SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_5_S6_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_5_S6_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 2542.46 s (35 us/read; 1.70 M reads/minute). === Summary === Total reads processed: 71,913,753 Reads with adapters: 21,261,023 (29.6%) Reads written (passing filters): 71,913,753 (100.0%) Total basepairs processed: 9,501,649,182 bp Quality-trimmed: 21,150,782 bp (0.2%) Total written (filtered): 9,451,599,234 bp (99.5%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 21261023 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 31.3% C: 13.2% G: 27.6% T: 27.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16006223 17978438.2 0 16006223 2 3731849 4494609.6 0 3731849 3 1307804 1123652.4 0 1307804 4 169001 280913.1 0 169001 5 28262 70228.3 0 28262 6 7445 17557.1 0 7445 7 615 4389.3 0 615 8 339 1097.3 0 339 9 454 274.3 0 45 409 10 549 68.6 1 3 546 11 155 17.1 1 1 154 12 50 4.3 1 1 49 13 40 4.3 1 0 40 14 55 4.3 1 1 54 15 62 4.3 1 0 62 16 71 4.3 1 0 71 17 72 4.3 1 0 72 18 88 4.3 1 0 88 19 49 4.3 1 3 46 20 66 4.3 1 0 66 21 60 4.3 1 0 60 22 79 4.3 1 0 79 23 70 4.3 1 0 70 24 56 4.3 1 1 55 25 63 4.3 1 0 63 26 68 4.3 1 0 68 27 91 4.3 1 3 88 28 63 4.3 1 0 63 29 74 4.3 1 0 74 30 65 4.3 1 0 65 31 62 4.3 1 0 62 32 102 4.3 1 0 102 33 77 4.3 1 0 77 34 67 4.3 1 2 65 35 77 4.3 1 0 77 36 75 4.3 1 0 75 37 88 4.3 1 0 88 38 69 4.3 1 0 69 39 56 4.3 1 0 56 40 86 4.3 1 0 86 41 73 4.3 1 1 72 42 66 4.3 1 0 66 43 60 4.3 1 0 60 44 61 4.3 1 0 61 45 78 4.3 1 1 77 46 51 4.3 1 0 51 47 91 4.3 1 1 90 48 77 4.3 1 0 77 49 52 4.3 1 0 52 50 63 4.3 1 0 63 51 69 4.3 1 0 69 52 64 4.3 1 0 64 53 68 4.3 1 0 68 54 82 4.3 1 0 82 55 88 4.3 1 0 88 56 62 4.3 1 3 59 57 81 4.3 1 0 81 58 67 4.3 1 0 67 59 42 4.3 1 0 42 60 62 4.3 1 0 62 61 53 4.3 1 0 53 62 63 4.3 1 0 63 63 68 4.3 1 1 67 64 61 4.3 1 1 60 65 168 4.3 1 0 168 66 55 4.3 1 0 55 67 47 4.3 1 0 47 68 57 4.3 1 0 57 69 78 4.3 1 0 78 70 64 4.3 1 0 64 71 77 4.3 1 0 77 72 77 4.3 1 0 77 73 70 4.3 1 0 70 74 49 4.3 1 0 49 75 71 4.3 1 0 71 76 41 4.3 1 0 41 77 70 4.3 1 0 70 78 51 4.3 1 0 51 79 44 4.3 1 0 44 80 69 4.3 1 0 69 81 54 4.3 1 0 54 82 55 4.3 1 0 55 83 60 4.3 1 0 60 84 64 4.3 1 2 62 85 53 4.3 1 0 53 86 41 4.3 1 0 41 87 64 4.3 1 0 64 88 60 4.3 1 0 60 89 44 4.3 1 0 44 90 49 4.3 1 0 49 91 55 4.3 1 1 54 92 61 4.3 1 0 61 93 73 4.3 1 0 73 94 66 4.3 1 0 66 95 50 4.3 1 0 50 96 76 4.3 1 0 76 97 59 4.3 1 0 59 98 56 4.3 1 0 56 99 66 4.3 1 0 66 100 55 4.3 1 0 55 101 60 4.3 1 0 60 102 63 4.3 1 0 63 103 53 4.3 1 0 53 104 45 4.3 1 0 45 105 57 4.3 1 0 57 106 67 4.3 1 0 67 107 55 4.3 1 1 54 108 49 4.3 1 0 49 109 50 4.3 1 0 50 110 49 4.3 1 0 49 111 52 4.3 1 0 52 112 48 4.3 1 0 48 113 77 4.3 1 0 77 114 62 4.3 1 0 62 115 54 4.3 1 0 54 116 41 4.3 1 0 41 117 40 4.3 1 0 40 118 54 4.3 1 0 54 119 68 4.3 1 0 68 120 60 4.3 1 0 60 121 47 4.3 1 0 47 122 58 4.3 1 0 58 123 48 4.3 1 0 48 124 126 4.3 1 0 126 125 54 4.3 1 0 54 126 40 4.3 1 0 40 127 43 4.3 1 0 43 128 31 4.3 1 0 31 129 58 4.3 1 1 57 130 36 4.3 1 0 36 131 55 4.3 1 0 55 132 41 4.3 1 0 41 133 41 4.3 1 0 41 134 52 4.3 1 0 52 135 70 4.3 1 1 69 136 48 4.3 1 0 48 137 44 4.3 1 0 44 138 45 4.3 1 1 44 139 71 4.3 1 0 71 140 53 4.3 1 0 53 141 42 4.3 1 0 42 142 40 4.3 1 0 40 143 48 4.3 1 0 48 144 55 4.3 1 0 55 145 49 4.3 1 0 49 146 17 4.3 1 0 17 147 22 4.3 1 0 22 148 8 4.3 1 0 8 149 8 4.3 1 0 8 150 13 4.3 1 0 13 151 8 4.3 1 0 8 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz ============================================= 71913753 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 71913753 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 179976 (0.25%)