/var/spool/slurm/d/job2098069/slurm_script: line 20: fg: no job control No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) Path to Cutadapt set as: '/gscratch/srlab/programs/miniconda3/bin/cutadapt' (user defined) 2.4 Cutadapt seems to be working fine (tested command '/gscratch/srlab/programs/miniconda3/bin/cutadapt --version') Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth10_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth10_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2619.14 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 84,306,567 Reads with adapters: 54,788,380 (65.0%) Reads written (passing filters): 84,306,567 (100.0%) Total basepairs processed: 12,645,985,050 bp Quality-trimmed: 16,741,512 bp (0.1%) Total written (filtered): 11,144,101,263 bp (88.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 54788380 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.3% C: 16.9% G: 14.5% T: 30.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 20087171 21076641.8 0 20087171 2 1813918 5269160.4 0 1813918 3 873915 1317290.1 0 873915 4 558229 329322.5 0 558229 5 415119 82330.6 0 415119 6 349731 20582.7 0 349731 7 372849 5145.7 0 372849 8 408592 1286.4 0 408592 9 374071 321.6 0 365399 8672 10 397601 80.4 1 373645 23956 11 412375 20.1 1 383235 29140 12 417766 5.0 1 391425 26341 13 401873 1.3 1 374959 26914 14 413498 1.3 1 383743 29755 15 410252 1.3 1 381745 28507 16 418895 1.3 1 388384 30511 17 433797 1.3 1 402985 30812 18 411876 1.3 1 385337 26539 19 405157 1.3 1 378241 26916 20 417320 1.3 1 389068 28252 21 425512 1.3 1 396360 29152 22 414020 1.3 1 386540 27480 23 426843 1.3 1 397519 29324 24 419542 1.3 1 388690 30852 25 419316 1.3 1 391778 27538 26 414854 1.3 1 387552 27302 27 426656 1.3 1 398584 28072 28 410941 1.3 1 385217 25724 29 418300 1.3 1 391761 26539 30 412229 1.3 1 388918 23311 31 406287 1.3 1 382845 23442 32 410526 1.3 1 387548 22978 33 409786 1.3 1 384961 24825 34 425411 1.3 1 400165 25246 35 398975 1.3 1 377322 21653 36 408651 1.3 1 384528 24123 37 410983 1.3 1 386751 24232 38 406065 1.3 1 382456 23609 39 403998 1.3 1 381336 22662 40 397942 1.3 1 375225 22717 41 434330 1.3 1 409437 24893 42 383620 1.3 1 360445 23175 43 397784 1.3 1 369631 28153 44 396544 1.3 1 370154 26390 45 522637 1.3 1 498900 23737 46 253725 1.3 1 236592 17133 47 381386 1.3 1 359409 21977 48 397939 1.3 1 375666 22273 49 377989 1.3 1 356497 21492 50 369415 1.3 1 346468 22947 51 405549 1.3 1 381238 24311 52 355894 1.3 1 336154 19740 53 350710 1.3 1 330270 20440 54 369432 1.3 1 347007 22425 55 370880 1.3 1 350472 20408 56 344709 1.3 1 324826 19883 57 358913 1.3 1 338694 20219 58 366734 1.3 1 346501 20233 59 335781 1.3 1 316350 19431 60 329821 1.3 1 312040 17781 61 307437 1.3 1 289200 18237 62 337215 1.3 1 317800 19415 63 339253 1.3 1 320983 18270 64 307533 1.3 1 290898 16635 65 284690 1.3 1 267115 17575 66 330662 1.3 1 311833 18829 67 324655 1.3 1 305761 18894 68 346463 1.3 1 326661 19802 69 343819 1.3 1 315151 28668 70 687320 1.3 1 661746 25574 71 75523 1.3 1 70809 4714 72 42649 1.3 1 37975 4674 73 120214 1.3 1 111212 9002 74 209861 1.3 1 197410 12451 75 233269 1.3 1 220078 13191 76 232990 1.3 1 219691 13299 77 227410 1.3 1 213929 13481 78 221915 1.3 1 208486 13429 79 215689 1.3 1 202835 12854 80 207250 1.3 1 194747 12503 81 201334 1.3 1 189702 11632 82 196748 1.3 1 184523 12225 83 190989 1.3 1 179763 11226 84 179219 1.3 1 168329 10890 85 175756 1.3 1 164936 10820 86 168289 1.3 1 158051 10238 87 167282 1.3 1 157274 10008 88 144104 1.3 1 134747 9357 89 135448 1.3 1 126378 9070 90 131499 1.3 1 122793 8706 91 127264 1.3 1 118736 8528 92 121114 1.3 1 113141 7973 93 113184 1.3 1 105860 7324 94 110374 1.3 1 102866 7508 95 104676 1.3 1 97419 7257 96 98069 1.3 1 91264 6805 97 91188 1.3 1 84762 6426 98 84155 1.3 1 78003 6152 99 78241 1.3 1 72477 5764 100 72641 1.3 1 67136 5505 101 69950 1.3 1 64581 5369 102 62894 1.3 1 58044 4850 103 57552 1.3 1 52942 4610 104 56649 1.3 1 51800 4849 105 52762 1.3 1 48230 4532 106 50188 1.3 1 45983 4205 107 47175 1.3 1 42914 4261 108 40194 1.3 1 36615 3579 109 34610 1.3 1 31470 3140 110 32291 1.3 1 29173 3118 111 28366 1.3 1 25552 2814 112 25385 1.3 1 22723 2662 113 23983 1.3 1 21292 2691 114 21024 1.3 1 18758 2266 115 20728 1.3 1 18438 2290 116 18385 1.3 1 16280 2105 117 18416 1.3 1 16258 2158 118 16190 1.3 1 14284 1906 119 13662 1.3 1 11866 1796 120 11982 1.3 1 10483 1499 121 10731 1.3 1 9124 1607 122 10985 1.3 1 9479 1506 123 12829 1.3 1 11132 1697 124 10226 1.3 1 8902 1324 125 11092 1.3 1 9647 1445 126 23421 1.3 1 20930 2491 127 20964 1.3 1 18444 2520 128 10521 1.3 1 9003 1518 129 9578 1.3 1 8324 1254 130 16881 1.3 1 15062 1819 131 35161 1.3 1 32891 2270 132 41035 1.3 1 38490 2545 133 59794 1.3 1 55833 3961 134 57318 1.3 1 53691 3627 135 18130 1.3 1 16692 1438 136 4809 1.3 1 4181 628 137 3107 1.3 1 2644 463 138 2705 1.3 1 2179 526 139 1017 1.3 1 724 293 140 980 1.3 1 691 289 141 368 1.3 1 214 154 142 237 1.3 1 143 94 143 211 1.3 1 121 90 144 476 1.3 1 337 139 145 1579 1.3 1 1325 254 146 2140 1.3 1 1799 341 147 16319 1.3 1 14071 2248 148 10062 1.3 1 8487 1575 149 2880 1.3 1 2480 400 150 38413 1.3 1 34718 3695 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_R1_001.fastq.gz ============================================= 84306567 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth10_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth10_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2698.65 s (32 us/read; 1.87 M reads/minute). === Summary === Total reads processed: 84,306,567 Reads with adapters: 53,624,774 (63.6%) Reads written (passing filters): 84,306,567 (100.0%) Total basepairs processed: 12,645,985,050 bp Quality-trimmed: 75,182,158 bp (0.6%) Total written (filtered): 11,165,536,073 bp (88.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 53624774 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.4% C: 13.8% G: 18.0% T: 31.