No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) Path to Cutadapt set as: 'cutadapt' (default) Cutadapt seems to be working fine (tested command 'cutadapt --version') AUTO-DETECTING ADAPTER TYPE =========================== Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz <<) Found perfect matches for the following adapter sequences: Adapter type Count Sequence Sequences analysed Percentage smallRNA 1 TGGAATTCTCGG 1000000 0.00 Nextera 0 CTGTCTCTTATA 1000000 0.00 Illumina 0 AGATCGGAAGAGC 1000000 0.00 Using smallRNA adapter for trimming (count: 1). Second best hit was Nextera (count: 0) gzip: stdout: Broken pipe Reducing length cutoff to 18bp for small RNA-Seq reads because a cutoff of 20bp may remove some short species of small RNAs if they had been trimmed by 1,2 or 3bp Setting the Illumina smallRNA 5' adapter as adapter 2: 'GATCGTCGGACT' Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_1_S3_L002_R1_001_val_1.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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_1_S3_L002_R1_001_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2879.23 s (35 us/read; 1.73 M reads/minute). === Summary === Total reads processed: 83,250,751 Reads with adapters: 31,902,917 (38.3%) Reads written (passing filters): 83,250,751 (100.0%) Total basepairs processed: 11,301,487,423 bp Quality-trimmed: 7,592,579 bp (0.1%) Total written (filtered): 11,249,045,252 bp (99.5%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 31902917 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 33.7% C: 8.8% G: 17.6% T: 39.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24138260 20812687.8 0 24138260 2 5462884 5203171.9 0 5462884 3 1774135 1300793.0 0 1774135 4 289598 325198.2 0 289598 5 150336 81299.6 0 150336 6 41866 20324.9 0 41866 7 12564 5081.2 0 12564 8 1209 1270.3 0 1209 9 534 317.6 0 79 455 10 1672 79.4 1 35 1637 11 1239 19.8 1 21 1218 12 292 5.0 1 6 286 13 237 5.0 1 0 237 14 204 5.0 1 0 204 15 168 5.0 1 2 166 16 200 5.0 1 3 197 17 193 5.0 1 0 193 18 227 5.0 1 3 224 19 181 5.0 1 4 177 20 225 5.0 1 2 223 21 202 5.0 1 0 202 22 203 5.0 1 1 202 23 283 5.0 1 4 279 24 290 5.0 1 3 287 25 256 5.0 1 2 254 26 210 5.0 1 4 206 27 235 5.0 1 0 235 28 231 5.0 1 3 228 29 284 5.0 1 7 277 30 214 5.0 1 1 213 31 260 5.0 1 1 259 32 224 5.0 1 0 224 33 241 5.0 1 1 240 34 257 5.0 1 1 256 35 243 5.0 1 6 237 36 225 5.0 1 4 221 37 256 5.0 1 2 254 38 256 5.0 1 2 254 39 248 5.0 1 1 247 40 197 5.0 1 3 194 41 197 5.0 1 4 193 42 208 5.0 1 6 202 43 241 5.0 1 2 239 44 201 5.0 1 2 199 45 209 5.0 1 2 207 46 233 5.0 1 1 232 47 204 5.0 1 4 200 48 196 5.0 1 0 196 49 221 5.0 1 4 217 50 266 5.0 1 1 265 51 219 5.0 1 0 219 52 259 5.0 1 0 259 53 239 5.0 1 1 238 54 238 5.0 1 3 235 55 273 5.0 1 4 269 56 235 5.0 1 3 232 57 266 5.0 1 3 263 58 258 5.0 1 3 255 59 269 5.0 1 2 267 60 200 5.0 1 0 200 61 213 5.0 1 3 210 62 216 5.0 1 4 212 63 200 5.0 1 3 197 64 266 5.0 1 2 264 65 232 5.0 1 0 232 66 223 5.0 1 1 222 67 238 5.0 1 3 235 68 233 5.0 1 0 233 69 187 5.0 1 2 185 70 250 5.0 1 5 245 71 230 5.0 1 0 230 72 230 5.0 1 3 227 73 181 5.0 1 2 179 74 199 5.0 1 2 197 75 212 5.0 1 2 210 76 271 5.0 1 1 270 77 217 5.0 1 4 213 78 209 5.0 1 1 208 79 198 5.0 1 0 198 80 222 5.0 1 4 218 81 209 5.0 1 0 209 82 203 5.0 1 1 202 83 168 5.0 1 1 167 84 253 5.0 1 1 252 85 222 5.0 1 0 222 86 224 5.0 1 4 220 87 221 5.0 1 1 220 88 245 5.0 1 9 236 89 213 5.0 1 2 211 90 189 5.0 1 0 189 91 166 5.0 1 1 165 92 237 5.0 1 3 234 93 201 5.0 1 4 197 94 160 5.0 1 5 155 95 232 5.0 1 2 230 96 225 5.0 1 2 223 97 225 5.0 1 0 225 98 172 5.0 1 2 170 99 235 5.0 1 6 229 100 168 5.0 1 1 167 101 246 5.0 1 3 243 102 191 5.0 1 4 187 103 237 5.0 1 3 234 104 206 5.0 1 0 206 105 186 5.0 1 0 186 106 165 5.0 1 0 165 107 214 5.0 1 5 209 108 188 5.0 1 2 186 109 178 5.0 1 1 177 110 193 5.0 1 3 190 111 181 5.0 1 2 179 112 190 5.0 1 3 187 113 248 5.0 1 1 247 114 211 5.0 1 3 208 115 182 5.0 1 2 180 116 162 5.0 1 3 159 117 165 5.0 1 1 164 118 188 5.0 1 1 187 119 205 5.0 1 2 203 120 156 5.0 1 2 154 121 207 5.0 1 3 204 122 179 5.0 1 1 178 123 200 5.0 1 2 198 124 178 5.0 1 1 177 125 168 5.0 1 1 167 126 199 5.0 1 1 198 127 150 5.0 1 2 148 128 188 5.0 1 0 188 129 172 5.0 1 1 171 130 166 5.0 1 2 164 131 188 5.0 1 0 188 132 155 5.0 1 0 155 133 187 5.0 1 4 183 134 157 5.0 1 