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.fastq.gz <<) Found perfect matches for the following adapter sequences: Adapter type Count Sequence Sequences analysed Percentage Nextera 205871 CTGTCTCTTATA 1000000 20.59 smallRNA 1 TGGAATTCTCGG 1000000 0.00 Illumina 0 AGATCGGAAGAGC 1000000 0.00 Using Nextera adapter for trimming (count: 205871). Second best hit was smallRNA (count: 1) gzip: stdout: Broken pipe Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/Library_Geoduck_MG_1_S3_L002_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_1_S3_L002_R1_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_1_S3_L002_R1_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_1_S3_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2897.19 s (35 us/read; 1.73 M reads/minute). === Summary === Total reads processed: 83,562,471 Reads with adapters: 38,392,912 (45.9%) Reads written (passing filters): 83,562,471 (100.0%) Total basepairs processed: 12,617,933,121 bp Quality-trimmed: 241,837,593 bp (1.9%) Total written (filtered): 11,342,814,479 bp (89.9%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 38392912 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.4% C: 33.7% G: 25.1% T: 24.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13870321 20890617.8 0 13870321 2 3335301 5222654.4 0 3335301 3 1043475 1305663.6 0 1043475 4 398194 326415.9 0 398194 5 278415 81604.0 0 278415 6 146118 20401.0 0 146118 7 160255 5100.2 0 160255 8 166688 1275.1 0 166688 9 205766 318.8 0 204471 1295 10 134850 79.7 1 129017 5833 11 183874 19.9 1 176793 7081 12 209435 5.0 1 201380 8055 13 253517 5.0 1 244238 9279 14 180337 5.0 1 174332 6005 15 258996 5.0 1 249336 9660 16 209555 5.0 1 201231 8324 17 190068 5.0 1 184234 5834 18 197520 5.0 1 191013 6507 19 108110 5.0 1 105012 3098 20 165276 5.0 1 158727 6549 21 210505 5.0 1 200652 9853 22 252929 5.0 1 244405 8524 23 165029 5.0 1 159499 5530 24 200834 5.0 1 195477 5357 25 222837 5.0 1 216873 5964 26 239329 5.0 1 232002 7327 27 293925 5.0 1 285727 8198 28 115347 5.0 1 111512 3835 29 196702 5.0 1 190279 6423 30 173191 5.0 1 168995 4196 31 110383 5.0 1 106998 3385 32 226587 5.0 1 221510 5077 33 137465 5.0 1 133994 3471 34 188166 5.0 1 183524 4642 35 239252 5.0 1 232636 6616 36 364315 5.0 1 355591 8724 37 102785 5.0 1 99575 3210 38 288040 5.0 1 281796 6244 39 54999 5.0 1 53323 1676 40 154448 5.0 1 150673 3775 41 191885 5.0 1 186039 5846 42 192440 5.0 1 188147 4293 43 202555 5.0 1 197703 4852 44 159796 5.0 1 156612 3184 45 453329 5.0 1 445550 7779 46 38215 5.0 1 36349 1866 47 201032 5.0 1 197434 3598 48 169680 5.0 1 166612 3068 49 203952 5.0 1 200125 3827 50 120637 5.0 1 117616 3021 51 145665 5.0 1 142275 3390 52 123054 5.0 1 120617 2437 53 180684 5.0 1 176429 4255 54 258874 5.0 1 252714 6160 55 322973 5.0 1 316754 6219 56 183280 5.0 1 179738 3542 57 149807 5.0 1 146986 2821 58 192892 5.0 1 189283 3609 59 194304 5.0 1 191017 3287 60 143274 5.0 1 140550 2724 61 132433 5.0 1 129808 2625 62 109366 5.0 1 107013 2353 63 170249 5.0 1 166484 3765 64 194641 5.0 1 190811 3830 65 201487 5.0 1 197327 4160 66 255760 5.0 1 250845 4915 67 217589 5.0 1 213440 4149 68 235836 5.0 1 231080 4756 69 246577 5.0 1 241387 5190 70 271012 5.0 1 265612 5400 71 393472 5.0 1 385928 7544 72 4243396 5.0 1 4218165 25231 73 834755 5.0 1 827481 7274 74 182416 5.0 1 180229 2187 75 74035 5.0 1 72725 1310 76 48967 5.0 1 47847 1120 77 50500 5.0 1 49387 1113 78 41173 5.0 1 40209 964 79 37506 5.0 1 36600 906 80 31703 5.0 1 30904 799 81 27904 5.0 1 27194 710 82 24980 5.0 1 24306 674 83 27330 5.0 1 26603 727 84 31648 5.0 1 30804 844 85 35461 5.0 1 34638 823 86 35257 5.0 1 34452 805 87 35427 5.0 1 34567 860 88 35041 5.0 1 34191 850 89 31687 5.0 1 30990 697 90 26319 5.0 1 25593 726 91 21452 5.0 1 20857 595 92 18055 5.0 1 17521 534 93 18279 5.0 1 17719 560 94 20868 5.0 1 20248 620 95 25493 5.0 1 24854 639 96 30556 5.0 1 29860 696 97 31023 5.0 1 30319 704 98 29547 5.0 1 28851 696 99 27291 5.0 1 26620 671 100 24215 5.0 1 23555 660 101 21225 5.0 1 20654 571 102 35197 5.0 1 34707 490 103 17220 5.0 1 16753 467 104 15509 5.0 1 15000 509 105 19433 5.0 1 18884 549 106 25150 5.0 1 24510 640 107 27422 5.0 1 26757 665 108 25314 5.0 1 24718 596 109 22005 5.0 1 21432 573 110 18929 5.0 1 18387 542 111 15129 5.0 1 14656 473 112 12063 5.0 1 11640 423 113 10585 5.0 1 10213 372 114 11785 5.0 1 11425 360 115 15067 5.0 1 14602 465 116 16848 5.0 1 16448 400 117 16323 5.0 1 15909 414 118 14611 5.0 1 14139 472 119 11623 5.0 1 11248 375 120 9061 5.0 1 8742 319 121 8552 5.0 1 8182 370 122 8236 5.0 1 7943 293 123 7738 5.0 1 7388 350 124 6343 5.0 1 6042 301 125 1532 5.0 1 1280 252 126 544 5.0 1 382 162 127 556 5.0 1 308 248 128 452 5.0 1 228 224 129 346 5.0 1 141 205 130 369 5.0 1 135 234 131 298 5.0 1 104 194 132 290 5.0 1 97 193 133 267 5.0 1 39 228 134 232 5.0 1 44 188 135 267 5.0 1 25 242 136 287 5.0 1 26 261 137 243 5.0 1 18 225 138 238 5.0 1 11 227 139 288 5.0 1 13 275 140 247 5.0 1 6 241 141 247 5.0 1 8 239 142 433 5.0 1 33 400 143 819 5.0 1 12 807 144 173 5.0 1 4 169 145 258 5.0 1 2 256 146 128 5.0 1 0 128 147 188 5.0 1 2 186 148 377 5.0 1 6 371 149 150 5.0 1 0 150 150 79 5.0 1 0 79 151 63 5.0 1 1 62 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_1_S3_L002_R1_001.fastq.gz ============================================= 83562471 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_01/Library_Geoduck_MG_1_S3_L002_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_1_S3_L002_R2_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_1_S3_L002_R2_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_1_S3_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 3003.16 s (36 us/read; 1.67 M reads/minute). === Summary === Total reads processed: 83,562,471 Reads with adapters: 38,976,691 (46.6%) Reads written (passing filters): 83,562,471 (100.0%) Total basepairs processed: 12,617,933,121 bp Quality-trimmed: 635,723,981 bp (5.0%) Total written (filtered): 10,961,342,640 bp (86.9%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 38976691 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 15.7% C: 35.1% G: 25.4% T: 23.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15985248 20890617.8 0 15985248 2 2627012 5222654.4 0 2627012 3 796767 1305663.6 0 796767 4 429050 326415.9 0 429050 5 317613 81604.0 0 317613 6 70847 20401.0 0 70847 7 172411 5100.2 0 172411 8 99936 1275.1 0 99936 9 243504 318.8 0 242492 1012 10 101789 79.7 1 86963 14826 11 199930 19.9 1 181681 18249 12 198461 5.0 1 180164 18297 13 306225 5.0 1 274776 31449 14 112339 5.0 1 100848 11491 15 304539 5.0 1 274391 30148 16 233147 5.0 1 208921 24226 17 101079 5.0 1 91745 9334 18 207715 5.0 1 186118 21597 19 193564 5.0 1 178163 15401 20 133698 5.0 1 121605 12093 21 127245 5.0 1 117135 10110 22 309141 5.0 1 283633 25508 23 101416 5.0 1 92303 9113 24 418239 5.0 1 387251 30988 25 208860 5.0 1 195437 13423 26 126211 5.0 1 116958 9253 27 160842 5.0 1 150939 9903 28 277558 5.0 1 262073 15485 29 142250 5.0 1 134318 7932 30 123649 5.0 1 116200 7449 31 183906 5.0 1 173414 10492 32 144806 5.0 1 137622 7184 33 128347 5.0 1 121334 7013 34 267701 5.0 1 255015 12686 35 220267 5.0 1 211967 8300 36 81538 5.0 1 76706 4832 37 203550 5.0 1 194248 9302 38 392847 5.0 1 376337 16510 39 178050 5.0 1 170010 8040 40 52141 5.0 1 49395 2746 41 110296 5.0 1 105771 4525 42 247384 5.0 1 240726 6658 43 125698 5.0 1 120762 4936 44 199058 5.0 1 193031 6027 45 235209 5.0 1 228574 6635 46 234181 5.0 1 227004 7177 47 171147 5.0 1 166343 4804 48 216342 5.0 1 210513 5829 49 122293 5.0 1 118792 3501 50 226118 5.0 1 220739 5379 51 44843 5.0 1 42790 2053 52 141470 5.0 1 137510 3960 53 175291 5.0 1 170146 5145 54 391152 5.0 1 382553 8599 55 94303 5.0 1 90753 3550 56 254503 5.0 1 246874 7629 57 363063 5.0 1 355127 7936 58 140400 5.0 1 137037 3363 59 110647 5.0 1 108053 2594 60 164297 5.0 1 160658 3639 61 121528 5.0 1 118184 3344 62 174843 5.0 1 170922 3921 63 265359 5.0 1 260233 5126 64 83357 5.0 1 81484 1873 65 129288 5.0 1 126903 2385 66 96911 5.0 1 94836 2075 67 281446 5.0 1 277124 4322 68 85202 5.0 1 83077 2125 69 140438 5.0 1 137910 2528 70 168623 5.0 1 165554 3069 71 99212 5.0 1 96947 2265 72 135577 5.0 1 132461 3116 73 163868 5.0 1 160423 3445 74 227202 5.0 1 222650 4552 75 390706 5.0 1 383560 7146 76 4064022 5.0 1 4037400 26622 77 786999 5.0 1 778958 8041 78 144903 5.0 1 142401 2502 79 45259 5.0 1 44001 1258 80 27900 5.0 1 26891 1009 81 22947 5.0 