SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_6_S5_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_6_S5_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 2603.18 s (35 us/read; 1.69 M reads/minute). === Summary === Total reads processed: 73,388,785 Reads with adapters: 22,452,935 (30.6%) Reads written (passing filters): 73,388,785 (100.0%) Total basepairs processed: 9,605,628,197 bp Quality-trimmed: 23,472,604 bp (0.2%) Total written (filtered): 9,551,866,968 bp (99.4%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 22452935 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 30.9% C: 14.3% G: 27.7% T: 27.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17201008 18347196.2 0 17201008 2 3669445 4586799.1 0 3669445 3 1328510 1146699.8 0 1328510 4 196833 286674.9 0 196833 5 36397 71668.7 0 36397 6 8572 17917.2 0 8572 7 751 4479.3 0 751 8 440 1119.8 0 440 9 564 280.0 0 97 467 10 607 70.0 1 6 601 11 192 17.5 1 0 192 12 74 4.4 1 2 72 13 51 4.4 1 0 51 14 64 4.4 1 1 63 15 67 4.4 1 1 66 16 72 4.4 1 0 72 17 108 4.4 1 0 108 18 92 4.4 1 1 91 19 52 4.4 1 0 52 20 91 4.4 1 3 88 21 109 4.4 1 4 105 22 109 4.4 1 0 109 23 64 4.4 1 0 64 24 70 4.4 1 2 68 25 72 4.4 1 0 72 26 70 4.4 1 0 70 27 98 4.4 1 0 98 28 76 4.4 1 0 76 29 95 4.4 1 1 94 30 80 4.4 1 0 80 31 71 4.4 1 1 70 32 81 4.4 1 2 79 33 81 4.4 1 3 78 34 90 4.4 1 1 89 35 78 4.4 1 0 78 36 79 4.4 1 2 77 37 86 4.4 1 2 84 38 84 4.4 1 3 81 39 67 4.4 1 0 67 40 87 4.4 1 2 85 41 89 4.4 1 0 89 42 79 4.4 1 1 78 43 70 4.4 1 0 70 44 91 4.4 1 1 90 45 73 4.4 1 0 73 46 73 4.4 1 1 72 47 103 4.4 1 0 103 48 90 4.4 1 1 89 49 81 4.4 1 0 81 50 75 4.4 1 1 74 51 83 4.4 1 0 83 52 78 4.4 1 0 78 53 73 4.4 1 0 73 54 71 4.4 1 0 71 55 67 4.4 1 0 67 56 87 4.4 1 2 85 57 93 4.4 1 1 92 58 85 4.4 1 3 82 59 73 4.4 1 0 73 60 67 4.4 1 1 66 61 63 4.4 1 0 63 62 66 4.4 1 0 66 63 80 4.4 1 0 80 64 69 4.4 1 0 69 65 103 4.4 1 1 102 66 69 4.4 1 2 67 67 92 4.4 1 0 92 68 86 4.4 1 1 85 69 69 4.4 1 0 69 70 81 4.4 1 1 80 71 88 4.4 1 0 88 72 69 4.4 1 0 69 73 81 4.4 1 0 81 74 67 4.4 1 0 67 75 77 4.4 1 0 77 76 81 4.4 1 2 79 77 87 4.4 1 0 87 78 52 4.4 1 0 52 79 66 4.4 1 1 65 80 80 4.4 1 0 80 81 71 4.4 1 0 71 82 73 4.4 1 2 71 83 64 4.4 1 0 64 84 77 4.4 1 0 77 85 61 4.4 1 0 61 86 49 4.4 1 0 49 87 88 4.4 1 2 86 88 58 4.4 1 0 58 89 68 4.4 1 1 67 90 49 4.4 1 0 49 91 60 4.4 1 0 60 92 78 4.4 1 1 77 93 60 4.4 1 1 59 94 52 4.4 1 1 51 95 61 4.4 1 1 60 96 71 4.4 1 0 71 97 59 4.4 1 7 52 98 64 4.4 1 0 64 99 69 4.4 1 0 69 100 81 4.4 1 0 81 101 62 4.4 1 0 62 102 76 4.4 1 0 76 103 47 4.4 1 0 47 104 57 4.4 1 1 56 105 52 4.4 1 0 52 106 52 4.4 1 0 52 107 73 4.4 1 0 73 108 83 4.4 1 0 83 109 60 4.4 1 3 57 110 86 4.4 1 0 86 111 73 4.4 1 0 73 112 45 4.4 1 1 44 113 69 4.4 1 0 69 114 82 4.4 1 1 81 115 61 4.4 1 0 61 116 46 4.4 1 1 45 117 64 4.4 1 0 64 118 52 4.4 1 0 52 119 70 4.4 1 0 70 120 74 4.4 1 0 74 121 60 4.4 1 0 60 122 58 4.4 1 0 58 123 61 4.4 1 1 60 124 63 4.4 1 1 62 125 56 4.4 1 2 54 126 71 4.4 1 0 71 127 66 4.4 1 2 64 128 59 4.4 1 0 59 129 57 4.4 1 0 57 130 48 4.4 1 0 48 131 59 4.4 1 1 58 132 72 4.4 1 0 72 133 55 4.4 1 0 55 134 51 4.4 1 0 51 135 59 4.4 1 0 59 136 46 4.4 1 0 46 137 35 4.4 1 2 33 138 43 4.4 1 1 42 139 80 4.4 1 0 80 140 70 4.4 1 0 70 141 63 4.4 1 0 63 142 54 4.4 1 0 54 143 75 4.4 1 0 75 144 72 4.4 1 0 72 145 59 4.4 1 0 59 146 33 4.4 1 0 33 147 14 4.4 1 0 14 148 6 4.4 1 0 6 149 6 4.4 1 0 6 150 15 4.4 1 0 15 151 8 4.4 1 0 8 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz ============================================= 73388785 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 73388785 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 196707 (0.27%)