0 157 135 171 5.0 1 1 170 136 166 5.0 1 2 164 137 160 5.0 1 1 159 138 186 5.0 1 3 183 139 187 5.0 1 1 186 140 184 5.0 1 0 184 141 132 5.0 1 0 132 142 101 5.0 1 2 99 143 88 5.0 1 3 85 144 75 5.0 1 0 75 145 123 5.0 1 2 121 146 104 5.0 1 1 103 147 207 5.0 1 0 207 148 158 5.0 1 1 157 149 81 5.0 1 0 81 150 140 5.0 1 1 139 151 2 5.0 1 0 2 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz ============================================= 83250751 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz_trimming_report.txt' 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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_1_S3_L002_R2_001_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 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 The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_1_S3_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_1_S3_L002_R2_001_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_1_S3_L002_R1_001_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_1_S3_L002_R2_001_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_1_S3_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_1_S3_L002_R2_001_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Total number of sequences analysed: 83250751 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 251699 (0.30%) >>> Now running FastQC on the validated data Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_1_S3_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_1_S3_L002_R2_001_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_2_S4_L002_R1_001_val_1.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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_2_S4_L002_R1_001_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2750.95 s (33 us/read; 1.79 M reads/minute). === Summary === Total reads processed: 82,206,331 Reads with adapters: 32,831,180 (39.9%) Reads written (passing filters): 82,206,331 (100.0%) Total basepairs processed: 10,973,171,706 bp Quality-trimmed: 6,128,036 bp (0.1%) Total written (filtered): 10,921,172,993 bp (99.5%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 32831180 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 35.1% C: 8.2% G: 16.7% T: 40.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 25154314 20551582.8 0 25154314 2 5441389 5137895.7 0 5441389 3 1658348 1284473.9 0 1658348 4 309694 321118.5 0 309694 5 167405 80279.6 0 167405 6 49246 20069.9 0 49246 7 14287 5017.5 0 14287 8 1584 1254.4 0 1584 9 689 313.6 0 81 608 10 1972 78.4 1 56 1916 11 1428 19.6 1 16 1412 12 318 4.9 1 4 314 13 244 4.9 1 1 243 14 247 4.9 1 3 244 15 245 4.9 1 0 245 16 212 4.9 1 0 212 17 220 4.9 1 1 219 18 235 4.9 1 5 230 19 247 4.9 1 1 246 20 263 4.9 1 10 253 21 219 4.9 1 0 219 22 214 4.9 1 4 210 23 301 4.9 1 2 299 24 304 4.9 1 1 303 25 319 4.9 1 3 316 26 260 4.9 1 2 258 27 274 4.9 1 0 274 28 247 4.9 1 6 241 29 284 4.9 1 0 284 30 209 4.9 1 6 203 31 257 4.9 1 1 256 32 308 4.9 1 5 303 33 254 4.9 1 0 254 34 229 4.9 1 2 227 35 286 4.9 1 7 279 36 232 4.9 1 3 229 37 242 4.9 1 6 236 38 268 4.9 1 1 267 39 252 4.9 1 2 250 40 242 4.9 1 1 241 41 267 4.9 1 3 264 42 242 4.9 1 5 237 43 266 4.9 1 1 265 44 250 4.9 1 3 247 45 227 4.9 1 0 227 46 261 4.9 1 6 255 47 218 4.9 1 0 218 48 248 4.9 1 2 246 49 225 4.9 1 0 225 50 283 4.9 1 1 282 51 253 4.9 1 2 251 52 198 4.9 1 5 193 53 234 4.9 1 1 233 54 273 4.9 1 0 273 55 277 4.9 1 5 272 56 284 4.9 1 2 282 57 254 4.9 1 0 254 58 206 4.9 1 1 205 59 253 4.9 1 0 253 60 185 4.9 1 4 181 61 245 4.9 1 0 245 62 245 4.9 1 0 245 63 243 4.9 1 2 241 64 216 4.9 1 1 215 65 236 4.9 1 5 231 66 259 4.9 1 2 257 67 241 4.9 1 0 241 68 257 4.9 1 4 253 69 221 4.9 1 4 217 70 229 4.9 1 1 228 71 232 4.9 1 3 229 72 240 4.9 1 0 240 73 238 4.9 1 1 237 74 227 4.9 1 5 222 75 253 4.9 1 1 252 76 243 4.9 1 2 241 77 212 4.9 1 1 211 78 210 4.9 1 3 207 79 183 4.9 1 0 183 80 241 4.9 1 5 236 81 177 4.9 1 1 176 82 201 4.9 1 1 200 83 238 4.9 1 7 231 84 238 4.9 1 0 238 85 215 4.9 1 0 215 86 203 4.9 1 1 202 87 221 4.9 1 5 216 88 228 4.9 1 2 226 89 224 4.9 1 1 223 90 201 4.9 1 0 201 91 234 4.9 1 3 231 92 247 4.9 1 1 246 93 235 4.9 1 3 232 94 173 4.9 1 4 169 95 236 4.9 1 2 234 96 214 4.9 1 3 211 97 186 4.9 1 4 182 98 218 4.9 1 2 216 99 242 4.9 1 6 236 100 187 4.9 1 2 185 101 222 4.9 1 2 220 102 197 4.9 1 3 