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19861880 21076641.8 0 19861880 2 1919691 5269160.4 0 1919691 3 938882 1317290.1 0 938882 4 581539 329322.5 0 581539 5 417710 82330.6 0 417710 6 337488 20582.7 0 337488 7 350550 5145.7 0 350550 8 408184 1286.4 0 408184 9 361115 321.6 0 355523 5592 10 382240 80.4 1 362108 20132 11 403125 20.1 1 374482 28643 12 438645 5.0 1 412693 25952 13 366854 1.3 1 339064 27790 14 399359 1.3 1 370774 28585 15 389746 1.3 1 362683 27063 16 421360 1.3 1 390121 31239 17 407725 1.3 1 380115 27610 18 385026 1.3 1 360065 24961 19 412814 1.3 1 385972 26842 20 419745 1.3 1 392160 27585 21 402299 1.3 1 373621 28678 22 411642 1.3 1 386608 25034 23 395427 1.3 1 370768 24659 24 409110 1.3 1 383132 25978 25 460076 1.3 1 433219 26857 26 363609 1.3 1 339230 24379 27 410710 1.3 1 383749 26961 28 388904 1.3 1 370127 18777 29 411926 1.3 1 389192 22734 30 395973 1.3 1 377516 18457 31 402573 1.3 1 381565 21008 32 393127 1.3 1 375243 17884 33 405440 1.3 1 384543 20897 34 395339 1.3 1 377122 18217 35 403096 1.3 1 383058 20038 36 469682 1.3 1 450927 18755 37 319186 1.3 1 301015 18171 38 414422 1.3 1 395297 19125 39 374689 1.3 1 357579 17110 40 401797 1.3 1 381569 20228 41 422375 1.3 1 395747 26628 42 376856 1.3 1 360778 16078 43 380787 1.3 1 360831 19956 44 485085 1.3 1 463953 21132 45 480769 1.3 1 456655 24114 46 495436 1.3 1 472137 23299 47 475183 1.3 1 460530 14653 48 191099 1.3 1 179403 11696 49 337830 1.3 1 322459 15371 50 348754 1.3 1 335301 13453 51 268498 1.3 1 255291 13207 52 351429 1.3 1 336964 14465 53 320857 1.3 1 305649 15208 54 510701 1.3 1 494536 16165 55 165726 1.3 1 154976 10750 56 351621 1.3 1 329864 21757 57 964943 1.3 1 937820 27123 58 170614 1.3 1 160589 10025 59 194970 1.3 1 182061 12909 60 577410 1.3 1 559224 18186 61 247581 1.3 1 236520 11061 62 277529 1.3 1 255766 21763 63 997327 1.3 1 970448 26879 64 396317 1.3 1 384091 12226 65 106341 1.3 1 100330 6011 66 148416 1.3 1 138514 9902 67 379450 1.3 1 367444 12006 68 193454 1.3 1 185270 8184 69 149441 1.3 1 141806 7635 70 234751 1.3 1 226478 8273 71 132306 1.3 1 126216 6090 72 128359 1.3 1 121745 6614 73 172501 1.3 1 164901 7600 74 164649 1.3 1 157171 7478 75 156766 1.3 1 149699 7067 76 125797 1.3 1 120623 5174 77 85434 1.3 1 80328 5106 78 155992 1.3 1 149110 6882 79 185685 1.3 1 178073 7612 80 194628 1.3 1 186786 7842 81 182472 1.3 1 174825 7647 82 177081 1.3 1 169246 7835 83 178185 1.3 1 170505 7680 84 167040 1.3 1 160177 6863 85 162923 1.3 1 155900 7023 86 149004 1.3 1 142542 6462 87 143532 1.3 1 137166 6366 88 134654 1.3 1 128858 5796 89 127832 1.3 1 122136 5696 90 123410 1.3 1 118178 5232 91 116022 1.3 1 110763 5259 92 109152 1.3 1 104048 5104 93 101287 1.3 1 96394 4893 94 97356 1.3 1 92882 4474 95 93231 1.3 1 88963 4268 96 88567 1.3 1 84313 4254 97 82806 1.3 1 78748 4058 98 77404 1.3 1 73679 3725 99 72610 1.3 1 69005 3605 100 67605 1.3 1 64115 3490 101 63637 1.3 1 60508 3129 102 56294 1.3 1 53295 2999 103 51177 1.3 1 48278 2899 104 50081 1.3 1 47279 2802 105 47068 1.3 1 44438 2630 106 45671 1.3 1 42954 2717 107 42278 1.3 1 39869 2409 108 36017 1.3 1 33715 2302 109 31799 1.3 1 29732 2067 110 29269 1.3 1 27294 1975 111 25299 1.3 1 23500 1799 112 22399 1.3 1 20610 1789 113 21352 1.3 1 19574 1778 114 19410 1.3 1 17712 1698 115 19560 1.3 1 17907 1653 116 18865 1.3 1 17204 1661 117 19197 1.3 1 17411 1786 118 16286 1.3 1 14784 1502 119 13223 1.3 1 11975 1248 120 11471 1.3 1 10215 1256 121 10557 1.3 1 9300 1257 122 10138 1.3 1 9061 1077 123 10990 1.3 1 9826 1164 124 9554 1.3 1 8514 1040 125 10377 1.3 1 9259 1118 126 20897 1.3 1 18962 1935 127 18296 1.3 1 16420 1876 128 9271 1.3 1 8180 1091 129 9240 1.3 1 8246 994 130 19574 1.3 1 17688 1886 131 37197 1.3 1 34730 2467 132 40733 1.3 1 38389 2344 133 67102 1.3 1 62904 4198 134 58466 1.3 1 54589 3877 135 17538 1.3 1 16342 1196 136 4875 1.3 1 4393 482 137 3204 1.3 1 2733 471 138 2278 1.3 1 1888 390 139 898 1.3 1 679 219 140 830 1.3 1 675 155 141 400 1.3 1 267 133 142 275 1.3 1 163 112 143 244 1.3 1 147 97 144 414 1.3 1 326 88 145 1650 1.3 1 1513 137 146 1285 1.3 1 1092 193 147 7354 1.3 1 6274 1080 148 4475 1.3 1 3775 700 149 1545 1.3 1 1335 210 150 16219 1.3 1 15040 1179 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth10_R2_001.fastq.gz ============================================= 84306567 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth10_R1_001_trimmed.fq.gz and Meth10_R2_001_trimmed.fq.gz file_1: Meth10_R1_001_trimmed.fq.gz, file_2: Meth10_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth10_R1_001_trimmed.fq.gz and Meth10_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth10_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth10_R2_001_val_2.fq.gz Total number of sequences analysed: 84306567 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 923660 (1.10%) >>> Now running FastQC on the validated data Meth10_R1_001_val_1.fq.gz<<< Started analysis of Meth10_R1_001_val_1.fq.gz Approx 5% complete for Meth10_R1_001_val_1.fq.gz Approx 10% complete for Meth10_R1_001_val_1.fq.gz Approx 15% complete for Meth10_R1_001_val_1.fq.gz Approx 20% complete for Meth10_R1_001_val_1.fq.gz Approx 25% complete for Meth10_R1_001_val_1.fq.gz Approx 30% complete for Meth10_R1_001_val_1.fq.gz Approx 35% complete for Meth10_R1_001_val_1.fq.gz Approx 40% complete for Meth10_R1_001_val_1.fq.gz Approx 45% complete for Meth10_R1_001_val_1.fq.gz Approx 50% complete for Meth10_R1_001_val_1.fq.gz Approx 55% complete for Meth10_R1_001_val_1.fq.gz Approx 60% complete for Meth10_R1_001_val_1.fq.gz Approx 65% complete for Meth10_R1_001_val_1.fq.gz Approx 70% complete for Meth10_R1_001_val_1.fq.gz Approx 75% complete for Meth10_R1_001_val_1.fq.gz Approx 80% complete for Meth10_R1_001_val_1.fq.gz Approx 85% complete for Meth10_R1_001_val_1.fq.gz Approx 90% complete for Meth10_R1_001_val_1.fq.gz Approx 95% complete for Meth10_R1_001_val_1.fq.gz Analysis complete for Meth10_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth10_R2_001_val_2.fq.gz<<< Started analysis of Meth10_R2_001_val_2.fq.gz Approx 5% complete for Meth10_R2_001_val_2.fq.gz Approx 10% complete for Meth10_R2_001_val_2.fq.gz Approx 15% complete for Meth10_R2_001_val_2.fq.gz Approx 20% complete for Meth10_R2_001_val_2.fq.gz Approx 25% complete for Meth10_R2_001_val_2.fq.gz Approx 30% complete for Meth10_R2_001_val_2.fq.gz Approx 35% complete for Meth10_R2_001_val_2.fq.gz Approx 40% complete for Meth10_R2_001_val_2.fq.gz Approx 45% complete for Meth10_R2_001_val_2.fq.gz Approx 50% complete for Meth10_R2_001_val_2.fq.gz Approx 55% complete for Meth10_R2_001_val_2.fq.gz Approx 60% complete for Meth10_R2_001_val_2.fq.gz Approx 65% complete for Meth10_R2_001_val_2.fq.gz Approx 70% complete for Meth10_R2_001_val_2.fq.gz Approx 75% complete for Meth10_R2_001_val_2.fq.gz Approx 80% complete for Meth10_R2_001_val_2.fq.gz Approx 85% complete for Meth10_R2_001_val_2.fq.gz Approx 90% complete for Meth10_R2_001_val_2.fq.gz Approx 95% complete for Meth10_R2_001_val_2.fq.gz Analysis complete for Meth10_R2_001_val_2.fq.gz Deleting both intermediate output files Meth10_R1_001_trimmed.fq.gz and Meth10_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth11_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth11_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_R1_001.