1 22158 789 82 17925 5.0 1 17189 736 83 18841 5.0 1 18067 774 84 24692 5.0 1 23696 996 85 29249 5.0 1 28377 872 86 36553 5.0 1 35389 1164 87 39381 5.0 1 38151 1230 88 37646 5.0 1 36681 965 89 32725 5.0 1 31842 883 90 26576 5.0 1 25736 840 91 21940 5.0 1 21129 811 92 18185 5.0 1 17508 677 93 17646 5.0 1 16897 749 94 20408 5.0 1 19729 679 95 25161 5.0 1 24357 804 96 29739 5.0 1 28847 892 97 31887 5.0 1 30920 967 98 28667 5.0 1 27763 904 99 25701 5.0 1 24816 885 100 22281 5.0 1 21396 885 101 17369 5.0 1 16757 612 102 14319 5.0 1 13630 689 103 13084 5.0 1 12383 701 104 14965 5.0 1 14139 826 105 20362 5.0 1 19289 1073 106 25963 5.0 1 24671 1292 107 27536 5.0 1 26653 883 108 25858 5.0 1 25025 833 109 22122 5.0 1 21347 775 110 18239 5.0 1 17598 641 111 14855 5.0 1 14317 538 112 11995 5.0 1 11490 505 113 9967 5.0 1 9516 451 114 10872 5.0 1 10404 468 115 14247 5.0 1 13763 484 116 16257 5.0 1 15728 529 117 15490 5.0 1 14967 523 118 13882 5.0 1 13361 521 119 11034 5.0 1 10595 439 120 8447 5.0 1 8037 410 121 8015 5.0 1 7609 406 122 7693 5.0 1 7318 375 123 7087 5.0 1 6742 345 124 5915 5.0 1 5619 296 125 1421 5.0 1 1170 251 126 621 5.0 1 368 253 127 534 5.0 1 289 245 128 419 5.0 1 204 215 129 364 5.0 1 123 241 130 438 5.0 1 154 284 131 350 5.0 1 101 249 132 349 5.0 1 99 250 133 276 5.0 1 50 226 134 262 5.0 1 45 217 135 246 5.0 1 34 212 136 270 5.0 1 50 220 137 266 5.0 1 32 234 138 281 5.0 1 19 262 139 289 5.0 1 26 263 140 234 5.0 1 13 221 141 273 5.0 1 18 255 142 424 5.0 1 40 384 143 598 5.0 1 25 573 144 191 5.0 1 7 184 145 192 5.0 1 7 185 146 103 5.0 1 4 99 147 204 5.0 1 7 197 148 303 5.0 1 13 290 149 161 5.0 1 1 160 150 87 5.0 1 1 86 151 36 5.0 1 0 36 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_1_S3_L002_R2_001.fastq.gz ============================================= 83562471 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_trimmed.fq.gz and Library_Geoduck_MG_1_S3_L002_R2_001_trimmed.fq.gz file_1: Library_Geoduck_MG_1_S3_L002_R1_001_trimmed.fq.gz, file_2: Library_Geoduck_MG_1_S3_L002_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_1_S3_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_1_S3_L002_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Total number of sequences analysed: 83562471 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 311720 (0.37%) >>> Now running FastQC on the validated data Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_1_S3_L002_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_1_S3_L002_R2_001_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_1_S3_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_1_S3_L002_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/Library_Geoduck_MG_2_S4_L002_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_2_S4_L002_R1_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_2_S4_L002_R1_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_2_S4_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2784.93 s (34 us/read; 1.78 M reads/minute). === Summary === Total reads processed: 82,486,730 Reads with adapters: 38,274,870 (46.4%) Reads written (passing filters): 82,486,730 (100.0%) Total basepairs processed: 12,455,496,230 bp Quality-trimmed: 264,631,747 bp (2.1%) Total written (filtered): 11,010,453,787 bp (88.4%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 38274870 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 17.1% C: 33.2% G: 23.1% T: 26.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11725056 20621682.5 0 11725056 2 3280128 5155420.6 0 3280128 3 963449 1288855.2 0 963449 4 401452 322213.8 0 401452 5 261325 80553.4 0 261325 6 158333 20138.4 0 158333 7 157607 5034.6 0 157607 8 171108 1258.6 0 171108 9 205103 314.7 0 203751 1352 10 137969 78.7 1 132074 5895 11 180155 19.7 1 173508 6647 12 213900 4.9 1 205595 8305 13 238400 4.9 1 229890 8510 14 195370 4.9 1 188715 6655 15 252163 4.9 1 242863 9300 16 216508 4.9 1 207634 8874 17 205638 4.9 1 199278 6360 18 191036 4.9 1 184900 6136 19 120447 4.9 1 116812 3635 20 166610 4.9 1 159936 6674 21 207880 4.9 1 198398 9482 22 249693 4.9 1 241559 8134 23 173429 4.9 1 167860 5569 24 206132 4.9 1 200823 5309 25 229667 4.9 1 223599 6068 26 247752 4.9 1 240522 7230 27 291878 4.9 1 284067 7811 28 130828 4.9 1 126695 4133 29 199559 4.9 1 193296 6263 30 173097 4.9 1 168864 4233 31 114253 4.9 1 110610 3643 32 207034 4.9 1 202218 4816 33 154640 4.9 1 150635 4005 34 237200 4.9 1 231064 6136 35 235068 4.9 1 229848 5220 36 212699 4.9 1 207829 4870 37 234889 4.9 1 228445 6444 38 224954 4.9 1 219263 5691 39 203397 4.9 1 197551 5846 40 193552 4.9 1 187411 6141 41 127103 4.9 1 123662 3441 42 200888 4.9 1 196045 4843 43 239476 4.9 1 233735 5741 44 171744 4.9 1 168191 3553 45 466702 4.9 1 458945 7757 46 51379 4.9 1 49260 2119 47 197247 4.9 1 194032 3215 48 193514 4.9 1 190060 3454 49 209464 4.9 1 205739 3725 50 136862 4.9 1 133560 3302 51 144293 4.9 1 140927 3366 52 137842 4.9 1 135078 2764 53 195711 4.9 1 191138 4573 54 261223 4.9 1 255142 6081 55 347395 4.9 1 340803 6592 56 207843 4.9 1 204044 3799 57 154897 4.9 1 152025 2872 58 215278 4.9 1 211116 4162 59 212556 4.9 1 208846 3710 60 154607 4.9 1 151744 2863 61 140087 4.9 1 137295 2792 62 125300 4.9 1 122588 2712 63 182736 4.9 1 178552 4184 64 220852 4.9 1 216486 4366 65 220283 4.9 1 215796 4487 66 285864 4.9 1 280390 5474 67 250173 4.9 1 245361 4812 68 265510 4.9 1 260221 5289 69 286648 4.9 1 280734 5914 70 316323 4.9 1 309924 6399 71 473200 4.9 1 464391 8809 72 5163834 4.9 1 5134507 29327 73 1022434 4.9 1 1013705 8729 74 223373 4.9 1 220799 2574 75 86601 4.9 1 85162 1439 76 55595 4.9 1 54368 1227 77 56037 4.9 1 54890 1147 78 47598 4.9 1 46535 1063 79 43401 4.9 1 42425 976 80 36923 4.9 1 35980 943 81 32142 4.9 1 31364 778 82 29493 4.9 1 28714 779 83 32336 4.9 1 31590 746 84 35856 4.9 1 34989 867 85 41646 4.9 1 40715 931 86 43060 4.9 1 42063 997 87 42339 4.9 1 41325 1014 88 41248 4.9 1 40274 974 89 37918 4.9 1 37105 813 90 31605 4.9 1 30831 774 91 25082 4.9 1 24369 713 92 21938 4.9 1 21315 623 93 21656 4.9 1 21029 627 94 25159 4.9 1 24383 776 95 30605 4.9 1 29842 763 96 37429 4.9 1 36542 887 97 37394 4.9 1 36619 775 98 35706 4.9 1 34853 853 99 32370 4.9 1 31587 783 100 28818 4.9 1 28117 701 101 24745 4.9 1 24135 610 102 35942 4.9 1 35410 532 103 19684 4.9 1 19182 502 104 19216 4.9 1 18660 556 105 25362 4.9 1 24645 717 106 31783 4.9 1 30989 794 107 35654 4.9 1 34844 810 108 33272 4.9 1 32430 842 109 28906 4.9 1 28203 703 110 24876 4.9 1 24215 661 111 20282 4.9 1 19778 504 112 16027 4.9 1 15519 508 113 13581 4.9 1 13118 463 114 14971 4.9 1 14504 467 115 19661 4.9 1 19171 490 116 22732 4.9 1 22212 520 117 22251 4.9 1 21743 508 118 20389 4.9 1 19897 492 119 16406 4.9 1 16007 399 120 13120 4.9 1 12695 425 121 12140 4.9 1 11700 440 122 11639 4.9 1 11226 413 123 10704 4.9 1 10326 378 124 8916 4.9 1 8602 314 125 2129 4.9 1 1926 203 126 867 4.9 1 655 212 127 628 4.9 1 424 204 128 552 4.9 1 287 265 129 366 4.9 1 148 218 130 413 4.9 1 181 232 131 359 4.9 1 102 257 132 352 4.9 1 135 217 133 269 4.9 1 43 226 134 299 4.9 1 40 259 135 273 4.9 1 27 246 136 270 4.9 1 27 243 137 220 4.9 1 13 207 138 291 4.9 1 9 282 139 261 4.9 1 4 257 140 217 4.9 1 9 208 141 226 4.9 1 9 217 142 408 4.9 1 29 379 143 858 4.9 1 14 844 144 169 4.9 1 2 167 145 243 4.9 1 4 239 146 75 4.9 1 0 75 147 168 4.9 1 1 167 148 429 4.9 1 6 423 149 155 4.9 1 0 155 150 106 4.9 1 2 104 151 54 4.9 1 0 54 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_2_S4_L002_R1_001.fastq.gz ============================================= 82486730 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_01/Library_Geoduck_MG_2_S4_L002_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_2_S4_L002_R2_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_2_S4_L002_R2_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_2_S4_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2891.36 s (35 us/read; 1.71 M reads/minute). === Summary === Total reads processed: 82,486,730 Reads with adapters: 38,987,648 (47.3%) Reads written (passing filters): 82,486,730 (100.0%) Total basepairs processed: 12,455,496,230 bp Quality-trimmed: 633,017,461 bp (5.1%) Total written (filtered): 10,655,835,190 bp (85.6%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 38987648 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.5% C: 34.5% G: 23.1% T: 25.