194 103 237 4.9 1 3 234 104 236 4.9 1 1 235 105 200 4.9 1 0 200 106 220 4.9 1 0 220 107 240 4.9 1 5 235 108 212 4.9 1 1 211 109 219 4.9 1 2 217 110 239 4.9 1 1 238 111 184 4.9 1 4 180 112 154 4.9 1 0 154 113 210 4.9 1 0 210 114 249 4.9 1 2 247 115 200 4.9 1 0 200 116 180 4.9 1 5 175 117 200 4.9 1 1 199 118 196 4.9 1 1 195 119 193 4.9 1 0 193 120 176 4.9 1 1 175 121 214 4.9 1 0 214 122 288 4.9 1 0 288 123 183 4.9 1 0 183 124 214 4.9 1 0 214 125 166 4.9 1 0 166 126 198 4.9 1 2 196 127 198 4.9 1 3 195 128 255 4.9 1 1 254 129 214 4.9 1 0 214 130 170 4.9 1 0 170 131 213 4.9 1 3 210 132 184 4.9 1 1 183 133 182 4.9 1 1 181 134 214 4.9 1 0 214 135 153 4.9 1 1 152 136 178 4.9 1 1 177 137 193 4.9 1 3 190 138 250 4.9 1 2 248 139 202 4.9 1 3 199 140 206 4.9 1 7 199 141 130 4.9 1 0 130 142 119 4.9 1 1 118 143 116 4.9 1 1 115 144 96 4.9 1 0 96 145 130 4.9 1 3 127 146 123 4.9 1 1 122 147 192 4.9 1 1 191 148 170 4.9 1 1 169 149 87 4.9 1 0 87 150 95 4.9 1 0 95 151 2 4.9 1 0 2 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz ============================================= 82206331 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_2_S4_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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_2_S4_L002_R2_001_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 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_2_S4_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 2870.62 s (35 us/read; 1.72 M reads/minute). === Summary === Total reads processed: 82,206,331 Reads with adapters: 25,143,341 (30.6%) Reads written (passing filters): 82,206,331 (100.0%) Total basepairs processed: 10,653,232,429 bp Quality-trimmed: 30,779,948 bp (0.3%) Total written (filtered): 10,588,614,497 bp (99.4%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 25143341 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 30.1% C: 14.9% G: 28.2% T: 26.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19313397 20551582.8 0 19313397 2 4142191 5137895.7 0 4142191 3 1428582 1284473.9 0 1428582 4 198307 321118.5 0 198307 5 36414 80279.6 0 36414 6 8949 20069.9 0 8949 7 950 5017.5 0 950 8 639 1254.4 0 639 9 748 313.6 0 130 618 10 789 78.4 1 8 781 11 219 19.6 1 2 217 12 76 4.9 1 0 76 13 75 4.9 1 0 75 14 84 4.9 1 0 84 15 82 4.9 1 1 81 16 107 4.9 1 0 107 17 121 4.9 1 1 120 18 119 4.9 1 0 119 19 125 4.9 1 1 124 20 123 4.9 1 2 121 21 132 4.9 1 1 131 22 135 4.9 1 0 135 23 92 4.9 1 1 91 24 96 4.9 1 0 96 25 93 4.9 1 0 93 26 112 4.9 1 1 111 27 112 4.9 1 3 109 28 112 4.9 1 1 111 29 111 4.9 1 1 110 30 109 4.9 1 0 109 31 96 4.9 1 1 95 32 116 4.9 1 0 116 33 111 4.9 1 3 108 34 121 4.9 1 0 121 35 102 4.9 1 1 101 36 108 4.9 1 0 108 37 106 4.9 1 0 106 38 104 4.9 1 0 104 39 128 4.9 1 0 128 40 93 4.9 1 1 92 41 80 4.9 1 0 80 42 91 4.9 1 0 91 43 114 4.9 1 0 114 44 91 4.9 1 0 91 45 97 4.9 1 0 97 46 96 4.9 1 0 96 47 119 4.9 1 0 119 48 96 4.9 1 0 96 49 96 4.9 1 0 96 50 124 4.9 1 0 124 51 107 4.9 1 1 106 52 115 4.9 1 1 114 53 89 4.9 1 1 88 54 83 4.9 1 0 83 55 113 4.9 1 0 113 56 89 4.9 1 0 89 57 106 4.9 1 1 105 58 108 4.9 1 0 108 59 95 4.9 1 1 94 60 124 4.9 1 0 124 61 84 4.9 1 0 84 62 104 4.9 1 0 104 63 78 4.9 1 0 78 64 107 4.9 1 0 107 65 159 4.9 1 0 159 66 93 4.9 1 1 92 67 85 4.9 1 0 85 68 102 4.9 1 3 99 69 97 4.9 1 1 96 70 99 4.9 1 2 97 71 83 4.9 1 1 82 72 89 4.9 1 0 89 73 99 4.9 1 0 99 74 90 4.9 1 1 89 75 74 4.9 1 1 73 76 89 4.9 1 0 89 77 85 4.9 1 0 85 78 100 4.9 1 3 97 79 83 4.9 1 0 83 80 120 4.9 1 0 120 81 86 4.9 1 0 86 82 68 4.9 1 2 66 83 85 4.9 1 1 84 84 94 4.9 1 0 94 85 62 4.9 1 0 62 86 91 4.9 1 2 89 87 81 4.9 1 0 81 88 76 4.9 1 0 76 89 87 4.9 1 1 86 90 86 4.9 1 2 84 91 72 4.9 1 0 72 92 80 4.9 1 1 79 93 87 4.9 1 1 86 94 67 4.9 1 0 67 95 68 4.9 1 0 68 96 81 4.9 1 0 81 97 60 4.9 1 0 60 98 98 4.9 1 3 95 99 103 4.9 1 1 102 100 92 4.9 1 1 91 101 92 4.9 1 0 92 102 88 4.9 1 0 88 103 78 4.9 1 0 78 104 80 4.9 1 1 79 105 78 4.9 1 0 78 106 82 4.9 1 0 82 107 78 4.9 1 0 78 108 88 4.9 1 0 88 109 66 4.9 1 0 66 110 72 4.9 1 0 72 111 77 4.9 1 1 76 112 65 4.9 1 0 65 113 74 4.9 1 1 73 114 90 4.9 1 0 90 115 106 4.9 1 0 106 116 56 4.9 1 0 56 117 70 4.9 1 0 70 118 72 4.9 1 0 72 119 83 4.9 1 0 83 120 67 4.9 1 0 67 121 49 4.9 1 0 49 122 60 4.9 1 0 60 123 60 4.9 1 0 60 124 100 4.9 1 0 100 125 92 4.9 1 2 90 126 51 4.9 1 1 50 127 62 