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 1776.03 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 57,269,773 Reads with adapters: 36,706,809 (64.1%) Reads written (passing filters): 57,269,773 (100.0%) Total basepairs processed: 8,590,465,950 bp Quality-trimmed: 10,574,753 bp (0.1%) Total written (filtered): 7,658,565,162 bp (89.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 36706809 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.8% C: 16.9% G: 13.9% T: 30.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13982278 14317443.2 0 13982278 2 1272605 3579360.8 0 1272605 3 616626 894840.2 0 616626 4 399599 223710.1 0 399599 5 297560 55927.5 0 297560 6 250136 13981.9 0 250136 7 266111 3495.5 0 266111 8 288918 873.9 0 288918 9 271113 218.5 0 265390 5723 10 279544 54.6 1 264129 15415 11 294465 13.7 1 274988 19477 12 298990 3.4 1 281558 17432 13 283809 0.9 1 266082 17727 14 291926 0.9 1 272443 19483 15 289444 0.9 1 270991 18453 16 291726 0.9 1 271848 19878 17 301649 0.9 1 281196 20453 18 287390 0.9 1 270155 17235 19 282484 0.9 1 265004 17480 20 288996 0.9 1 271191 17805 21 293094 0.9 1 274500 18594 22 289715 0.9 1 272137 17578 23 294469 0.9 1 275458 19011 24 291501 0.9 1 270616 20885 25 286994 0.9 1 268986 18008 26 286191 0.9 1 268476 17715 27 293187 0.9 1 275154 18033 28 280749 0.9 1 264395 16354 29 285836 0.9 1 268364 17472 30 282183 0.9 1 267200 14983 31 276439 0.9 1 261052 15387 32 278845 0.9 1 263555 15290 33 278270 0.9 1 261863 16407 34 280484 0.9 1 264520 15964 35 270772 0.9 1 256556 14216 36 273552 0.9 1 258558 14994 37 270503 0.9 1 256113 14390 38 269801 0.9 1 254354 15447 39 307927 0.9 1 292977 14950 40 228292 0.9 1 213693 14599 41 262916 0.9 1 247928 14988 42 310441 0.9 1 295775 14666 43 214783 0.9 1 200500 14283 44 261094 0.9 1 244473 16621 45 348358 0.9 1 333791 14567 46 155990 0.9 1 145446 10544 47 246315 0.9 1 233080 13235 48 253542 0.9 1 239845 13697 49 242860 0.9 1 229843 13017 50 236542 0.9 1 222793 13749 51 256172 0.9 1 241268 14904 52 230905 0.9 1 218690 12215 53 225380 0.9 1 213051 12329 54 232326 0.9 1 219163 13163 55 232548 0.9 1 220387 12161 56 218193 0.9 1 206384 11809 57 223916 0.9 1 211977 11939 58 230390 0.9 1 218148 12242 59 207275 0.9 1 195384 11891 60 206194 0.9 1 195797 10397 61 195645 0.9 1 185124 10521 62 208679 0.9 1 197641 11038 63 208281 0.9 1 197739 10542 64 194879 0.9 1 184959 9920 65 174970 0.9 1 164625 10345 66 200053 0.9 1 189080 10973 67 204501 0.9 1 193222 11279 68 217395 0.9 1 205150 12245 69 211131 0.9 1 194236 16895 70 433015 0.9 1 417582 15433 71 38685 0.9 1 36188 2497 72 21854 0.9 1 19319 2535 73 72469 0.9 1 67203 5266 74 127570 0.9 1 120370 7200 75 140965 0.9 1 133156 7809 76 141040 0.9 1 133125 7915 77 136732 0.9 1 129051 7681 78 133000 0.9 1 125447 7553 79 130736 0.9 1 123441 7295 80 123899 0.9 1 116847 7052 81 120530 0.9 1 113828 6702 82 116290 0.9 1 109538 6752 83 113154 0.9 1 106811 6343 84 108150 0.9 1 101817 6333 85 104580 0.9 1 98445 6135 86 100366 0.9 1 94548 5818 87 98603 0.9 1 93171 5432 88 86456 0.9 1 81142 5314 89 82757 0.9 1 77660 5097 90 79793 0.9 1 74838 4955 91 77171 0.9 1 72293 4878 92 72816 0.9 1 68413 4403 93 69895 0.9 1 65420 4475 94 65365 0.9 1 61111 4254 95 61385 0.9 1 57350 4035 96 57430 0.9 1 53681 3749 97 54052 0.9 1 50321 3731 98 50877 0.9 1 47462 3415 99 47187 0.9 1 43985 3202 100 43700 0.9 1 40634 3066 101 40961 0.9 1 37957 3004 102 37929 0.9 1 35132 2797 103 35167 0.9 1 32514 2653 104 32627 0.9 1 30181 2446 105 29931 0.9 1 27484 2447 106 28066 0.9 1 25789 2277 107 25817 0.9 1 23703 2114 108 22839 0.9 1 20877 1962 109 19830 0.9 1 18204 1626 110 17973 0.9 1 16390 1583 111 16561 0.9 1 14903 1658 112 14658 0.9 1 13236 1422 113 13084 0.9 1 11717 1367 114 11483 0.9 1 10188 1295 115 10860 0.9 1 9574 1286 116 9285 0.9 1 8192 1093 117 8359 0.9 1 7430 929 118 7648 0.9 1 6652 996 119 6490 0.9 1 5641 849 120 5765 0.9 1 4943 822 121 5033 0.9 1 4278 755 122 4865 0.9 1 4139 726 123 4372 0.9 1 3730 642 124 3987 0.9 1 3368 619 125 4223 0.9 1 3593 630 126 7107 0.9 1 6256 851 127 6334 0.9 1 5554 780 128 3487 0.9 1 2933 554 129 3044 0.9 1 2511 533 130 4342 0.9 1 3706 636 131 8508 0.9 1 7754 754 132 11085 0.9 1 10293 792 133 17731 0.9 1 16507 1224 134 18066 0.9 1 16825 1241 135 5794 0.9 1 5274 520 136 1625 0.9 1 1370 255 137 938 0.9 1 721 217 138 798 0.9 1 569 229 139 380 0.9 1 255 125 140 308 0.9 1 208 100 141 151 0.9 1 74 77 142 113 0.9 1 55 58 143 76 0.9 1 46 30 144 164 0.9 1 131 33 145 570 0.9 1 476 94 146 636 0.9 1 513 123 147 3935 0.9 1 3353 582 148 2549 0.9 1 2094 455 149 1118 0.9 1 939 179 150 13768 0.9 1 12403 1365 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_R1_001.fastq.gz ============================================= 57269773 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth11_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth11_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_R2_001.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 1845.06 s (32 us/read; 1.86 M reads/minute). === Summary === Total reads processed: 57,269,773 Reads with adapters: 35,875,658 (62.6%) Reads written (passing filters): 57,269,773 (100.0%) Total basepairs processed: 8,590,465,950 bp Quality-trimmed: 49,403,829 bp (0.6%) Total written (filtered): 7,661,639,634 bp (89.