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13910710 20621682.5 0 13910710 2 2695279 5155420.6 0 2695279 3 770577 1288855.2 0 770577 4 390113 322213.8 0 390113 5 299924 80553.4 0 299924 6 73228 20138.4 0 73228 7 160155 5034.6 0 160155 8 107901 1258.6 0 107901 9 247142 314.7 0 246070 1072 10 120703 78.7 1 104350 16353 11 175993 19.7 1 159643 16350 12 206721 4.9 1 187703 19018 13 298053 4.9 1 267467 30586 14 125653 4.9 1 112694 12959 15 325134 4.9 1 292269 32865 16 248621 4.9 1 222514 26107 17 95064 4.9 1 85766 9298 18 204755 4.9 1 183993 20762 19 201420 4.9 1 184892 16528 20 131627 4.9 1 119500 12127 21 125858 4.9 1 115771 10087 22 316712 4.9 1 290900 25812 23 109276 4.9 1 99224 10052 24 418959 4.9 1 388236 30723 25 213351 4.9 1 199865 13486 26 120373 4.9 1 111536 8837 27 162959 4.9 1 152944 10015 28 296398 4.9 1 279878 16520 29 175517 4.9 1 166199 9318 30 80658 4.9 1 75275 5383 31 210048 4.9 1 199508 10540 32 125298 4.9 1 119761 5537 33 71195 4.9 1 66812 4383 34 363227 4.9 1 347637 15590 35 36608 4.9 1 32874 3734 36 215646 4.9 1 206249 9397 37 338986 4.9 1 322990 15996 38 96014 4.9 1 90530 5484 39 279139 4.9 1 269049 10090 40 52571 4.9 1 48553 4018 41 230935 4.9 1 219825 11110 42 238023 4.9 1 228797 9226 43 258892 4.9 1 250155 8737 44 120071 4.9 1 115118 4953 45 305797 4.9 1 296950 8847 46 226089 4.9 1 218256 7833 47 192737 4.9 1 187055 5682 48 223263 4.9 1 216787 6476 49 148310 4.9 1 144121 4189 50 264029 4.9 1 257290 6739 51 44237 4.9 1 42021 2216 52 168160 4.9 1 163244 4916 53 186692 4.9 1 180913 5779 54 409214 4.9 1 400223 8991 55 133371 4.9 1 128894 4477 56 274187 4.9 1 265261 8926 57 353998 4.9 1 346144 7854 58 143566 4.9 1 140034 3532 59 146730 4.9 1 143317 3413 60 147040 4.9 1 143374 3666 61 128603 4.9 1 124891 3712 62 222973 4.9 1 218043 4930 63 275007 4.9 1 269512 5495 64 103158 4.9 1 100902 2256 65 133161 4.9 1 130669 2492 66 109562 4.9 1 107151 2411 67 328924 4.9 1 323700 5224 68 70562 4.9 1 68568 1994 69 156552 4.9 1 153358 3194 70 207285 4.9 1 203518 3767 71 98837 4.9 1 96597 2240 72 155917 4.9 1 152323 3594 73 191980 4.9 1 188075 3905 74 289460 4.9 1 284064 5396 75 518213 4.9 1 509442 8771 76 4949229 4.9 1 4918275 30954 77 912962 4.9 1 903824 9138 78 159126 4.9 1 156517 2609 79 51275 4.9 1 49892 1383 80 31376 4.9 1 30308 1068 81 26207 4.9 1 25352 855 82 20721 4.9 1 19819 902 83 22063 4.9 1 21219 844 84 29535 4.9 1 28484 1051 85 35047 4.9 1 34033 1014 86 42921 4.9 1 41648 1273 87 45531 4.9 1 44334 1197 88 43008 4.9 1 41926 1082 89 36863 4.9 1 35874 989 90 30007 4.9 1 29099 908 91 24226 4.9 1 23410 816 92 20240 4.9 1 19484 756 93 20103 4.9 1 19351 752 94 23388 4.9 1 22651 737 95 29024 4.9 1 28203 821 96 33995 4.9 1 33024 971 97 36351 4.9 1 35363 988 98 33941 4.9 1 32966 975 99 30349 4.9 1 29392 957 100 27084 4.9 1 26122 962 101 20717 4.9 1 19967 750 102 17063 4.9 1 16392 671 103 15358 4.9 1 14644 714 104 17857 4.9 1 17025 832 105 25376 4.9 1 24303 1073 106 32854 4.9 1 31455 1399 107 35690 4.9 1 34681 1009 108 33331 4.9 1 32446 885 109 28674 4.9 1 27886 788 110 23983 4.9 1 23268 715 111 19187 4.9 1 18599 588 112 15553 4.9 1 14990 563 113 12743 4.9 1 12222 521 114 13806 4.9 1 13269 537 115 18519 4.9 1 17949 570 116 21697 4.9 1 21071 626 117 20834 4.9 1 20249 585 118 19233 4.9 1 18681 552 119 15360 4.9 1 14867 493 120 12174 4.9 1 11732 442 121 11091 4.9 1 10673 418 122 10559 4.9 1 10131 428 123 9844 4.9 1 9475 369 124 8126 4.9 1 7815 311 125 1999 4.9 1 1754 245 126 866 4.9 1 617 249 127 635 4.9 1 373 262 128 493 4.9 1 277 216 129 371 4.9 1 140 231 130 392 4.9 1 177 215 131 317 4.9 1 103 214 132 389 4.9 1 141 248 133 295 4.9 1 59 236 134 284 4.9 1 52 232 135 247 4.9 1 33 214 136 256 4.9 1 37 219 137 234 4.9 1 20 214 138 292 4.9 1 20 272 139 271 4.9 1 9 262 140 256 4.9 1 17 239 141 302 4.9 1 23 279 142 478 4.9 1 27 451 143 632 4.9 1 27 605 144 185 4.9 1 4 181 145 208 4.9 1 4 204 146 142 4.9 1 2 140 147 218 4.9 1 3 215 148 311 4.9 1 8 303 149 159 4.9 1 1 158 150 66 4.9 1 0 66 151 48 4.9 1 0 48 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_2_S4_L002_R2_001.fastq.gz ============================================= 82486730 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_trimmed.fq.gz and Library_Geoduck_MG_2_S4_L002_R2_001_trimmed.fq.gz file_1: Library_Geoduck_MG_2_S4_L002_R1_001_trimmed.fq.gz, file_2: Library_Geoduck_MG_2_S4_L002_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_2_S4_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_2_S4_L002_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Total number of sequences analysed: 82486730 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 280399 (0.34%) >>> Now running FastQC on the validated data Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_2_S4_L002_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_2_S4_L002_R2_001_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_2_S4_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_2_S4_L002_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/Library_Geoduck_MG_3_S1_L002_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_3_S1_L002_R1_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_3_S1_L002_R1_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_3_S1_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2696.49 s (30 us/read; 1.98 M reads/minute). === Summary === Total reads processed: 88,941,440 Reads with adapters: 50,629,031 (56.9%) Reads written (passing filters): 88,941,440 (100.0%) Total basepairs processed: 13,430,157,440 bp Quality-trimmed: 516,821,182 bp (3.8%) Total written (filtered): 10,822,883,249 bp (80.6%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 50629031 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 15.3% C: 35.8% G: 22.4% T: 26.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10740819 22235360.0 0 10740819 2 2883216 5558840.0 0 2883216 3 876631 1389710.0 0 876631 4 428102 347427.5 0 428102 5 300091 86856.9 0 300091 6 162824 21714.2 0 162824 7 174352 5428.6 0 174352 8 192916 1357.1 0 192916 9 249121 339.3 0 247908 1213 10 168134 84.8 1 160539 7595 11 230929 21.2 1 221387 9542 12 267207 5.3 1 255413 11794 13 312130 5.3 1 299434 12696 14 213034 5.3 1 204426 8608 15 302846 5.3 1 289994 12852 16 240887 5.3 1 228847 12040 17 234852 5.3 1 226509 8343 18 218700 5.3 1 210438 8262 19 140320 5.3 1 135591 4729 20 211892 5.3 1 202001 9891 21 305234 5.3 1 288808 16426 22 307747 5.3 1 296537 11210 23 233822 5.3 1 225938 7884 24 240902 5.3 1 234134 6768 25 279973 5.3 1 271379 8594 26 300986 5.3 1 290509 10477 27 363401 5.3 1 351076 12325 28 147245 5.3 1 141480 5765 29 264658 5.3 1 254130 10528 30 228810 5.3 1 222005 6805 31 171549 5.3 1 165588 5961 32 306117 5.3 1 298452 7665 33 179650 5.3 1 174397 5253 34 311089 5.3 1 301891 9198 35 463030 5.3 1 449805 13225 36 166627 5.3 1 162418 4209 37 374065 5.3 1 364921 9144 38 150371 5.3 1 146388 3983 39 217970 5.3 1 211431 6539 40 268012 5.3 1 259126 8886 41 167180 5.3 1 161973 5207 42 326977 5.3 1 317552 9425 43 489606 5.3 1 475667 13939 44 125130 5.3 1 121009 4121 45 601345 5.3 1 589060 12285 46 51836 5.3 1 48806 3030 47 288279 5.3 1 282462 5817 48 232041 5.3 1 227055 4986 49 288602 5.3 1 282315 6287 50 180243 5.3 1 175031 5212 51 232991 5.3 1 226936 6055 52 193530 5.3 1 189241 4289 53 298785 5.3 1 290922 7863 54 431689 5.3 1 420510 11179 55 488841 5.3 1 478312 10529 56 300200 5.3 1 294018 6182 57 223007 5.3 1 218284 4723 58 305256 5.3 1 298834 6422 59 300700 5.3 1 294879 5821 60 223286 5.3 1 218347 4939 61 230740 5.3 1 225737 5003 62 187265 5.3 1 183011 4254 63 300940 5.3 1 293573 7367 64 358761 5.3 1 350998 7763 65 373143 5.3 1 364738 8405 66 453347 5.3 1 443705 9642 67 398605 5.3 1 390327 8278 68 412659 5.3 1 403616 9043 69 469462 5.3 1 458745 10717 70 550178 5.3 1 537905 12273 71 881154 5.3 1 862584 18570 72 10679297 5.3 1 10616312 62985 73 2123436 5.3 1 2104474 18962 74 461073 5.3 1 455657 5416 75 166170 5.3 1 163243 2927 76 100997 5.3 1 98714 2283 77 96795 5.3 1 94701 2094 78 80577 5.3 1 78645 1932 79 71982 5.3 1 70353 1629 80 63975 5.3 1 62415 1560 81 59274 5.3 1 57741 1533 82 57183 5.3 1 55813 1370 83 64180 5.3 1 62743 1437 84 71948 5.3 1 70284 1664 85 80395 5.3 1 78668 1727 86 81442 5.3 1 79596 1846 87 80411 5.3 1 78583 1828 88 78453 5.3 1 76670 1783 89 71272 5.3 1 69682 1590 90 61015 5.3 1 59629 1386 91 50213 5.3 1 48967 1246 92 43715 5.3 1 42560 1155 93 45406 5.3 1 44261 1145 94 53143 5.3 1 51776 1367 95 64410 5.3 1 63005 1405 96 76734 5.3 1 75032 1702 97 78517 5.3 1 76762 1755 98 75342 5.3 