4.9 1 0 62 128 70 4.9 1 0 70 129 50 4.9 1 0 50 130 69 4.9 1 0 69 131 71 4.9 1 0 71 132 84 4.9 1 0 84 133 73 4.9 1 0 73 134 70 4.9 1 0 70 135 78 4.9 1 1 77 136 70 4.9 1 1 69 137 58 4.9 1 2 56 138 66 4.9 1 2 64 139 81 4.9 1 0 81 140 74 4.9 1 0 74 141 76 4.9 1 0 76 142 67 4.9 1 0 67 143 112 4.9 1 1 111 144 77 4.9 1 0 77 145 67 4.9 1 0 67 146 34 4.9 1 0 34 147 23 4.9 1 0 23 148 17 4.9 1 0 17 149 22 4.9 1 0 22 150 19 4.9 1 0 19 151 14 4.9 1 0 14 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz ============================================= 82206331 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_2_S4_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_2_S4_L002_R2_001_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_2_S4_L002_R1_001_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_2_S4_L002_R2_001_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_2_S4_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_2_S4_L002_R2_001_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Total number of sequences analysed: 82206331 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 290422 (0.35%) >>> Now running FastQC on the validated data Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_2_S4_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_2_S4_L002_R2_001_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_3_S1_L002_R1_001_val_1.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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_3_S1_L002_R1_001_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2677.82 s (30 us/read; 1.99 M reads/minute). === Summary === Total reads processed: 88,647,204 Reads with adapters: 34,402,376 (38.8%) Reads written (passing filters): 88,647,204 (100.0%) Total basepairs processed: 10,786,340,239 bp Quality-trimmed: 8,243,040 bp (0.1%) Total written (filtered): 10,730,992,217 bp (99.5%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 34402376 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 36.6% C: 8.7% G: 18.2% T: 36.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 26415990 22161801.0 0 26415990 2 5891012 5540450.2 0 5891012 3 1599136 1385112.6 0 1599136 4 265923 346278.1 0 265923 5 140882 86569.5 0 140882 6 46671 21642.4 0 46671 7 10088 5410.6 0 10088 8 1910 1352.6 0 1910 9 990 338.2 0 90 900 10 2093 84.5 1 33 2060 11 1509 21.1 1 14 1495 12 269 5.3 1 2 267 13 253 5.3 1 0 253 14 195 5.3 1 7 188 15 166 5.3 1 2 164 16 198 5.3 1 7 191 17 148 5.3 1 0 148 18 225 5.3 1 6 219 19 186 5.3 1 1 185 20 303 5.3 1 2 301 21 237 5.3 1 1 236 22 227 5.3 1 3 224 23 290 5.3 1 4 286 24 268 5.3 1 1 267 25 258 5.3 1 2 256 26 250 5.3 1 1 249 27 238 5.3 1 4 234 28 256 5.3 1 7 249 29 234 5.3 1 0 234 30 214 5.3 1 6 208 31 229 5.3 1 1 228 32 233 5.3 1 1 232 33 211 5.3 1 0 211 34 230 5.3 1 1 229 35 256 5.3 1 4 252 36 248 5.3 1 4 244 37 196 5.3 1 3 193 38 210 5.3 1 3 207 39 228 5.3 1 8 220 40 223 5.3 1 13 210 41 200 5.3 1 2 198 42 231 5.3 1 4 227 43 232 5.3 1 4 228 44 225 5.3 1 7 218 45 202 5.3 1 11 191 46 225 5.3 1 3 222 47 219 5.3 1 2 217 48 235 5.3 1 0 235 49 211 5.3 1 8 203 50 244 5.3 1 1 243 51 223 5.3 1 0 223 52 210 5.3 1 8 202 53 235 5.3 1 1 234 54 237 5.3 1 11 226 55 232 5.3 1 6 226 56 240 5.3 1 4 236 57 192 5.3 1 4 188 58 217 5.3 1 0 217 59 220 5.3 1 1 219 60 173 5.3 1 1 172 61 166 5.3 1 2 164 62 164 5.3 1 3 161 63 199 5.3 1 2 197 64 201 5.3 1 5 196 65 177 5.3 1 4 173 66 193 5.3 1 4 189 67 171 5.3 1 4 167 68 187 5.3 1 3 184 69 186 5.3 1 1 185 70 205 5.3 1 1 204 71 201 5.3 1 2 199 72 221 5.3 1 4 217 73 185 5.3 1 0 185 74 205 5.3 1 1 204 75 198 5.3 1 1 197 76 190 5.3 1 0 190 77 218 5.3 1 1 217 78 238 5.3 1 1 237 79 199 5.3 1 2 197 80 186 5.3 1 1 185 81 164 5.3 1 0 164 82 182 5.3 1 1 181 83 203 5.3 1 7 196 84 189 5.3 1 0 189 85 197 5.3 1 1 196 86 212 5.3 1 0 212 87 152 5.3 1 0 152 88 161 5.3 1 1 160 89 197 5.3 1 2 195 90 183 5.3 1 4 179 91 178 5.3 1 5 173 92 178 5.3 1 3 175 93 175 5.3 1 4 171 94 189 5.3 1 3 186 95 194 5.3 1 2 192 96 195 5.3 1 2 193 97 210 5.3 1 3 207 98 182 5.3 1 2 180 99 180 5.3 1 0 180 100 153 5.3 1 0 153 101 201 5.3 1 2 199 102 196 5.3 1 0 196 103 185 5.3 1 0 185 104 187 5.3 1 3 184 105 180 5.3 1 2 178 106 165 5.3 1 1 164 107 189 5.3 1 0 189 108 190 5.3 1 1 189 109 158 5.3 1 3 155 110 180 5.3 1 0 180 111 165 5.3 1 2 163 112 140 5.3 1 