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 35875658 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.6% C: 13.2% G: 17.9% T: 32.3% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13652070 14317443.2 0 13652070 2 1371554 3579360.8 0 1371554 3 670390 894840.2 0 670390 4 417479 223710.1 0 417479 5 303084 55927.5 0 303084 6 241419 13981.9 0 241419 7 247953 3495.5 0 247953 8 300759 873.9 0 300759 9 244986 218.5 0 241363 3623 10 267107 54.6 1 251813 15294 11 288379 13.7 1 266578 21801 12 308750 3.4 1 288531 20219 13 263280 0.9 1 242595 20685 14 283158 0.9 1 261771 21387 15 273211 0.9 1 254413 18798 16 295565 0.9 1 272704 22861 17 291590 0.9 1 270953 20637 18 257791 0.9 1 240881 16910 19 298939 0.9 1 278827 20112 20 294388 0.9 1 275007 19381 21 259793 0.9 1 240679 19114 22 288102 0.9 1 269983 18119 23 272758 0.9 1 255357 17401 24 302255 0.9 1 282101 20154 25 346143 0.9 1 327110 19033 26 221906 0.9 1 206394 15512 27 257508 0.9 1 239993 17515 28 266794 0.9 1 253852 12942 29 278302 0.9 1 262931 15371 30 273410 0.9 1 259852 13558 31 269441 0.9 1 255190 14251 32 265656 0.9 1 252921 12735 33 274926 0.9 1 259601 15325 34 266938 0.9 1 254391 12547 35 325149 0.9 1 310396 14753 36 211849 0.9 1 198782 13067 37 275447 0.9 1 260850 14597 38 262895 0.9 1 248000 14895 39 250310 0.9 1 239428 10882 40 261993 0.9 1 247371 14622 41 267420 0.9 1 254707 12713 42 268773 0.9 1 255253 13520 43 234071 0.9 1 222435 11636 44 301151 0.9 1 286586 14565 45 280759 0.9 1 265724 15035 46 299635 0.9 1 284753 14882 47 312695 0.9 1 301613 11082 48 157512 0.9 1 149001 8511 49 213512 0.9 1 203376 10136 50 235473 0.9 1 226110 9363 51 178012 0.9 1 169464 8548 52 234813 0.9 1 224858 9955 53 209236 0.9 1 199293 9943 54 316092 0.9 1 305412 10680 55 112244 0.9 1 105473 6771 56 220830 0.9 1 208113 12717 57 508437 0.9 1 492031 16406 58 107616 0.9 1 101036 6580 59 141028 0.9 1 132803 8225 60 328748 0.9 1 317231 11517 61 170989 0.9 1 163213 7776 62 190271 0.9 1 176527 13744 63 598469 0.9 1 582057 16412 64 196175 0.9 1 189111 7064 65 75303 0.9 1 71391 3912 66 93127 0.9 1 86983 6144 67 252236 0.9 1 243838 8398 68 139122 0.9 1 133347 5775 69 101848 0.9 1 96919 4929 70 148277 0.9 1 142823 5454 71 96395 0.9 1 92108 4287 72 94572 0.9 1 89902 4670 73 122596 0.9 1 117135 5461 74 117845 0.9 1 112409 5436 75 114732 0.9 1 109854 4878 76 85369 0.9 1 81892 3477 77 49961 0.9 1 47013 2948 78 91492 0.9 1 87404 4088 79 112415 0.9 1 107577 4838 80 115758 0.9 1 110808 4950 81 110029 0.9 1 105236 4793 82 106598 0.9 1 101879 4719 83 107411 0.9 1 102853 4558 84 102221 0.9 1 97792 4429 85 99548 0.9 1 95304 4244 86 91834 0.9 1 88022 3812 87 87435 0.9 1 83652 3783 88 82206 0.9 1 78618 3588 89 78920 0.9 1 75577 3343 90 75420 0.9 1 72180 3240 91 71229 0.9 1 68159 3070 92 66879 0.9 1 63939 2940 93 63376 0.9 1 60471 2905 94 58378 0.9 1 55732 2646 95 55848 0.9 1 53239 2609 96 52506 0.9 1 49995 2511 97 49733 0.9 1 47319 2414 98 47175 0.9 1 44951 2224 99 44576 0.9 1 42258 2318 100 41299 0.9 1 39149 2150 101 37729 0.9 1 35880 1849 102 34327 0.9 1 32542 1785 103 31505 0.9 1 29933 1572 104 29038 0.9 1 27496 1542 105 27014 0.9 1 25593 1421 106 25246 0.9 1 23877 1369 107 23541 0.9 1 22243 1298 108 20574 0.9 1 19364 1210 109 18140 0.9 1 17020 1120 110 16344 0.9 1 15303 1041 111 14718 0.9 1 13778 940 112 13229 0.9 1 12375 854 113 11880 0.9 1 10969 911 114 10325 0.9 1 9514 811 115 9876 0.9 1 9056 820 116 8659 0.9 1 7917 742 117 7984 0.9 1 7254 730 118 7051 0.9 1 6346 705 119 6120 0.9 1 5502 618 120 5404 0.9 1 4811 593 121 4475 0.9 1 3981 494 122 4366 0.9 1 3809 557 123 4026 0.9 1 3465 561 124 3652 0.9 1 3170 482 125 3933 0.9 1 3413 520 126 6525 0.9 1 5801 724 127 5731 0.9 1 5038 693 128 3229 0.9 1 2781 448 129 2875 0.9 1 2498 377 130 4906 0.9 1 4365 541 131 9003 0.9 1 8372 631 132 11425 0.9 1 10654 771 133 20494 0.9 1 19096 1398 134 19061 0.9 1 17759 1302 135 5795 0.9 1 5297 498 136 1682 0.9 1 1494 188 137 1060 0.9 1 890 170 138 733 0.9 1 578 155 139 345 0.9 1 259 86 140 325 0.9 1 255 70 141 178 0.9 1 98 80 142 100 0.9 1 57 43 143 102 0.9 1 66 36 144 193 0.9 1 140 53 145 617 0.9 1 561 56 146 465 0.9 1 385 80 147 2118 0.9 1 1805 313 148 1327 0.9 1 1096 231 149 604 0.9 1 524 80 150 6552 0.9 1 6036 516 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth11_R2_001.fastq.gz ============================================= 57269773 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth11_R1_001_trimmed.fq.gz and Meth11_R2_001_trimmed.fq.gz file_1: Meth11_R1_001_trimmed.fq.gz, file_2: Meth11_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth11_R1_001_trimmed.fq.gz and Meth11_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth11_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth11_R2_001_val_2.fq.gz Total number of sequences analysed: 57269773 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 424184 (0.74%) >>> Now running FastQC on the validated data Meth11_R1_001_val_1.fq.gz<<< Started analysis of Meth11_R1_001_val_1.fq.gz Approx 5% complete for Meth11_R1_001_val_1.fq.gz Approx 10% complete for Meth11_R1_001_val_1.fq.gz Approx 15% complete for Meth11_R1_001_val_1.fq.gz Approx 20% complete for Meth11_R1_001_val_1.fq.gz Approx 25% complete for Meth11_R1_001_val_1.fq.gz Approx 30% complete for Meth11_R1_001_val_1.fq.gz Approx 35% complete for Meth11_R1_001_val_1.fq.gz Approx 40% complete for Meth11_R1_001_val_1.fq.gz Approx 45% complete for Meth11_R1_001_val_1.fq.gz Approx 50% complete for Meth11_R1_001_val_1.fq.gz Approx 55% complete for Meth11_R1_001_val_1.fq.gz Approx 60% complete for Meth11_R1_001_val_1.fq.gz Approx 65% complete for Meth11_R1_001_val_1.fq.gz Approx 70% complete for Meth11_R1_001_val_1.fq.gz Approx 75% complete for Meth11_R1_001_val_1.fq.gz Approx 80% complete for Meth11_R1_001_val_1.fq.gz Approx 85% complete for Meth11_R1_001_val_1.fq.gz Approx 90% complete for Meth11_R1_001_val_1.fq.gz Approx 95% complete for Meth11_R1_001_val_1.fq.gz Analysis complete for Meth11_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth11_R2_001_val_2.fq.gz<<< Started analysis of Meth11_R2_001_val_2.fq.gz Approx 5% complete for Meth11_R2_001_val_2.fq.gz Approx 10% complete for Meth11_R2_001_val_2.fq.gz Approx 15% complete for Meth11_R2_001_val_2.fq.gz Approx 20% complete for Meth11_R2_001_val_2.fq.gz Approx 25% complete for Meth11_R2_001_val_2.fq.gz Approx 30% complete for Meth11_R2_001_val_2.fq.gz Approx 35% complete for Meth11_R2_001_val_2.fq.gz Approx 40% complete for Meth11_R2_001_val_2.fq.gz Approx 45% complete for Meth11_R2_001_val_2.fq.gz Approx 50% complete for Meth11_R2_001_val_2.fq.gz Approx 55% complete for Meth11_R2_001_val_2.fq.gz