1 73691 1651 99 70231 5.3 1 68727 1504 100 64101 5.3 1 62713 1388 101 56094 5.3 1 54918 1176 102 84263 5.3 1 83207 1056 103 45976 5.3 1 45014 962 104 44715 5.3 1 43553 1162 105 56702 5.3 1 55411 1291 106 72139 5.3 1 70616 1523 107 80442 5.3 1 78860 1582 108 77200 5.3 1 75509 1691 109 70196 5.3 1 68755 1441 110 62426 5.3 1 61045 1381 111 52310 5.3 1 51137 1173 112 42602 5.3 1 41591 1011 113 36195 5.3 1 35299 896 114 38194 5.3 1 37318 876 115 46041 5.3 1 45040 1001 116 51763 5.3 1 50730 1033 117 51633 5.3 1 50621 1012 118 50847 5.3 1 49849 998 119 43544 5.3 1 42641 903 120 38342 5.3 1 37473 869 121 36945 5.3 1 36095 850 122 36026 5.3 1 35193 833 123 35046 5.3 1 34263 783 124 28685 5.3 1 28058 627 125 8381 5.3 1 8068 313 126 2841 5.3 1 2563 278 127 1824 5.3 1 1566 258 128 1320 5.3 1 1033 287 129 792 5.3 1 541 251 130 748 5.3 1 439 309 131 565 5.3 1 300 265 132 588 5.3 1 368 220 133 377 5.3 1 137 240 134 389 5.3 1 106 283 135 296 5.3 1 72 224 136 336 5.3 1 71 265 137 214 5.3 1 30 184 138 306 5.3 1 9 297 139 280 5.3 1 9 271 140 252 5.3 1 14 238 141 337 5.3 1 18 319 142 608 5.3 1 36 572 143 933 5.3 1 21 912 144 177 5.3 1 4 173 145 249 5.3 1 10 239 146 127 5.3 1 8 119 147 221 5.3 1 3 218 148 484 5.3 1 3 481 149 184 5.3 1 7 177 150 69 5.3 1 0 69 151 81 5.3 1 0 81 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_3_S1_L002_R1_001.fastq.gz ============================================= 88941440 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_01/Library_Geoduck_MG_3_S1_L002_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_3_S1_L002_R2_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_3_S1_L002_R2_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_3_S1_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2762.49 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 88,941,440 Reads with adapters: 50,557,832 (56.8%) Reads written (passing filters): 88,941,440 (100.0%) Total basepairs processed: 13,430,157,440 bp Quality-trimmed: 817,901,180 bp (6.1%) Total written (filtered): 10,526,515,424 bp (78.4%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 50557832 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 15.0% C: 36.6% G: 22.3% T: 26.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12102841 22235360.0 0 12102841 2 2391957 5558840.0 0 2391957 3 704014 1389710.0 0 704014 4 455591 347427.5 0 455591 5 345251 86856.9 0 345251 6 81488 21714.2 0 81488 7 180140 5428.6 0 180140 8 123502 1357.1 0 123502 9 310834 339.3 0 309842 992 10 114893 84.8 1 97438 17455 11 281746 21.2 1 255544 26202 12 245722 5.3 1 222682 23040 13 356413 5.3 1 320163 36250 14 135736 5.3 1 120635 15101 15 391698 5.3 1 351844 39854 16 272643 5.3 1 241119 31524 17 129881 5.3 1 116556 13325 18 239054 5.3 1 212999 26055 19 271998 5.3 1 247814 24184 20 168031 5.3 1 151910 16121 21 188448 5.3 1 173052 15396 22 395187 5.3 1 361084 34103 23 155232 5.3 1 141379 13853 24 533386 5.3 1 492217 41169 25 290378 5.3 1 270257 20121 26 153242 5.3 1 140952 12290 27 231867 5.3 1 216439 15428 28 390044 5.3 1 366683 23361 29 225393 5.3 1 212347 13046 30 143974 5.3 1 134430 9544 31 296372 5.3 1 279613 16759 32 235990 5.3 1 224928 11062 33 321040 5.3 1 307150 13890 34 143159 5.3 1 135599 7560 35 277226 5.3 1 265485 11741 36 226287 5.3 1 216569 9718 37 223010 5.3 1 213816 9194 38 359798 5.3 1 346337 13461 39 112910 5.3 1 105841 7069 40 355835 5.3 1 343458 12377 41 161130 5.3 1 153974 7156 42 261534 5.3 1 253881 7653 43 234303 5.3 1 226171 8132 44 244133 5.3 1 236223 7910 45 422777 5.3 1 410467 12310 46 296231 5.3 1 285560 10671 47 264373 5.3 1 256775 7598 48 274577 5.3 1 266398 8179 49 212398 5.3 1 206326 6072 50 341689 5.3 1 332576 9113 51 88988 5.3 1 85199 3789 52 237057 5.3 1 229743 7314 53 303740 5.3 1 294502 9238 54 624564 5.3 1 610862 13702 55 175759 5.3 1 169184 6575 56 407889 5.3 1 395556 12333 57 528052 5.3 1 516522 11530 58 230360 5.3 1 224543 5817 59 183603 5.3 1 179115 4488 60 265039 5.3 1 258888 6151 61 211479 5.3 1 206057 5422 62 312441 5.3 1 305492 6949 63 441351 5.3 1 433069 8282 64 163490 5.3 1 159931 3559 65 201579 5.3 1 197463 4116 66 193377 5.3 1 188529 4848 67 487211 5.3 1 477782 9429 68 125512 5.3 1 121892 3620 69 251167 5.3 1 245913 5254 70 313636 5.3 1 307800 5836 71 170362 5.3 1 166502 3860 72 267450 5.3 1 261407 6043 73 344621 5.3 1 337473 7148 74 518975 5.3 1 508825 10150 75 898294 5.3 1 880531 17763 76 10607721 5.3 1 10542674 65047 77 1892842 5.3 1 1873852 18990 78 325694 5.3 1 320679 5015 79 93750 5.3 1 91417 2333 80 53885 5.3 1 52053 1832 81 46978 5.3 1 45620 1358 82 38534 5.3 1 37196 1338 83 42265 5.3 1 40841 1424 84 58325 5.3 1 56350 1975 85 67543 5.3 1 65782 1761 86 83063 5.3 1 80837 2226 87 89502 5.3 1 87180 2322 88 86122 5.3 1 84194 1928 89 73197 5.3 1 71564 1633 90 61360 5.3 1 59707 1653 91 50131 5.3 1 48824 1307 92 43514 5.3 1 42267 1247 93 43500 5.3 1 42107 1393 94 50322 5.3 1 49081 1241 95 62030 5.3 1 60591 1439 96 72189 5.3 1 70524 1665 97 77922 5.3 1 76034 1888 98 73215 5.3 1 71294 1921 99 65787 5.3 1 63986 1801 100 58494 5.3 1 56792 1702 101 47077 5.3 1 45781 1296 102 38926 5.3 1 37661 1265 103 35991 5.3 1 34764 1227 104 41487 5.3 1 39846 1641 105 55113 5.3 1 53213 1900 106 70052 5.3 1 67538 2514 107 75976 5.3 1 74127 1849 108 73714 5.3 1 72064 1650 109 66456 5.3 1 65022 1434 110 57312 5.3 1 56062 1250 111 47748 5.3 1 46657 1091 112 38827 5.3 1 37888 939 113 32164 5.3 1 31369 795 114 33636 5.3 1 32845 791 115 41023 5.3 1 40089 934 116 47155 5.3 1 46125 1030 117 47742 5.3 1 46704 1038 118 46422 5.3 1 45435 987 119 40578 5.3 1 39739 839 120 35223 5.3 1 34440 783 121 33922 5.3 1 33156 766 122 32911 5.3 1 32153 758 123 31413 5.3 1 30688 725 124 26227 5.3 1 25686 541 125 7658 5.3 1 7294 364 126 2683 5.3 1 2432 251 127 1777 5.3 1 1488 289 128 1301 5.3 1 978 323 129 724 5.3 1 469 255 130 708 5.3 1 427 281 131 523 5.3 1 272 251 132 607 5.3 1 342 265 133 389 5.3 1 109 280 134 362 5.3 1 114 248 135 361 5.3 1 69 292 136 290 5.3 1 74 216 137 269 5.3 1 36 233 138 306 5.3 1 20 286 139 249 5.3 1 11 238 140 304 5.3 1 17 287 141 390 5.3 1 25 365 142 564 5.3 1 67 497 143 717 5.3 1 37 680 144 174 5.3 1 5 169 145 201 5.3 1 4 197 146 128 5.3 1 0 128 147 211 5.3 1 6 205 148 324 5.3 1 9 315 149 161 5.3 1 3 158 150 80 5.3 1 3 77 151 39 5.3 1 1 38 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_3_S1_L002_R2_001.fastq.gz ============================================= 88941440 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_trimmed.fq.gz and Library_Geoduck_MG_3_S1_L002_R2_001_trimmed.fq.gz file_1: Library_Geoduck_MG_3_S1_L002_R1_001_trimmed.fq.gz, file_2: Library_Geoduck_MG_3_S1_L002_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_3_S1_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_3_S1_L002_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Total number of sequences analysed: 88941440 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 294236 (0.33%) >>> Now running FastQC on the validated data Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_3_S1_L002_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_3_S1_L002_R2_001_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_3_S1_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_3_S1_L002_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/Library_Geoduck_MG_5_S6_L002_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_5_S6_L002_R1_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_5_S6_L002_R1_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_5_S6_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2451.22 s (34 us/read; 1.77 M reads/minute). === Summary === Total reads processed: 72,142,506 Reads with adapters: 31,733,399 (44.0%) Reads written (passing filters): 72,142,506 (100.0%) Total basepairs processed: 10,893,518,406 bp Quality-trimmed: 182,199,295 bp (1.7%) Total written (filtered): 9,783,609,794 bp (89.8%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 31733399 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 17.6% C: 32.3% G: 22.3% T: 27.