1 139 113 205 5.3 1 3 202 114 158 5.3 1 2 156 115 150 5.3 1 0 150 116 149 5.3 1 2 147 117 156 5.3 1 2 154 118 152 5.3 1 3 149 119 171 5.3 1 1 170 120 142 5.3 1 2 140 121 165 5.3 1 0 165 122 221 5.3 1 3 218 123 183 5.3 1 2 181 124 171 5.3 1 1 170 125 152 5.3 1 0 152 126 161 5.3 1 1 160 127 154 5.3 1 1 153 128 166 5.3 1 0 166 129 159 5.3 1 4 155 130 171 5.3 1 0 171 131 132 5.3 1 3 129 132 162 5.3 1 2 160 133 134 5.3 1 4 130 134 147 5.3 1 0 147 135 124 5.3 1 1 123 136 138 5.3 1 0 138 137 148 5.3 1 2 146 138 159 5.3 1 1 158 139 170 5.3 1 1 169 140 167 5.3 1 1 166 141 98 5.3 1 0 98 142 85 5.3 1 0 85 143 57 5.3 1 0 57 144 50 5.3 1 2 48 145 123 5.3 1 0 123 146 72 5.3 1 0 72 147 154 5.3 1 1 153 148 113 5.3 1 2 111 149 57 5.3 1 1 56 150 111 5.3 1 1 110 151 3 5.3 1 0 3 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz ============================================= 88647204 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz_trimming_report.txt' 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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_3_S1_L002_R2_001_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 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 The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_3_S1_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_3_S1_L002_R2_001_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_3_S1_L002_R1_001_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_3_S1_L002_R2_001_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_3_S1_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_3_S1_L002_R2_001_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Total number of sequences analysed: 88647204 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 696909 (0.79%) >>> Now running FastQC on the validated data Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_3_S1_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_3_S1_L002_R2_001_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_5_S6_L002_R1_001_val_1.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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_5_S6_L002_R1_001_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2444.45 s (34 us/read; 1.77 M reads/minute). === Summary === Total reads processed: 71,913,753 Reads with adapters: 29,525,363 (41.1%) Reads written (passing filters): 71,913,753 (100.0%) Total basepairs processed: 9,752,811,927 bp Quality-trimmed: 3,952,574 bp (0.0%) Total written (filtered): 9,707,701,519 bp (99.5%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 29525363 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 35.6% C: 7.6% G: 15.7% T: 41.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22874628 17978438.2 0 22874628 2 4654313 4494609.6 0 4654313 3 1447610 1123652.4 0 1447610 4 293768 280913.1 0 293768 5 159482 70228.3 0 159482 6 47395 17557.1 0 47395 7 13696 4389.3 0 13696 8 1513 1097.3 0 1513 9 654 274.3 0 69 585 10 1858 68.6 1 37 1821 11 1303 17.1 1 16 1287 12 297 4.3 1 4 293 13 256 4.3 1 4 252 14 245 4.3 1 6 239 15 198 4.3 1 2 196 16 192 4.3 1 0 192 17 199 4.3 1 0 199 18 195 4.3 1 8 187 19 175 4.3 1 0 175 20 332 4.3 1 2 330 21 239 4.3 1 1 238 22 194 4.3 1 1 193 23 319 4.3 1 6 313 24 264 4.3 1 1 263 25 257 4.3 1 0 257 26 279 4.3 1 1 278 27 221 4.3 1 0 221 28 222 4.3 1 1 221 29 228 4.3 1 0 228 30 195 4.3 1 7 188 31 256 4.3 1 1 255 32 302 4.3 1 0 302 33 211 4.3 1 1 210 34 238 4.3 1 0 238 35 243 4.3 1 6 237 36 216 4.3 1 0 216 37 255 4.3 1 0 255 38 251 4.3 1 0 251 39 210 4.3 1 4 206 40 224 4.3 1 1 223 41 191 4.3 1 2 189 42 226 4.3 1 1 225 43 225 4.3 1 0 225 44 215 4.3 1 4 211 45 181 4.3 1 1 180 46 255 4.3 1 3 252 47 208 4.3 1 1 207 48 234 4.3 1 0 234 49 200 4.3 1 1 199 50 217 4.3 1 3 214 51 184 4.3 1 1 183 52 234 4.3 1 5 229 53 210 4.3 1 0 210 54 273 4.3 1 0 273 55 246 4.3 1 3 243 56 222 4.3 1 1 221 57 242 4.3 1 2 240 58 232 4.3 1 2 230 59 268 4.3 1 1 267 60 218 4.3 1 0 218 61 227 4.3 1 0 227 62 206 4.3 1 1 205 63 202 4.3 1 3 199 64 242 4.3 1 5 237 65 233 4.3 1 1 232 66 237 4.3 1 5 232 67 267 4.3 1 1 266 68 254 4.3 1 5 249 69 183 4.3 1 7 176 70 203 4.3 1 2 201 71 202 4.3 1 1 201 72 250 4.3 1 3 247 73 248 4.3 1 4 244 74 264 4.3 1 0 264 75 186 4.3 1 1 185 76 287 4.3 1 7 280 77 202 4.3 1 0 202 78 153 4.3 1 0 153 79 189 4.3 1 1 188 80 