Approx 60% complete for Meth11_R2_001_val_2.fq.gz Approx 65% complete for Meth11_R2_001_val_2.fq.gz Approx 70% complete for Meth11_R2_001_val_2.fq.gz Approx 75% complete for Meth11_R2_001_val_2.fq.gz Approx 80% complete for Meth11_R2_001_val_2.fq.gz Approx 85% complete for Meth11_R2_001_val_2.fq.gz Approx 90% complete for Meth11_R2_001_val_2.fq.gz Approx 95% complete for Meth11_R2_001_val_2.fq.gz Analysis complete for Meth11_R2_001_val_2.fq.gz Deleting both intermediate output files Meth11_R1_001_trimmed.fq.gz and Meth11_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth12_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth12_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_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 90000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 3034.05 s (32 us/read; 1.88 M reads/minute). === Summary === Total reads processed: 95,078,293 Reads with adapters: 58,848,167 (61.9%) Reads written (passing filters): 95,078,293 (100.0%) Total basepairs processed: 14,261,743,950 bp Quality-trimmed: 18,533,032 bp (0.1%) Total written (filtered): 12,932,762,956 bp (90.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58848167 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.5% C: 15.8% G: 14.1% T: 30.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24724303 23769573.2 0 24724303 2 2192576 5942393.3 0 2192576 3 1042067 1485598.3 0 1042067 4 655261 371399.6 0 655261 5 477537 92849.9 0 477537 6 396153 23212.5 0 396153 7 423130 5803.1 0 423130 8 457423 1450.8 0 457423 9 424500 362.7 0 413006 11494 10 446196 90.7 1 415544 30652 11 465143 22.7 1 427929 37214 12 468903 5.7 1 434676 34227 13 448507 1.4 1 414045 34462 14 465166 1.4 1 427289 37877 15 459814 1.4 1 422900 36914 16 461078 1.4 1 422731 38347 17 475933 1.4 1 437158 38775 18 453848 1.4 1 419943 33905 19 447533 1.4 1 413539 33994 20 457023 1.4 1 421300 35723 21 463475 1.4 1 426882 36593 22 450325 1.4 1 416322 34003 23 463871 1.4 1 427287 36584 24 450594 1.4 1 411685 38909 25 449609 1.4 1 414677 34932 26 446248 1.4 1 411995 34253 27 452244 1.4 1 418059 34185 28 439004 1.4 1 407592 31412 29 440489 1.4 1 408593 31896 30 435869 1.4 1 407591 28278 31 427568 1.4 1 399209 28359 32 429685 1.4 1 401802 27883 33 423814 1.4 1 394888 28926 34 432669 1.4 1 403029 29640 35 425569 1.4 1 395136 30433 36 413069 1.4 1 386424 26645 37 417282 1.4 1 389564 27718 38 411299 1.4 1 384463 26836 39 422142 1.4 1 393672 28470 40 399257 1.4 1 373795 25462 41 393915 1.4 1 367460 26455 42 399370 1.4 1 372928 26442 43 407366 1.4 1 379096 28270 44 381801 1.4 1 352422 29379 45 534446 1.4 1 507061 27385 46 220922 1.4 1 202544 18378 47 368220 1.4 1 344111 24109 48 375094 1.4 1 350570 24524 49 364701 1.4 1 341114 23587 50 350179 1.4 1 326143 24036 51 366664 1.4 1 340938 25726 52 349018 1.4 1 326564 22454 53 334697 1.4 1 312062 22635 54 338534 1.4 1 315306 23228 55 336212 1.4 1 314235 21977 56 320047 1.4 1 298360 21687 57 321649 1.4 1 299684 21965 58 336816 1.4 1 315144 21672 59 289180 1.4 1 268762 20418 60 302150 1.4 1 282506 19644 61 289047 1.4 1 269271 19776 62 297706 1.4 1 277515 20191 63 286345 1.4 1 266938 19407 64 285442 1.4 1 266817 18625 65 248921 1.4 1 231411 17510 66 274014 1.4 1 254524 19490 67 298134 1.4 1 276712 21422 68 306160 1.4 1 284848 21312 69 288858 1.4 1 259564 29294 70 556317 1.4 1 531457 24860 71 55700 1.4 1 51368 4332 72 42209 1.4 1 36813 5396 73 118301 1.4 1 108470 9831 74 179033 1.4 1 166018 13015 75 191576 1.4 1 178006 13570 76 188227 1.4 1 174899 13328 77 182972 1.4 1 169832 13140 78 175656 1.4 1 162812 12844 79 169131 1.4 1 156733 12398 80 162761 1.4 1 151022 11739 81 156178 1.4 1 144598 11580 82 151404 1.4 1 140246 11158 83 144686 1.4 1 134062 10624 84 138872 1.4 1 128480 10392 85 132517 1.4 1 122836 9681 86 129438 1.4 1 119634 9804 87 125561 1.4 1 116434 9127 88 103118 1.4 1 94450 8668 89 97569 1.4 1 89261 8308 90 95148 1.4 1 87165 7983 91 91487 1.4 1 84101 7386 92 87383 1.4 1 80244 7139 93 81992 1.4 1 74884 7108 94 77741 1.4 1 71106 6635 95 72595 1.4 1 66315 6280 96 67892 1.4 1 61974 5918 97 62665 1.4 1 57134 5531 98 57692 1.4 1 52622 5070 99 53385 1.4 1 48487 4898 100 50323 1.4 1 45734 4589 101 46686 1.4 1 42289 4397 102 42837 1.4 1 38705 4132 103 39166 1.4 1 35204 3962 104 36994 1.4 1 33188 3806 105 34010 1.4 1 30482 3528 106 32507 1.4 1 29041 3466 107 29864 1.4 1 26595 3269 108 26390 1.4 1 23241 3149 109 23862 1.4 1 21026 2836 110 22353 1.4 1 19573 2780 111 19709 1.4 1 17428 2281 112 18468 1.4 1 16117 2351 113 17589 1.4 1 15276 2313 114 15699 1.4 1 13592 2107 115 15013 1.4 1 12954 2059 116 13696 1.4 1 11832 1864 117 13376 1.4 1 11519 1857 118 11439 1.4 1 9831 1608 119 10494 1.4 1 8923 1571 120 9208 1.4 1 7771 1437 121 8368 1.4 1 7017 1351 122 8186 1.4 1 6943 1243 123 9576 1.4 1 8158 1418 124 7534 1.4 1 6250 1284 125 7307 1.4 1 6055 1252 126 11486 1.4 1 10127 1359 127 10120 1.4 1 8809 1311 128 6795 1.4 1 5762 1033 129 6533 1.4 1 5639 894 130 8401 1.4 1 7399 1002 131 11952 1.4 1 10963 989 132 11110 1.4 1 10171 939 133 15296 1.4 1 14043 1253 134 13019 1.4 1 11987 1032 135 4296 1.4 1 3733 563 136 1761 1.4 1 1388 373 137 1288 1.4 1 1033 255 138 1262 1.4 1 1012 250 139 809 1.4 1 513 296 140 593 1.4 1 393 200 141 347 1.4 1 222 125 142 271 1.4 1 139 132 143 182 1.4 1 133 49 144 193 1.4 1 124 69 145 447 1.4 1 376 71 146 752 1.4 1 655 97 147 5650 1.4 1 5121 529 148 3130 1.4 1 2811 319 149 668 1.4 1 608 60 150 10162 1.4 1 9584 578 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_R1_001.fastq.gz ============================================= 95078293 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth12_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth12_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_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 90000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 3104.61 s (33 us/read; 1.84 M reads/minute). === Summary === Total reads processed: 95,078,293 Reads with adapters: 57,113,586 (60.1%) Reads written (passing filters): 95,078,293 (100.0%) Total basepairs processed: 14,261,743,950 bp Quality-trimmed: 92,575,641 bp (0.6%) Total written (filtered): 12,953,429,284 bp (90.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 57113586 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.6% C: 13.2% G: 17.1% T: 32.