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9833737 18035626.5 0 9833737 2 2999659 4508906.6 0 2999659 3 844695 1127226.7 0 844695 4 358458 281806.7 0 358458 5 233858 70451.7 0 233858 6 138002 17612.9 0 138002 7 141418 4403.2 0 141418 8 150631 1100.8 0 150631 9 177638 275.2 0 176450 1188 10 126523 68.8 1 121480 5043 11 152994 17.2 1 147475 5519 12 190226 4.3 1 182986 7240 13 206023 4.3 1 199191 6832 14 171362 4.3 1 165850 5512 15 217361 4.3 1 210051 7310 16 189085 4.3 1 181932 7153 17 185794 4.3 1 180385 5409 18 160865 4.3 1 155933 4932 19 108848 4.3 1 105686 3162 20 146247 4.3 1 140767 5480 21 194372 4.3 1 186033 8339 22 192197 4.3 1 186412 5785 23 162000 4.3 1 157253 4747 24 169958 4.3 1 165887 4071 25 198714 4.3 1 193609 5105 26 214676 4.3 1 208712 5964 27 260822 4.3 1 254664 6158 28 100855 4.3 1 97860 2995 29 166673 4.3 1 162076 4597 30 134446 4.3 1 131766 2680 31 117193 4.3 1 114120 3073 32 162194 4.3 1 158800 3394 33 150086 4.3 1 146800 3286 34 169907 4.3 1 166442 3465 35 210457 4.3 1 204885 5572 36 246020 4.3 1 239382 6638 37 182412 4.3 1 179066 3346 38 130670 4.3 1 127768 2902 39 155875 4.3 1 151782 4093 40 169586 4.3 1 164900 4686 41 132785 4.3 1 128879 3906 42 146511 4.3 1 142064 4447 43 284956 4.3 1 277416 7540 44 99308 4.3 1 96832 2476 45 394462 4.3 1 387839 6623 46 36755 4.3 1 35031 1724 47 174118 4.3 1 171161 2957 48 167799 4.3 1 164855 2944 49 167893 4.3 1 164870 3023 50 123538 4.3 1 120717 2821 51 120305 4.3 1 117576 2729 52 112322 4.3 1 110111 2211 53 160808 4.3 1 157183 3625 54 218609 4.3 1 213394 5215 55 292218 4.3 1 286594 5624 56 164816 4.3 1 161751 3065 57 138962 4.3 1 136362 2600 58 178897 4.3 1 175592 3305 59 172817 4.3 1 169923 2894 60 131124 4.3 1 128758 2366 61 115464 4.3 1 113289 2175 62 98925 4.3 1 96912 2013 63 150849 4.3 1 147380 3469 64 175307 4.3 1 171833 3474 65 180494 4.3 1 176840 3654 66 228477 4.3 1 224252 4225 67 202051 4.3 1 198354 3697 68 213709 4.3 1 209582 4127 69 228216 4.3 1 223672 4544 70 246543 4.3 1 241730 4813 71 362823 4.3 1 356208 6615 72 3867212 4.3 1 3845188 22024 73 761150 4.3 1 754576 6574 74 166715 4.3 1 164768 1947 75 64897 4.3 1 63809 1088 76 43443 4.3 1 42471 972 77 43249 4.3 1 42250 999 78 36989 4.3 1 36133 856 79 33052 4.3 1 32237 815 80 29008 4.3 1 28319 689 81 25256 4.3 1 24612 644 82 22598 4.3 1 22015 583 83 24044 4.3 1 23447 597 84 26648 4.3 1 25910 738 85 30827 4.3 1 30159 668 86 31886 4.3 1 31149 737 87 32642 4.3 1 31852 790 88 31909 4.3 1 31205 704 89 29127 4.3 1 28420 707 90 23594 4.3 1 22921 673 91 18651 4.3 1 18107 544 92 15502 4.3 1 15050 452 93 15637 4.3 1 15166 471 94 18011 4.3 1 17438 573 95 23082 4.3 1 22488 594 96 27499 4.3 1 26854 645 97 28133 4.3 1 27449 684 98 26576 4.3 1 25950 626 99 23562 4.3 1 22979 583 100 20601 4.3 1 20056 545 101 17318 4.3 1 16846 472 102 21484 4.3 1 21036 448 103 13333 4.3 1 12948 385 104 13506 4.3 1 13054 452 105 18165 4.3 1 17678 487 106 23200 4.3 1 22574 626 107 25746 4.3 1 25157 589 108 23846 4.3 1 23219 627 109 20651 4.3 1 20039 612 110 16853 4.3 1 16352 501 111 13534 4.3 1 13127 407 112 10621 4.3 1 10266 355 113 9008 4.3 1 8730 278 114 10237 4.3 1 9870 367 115 13508 4.3 1 13106 402 116 15797 4.3 1 15367 430 117 15162 4.3 1 14754 408 118 13440 4.3 1 13070 370 119 10422 4.3 1 10080 342 120 8152 4.3 1 7842 310 121 7333 4.3 1 7020 313 122 6850 4.3 1 6578 272 123 6332 4.3 1 6053 279 124 5153 4.3 1 4902 251 125 1214 4.3 1 1033 181 126 443 4.3 1 278 165 127 367 4.3 1 185 182 128 287 4.3 1 113 174 129 249 4.3 1 61 188 130 297 4.3 1 62 235 131 250 4.3 1 45 205 132 262 4.3 1 47 215 133 212 4.3 1 29 183 134 254 4.3 1 20 234 135 206 4.3 1 7 199 136 189 4.3 1 8 181 137 197 4.3 1 4 193 138 230 4.3 1 6 224 139 207 4.3 1 6 201 140 198 4.3 1 4 194 141 231 4.3 1 7 224 142 343 4.3 1 14 329 143 812 4.3 1 14 798 144 190 4.3 1 1 189 145 207 4.3 1 1 206 146 114 4.3 1 0 114 147 168 4.3 1 0 168 148 401 4.3 1 2 399 149 177 4.3 1 1 176 150 97 4.3 1 0 97 151 48 4.3 1 3 45 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_5_S6_L002_R1_001.fastq.gz ============================================= 72142506 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_01/Library_Geoduck_MG_5_S6_L002_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_5_S6_L002_R2_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_5_S6_L002_R2_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_5_S6_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2548.95 s (35 us/read; 1.70 M reads/minute). === Summary === Total reads processed: 72,142,506 Reads with adapters: 32,074,902 (44.5%) Reads written (passing filters): 72,142,506 (100.0%) Total basepairs processed: 10,893,518,406 bp Quality-trimmed: 470,539,858 bp (4.3%) Total written (filtered): 9,503,775,392 bp (87.2%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 32074902 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 17.1% C: 33.3% G: 22.4% T: 27.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11307470 18035626.5 0 11307470 2 2484973 4508906.6 0 2484973 3 637659 1127226.7 0 637659 4 409601 281806.7 0 409601 5 264543 70451.7 0 264543 6 71888 17612.9 0 71888 7 145923 4403.2 0 145923 8 97639 1100.8 0 97639 9 226293 275.2 0 225304 989 10 89599 68.8 1 77343 12256 11 182727 17.2 1 167164 15563 12 179100 4.3 1 164096 15004 13 261706 4.3 1 237527 24179 14 105947 4.3 1 95776 10171 15 265605 4.3 1 241818 23787 16 210655 4.3 1 190587 20068 17 101016 4.3 1 92642 8374 18 171663 4.3 1 155176 16487 19 187990 4.3 1 173831 14159 20 110613 4.3 1 101198 9415 21 118508 4.3 1 109730 8778 22 274149 4.3 1 253126 21023 23 90441 4.3 1 82687 7754 24 360500 4.3 1 336352 24148 25 199998 4.3 1 187858 12140 26 111309 4.3 1 103725 7584 27 149081 4.3 1 140654 8427 28 248423 4.3 1 235687 12736 29 122477 4.3 1 116311 6166 30 107749 4.3 1 101542 6207 31 162871 4.3 1 154226 8645 32 120631 4.3 1 115234 5397 33 118489 4.3 1 112271 6218 34 245793 4.3 1 234939 10854 35 190517 4.3 1 183691 6826 36 79929 4.3 1 75288 4641 37 185327 4.3 1 177678 7649 38 350817 4.3 1 337845 12972 39 160243 4.3 1 153509 6734 40 49523 4.3 1 47055 2468 41 99720 4.3 1 95846 3874 42 209961 4.3 1 204671 5290 43 122898 4.3 1 118531 4367 44 166079 4.3 1 161517 4562 45 218520 4.3 1 212794 5726 46 216230 4.3 1 210165 6065 47 150848 4.3 1 146896 3952 48 195313 4.3 1 190410 4903 49 119864 4.3 1 116907 2957 50 198149 4.3 1 193710 4439 51 44470 4.3 1 42705 1765 52 125312 4.3 1 122091 3221 53 160350 4.3 1 156164 4186 54 350097 4.3 1 343329 6768 55 90527 4.3 1 87468 3059 56 228576 4.3 1 222949 5627 57 314847 4.3 1 308798 6049 58 130101 4.3 1 127078 3023 59 103061 4.3 1 100655 2406 60 145738 4.3 1 142665 3073 61 110959 4.3 1 108380 2579 62 157053 4.3 1 153657 3396 63 232486 4.3 1 228299 4187 64 77784 4.3 1 76130 1654 65 113617 4.3 1 111623 1994 66 91230 4.3 1 89405 1825 67 255083 4.3 1 251507 3576 68 76869 4.3 1 75081 1788 69 130744 4.3 1 128354 2390 70 155408 4.3 1 152773 2635 71 87764 4.3 1 85962 1802 72 122270 4.3 1 119725 2545 73 148448 4.3 1 145724 2724 74 209849 4.3 1 206144 3705 75 367609 4.3 1 361553 6056 76 3686459 4.3 1 3664819 21640 77 697823 4.3 1 691400 6423 78 126948 4.3 1 125058 1890 79 40096 4.3 1 39112 984 80 24645 4.3 1 23902 743 81 20367 4.3 1 19755 612 82 16078 4.3 1 15494 584 83 16099 4.3 1 15502 597 84 22100 4.3 1 21363 737 85 27271 4.3 1 26557 714 86 32766 4.3 1 31943 823 87 35764 4.3 1 34863 901 88 34412 4.3 1 33651 761 89 29649 4.3 1 28854 795 90 24331 4.3 1 23662 669 91 19647 4.3 1 19057 590 92 16184 4.3 1 15655 529 93 15805 4.3 1 15266 539 94 18042 4.3 1 17484 558 95 23214 4.3 1 22574 640 96 27102 4.3 1 26399 703 97 29599 4.3 1 28831 768 98 26939 4.3 1 26231 708 99 23593 4.3 1 22861 732 100 20037 4.3 1 19411 626 101 15643 4.3 1 15085 558 102 12701 4.3 1 12170 531 103 11370 4.3 1 10864 506 104 13052 4.3 1 12479 573 105 18499 4.3 1 17748 751 106 23737 4.3 1 22878 859 107 25678 4.3 1 25001 677 108 24121 4.3 1 23475 646 109 21133 4.3 1 20494 639 110 16788 4.3 1 16309 479 111 13356 4.3 1 12937 419 112 10717 4.3 1 10310 407 113 8871 4.3 1 8444 427 114 9976 4.3 1 9609 367 115 13191 4.3 1 12784 407 116 15663 4.3 1 15218 445 117 14717 4.3 1 14265 452 118 13298 4.3 1 12886 412 119 10198 4.3 1 9859 339 120 7835 4.3 1 7503 332 121 6923 4.3 1 6583 340 122 6487 4.3 1 6134 353 123 6011 4.3 1 5666 345 124 5052 4.3 1 4766 286 125 1232 4.3 1 993 239 126 453 4.3 1 276 177 127 417 4.3 1 198 219 128 338 4.3 1 117 221 129 278 4.3 1 74 204 130 327 4.3 1 76 251 131 235 4.3 1 44 191 132 245 4.3 1 46 199 133 201 4.3 1 26 175 134 217 4.3 1 19 198 135 219 4.3 1 9 210 136 233 4.3 1 11 222 137 183 4.3 1 13 170 138 242 4.3 1 8 234 139 251 4.3 1 7 244 140 235 4.3 1 11 224 141 245 4.3 1 5 240 142 401 4.3 1 25 376 143 537 4.3 1 15 522 144 182 4.3 1 6 176 145 176 4.3 1 2 174 146 99 4.3 1 1 98 147 204 4.3 1 2 202 148 315 4.3 1 3 312 149 117 4.3 1 1 116 150 65 4.3 1 4 61 151 49 4.3 1 3 46 