223 4.3 1 2 221 81 163 4.3 1 0 163 82 184 4.3 1 1 183 83 229 4.3 1 4 225 84 247 4.3 1 1 246 85 214 4.3 1 3 211 86 212 4.3 1 1 211 87 229 4.3 1 1 228 88 195 4.3 1 2 193 89 211 4.3 1 4 207 90 204 4.3 1 0 204 91 165 4.3 1 3 162 92 204 4.3 1 0 204 93 167 4.3 1 4 163 94 163 4.3 1 3 160 95 240 4.3 1 4 236 96 218 4.3 1 0 218 97 252 4.3 1 0 252 98 209 4.3 1 0 209 99 228 4.3 1 1 227 100 195 4.3 1 1 194 101 256 4.3 1 5 251 102 221 4.3 1 7 214 103 200 4.3 1 1 199 104 211 4.3 1 1 210 105 192 4.3 1 1 191 106 216 4.3 1 0 216 107 206 4.3 1 2 204 108 204 4.3 1 2 202 109 187 4.3 1 0 187 110 206 4.3 1 4 202 111 153 4.3 1 1 152 112 159 4.3 1 2 157 113 209 4.3 1 1 208 114 225 4.3 1 3 222 115 182 4.3 1 1 181 116 167 4.3 1 4 163 117 231 4.3 1 0 231 118 195 4.3 1 1 194 119 199 4.3 1 0 199 120 154 4.3 1 3 151 121 197 4.3 1 0 197 122 193 4.3 1 4 189 123 195 4.3 1 0 195 124 173 4.3 1 0 173 125 214 4.3 1 2 212 126 165 4.3 1 0 165 127 212 4.3 1 9 203 128 258 4.3 1 1 257 129 238 4.3 1 11 227 130 190 4.3 1 1 189 131 228 4.3 1 1 227 132 186 4.3 1 2 184 133 149 4.3 1 0 149 134 202 4.3 1 3 199 135 132 4.3 1 0 132 136 191 4.3 1 1 190 137 187 4.3 1 2 185 138 218 4.3 1 1 217 139 220 4.3 1 4 216 140 199 4.3 1 1 198 141 136 4.3 1 0 136 142 99 4.3 1 2 97 143 109 4.3 1 0 109 144 94 4.3 1 0 94 145 152 4.3 1 1 151 146 132 4.3 1 3 129 147 199 4.3 1 0 199 148 132 4.3 1 1 131 149 74 4.3 1 1 73 150 110 4.3 1 1 109 151 5 4.3 1 0 5 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz ============================================= 71913753 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz_trimming_report.txt' 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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_5_S6_L002_R2_001_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 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 The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_5_S6_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_5_S6_L002_R2_001_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_5_S6_L002_R1_001_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_5_S6_L002_R2_001_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_5_S6_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_5_S6_L002_R2_001_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Total number of sequences analysed: 71913753 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 179976 (0.25%) >>> Now running FastQC on the validated data Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_5_S6_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_5_S6_L002_R2_001_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_6_S5_L002_R1_001_val_1.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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_6_S5_L002_R1_001_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2491.23 s (34 us/read; 1.77 M reads/minute). === Summary === Total reads processed: 73,388,785 Reads with adapters: 29,397,922 (40.1%) Reads written (passing filters): 73,388,785 (100.0%) Total basepairs processed: 9,860,957,526 bp Quality-trimmed: 4,346,715 bp (0.0%) Total written (filtered): 9,815,588,776 bp (99.5%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 29397922 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 35.2% C: 8.3% G: 16.1% T: 40.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 22459608 18347196.2 0 22459608 2 4874628 4586799.1 0 4874628 3 1560261 1146699.8 0 1560261 4 271652 286674.9 0 271652 5 146370 71668.7 0 146370 6 42723 17917.2 0 42723 7 12349 4479.3 0 12349 8 1436 1119.8 0 1436 9 556 280.0 0 59 497 10 1682 70.0 1 16 1666 11 1152 17.5 1 9 1143 12 259 4.4 1 1 258 13 204 4.4 1 0 204 14 237 4.4 1 3 234 15 175 4.4 1 0 175 16 144 4.4 1 1 143 17 157 4.4 1 0 157 18 211 4.4 1 0 211 19 178 4.4 1 0 178 20 209 4.4 1 1 208 21 201 4.4 1 1 200 22 195 4.4 1 2 193 23 290 4.4 1 4 286 24 261 4.4 1 4 257 25 253 4.4 1 3 250 26 238 4.4 1 1 237 27 220 4.4 1 5 215 28 178 4.4 1 1 177 29 243 4.4 1 1 242 30 219 4.4 1 3 216 31 210 4.4 1 1 209 32 197 4.4 1 2 195 33 218 4.4 1 0 218 34 185 4.4 1 0 185 35 225 4.4 1 3 222 36 219 4.4 1 3 216 37 193 4.4 1 1 192 38 243 4.4 1 0 243 39 232 4.4 1 2 230 40 197 4.4 1 0 197 41 199 4.4 1 0 199 42 211 4.4 1 1 210 43 239 4.4 1 4 235 44 215 4.4 1 4 211 45 189 4.4 1 0 189 46 242 4.4 1 