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 24193020 23769573.2 0 24193020 2 2321427 5942393.3 0 2321427 3 1112927 1485598.3 0 1112927 4 680627 371399.6 0 680627 5 483619 92849.9 0 483619 6 382658 23212.5 0 382658 7 400756 5803.1 0 400756 8 476670 1450.8 0 476670 9 382416 362.7 0 375652 6764 10 426382 90.7 1 397796 28586 11 452408 22.7 1 414474 37934 12 485108 5.7 1 449176 35932 13 411618 1.4 1 375474 36144 14 446720 1.4 1 409328 37392 15 434065 1.4 1 399571 34494 16 462921 1.4 1 423521 39400 17 453970 1.4 1 418071 35899 18 412189 1.4 1 381021 31168 19 465881 1.4 1 430523 35358 20 454382 1.4 1 420028 34354 21 417482 1.4 1 383546 33936 22 444470 1.4 1 412491 31979 23 425227 1.4 1 394687 30540 24 454574 1.4 1 419702 34872 25 515764 1.4 1 481969 33795 26 369041 1.4 1 340356 28685 27 406916 1.4 1 375617 31299 28 415828 1.4 1 392669 23159 29 425658 1.4 1 399987 25671 30 427967 1.4 1 404675 23292 31 404403 1.4 1 381603 22800 32 417365 1.4 1 394613 22752 33 421253 1.4 1 398025 23228 34 402594 1.4 1 378677 23917 35 411229 1.4 1 389344 21885 36 453720 1.4 1 428393 25327 37 426906 1.4 1 403017 23889 38 427072 1.4 1 401798 25274 39 370033 1.4 1 350285 19748 40 395729 1.4 1 373590 22139 41 354046 1.4 1 333306 20740 42 385438 1.4 1 367338 18100 43 351442 1.4 1 330773 20669 44 509041 1.4 1 483534 25507 45 594107 1.4 1 565356 28751 46 317778 1.4 1 296250 21528 47 639123 1.4 1 617320 21803 48 113143 1.4 1 103819 9324 49 276243 1.4 1 261915 14328 50 270853 1.4 1 258851 12002 51 213056 1.4 1 200612 12444 52 263221 1.4 1 249959 13262 53 314479 1.4 1 296892 17587 54 505518 1.4 1 486843 18675 55 130184 1.4 1 119778 10406 56 328479 1.4 1 302626 25853 57 1110749 1.4 1 1075017 35732 58 157937 1.4 1 147605 10332 59 133513 1.4 1 120361 13152 60 607224 1.4 1 584749 22475 61 162404 1.4 1 153913 8491 62 168482 1.4 1 150480 18002 63 783592 1.4 1 754929 28663 64 505892 1.4 1 487511 18381 65 72148 1.4 1 66779 5369 66 124265 1.4 1 115472 8793 67 232144 1.4 1 223086 9058 68 113041 1.4 1 106634 6407 69 114501 1.4 1 107433 7068 70 170025 1.4 1 162729 7296 71 82166 1.4 1 77671 4495 72 71726 1.4 1 67090 4636 73 96300 1.4 1 91117 5183 74 93733 1.4 1 89063 4670 75 78851 1.4 1 74152 4699 76 71610 1.4 1 67074 4536 77 100323 1.4 1 94686 5637 78 135245 1.4 1 128265 6980 79 146731 1.4 1 139375 7356 80 153260 1.4 1 145549 7711 81 140021 1.4 1 133104 6917 82 130993 1.4 1 124085 6908 83 128099 1.4 1 121346 6753 84 122775 1.4 1 116305 6470 85 115824 1.4 1 109797 6027 86 108084 1.4 1 102249 5835 87 101586 1.4 1 96167 5419 88 94186 1.4 1 88986 5200 89 89268 1.4 1 84454 4814 90 85446 1.4 1 80746 4700 91 79463 1.4 1 74923 4540 92 74553 1.4 1 70313 4240 93 69532 1.4 1 65452 4080 94 65867 1.4 1 61984 3883 95 62796 1.4 1 59022 3774 96 59091 1.4 1 55464 3627 97 54962 1.4 1 51600 3362 98 50891 1.4 1 47713 3178 99 47043 1.4 1 44089 2954 100 44441 1.4 1 41505 2936 101 40672 1.4 1 37829 2843 102 36611 1.4 1 34115 2496 103 33247 1.4 1 30785 2462 104 31409 1.4 1 29137 2272 105 29212 1.4 1 27062 2150 106 28217 1.4 1 26200 2017 107 25665 1.4 1 23681 1984 108 22174 1.4 1 20404 1770 109 20157 1.4 1 18482 1675 110 18992 1.4 1 17269 1723 111 17255 1.4 1 15590 1665 112 15341 1.4 1 13808 1533 113 15075 1.4 1 13656 1419 114 13564 1.4 1 12115 1449 115 13158 1.4 1 11734 1424 116 12995 1.4 1 11653 1342 117 12776 1.4 1 11406 1370 118 10678 1.4 1 9485 1193 119 9111 1.4 1 7944 1167 120 8420 1.4 1 7308 1112 121 7655 1.4 1 6652 1003 122 7350 1.4 1 6355 995 123 8082 1.4 1 7049 1033 124 6446 1.4 1 5619 827 125 6500 1.4 1 5610 890 126 10458 1.4 1 9294 1164 127 9129 1.4 1 8095 1034 128 6081 1.4 1 5290 791 129 5996 1.4 1 5228 768 130 8988 1.4 1 8142 846 131 12230 1.4 1 11354 876 132 10519 1.4 1 9681 838 133 16022 1.4 1 14912 1110 134 12285 1.4 1 11366 919 135 3865 1.4 1 3436 429 136 1669 1.4 1 1394 275 137 1290 1.4 1 1063 227 138 1185 1.4 1 977 208 139 704 1.4 1 527 177 140 741 1.4 1 575 166 141 476 1.4 1 343 133 142 294 1.4 1 213 81 143 286 1.4 1 174 112 144 224 1.4 1 171 53 145 534 1.4 1 487 47 146 450 1.4 1 389 61 147 2769 1.4 1 2540 229 148 1423 1.4 1 1291 132 149 450 1.4 1 429 21 150 4827 1.4 1 4616 211 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth12_R2_001.fastq.gz ============================================= 95078293 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth12_R1_001_trimmed.fq.gz and Meth12_R2_001_trimmed.fq.gz file_1: Meth12_R1_001_trimmed.fq.gz, file_2: Meth12_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth12_R1_001_trimmed.fq.gz and Meth12_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth12_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth12_R2_001_val_2.fq.gz Total number of sequences analysed: 95078293 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 655588 (0.69%) >>> Now running FastQC on the validated data Meth12_R1_001_val_1.fq.gz<<< Started analysis of Meth12_R1_001_val_1.fq.gz Approx 5% complete for Meth12_R1_001_val_1.fq.gz Approx 10% complete for Meth12_R1_001_val_1.fq.gz Approx 15% complete for Meth12_R1_001_val_1.fq.gz Approx 20% complete for Meth12_R1_001_val_1.fq.gz Approx 25% complete for Meth12_R1_001_val_1.fq.gz Approx 30% complete for Meth12_R1_001_val_1.fq.gz Approx 35% complete for Meth12_R1_001_val_1.fq.gz Approx 40% complete for Meth12_R1_001_val_1.fq.gz Approx 45% complete for Meth12_R1_001_val_1.fq.gz Approx 50% complete for Meth12_R1_001_val_1.fq.gz Approx 55% complete for Meth12_R1_001_val_1.fq.gz Approx 60% complete for Meth12_R1_001_val_1.fq.gz Approx 65% complete for Meth12_R1_001_val_1.fq.gz Approx 70% complete for Meth12_R1_001_val_1.fq.gz Approx 75% complete for Meth12_R1_001_val_1.fq.gz Approx 80% complete for Meth12_R1_001_val_1.fq.gz Approx 85% complete for Meth12_R1_001_val_1.fq.gz Approx 90% complete for Meth12_R1_001_val_1.fq.gz Approx 95% complete for Meth12_R1_001_val_1.fq.gz Analysis complete for Meth12_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth12_R2_001_val_2.fq.gz<<< Started analysis of Meth12_R2_001_val_2.fq.gz Approx 5% complete for Meth12_R2_001_val_2.fq.gz Approx 10% complete for Meth12_R2_001_val_2.fq.gz Approx 15% complete for Meth12_R2_001_val_2.fq.gz Approx 20% complete for Meth12_R2_001_val_2.fq.gz Approx 25% complete for Meth12_R2_001_val_2.fq.gz Approx 30% complete