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_5_S6_L002_R2_001.fastq.gz ============================================= 72142506 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_trimmed.fq.gz and Library_Geoduck_MG_5_S6_L002_R2_001_trimmed.fq.gz file_1: Library_Geoduck_MG_5_S6_L002_R1_001_trimmed.fq.gz, file_2: Library_Geoduck_MG_5_S6_L002_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_5_S6_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_5_S6_L002_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Total number of sequences analysed: 72142506 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 228753 (0.32%) >>> Now running FastQC on the validated data Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_5_S6_L002_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_5_S6_L002_R2_001_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_5_S6_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_5_S6_L002_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/Library_Geoduck_MG_6_S5_L002_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_6_S5_L002_R1_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_6_S5_L002_R1_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_6_S5_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2510.85 s (34 us/read; 1.76 M reads/minute). === Summary === Total reads processed: 73,610,508 Reads with adapters: 34,027,761 (46.2%) Reads written (passing filters): 73,610,508 (100.0%) Total basepairs processed: 11,115,186,708 bp Quality-trimmed: 200,453,105 bp (1.8%) Total written (filtered): 9,890,564,008 bp (89.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 34027761 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.8% C: 33.1% G: 23.6% T: 26.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 10419042 18402627.0 0 10419042 2 2972643 4600656.8 0 2972643 3 908699 1150164.2 0 908699 4 357980 287541.0 0 357980 5 251321 71885.3 0 251321 6 138865 17971.3 0 138865 7 148822 4492.8 0 148822 8 158465 1123.2 0 158465 9 190634 280.8 0 189334 1300 10 127433 70.2 1 122111 5322 11 168478 17.6 1 162191 6287 12 199510 4.4 1 191691 7819 13 225998 4.4 1 217700 8298 14 177156 4.4 1 171162 5994 15 234584 4.4 1 226080 8504 16 198858 4.4 1 191139 7719 17 191123 4.4 1 185245 5878 18 178495 4.4 1 172778 5717 19 109217 4.4 1 105914 3303 20 156180 4.4 1 149920 6260 21 199843 4.4 1 190602 9241 22 229926 4.4 1 222565 7361 23 160663 4.4 1 155332 5331 24 189233 4.4 1 184218 5015 25 212744 4.4 1 206776 5968 26 230380 4.4 1 223336 7044 27 275391 4.4 1 268286 7105 28 115258 4.4 1 111493 3765 29 182231 4.4 1 176499 5732 30 161880 4.4 1 158009 3871 31 109720 4.4 1 106312 3408 32 196618 4.4 1 191998 4620 33 155576 4.4 1 151780 3796 34 223933 4.4 1 218073 5860 35 179085 4.4 1 175124 3961 36 382074 4.4 1 373523 8551 37 51415 4.4 1 49695 1720 38 208735 4.4 1 204373 4362 39 133891 4.4 1 130380 3511 40 141199 4.4 1 137653 3546 41 141433 4.4 1 137945 3488 42 167240 4.4 1 162717 4523 43 266848 4.4 1 259389 7459 44 151264 4.4 1 147592 3672 45 435130 4.4 1 427147 7983 46 43271 4.4 1 41260 2011 47 192372 4.4 1 188955 3417 48 175208 4.4 1 171910 3298 49 193059 4.4 1 189395 3664 50 123629 4.4 1 120578 3051 51 135572 4.4 1 132432 3140 52 121540 4.4 1 119019 2521 53 176343 4.4 1 172178 4165 54 246205 4.4 1 240342 5863 55 317966 4.4 1 311627 6339 56 185183 4.4 1 181656 3527 57 139994 4.4 1 137228 2766 58 192702 4.4 1 188942 3760 59 193828 4.4 1 190398 3430 60 137239 4.4 1 134591 2648 61 129484 4.4 1 126877 2607 62 107127 4.4 1 104790 2337 63 164918 4.4 1 161127 3791 64 193713 4.4 1 189826 3887 65 200176 4.4 1 196084 4092 66 255550 4.4 1 250630 4920 67 218060 4.4 1 213754 4306 68 234322 4.4 1 229538 4784 69 249930 4.4 1 244668 5262 70 272085 4.4 1 266604 5481 71 404097 4.4 1 396277 7820 72 4316798 4.4 1 4290132 26666 73 856365 4.4 1 848645 7720 74 186896 4.4 1 184648 2248 75 72978 4.4 1 71709 1269 76 49783 4.4 1 48614 1169 77 49628 4.4 1 48517 1111 78 40674 4.4 1 39679 995 79 36778 4.4 1 35979 799 80 30462 4.4 1 29700 762 81 27342 4.4 1 26640 702 82 25172 4.4 1 24517 655 83 27025 4.4 1 26361 664 84 30366 4.4 1 29598 768 85 35406 4.4 1 34594 812 86 36296 4.4 1 35495 801 87 36165 4.4 1 35229 936 88 35244 4.4 1 34378 866 89 32654 4.4 1 31795 859 90 26622 4.4 1 25953 669 91 21181 4.4 1 20586 595 92 18126 4.4 1 17627 499 93 18147 4.4 1 17605 542 94 20897 4.4 1 20186 711 95 26232 4.4 1 25551 681 96 31860 4.4 1 31084 776 97 32298 4.4 1 31477 821 98 30420 4.4 1 29654 766 99 27330 4.4 1 26625 705 100 24071 4.4 1 23440 631 101 20090 4.4 1 19569 521 102 26131 4.4 1 25611 520 103 15595 4.4 1 15164 431 104 15907 4.4 1 15388 519 105 20827 4.4 1 20207 620 106 26375 4.4 1 25644 731 107 29802 4.4 1 29133 669 108 27794 4.4 1 27094 700 109 23598 4.4 1 22961 637 110 20007 4.4 1 19449 558 111 15766 4.4 1 15317 449 112 12499 4.4 1 12097 402 113 10620 4.4 1 10199 421 114 12004 4.4 1 11600 404 115 15542 4.4 1 15057 485 116 18195 4.4 1 17703 492 117 17751 4.4 1 17304 447 118 15946 4.4 1 15474 472 119 12198 4.4 1 11814 384 120 9382 4.4 1 8998 384 121 8815 4.4 1 8469 346 122 8324 4.4 1 8000 324 123 7644 4.4 1 7327 317 124 6260 4.4 1 6003 257 125 1445 4.4 1 1238 207 126 557 4.4 1 350 207 127 477 4.4 1 229 248 128 347 4.4 1 129 218 129 301 4.4 1 76 225 130 290 4.4 1 70 220 131 241 4.4 1 56 185 132 316 4.4 1 72 244 133 270 4.4 1 25 245 134 202 4.4 1 12 190 135 206 4.4 1 12 194 136 208 4.4 1 14 194 137 187 4.4 1 7 180 138 260 4.4 1 4 256 139 267 4.4 1 9 258 140 196 4.4 1 7 189 141 249 4.4 1 6 243 142 449 4.4 1 26 423 143 787 4.4 1 12 775 144 168 4.4 1 3 165 145 260 4.4 1 5 255 146 117 4.4 1 1 116 147 170 4.4 1 2 168 148 432 4.4 1 4 428 149 143 4.4 1 3 140 150 92 4.4 1 0 92 151 50 4.4 1 0 50 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_6_S5_L002_R1_001.fastq.gz ============================================= 73610508 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_01/Library_Geoduck_MG_6_S5_L002_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_6_S5_L002_R2_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_6_S5_L002_R2_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_6_S5_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2605.73 s (35 us/read; 1.69 M reads/minute). === Summary === Total reads processed: 73,610,508 Reads with adapters: 34,531,336 (46.9%) Reads written (passing filters): 73,610,508 (100.0%) Total basepairs processed: 11,115,186,708 bp Quality-trimmed: 493,115,597 bp (4.4%) Total written (filtered): 9,607,718,782 bp (86.4%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 34531336 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.2% C: 34.2% G: 23.7% T: 25.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 12164809 18402627.0 0 12164809 2 2460932 4600656.8 0 2460932 3 728552 1150164.2 0 728552 4 359916 287541.0 0 359916 5 279786 71885.3 0 279786 6 68028 17971.3 0 68028 7 150411 4492.8 0 150411 8 100927 1123.2 0 100927 9 233433 280.8 0 232415 1018 10 111315 70.2 1 96495 14820 11 164501 17.6 1 149749 14752 12 193744 4.4 1 176581 17163 13 277141 4.4 1 249324 27817 14 115994 4.4 1 104380 11614 15 302492 4.4 1 272877 29615 16 230694 4.4 1 207676 23018 17 88270 4.4 1 79931 8339 18 190873 4.4 1 172390 18483 19 185039 4.4 1 170654 14385 20 122969 4.4 1 112168 10801 21 116784 4.4 1 107713 9071 22 294009 4.4 1 270610 23399 23 102074 4.4 1 93065 9009 24 389547 4.4 1 362165 27382 25 196340 4.4 1 184212 12128 26 112092 4.4 1 104179 7913 27 150664 4.4 1 141680 8984 28 274805 4.4 1 259720 15085 29 163866 4.4 1 155380 8486 30 74321 4.4 1 69427 4894 31 194339 4.4 1 184731 9608 32 116377 4.4 1 111425 4952 33 65516 4.4 1 61663 3853 34 336323 4.4 1 322627 13696 35 33434 4.4 1 30315 3119 36 199110 4.4 1 190961 8149 37 314927 4.4 1 300656 14271 38 86329 4.4 1 81442 4887 39 258989 4.4 1 249915 9074 40 47772 4.4 1 44321 3451 41 209697 4.4 1 199902 9795 42 221086 4.4 1 213093 7993 43 235755 4.4 1 228133 7622 44 110648 4.4 1 106346 4302 45 280672 4.4 1 272906 7766 46 205643 4.4 1 198827 6816 47 177230 4.4 1 172233 4997 48 205148 4.4 1 199584 5564 49 135485 4.4 1 131942 3543 50 239675 4.4 1 234010 5665 51 39624 4.4 1 37716 1908 52 150612 4.4 1 146653 3959 53 168171 4.4 1 163308 4863 54 370553 4.4 1 363169 7384 55 119427 4.4 1 115552 3875 56 245761 4.4 1 238473 7288 57 320546 4.4 1 313794 6752 58 130334 4.4 1 127167 3167 59 132351 4.4 1 129474 2877 60 133192 4.4 1 130031 3161 61 114555 4.4 1 111446 3109 62 198186 4.4 1 193904 4282 63 