0 242 47 205 4.4 1 0 205 48 215 4.4 1 1 214 49 209 4.4 1 0 209 50 185 4.4 1 2 183 51 186 4.4 1 0 186 52 214 4.4 1 7 207 53 212 4.4 1 0 212 54 227 4.4 1 1 226 55 192 4.4 1 2 190 56 186 4.4 1 5 181 57 213 4.4 1 1 212 58 203 4.4 1 0 203 59 233 4.4 1 3 230 60 164 4.4 1 6 158 61 167 4.4 1 3 164 62 202 4.4 1 5 197 63 200 4.4 1 0 200 64 179 4.4 1 1 178 65 191 4.4 1 0 191 66 195 4.4 1 4 191 67 194 4.4 1 2 192 68 204 4.4 1 6 198 69 184 4.4 1 2 182 70 197 4.4 1 2 195 71 208 4.4 1 0 208 72 182 4.4 1 1 181 73 164 4.4 1 0 164 74 215 4.4 1 1 214 75 161 4.4 1 7 154 76 221 4.4 1 1 220 77 203 4.4 1 3 200 78 167 4.4 1 0 167 79 180 4.4 1 1 179 80 178 4.4 1 0 178 81 153 4.4 1 0 153 82 155 4.4 1 0 155 83 163 4.4 1 0 163 84 225 4.4 1 0 225 85 183 4.4 1 0 183 86 153 4.4 1 1 152 87 184 4.4 1 1 183 88 189 4.4 1 0 189 89 189 4.4 1 1 188 90 170 4.4 1 0 170 91 191 4.4 1 5 186 92 219 4.4 1 0 219 93 168 4.4 1 3 165 94 179 4.4 1 3 176 95 201 4.4 1 1 200 96 192 4.4 1 0 192 97 188 4.4 1 2 186 98 167 4.4 1 0 167 99 192 4.4 1 0 192 100 167 4.4 1 2 165 101 180 4.4 1 0 180 102 181 4.4 1 4 177 103 173 4.4 1 0 173 104 159 4.4 1 0 159 105 163 4.4 1 0 163 106 167 4.4 1 1 166 107 226 4.4 1 2 224 108 179 4.4 1 0 179 109 143 4.4 1 0 143 110 182 4.4 1 1 181 111 160 4.4 1 1 159 112 160 4.4 1 0 160 113 190 4.4 1 0 190 114 181 4.4 1 0 181 115 171 4.4 1 5 166 116 146 4.4 1 2 144 117 198 4.4 1 2 196 118 178 4.4 1 0 178 119 186 4.4 1 1 185 120 185 4.4 1 1 184 121 146 4.4 1 0 146 122 178 4.4 1 1 177 123 134 4.4 1 0 134 124 184 4.4 1 0 184 125 170 4.4 1 0 170 126 162 4.4 1 1 161 127 108 4.4 1 2 106 128 198 4.4 1 1 197 129 160 4.4 1 2 158 130 151 4.4 1 1 150 131 195 4.4 1 1 194 132 125 4.4 1 1 124 133 125 4.4 1 0 125 134 147 4.4 1 1 146 135 159 4.4 1 0 159 136 133 4.4 1 1 132 137 144 4.4 1 1 143 138 205 4.4 1 0 205 139 163 4.4 1 0 163 140 152 4.4 1 0 152 141 92 4.4 1 1 91 142 95 4.4 1 0 95 143 77 4.4 1 0 77 144 63 4.4 1 0 63 145 146 4.4 1 0 146 146 117 4.4 1 0 117 147 227 4.4 1 0 227 148 124 4.4 1 0 124 149 70 4.4 1 0 70 150 96 4.4 1 1 95 151 1 4.4 1 0 1 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz ============================================= 73388785 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz_trimming_report.txt' 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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_6_S5_L002_R2_001_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 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 The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_6_S5_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_6_S5_L002_R2_001_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_6_S5_L002_R1_001_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_6_S5_L002_R2_001_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_6_S5_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_6_S5_L002_R2_001_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Total number of sequences analysed: 73388785 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 196707 (0.27%) >>> Now running FastQC on the validated data Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_6_S5_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_6_S5_L002_R2_001_val_2_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_7_S2_L002_R1_001_val_1.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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_7_S2_L002_R1_001_val_1_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'TGGAATTCTCGG' from file Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2941.23 s (33 us/read; 1.80 M reads/minute). === Summary === Total reads processed: 88,036,439 Reads with adapters: 35,638,015 (40.5%) Reads written (passing filters): 88,036,439 (100.0%) Total basepairs processed: 11,754,350,316 bp Quality-trimmed: 4,836,285 bp (0.0%) Total written (filtered): 11,699,753,699 bp (99.5%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 35638015 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 35.7% C: 8.2% G: 15.7% T: 40.