401 22009109.8 0 20034401 2 4422645 5502277.4 0 4422645 3 1624365 1375569.4 0 1624365 4 237851 343892.3 0 237851 5 39616 85973.1 0 39616 6 9538 21493.3 0 9538 7 913 5373.3 0 913 8 577 1343.3 0 577 9 570 335.8 0 108 462 10 716 84.0 1 3 713 11 216 21.0 1 0 216 12 63 5.2 1 0 63 13 71 5.2 1 1 70 14 67 5.2 1 0 67 15 79 5.2 1 0 79 16 93 5.2 1 0 93 17 123 5.2 1 0 123 18 98 5.2 1 1 97 19 86 5.2 1 0 86 20 93 5.2 1 0 93 21 120 5.2 1 0 120 22 83 5.2 1 0 83 23 85 5.2 1 0 85 24 92 5.2 1 0 92 25 80 5.2 1 0 80 26 101 5.2 1 1 100 27 98 5.2 1 0 98 28 88 5.2 1 0 88 29 105 5.2 1 1 104 30 78 5.2 1 1 77 31 83 5.2 1 0 83 32 98 5.2 1 1 97 33 113 5.2 1 1 112 34 98 5.2 1 0 98 35 84 5.2 1 1 83 36 101 5.2 1 0 101 37 94 5.2 1 1 93 38 92 5.2 1 0 92 39 97 5.2 1 1 96 40 112 5.2 1 1 111 41 109 5.2 1 0 109 42 95 5.2 1 1 94 43 84 5.2 1 0 84 44 84 5.2 1 1 83 45 100 5.2 1 0 100 46 85 5.2 1 2 83 47 70 5.2 1 1 69 48 69 5.2 1 0 69 49 69 5.2 1 0 69 50 87 5.2 1 0 87 51 78 5.2 1 0 78 52 74 5.2 1 4 70 53 89 5.2 1 0 89 54 86 5.2 1 3 83 55 83 5.2 1 1 82 56 84 5.2 1 1 83 57 112 5.2 1 0 112 58 93 5.2 1 0 93 59 88 5.2 1 2 86 60 89 5.2 1 0 89 61 91 5.2 1 1 90 62 83 5.2 1 0 83 63 111 5.2 1 1 110 64 91 5.2 1 0 91 65 76 5.2 1 2 74 66 79 5.2 1 2 77 67 98 5.2 1 0 98 68 90 5.2 1 2 88 69 75 5.2 1 0 75 70 97 5.2 1 1 96 71 104 5.2 1 0 104 72 87 5.2 1 0 87 73 90 5.2 1 1 89 74 70 5.2 1 0 70 75 80 5.2 1 1 79 76 104 5.2 1 2 102 77 80 5.2 1 1 79 78 70 5.2 1 1 69 79 78 5.2 1 0 78 80 87 5.2 1 1 86 81 85 5.2 1 1 84 82 41 5.2 1 0 41 83 85 5.2 1 0 85 84 65 5.2 1 0 65 85 87 5.2 1 0 87 86 57 5.2 1 0 57 87 86 5.2 1 1 85 88 80 5.2 1 1 79 89 67 5.2 1 6 61 90 68 5.2 1 1 67 91 53 5.2 1 0 53 92 72 5.2 1 1 71 93 106 5.2 1 2 104 94 53 5.2 1 0 53 95 94 5.2 1 0 94 96 90 5.2 1 0 90 97 75 5.2 1 0 75 98 66 5.2 1 2 64 99 66 5.2 1 3 63 100 73 5.2 1 1 72 101 68 5.2 1 0 68 102 64 5.2 1 1 63 103 80 5.2 1 0 80 104 58 5.2 1 0 58 105 75 5.2 1 0 75 106 93 5.2 1 0 93 107 61 5.2 1 0 61 108 61 5.2 1 1 60 109 58 5.2 1 0 58 110 72 5.2 1 0 72 111 78 5.2 1 0 78 112 63 5.2 1 1 62 113 77 5.2 1 0 77 114 70 5.2 1 0 70 115 64 5.2 1 0 64 116 51 5.2 1 0 51 117 64 5.2 1 1 63 118 55 5.2 1 0 55 119 61 5.2 1 0 61 120 65 5.2 1 0 65 121 66 5.2 1 0 66 122 99 5.2 1 2 97 123 59 5.2 1 0 59 124 70 5.2 1 0 70 125 59 5.2 1 2 57 126 70 5.2 1 2 68 127 62 5.2 1 0 62 128 46 5.2 1 1 45 129 59 5.2 1 0 59 130 52 5.2 1 4 48 131 62 5.2 1 1 61 132 71 5.2 1 1 70 133 60 5.2 1 0 60 134 72 5.2 1 1 71 135 56 5.2 1 1 55 136 55 5.2 1 3 52 137 52 5.2 1 0 52 138 51 5.2 1 0 51 139 59 5.2 1 0 59 140 98 5.2 1 0 98 141 70 5.2 1 0 70 142 37 5.2 1 0 37 143 82 5.2 1 2 80 144 71 5.2 1 0 71 145 75 5.2 1 0 75 146 44 5.2 1 0 44 147 26 5.2 1 0 26 148 10 5.2 1 0 10 149 10 5.2 1 0 10 150 11 5.2 1 0 11 151 8 5.2 1 0 8 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz ============================================= 88036439 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 88036439 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 239535 (0.27%)