245945 4.4 1 241338 4607 64 91699 4.4 1 89744 1955 65 118346 4.4 1 116078 2268 66 98150 4.4 1 96080 2070 67 297293 4.4 1 292886 4407 68 63685 4.4 1 61951 1734 69 141067 4.4 1 138358 2709 70 184352 4.4 1 181206 3146 71 86386 4.4 1 84479 1907 72 137311 4.4 1 134540 2771 73 167952 4.4 1 164779 3173 74 251865 4.4 1 247453 4412 75 450167 4.4 1 442872 7295 76 4130506 4.4 1 4105472 25034 77 765948 4.4 1 758540 7408 78 133936 4.4 1 131859 2077 79 43971 4.4 1 42827 1144 80 27103 4.4 1 26206 897 81 22516 4.4 1 21791 725 82 17644 4.4 1 17028 616 83 18841 4.4 1 18158 683 84 24838 4.4 1 23969 869 85 30169 4.4 1 29346 823 86 36546 4.4 1 35546 1000 87 39797 4.4 1 38756 1041 88 37128 4.4 1 36183 945 89 32141 4.4 1 31286 855 90 26115 4.4 1 25379 736 91 21126 4.4 1 20516 610 92 17388 4.4 1 16814 574 93 16699 4.4 1 16074 625 94 19418 4.4 1 18821 597 95 24671 4.4 1 23971 700 96 28934 4.4 1 28161 773 97 31377 4.4 1 30502 875 98 29002 4.4 1 28172 830 99 25798 4.4 1 25023 775 100 21968 4.4 1 21248 720 101 17019 4.4 1 16424 595 102 13764 4.4 1 13201 563 103 12490 4.4 1 11929 561 104 14699 4.4 1 14001 698 105 20374 4.4 1 19479 895 106 26538 4.4 1 25576 962 107 28904 4.4 1 28076 828 108 27927 4.4 1 27165 762 109 23842 4.4 1 23136 706 110 19421 4.4 1 18829 592 111 15099 4.4 1 14631 468 112 12109 4.4 1 11683 426 113 9886 4.4 1 9490 396 114 10807 4.4 1 10443 364 115 14232 4.4 1 13799 433 116 17052 4.4 1 16560 492 117 16312 4.4 1 15836 476 118 14707 4.4 1 14271 436 119 11459 4.4 1 11034 425 120 8656 4.4 1 8297 359 121 7898 4.4 1 7522 376 122 7580 4.4 1 7256 324 123 7134 4.4 1 6795 339 124 5533 4.4 1 5234 299 125 1330 4.4 1 1133 197 126 508 4.4 1 304 204 127 473 4.4 1 242 231 128 340 4.4 1 138 202 129 286 4.4 1 69 217 130 295 4.4 1 68 227 131 284 4.4 1 60 224 132 336 4.4 1 75 261 133 233 4.4 1 26 207 134 234 4.4 1 22 212 135 195 4.4 1 9 186 136 258 4.4 1 24 234 137 183 4.4 1 13 170 138 265 4.4 1 6 259 139 248 4.4 1 8 240 140 246 4.4 1 10 236 141 262 4.4 1 7 255 142 423 4.4 1 16 407 143 620 4.4 1 20 600 144 184 4.4 1 10 174 145 188 4.4 1 7 181 146 110 4.4 1 3 107 147 201 4.4 1 4 197 148 337 4.4 1 8 329 149 148 4.4 1 2 146 150 73 4.4 1 0 73 151 41 4.4 1 0 41 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_6_S5_L002_R2_001.fastq.gz ============================================= 73610508 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_trimmed.fq.gz and Library_Geoduck_MG_6_S5_L002_R2_001_trimmed.fq.gz file_1: Library_Geoduck_MG_6_S5_L002_R1_001_trimmed.fq.gz, file_2: Library_Geoduck_MG_6_S5_L002_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_6_S5_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_6_S5_L002_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Total number of sequences analysed: 73610508 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 221723 (0.30%) >>> Now running FastQC on the validated data Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_6_S5_L002_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_6_S5_L002_R2_001_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_6_S5_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_6_S5_L002_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/home/sam/analyses/20181211_metagenomics_fastqc_trimgalore/20181211_metagenomics_trimgalore_01/Library_Geoduck_MG_7_S2_L002_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_7_S2_L002_R1_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_7_S2_L002_R1_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_7_S2_L002_R1_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 2970.78 s (34 us/read; 1.78 M reads/minute). === Summary === Total reads processed: 88,314,076 Reads with adapters: 41,704,051 (47.2%) Reads written (passing filters): 88,314,076 (100.0%) Total basepairs processed: 13,335,425,476 bp Quality-trimmed: 243,789,443 bp (1.8%) Total written (filtered): 11,791,021,808 bp (88.4%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 41704051 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.8% C: 33.2% G: 23.0% T: 27.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 11837322 22078519.0 0 11837322 2 3527103 5519629.8 0 3527103 3 1055780 1379907.4 0 1055780 4 460645 344976.9 0 460645 5 315456 86244.2 0 315456 6 188628 21561.1 0 188628 7 190525 5390.3 0 190525 8 207470 1347.6 0 207470 9 251241 336.9 0 249787 1454 10 167709 84.2 1 161196 6513 11 221233 21.1 1 213547 7686 12 262000 5.3 1 252369 9631 13 297890 5.3 1 287833 10057 14 230702 5.3 1 223429 7273 15 309660 5.3 1 299147 10513 16 260728 5.3 1 251292 9436 17 242656 5.3 1 235323 7333 18 237876 5.3 1 230817 7059 19 139718 5.3 1 135765 3953 20 202049 5.3 1 194615 7434 21 251904 5.3 1 241137 10767 22 303447 5.3 1 294210 9237 23 211360 5.3 1 204823 6537 24 250316 5.3 1 244006 6310 25 278768 5.3 1 271545 7223 26 299714 5.3 1 291442 8272 27 355283 5.3 1 346826 8457 28 152942 5.3 1 148316 4626 29 238366 5.3 1 231246 7120 30 210978 5.3 1 206422 4556 31 142801 5.3 1 138596 4205 32 275083 5.3 1 269385 5698 33 177507 5.3 1 173537 3970 34 230569 5.3 1 225408 5161 35 299884 5.3 1 292046 7838 36 455969 5.3 1 446019 9950 37 132116 5.3 1 128178 3938 38 359119 5.3 1 351705 7414 39 71721 5.3 1 69697 2024 40 193980 5.3 1 189437 4543 41 235364 5.3 1 229027 6337 42 239292 5.3 1 234294 4998 43 256044 5.3 1 250073 5971 44 203721 5.3 1 199825 3896 45 567194 5.3 1 558017 9177 46 49086 5.3 1 46905 2181 47 252827 5.3 1 248801 4026 48 215878 5.3 1 212344 3534 49 255712 5.3 1 251231 4481 50 154568 5.3 1 150928 3640 51 178393 5.3 1 174448 3945 52 155561 5.3 1 152621 2940 53 226654 5.3 1 221610 5044 54 320581 5.3 1 313548 7033 55 407318 5.3 1 399861 7457 56 237563 5.3 1 233312 4251 57 185492 5.3 1 182108 3384 58 248685 5.3 1 244214 4471 59 248466 5.3 1 244446 4020 60 180262 5.3 1 177007 3255 61 165164 5.3 1 162055 3109 62 139065 5.3 1 136159 2906 63 212290 5.3 1 207804 4486 64 247953 5.3 1 243312 4641 65 255639 5.3 1 250695 4944 66 327156 5.3 1 321087 6069 67 281328 5.3 1 276128 5200 68 302626 5.3 1 296931 5695 69 317025 5.3 1 310666 6359 70 344575 5.3 1 337918 6657 71 503276 5.3 1 493996 9280 72 5408619 5.3 1 5377829 30790 73 1069104 5.3 1 1060010 9094 74 235268 5.3 1 232645 2623 75 94504 5.3 1 92878 1626 76 63361 5.3 1 62005 1356 77 64135 5.3 1 62847 1288 78 52148 5.3 1 50985 1163 79 47636 5.3 1 46650 986 80 40296 5.3 1 39394 902 81 35402 5.3 1 34516 886 82 31834 5.3 1 31074 760 83 34390 5.3 1 33526 864 84 39046 5.3 1 38168 878 85 45220 5.3 1 44310 910 86 45545 5.3 1 44554 991 87 45136 5.3 1 44123 1013 88 44261 5.3 1 43299 962 89 40216 5.3 1 39310 906 90 33495 5.3 1 32741 754 91 26435 5.3 1 25779 656 92 22863 5.3 1 22247 616 93 22930 5.3 1 22312 618 94 26357 5.3 1 25697 660 95 32797 5.3 1 31989 808 96 39714 5.3 1 38882 832 97 40006 5.3 1 39125 881 98 37463 5.3 1 36628 835 99 34380 5.3 1 33603 777 100 29953 5.3 1 29256 697 101 26228 5.3 1 25604 624 102 39583 5.3 1 39031 552 103 20525 5.3 1 20047 478 104 19605 5.3 1 19099 506 105 25882 5.3 1 25264 618 106 32778 5.3 1 31934 844 107 36206 5.3 1 35451 755 108 33501 5.3 1 32769 732 109 28532 5.3 1 27840 692 110 24453 5.3 1 23875 578 111 19581 5.3 1 19097 484 112 15397 5.3 1 14913 484 113 13215 5.3 1 12779 436 114 14860 5.3 1 14402 458 115 19757 5.3 1 19247 510 116 22791 5.3 1 22282 509 117 21938 5.3 1 21393 545 118 19251 5.3 1 18784 467 119 15093 5.3 1 14669 424 120 11635 5.3 1 11263 372 121 10520 5.3 1 10184 336 122 10224 5.3 1 9899 325 123 9571 5.3 1 9177 394 124 7735 5.3 1 7443 292 125 1642 5.3 1 1443 199 126 596 5.3 1 359 237 127 551 5.3 1 294 257 128 367 5.3 1 152 215 129 326 5.3 1 102 224 130 354 5.3 1 88 266 131 295 5.3 1 64 231 132 327 5.3 1 69 258 133 260 5.3 1 24 236 134 215 5.3 1 15 200 135 244 5.3 1 14 230 136 243 5.3 1 7 236 137 220 5.3 1 18 202 138 305 5.3 1 5 300 139 307 5.3 1 5 302 140 231 5.3 1 9 222 141 302 5.3 1 7 295 142 436 5.3 1 26 410 143 871 5.3 1 15 856 144 219 5.3 1 3 216 145 283 5.3 1 3 280 146 109 5.3 1 0 109 147 169 5.3 1 0 169 148 485 5.3 1 5 480 149 184 5.3 1 0 184 150 98 5.3 1 1 97 151 61 5.3 1 1 60 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_7_S2_L002_R1_001.fastq.gz ============================================= 88314076 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_01/Library_Geoduck_MG_7_S2_L002_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: Library_Geoduck_MG_7_S2_L002_R2_001.fastq.