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 27394243 22009109.8 0 27394243 2 5797880 5502277.4 0 5797880 3 1805026 1375569.4 0 1805026 4 337285 343892.3 0 337285 5 188941 85973.1 0 188941 6 57639 21493.3 0 57639 7 16581 5373.3 0 16581 8 2106 1343.3 0 2106 9 717 335.8 0 104 613 10 2296 84.0 1 60 2236 11 1692 21.0 1 13 1679 12 376 5.2 1 4 372 13 247 5.2 1 0 247 14 286 5.2 1 4 282 15 280 5.2 1 2 278 16 223 5.2 1 1 222 17 217 5.2 1 1 216 18 260 5.2 1 8 252 19 227 5.2 1 3 224 20 325 5.2 1 2 323 21 248 5.2 1 0 248 22 255 5.2 1 4 251 23 340 5.2 1 0 340 24 362 5.2 1 0 362 25 321 5.2 1 1 320 26 323 5.2 1 2 321 27 270 5.2 1 2 268 28 278 5.2 1 4 274 29 329 5.2 1 9 320 30 260 5.2 1 5 255 31 258 5.2 1 3 255 32 317 5.2 1 5 312 33 281 5.2 1 6 275 34 257 5.2 1 1 256 35 270 5.2 1 3 267 36 279 5.2 1 2 277 37 282 5.2 1 5 277 38 265 5.2 1 3 262 39 295 5.2 1 1 294 40 314 5.2 1 0 314 41 278 5.2 1 6 272 42 222 5.2 1 6 216 43 281 5.2 1 3 278 44 292 5.2 1 6 286 45 229 5.2 1 4 225 46 312 5.2 1 2 310 47 287 5.2 1 5 282 48 256 5.2 1 1 255 49 247 5.2 1 1 246 50 267 5.2 1 0 267 51 226 5.2 1 2 224 52 254 5.2 1 2 252 53 258 5.2 1 1 257 54 268 5.2 1 5 263 55 270 5.2 1 2 268 56 262 5.2 1 8 254 57 286 5.2 1 0 286 58 279 5.2 1 1 278 59 268 5.2 1 0 268 60 238 5.2 1 2 236 61 246 5.2 1 5 241 62 266 5.2 1 1 265 63 240 5.2 1 0 240 64 235 5.2 1 3 232 65 286 5.2 1 2 284 66 239 5.2 1 1 238 67 295 5.2 1 4 291 68 229 5.2 1 3 226 69 216 5.2 1 1 215 70 256 5.2 1 0 256 71 257 5.2 1 2 255 72 260 5.2 1 1 259 73 242 5.2 1 1 241 74 250 5.2 1 0 250 75 248 5.2 1 5 243 76 238 5.2 1 6 232 77 268 5.2 1 3 265 78 242 5.2 1 2 240 79 261 5.2 1 2 259 80 236 5.2 1 0 236 81 240 5.2 1 2 238 82 220 5.2 1 1 219 83 258 5.2 1 5 253 84 234 5.2 1 0 234 85 265 5.2 1 2 263 86 255 5.2 1 4 251 87 239 5.2 1 2 237 88 246 5.2 1 1 245 89 284 5.2 1 1 283 90 184 5.2 1 0 184 91 232 5.2 1 0 232 92 217 5.2 1 4 213 93 242 5.2 1 2 240 94 206 5.2 1 2 204 95 246 5.2 1 2 244 96 215 5.2 1 7 208 97 213 5.2 1 3 210 98 230 5.2 1 0 230 99 264 5.2 1 3 261 100 220 5.2 1 4 216 101 290 5.2 1 2 288 102 228 5.2 1 6 222 103 243 5.2 1 4 239 104 246 5.2 1 0 246 105 192 5.2 1 0 192 106 226 5.2 1 0 226 107 288 5.2 1 3 285 108 232 5.2 1 1 231 109 238 5.2 1 1 237 110 288 5.2 1 1 287 111 248 5.2 1 1 247 112 156 5.2 1 6 150 113 252 5.2 1 1 251 114 258 5.2 1 1 257 115 252 5.2 1 4 248 116 221 5.2 1 5 216 117 193 5.2 1 5 188 118 250 5.2 1 3 247 119 258 5.2 1 0 258 120 213 5.2 1 1 212 121 247 5.2 1 1 246 122 256 5.2 1 0 256 123 220 5.2 1 1 219 124 205 5.2 1 2 203 125 217 5.2 1 1 216 126 228 5.2 1 4 224 127 230 5.2 1 12 218 128 266 5.2 1 1 265 129 236 5.2 1 1 235 130 187 5.2 1 1 186 131 213 5.2 1 0 213 132 197 5.2 1 2 195 133 162 5.2 1 2 160 134 193 5.2 1 4 189 135 195 5.2 1 0 195 136 207 5.2 1 4 203 137 181 5.2 1 5 176 138 251 5.2 1 2 249 139 203 5.2 1 0 203 140 224 5.2 1 0 224 141 120 5.2 1 0 120 142 121 5.2 1 1 120 143 89 5.2 1 0 89 144 109 5.2 1 1 108 145 129 5.2 1 3 126 146 114 5.2 1 0 114 147 250 5.2 1 3 247 148 130 5.2 1 2 128 149 83 5.2 1 0 83 150 127 5.2 1 1 126 151 2 5.2 1 0 2 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz ============================================= 88036439 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_02/Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz_trimming_report.txt' 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(s) will be GZIP compressed Writing final adapter and quality trimmed output to Library_Geoduck_MG_7_S2_L002_R2_001_val_2_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'GATCGTCGGACT' from file Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 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 The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Library_Geoduck_MG_7_S2_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_7_S2_L002_R2_001_val_2_trimmed.fq.gz file_1: Library_Geoduck_MG_7_S2_L002_R1_001_val_1_trimmed.fq.gz, file_2: Library_Geoduck_MG_7_S2_L002_R2_001_val_2_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_7_S2_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_7_S2_L002_R2_001_val_2_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Total number of sequences analysed: 88036439 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 239535 (0.27%) >>> Now running FastQC on the validated data Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_7_S2_L002_R1_001_val_1_trimmed.fq.gz and Library_Geoduck_MG_7_S2_L002_R2_001_val_2_trimmed.fq.gz ==================================================================================================== gzip: stdout: Broken pipe