for Meth12_R2_001_val_2.fq.gz Approx 35% complete for Meth12_R2_001_val_2.fq.gz Approx 40% complete for Meth12_R2_001_val_2.fq.gz Approx 45% complete for Meth12_R2_001_val_2.fq.gz Approx 50% complete for Meth12_R2_001_val_2.fq.gz Approx 55% complete for Meth12_R2_001_val_2.fq.gz Approx 60% complete for Meth12_R2_001_val_2.fq.gz Approx 65% complete for Meth12_R2_001_val_2.fq.gz Approx 70% complete for Meth12_R2_001_val_2.fq.gz Approx 75% complete for Meth12_R2_001_val_2.fq.gz Approx 80% complete for Meth12_R2_001_val_2.fq.gz Approx 85% complete for Meth12_R2_001_val_2.fq.gz Approx 90% complete for Meth12_R2_001_val_2.fq.gz Approx 95% complete for Meth12_R2_001_val_2.fq.gz Analysis complete for Meth12_R2_001_val_2.fq.gz Deleting both intermediate output files Meth12_R1_001_trimmed.fq.gz and Meth12_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth1_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth1_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2350.59 s (31 us/read; 1.92 M reads/minute). === Summary === Total reads processed: 75,063,646 Reads with adapters: 48,328,955 (64.4%) Reads written (passing filters): 75,063,646 (100.0%) Total basepairs processed: 11,259,546,900 bp Quality-trimmed: 13,767,880 bp (0.1%) Total written (filtered): 10,038,125,535 bp (89.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 48328955 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.1% C: 16.0% G: 14.0% T: 30.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18710709 18765911.5 0 18710709 2 1656344 4691477.9 0 1656344 3 816816 1172869.5 0 816816 4 516096 293217.4 0 516096 5 376016 73304.3 0 376016 6 315457 18326.1 0 315457 7 337109 4581.5 0 337109 8 369652 1145.4 0 369652 9 335509 286.3 0 327477 8032 10 357252 71.6 1 335442 21810 11 372080 17.9 1 345243 26837 12 376270 4.5 1 351799 24471 13 361054 1.1 1 335856 25198 14 375182 1.1 1 347566 27616 15 370274 1.1 1 344585 25689 16 378696 1.1 1 350698 27998 17 390340 1.1 1 361837 28503 18 369733 1.1 1 344851 24882 19 365329 1.1 1 340187 25142 20 372175 1.1 1 346848 25327 21 378433 1.1 1 351678 26755 22 371144 1.1 1 345973 25171 23 382287 1.1 1 355300 26987 24 374251 1.1 1 345132 29119 25 373180 1.1 1 347857 25323 26 369424 1.1 1 344363 25061 27 379615 1.1 1 354423 25192 28 369357 1.1 1 345908 23449 29 366320 1.1 1 342423 23897 30 366803 1.1 1 345225 21578 31 362760 1.1 1 340028 22732 32 400561 1.1 1 377808 22753 33 328870 1.1 1 307922 20948 34 370029 1.1 1 346926 23103 35 359381 1.1 1 337247 22134 36 366007 1.1 1 342210 23797 37 354073 1.1 1 333404 20669 38 359650 1.1 1 337399 22251 39 356932 1.1 1 335239 21693 40 358506 1.1 1 336483 22023 41 349540 1.1 1 327051 22489 42 381911 1.1 1 360544 21367 43 309857 1.1 1 287977 21880 44 342623 1.1 1 317606 25017 45 487516 1.1 1 466022 21494 46 182025 1.1 1 167416 14609 47 325619 1.1 1 306447 19172 48 330513 1.1 1 310694 19819 49 330610 1.1 1 311613 18997 50 313977 1.1 1 294522 19455 51 322321 1.1 1 301535 20786 52 317755 1.1 1 299076 18679 53 305793 1.1 1 287161 18632 54 308320 1.1 1 288750 19570 55 308849 1.1 1 290247 18602 56 296634 1.1 1 278525 18109 57 297862 1.1 1 279673 18189 58 311936 1.1 1 294182 17754 59 264874 1.1 1 248209 16665 60 281522 1.1 1 265089 16433 61 267748 1.1 1 251495 16253 62 273594 1.1 1 257005 16589 63 264311 1.1 1 248380 15931 64 271183 1.1 1 255859 15324 65 228552 1.1 1 214019 14533 66 252781 1.1 1 236108 16673 67 291928 1.1 1 273531 18397 68 298209 1.1 1 280575 17634 69 273052 1.1 1 248426 24626 70 535664 1.1 1 515290 20374 71 39169 1.1 1 36074 3095 72 29751 1.1 1 25209 4542 73 116623 1.1 1 107809 8814 74 174109 1.1 1 163139 10970 75 187073 1.1 1 175273 11800 76 183577 1.1 1 172180 11397 77 176884 1.1 1 165498 11386 78 170780 1.1 1 159859 10921 79 164622 1.1 1 154127 10495 80 159951 1.1 1 149653 10298 81 153932 1.1 1 143914 10018 82 147439 1.1 1 137900 9539 83 143214 1.1 1 134040 9174 84 137291 1.1 1 128259 9032 85 132225 1.1 1 123566 8659 86 125531 1.1 1 117378 8153 87 123532 1.1 1 115683 7849 88 107193 1.1 1 99639 7554 89 100482 1.1 1 93344 7138 90 98338 1.1 1 91292 7046 91 93064 1.1 1 86350 6714 92 89428 1.1 1 82811 6617 93 83308 1.1 1 77158 6150 94 79442 1.1 1 73600 5842 95 74504 1.1 1 68842 5662 96 69303 1.1 1 63977 5326 97 64086 1.1 1 58962 5124 98 59263 1.1 1 54478 4785 99 55431 1.1 1 50932 4499 100 51141 1.1 1 46801 4340 101 48209 1.1 1 44018 4191 102 43538 1.1 1 39871 3667 103 39805 1.1 1 36098 3707 104 38756 1.1 1 35097 3659 105 35421 1.1 1 31970 3451 106 33268 1.1 1 30122 3146 107 29612 1.1 1 26680 2932 108 26797 1.1 1 24049 2748 109 23707 1.1 1 21229 2478 110 21294 1.1 1 19095 2199 111 19347 1.1 1 16984 2363 112 16813 1.1 1 14814 1999 113 16091 1.1 1 14158 1933 114 13670 1.1 1 11893 1777 115 13296 1.1 1 11498 1798 116 11809 1.1 1 10128 1681 117 11544 1.1 1 10095 1449 118 9929 1.1 1 8552 1377 119 8573 1.1 1 7300 1273 120 7809 1.1 1 6511 1298 121 6728 1.1 1 5618 1110 122 7027 1.1 1 5901 1126 123 7546 1.1 1 6434 1112 124 6267 1.1 1 5356 911 125 7049 1.1 1 5992 1057 126 14598 1.1 1 12783 1815 127 13298 1.1 1 11606 1692 128 7112 1.1 1 6061 1051 129 6533 1.1 1 5591 942 130 10720 1.1 1 9489 1231 131 20639 1.1 1 19294 1345 132 24336 1.1 1 22602 1734 133 36762 1.1 1 34343 2419 134 35478 1.1 1 33207 2271 135 11882 1.1 1 10868 1014 136 3678 1.1 1 3202 476 137 2423 1.1 1 2056 367 138 2237 1.1 1 1784 453 139 911 1.1 1 660 251 140 744 1.1 1 534 210 141 277 1.1 1 188 89 142 192 1.1 1 107 85 143 207 1.1 1 148 59 144 361 1.1 1 291 70 145 1422 1.1 1 1247 175 146 1707 1.1 1 1433 274 147 10742 1.1 1 9315 1427 148 6295 1.1 1 5220 1075 149 2023 1.1 1 1738 285 150 23032 1.1 1 20646 2386 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_R1_001.fastq.gz ============================================= 75063646 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth1_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth1_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2419.51 s (32 us/read; 1.86 M reads/minute). === Summary === Total reads processed: 75,063,646 Reads with adapters: 47,220,569 (62.9%) Reads written (passing filters): 75,063,646 (100.0%) Total basepairs processed: 11,259,546,900 bp Quality-trimmed: 59,942,666 bp (0.5%) Total written (filtered): 10,051,947,808 bp (89.