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: 'CTGTCTCTTATA' (Nextera Transposase sequence; auto-detected) Maximum trimming error rate: 0.1 (default) Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 20 bp 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_01/20181211_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_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'CTGTCTCTTATA' from file Library_Geoduck_MG_7_S2_L002_R2_001.fastq.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 CTGTCTCTTATA Library_Geoduck_MG_7_S2_L002_R2_001.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 3090.17 s (35 us/read; 1.71 M reads/minute). === Summary === Total reads processed: 88,314,076 Reads with adapters: 42,085,008 (47.7%) Reads written (passing filters): 88,314,076 (100.0%) Total basepairs processed: 13,335,425,476 bp Quality-trimmed: 580,847,327 bp (4.4%) Total written (filtered): 11,470,592,114 bp (86.0%) === Adapter 1 === Sequence: CTGTCTCTTATA; Type: regular 3'; Length: 12; Trimmed: 42085008 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 16.3% C: 34.2% G: 23.1% T: 26.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13815390 22078519.0 0 13815390 2 2903007 5519629.8 0 2903007 3 858433 1379907.4 0 858433 4 444846 344976.9 0 444846 5 356245 86244.2 0 356245 6 88425 21561.1 0 88425 7 192578 5390.3 0 192578 8 134365 1347.6 0 134365 9 302952 336.9 0 301713 1239 10 147983 84.2 1 128845 19138 11 214261 21.1 1 195344 18917 12 257575 5.3 1 235067 22508 13 358131 5.3 1 323251 34880 14 154590 5.3 1 139441 15149 15 390204 5.3 1 352897 37307 16 301173 5.3 1 271471 29702 17 116222 5.3 1 105407 10815 18 244462 5.3 1 221166 23296 19 243108 5.3 1 224270 18838 20 158469 5.3 1 144680 13789 21 154476 5.3 1 142774 11702 22 380789 5.3 1 350660 30129 23 133812 5.3 1 122174 11638 24 502426 5.3 1 467946 34480 25 257212 5.3 1 241585 15627 26 147897 5.3 1 137502 10395 27 198670 5.3 1 186943 11727 28 354573 5.3 1 335535 19038 29 206095 5.3 1 195568 10527 30 94303 5.3 1 88247 6056 31 269195 5.3 1 256089 13106 32 153503 5.3 1 147100 6403 33 87009 5.3 1 81814 5195 34 438335 5.3 1 420537 17798 35 43851 5.3 1 39862 3989 36 259925 5.3 1 249150 10775 37 404204 5.3 1 386211 17993 38 114808 5.3 1 108521 6287 39 336591 5.3 1 324557 12034 40 63973 5.3 1 59089 4884 41 274501 5.3 1 261632 12869 42 287294 5.3 1 276699 10595 43 304894 5.3 1 294932 9962 44 144286 5.3 1 138653 5633 45 362621 5.3 1 353064 9557 46 265796 5.3 1 256904 8892 47 230798 5.3 1 224183 6615 48 261645 5.3 1 254507 7138 49 175700 5.3 1 171155 4545 50 307800 5.3 1 300542 7258 51 50823 5.3 1 48523 2300 52 196137 5.3 1 190871 5266 53 218924 5.3 1 212377 6547 54 468463 5.3 1 458870 9593 55 160927 5.3 1 155823 5104 56 325655 5.3 1 315119 10536 57 418012 5.3 1 409075 8937 58 168897 5.3 1 164897 4000 59 170877 5.3 1 167072 3805 60 173407 5.3 1 169369 4038 61 150736 5.3 1 146535 4201 62 254742 5.3 1 249322 5420 63 317446 5.3 1 311442 6004 64 116976 5.3 1 114609 2367 65 152947 5.3 1 150134 2813 66 124491 5.3 1 121807 2684 67 381882 5.3 1 376181 5701 68 81616 5.3 1 79507 2109 69 181354 5.3 1 177709 3645 70 236502 5.3 1 232200 4302 71 112714 5.3 1 110366 2348 72 176074 5.3 1 172441 3633 73 214263 5.3 1 210268 3995 74 323279 5.3 1 317611 5668 75 573931 5.3 1 564593 9338 76 5123114 5.3 1 5091744 31370 77 944898 5.3 1 935759 9139 78 165918 5.3 1 163262 2656 79 54730 5.3 1 53273 1457 80 34966 5.3 1 33856 1110 81 28604 5.3 1 27740 864 82 22339 5.3 1 21467 872 83 24071 5.3 1 23180 891 84 31098 5.3 1 30000 1098 85 37724 5.3 1 36697 1027 86 45682 5.3 1 44441 1241 87 48954 5.3 1 47620 1334 88 46094 5.3 1 44960 1134 89 40067 5.3 1 38935 1132 90 32234 5.3 1 31361 873 91 25905 5.3 1 25071 834 92 21664 5.3 1 20931 733 93 21322 5.3 1 20463 859 94 24588 5.3 1 23852 736 95 30848 5.3 1 29989 859 96 35741 5.3 1 34789 952 97 38815 5.3 1 37746 1069 98 35781 5.3 1 34738 1043 99 31719 5.3 1 30792 927 100 27260 5.3 1 26353 907 101 21446 5.3 1 20750 696 102 17268 5.3 1 16534 734 103 15585 5.3 1 14849 736 104 18416 5.3 1 17556 860 105 25870 5.3 1 24747 1123 106 33367 5.3 1 31973 1394 107 35823 5.3 1 34851 972 108 33683 5.3 1 32816 867 109 28611 5.3 1 27816 795 110 23616 5.3 1 22938 678 111 18775 5.3 1 18257 518 112 14563 5.3 1 14065 498 113 12481 5.3 1 12025 456 114 13547 5.3 1 13027 520 115 18671 5.3 1 18103 568 116 21513 5.3 1 20953 560 117 20559 5.3 1 19985 574 118 18201 5.3 1 17684 517 119 14031 5.3 1 13547 484 120 10716 5.3 1 10331 385 121 9576 5.3 1 9192 384 122 9187 5.3 1 8828 359 123 8492 5.3 1 8107 385 124 7137 5.3 1 6829 308 125 1583 5.3 1 1314 269 126 578 5.3 1 336 242 127 563 5.3 1 304 259 128 400 5.3 1 172 228 129 313 5.3 1 88 225 130 327 5.3 1 89 238 131 243 5.3 1 57 186 132 308 5.3 1 62 246 133 266 5.3 1 32 234 134 239 5.3 1 26 213 135 218 5.3 1 20 198 136 250 5.3 1 16 234 137 261 5.3 1 11 250 138 314 5.3 1 7 307 139 299 5.3 1 3 296 140 270 5.3 1 14 256 141 255 5.3 1 13 242 142 506 5.3 1 31 475 143 758 5.3 1 29 729 144 205 5.3 1 5 200 145 207 5.3 1 7 200 146 105 5.3 1 4 101 147 187 5.3 1 3 184 148 350 5.3 1 7 343 149 159 5.3 1 1 158 150 59 5.3 1 2 57 151 39 5.3 1 0 39 RUN STATISTICS FOR INPUT FILE: Library_Geoduck_MG_7_S2_L002_R2_001.fastq.gz ============================================= 88314076 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_trimmed.fq.gz and Library_Geoduck_MG_7_S2_L002_R2_001_trimmed.fq.gz file_1: Library_Geoduck_MG_7_S2_L002_R1_001_trimmed.fq.gz, file_2: Library_Geoduck_MG_7_S2_L002_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Library_Geoduck_MG_7_S2_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_7_S2_L002_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Total number of sequences analysed: 88314076 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 277637 (0.31%) >>> Now running FastQC on the validated data Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz<<< Started analysis of Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 5% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 10% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 15% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 20% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 25% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 30% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 35% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 40% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 45% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 50% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 55% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 60% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 65% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 70% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 75% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 80% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 85% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 90% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz Approx 95% complete for Library_Geoduck_MG_7_S2_L002_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz<<< Started analysis of Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 5% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 10% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 15% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 20% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 25% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 30% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 35% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 40% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 45% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 50% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 55% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 60% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 65% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 70% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 75% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 80% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 85% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 90% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Approx 95% complete for Library_Geoduck_MG_7_S2_L002_R2_001_val_2.fq.gz Deleting both intermediate output files Library_Geoduck_MG_7_S2_L002_R1_001_trimmed.fq.gz and Library_Geoduck_MG_7_S2_L002_R2_001_trimmed.fq.gz ==================================================================================================== gzip: stdout: Broken pipe