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 47220569 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.3% C: 12.8% G: 17.4% T: 32.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18441421 18765911.5 0 18441421 2 1750991 4691477.9 0 1750991 3 877760 1172869.5 0 877760 4 542351 293217.4 0 542351 5 379149 73304.3 0 379149 6 303548 18326.1 0 303548 7 312527 4581.5 0 312527 8 362510 1145.4 0 362510 9 328504 286.3 0 323925 4579 10 338715 71.6 1 321858 16857 11 365879 17.9 1 339451 26428 12 397669 4.5 1 374189 23480 13 325125 1.1 1 301399 23726 14 360991 1.1 1 335177 25814 15 349921 1.1 1 325228 24693 16 382894 1.1 1 354217 28677 17 367351 1.1 1 342834 24517 18 338458 1.1 1 316318 22140 19 376286 1.1 1 352494 23792 20 379077 1.1 1 354928 24149 21 343774 1.1 1 318864 24910 22 366212 1.1 1 344159 22053 23 350055 1.1 1 328241 21814 24 376199 1.1 1 352432 23767 25 423461 1.1 1 399691 23770 26 307403 1.1 1 285842 21561 27 359312 1.1 1 334581 24731 28 345619 1.1 1 329168 16451 29 359270 1.1 1 339106 20164 30 354441 1.1 1 337793 16648 31 355057 1.1 1 336449 18608 32 350452 1.1 1 334307 16145 33 352943 1.1 1 335135 17808 34 358015 1.1 1 338908 19107 35 464708 1.1 1 445740 18968 36 273302 1.1 1 255292 18010 37 325079 1.1 1 311126 13953 38 335525 1.1 1 318863 16662 39 337577 1.1 1 322860 14717 40 367020 1.1 1 349128 17892 41 319224 1.1 1 304174 15050 42 332649 1.1 1 318337 14312 43 323823 1.1 1 308429 15394 44 334118 1.1 1 319822 14296 45 343494 1.1 1 326408 17086 46 358115 1.1 1 338836 19279 47 402427 1.1 1 387903 14524 48 283932 1.1 1 271129 12803 49 274857 1.1 1 261030 13827 50 315849 1.1 1 303139 12710 51 266831 1.1 1 254373 12458 52 311199 1.1 1 297931 13268 53 287934 1.1 1 274634 13300 54 385122 1.1 1 371431 13691 55 190442 1.1 1 179926 10516 56 295821 1.1 1 280546 15275 57 513539 1.1 1 495845 17694 58 168861 1.1 1 159586 9275 59 223841 1.1 1 212609 11232 60 384551 1.1 1 370691 13860 61 242884 1.1 1 232450 10434 62 233434 1.1 1 216179 17255 63 771347 1.1 1 750613 20734 64 193966 1.1 1 186184 7782 65 119008 1.1 1 112900 6108 66 137693 1.1 1 128970 8723 67 347444 1.1 1 336043 11401 68 204788 1.1 1 196327 8461 69 171955 1.1 1 164002 7953 70 219714 1.1 1 211438 8276 71 159973 1.1 1 153139 6834 72 143819 1.1 1 136598 7221 73 175548 1.1 1 167699 7849 74 158126 1.1 1 150516 7610 75 153760 1.1 1 147027 6733 76 103682 1.1 1 99086 4596 77 77177 1.1 1 72994 4183 78 125043 1.1 1 119651 5392 79 142945 1.1 1 136911 6034 80 147419 1.1 1 141242 6177 81 137880 1.1 1 131886 5994 82 133886 1.1 1 128062 5824 83 133032 1.1 1 127354 5678 84 127298 1.1 1 121870 5428 85 123895 1.1 1 118634 5261 86 113116 1.1 1 108201 4915 87 108156 1.1 1 103506 4650 88 101256 1.1 1 96922 4334 89 94739 1.1 1 90468 4271 90 91660 1.1 1 87538 4122 91 85089 1.1 1 81271 3818 92 80648 1.1 1 76884 3764 93 74350 1.1 1 70748 3602 94 70493 1.1 1 67010 3483 95 66098 1.1 1 62873 3225 96 62060 1.1 1 58962 3098 97 57590 1.1 1 54784 2806 98 54344 1.1 1 51575 2769 99 51367 1.1 1 48831 2536 100 47029 1.1 1 44560 2469 101 43951 1.1 1 41556 2395 102 38875 1.1 1 36878 1997 103 35306 1.1 1 33351 1955 104 34244 1.1 1 32195 2049 105 31669 1.1 1 29822 1847 106 29834 1.1 1 28041 1793 107 26571 1.1 1 24760 1811 108 23726 1.1 1 22206 1520 109 21391 1.1 1 19943 1448 110 19404 1.1 1 18072 1332 111 17107 1.1 1 15751 1356 112 14754 1.1 1 13496 1258 113 14189 1.1 1 13010 1179 114 12289 1.1 1 11217 1072 115 12191 1.1 1 11066 1125 116 11581 1.1 1 10479 1102 117 11369 1.1 1 10357 1012 118 9875 1.1 1 8914 961 119 7988 1.1 1 7169 819 120 7173 1.1 1 6327 846 121 6417 1.1 1 5647 770 122 6411 1.1 1 5646 765 123 6823 1.1 1 5985 838 124 6037 1.1 1 5272 765 125 6389 1.1 1 5701 688 126 13004 1.1 1 11810 1194 127 11807 1.1 1 10602 1205 128 6653 1.1 1 5821 832 129 6063 1.1 1 5404 659 130 12206 1.1 1 11167 1039 131 21489 1.1 1 20251 1238 132 23857 1.1 1 22552 1305 133 40790 1.1 1 38491 2299 134 36238 1.1 1 34039 2199 135 11536 1.1 1 10764 772 136 3632 1.1 1 3307 325 137 2534 1.1 1 2245 289 138 1913 1.1 1 1618 295 139 782 1.1 1 648 134 140 600 1.1 1 481 119 141 277 1.1 1 192 85 142 223 1.1 1 147 76 143 239 1.1 1 171 68 144 420 1.1 1 341 79 145 1534 1.1 1 1415 119 146 1169 1.1 1 1053 116 147 5852 1.1 1 5228 624 148 3276 1.1 1 2839 437 149 1056 1.1 1 928 128 150 10964 1.1 1 10259 705 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth1_R2_001.fastq.gz ============================================= 75063646 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth1_R1_001_trimmed.fq.gz and Meth1_R2_001_trimmed.fq.gz file_1: Meth1_R1_001_trimmed.fq.gz, file_2: Meth1_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth1_R1_001_trimmed.fq.gz and Meth1_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth1_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth1_R2_001_val_2.fq.gz Total number of sequences analysed: 75063646 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 638951 (0.85%) >>> Now running FastQC on the validated data Meth1_R1_001_val_1.fq.gz<<< Started analysis of Meth1_R1_001_val_1.fq.gz Approx 5% complete for Meth1_R1_001_val_1.fq.gz Approx 10% complete for Meth1_R1_001_val_1.fq.gz Approx 15% complete for Meth1_R1_001_val_1.fq.gz Approx 20% complete for Meth1_R1_001_val_1.fq.gz Approx 25% complete for Meth1_R1_001_val_1.fq.gz Approx 30% complete for Meth1_R1_001_val_1.fq.gz Approx 35% complete for Meth1_R1_001_val_1.fq.gz Approx 40% complete for Meth1_R1_001_val_1.fq.gz Approx 45% complete for Meth1_R1_001_val_1.fq.gz Approx 50% complete for Meth1_R1_001_val_1.fq.gz Approx 55% complete for Meth1_R1_001_val_1.fq.gz Approx 60% complete for Meth1_R1_001_val_1.fq.gz Approx 65% complete for Meth1_R1_001_val_1.fq.gz Approx 70% complete for Meth1_R1_001_val_1.fq.gz Approx 75% complete for Meth1_R1_001_val_1.fq.gz Approx 80% complete for Meth1_R1_001_val_1.fq.gz Approx 85% complete for Meth1_R1_001_val_1.fq.gz Approx 90% complete for Meth1_R1_001_val_1.fq.gz Approx 95% complete for Meth1_R1_001_val_1.fq.gz Analysis complete for Meth1_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth1_R2_001_val_2.fq.gz<<< Started analysis of Meth1_R2_001_val_2.fq.gz Approx 5% complete for Meth1_R2_001_val_2.fq.gz Approx 10% complete for Meth1_R2_001_val_2.fq.gz Approx 15% complete for Meth1_R2_001_val_2.fq.gz Approx 20% complete for Meth1_R2_001_val_2.fq.gz Approx 25% complete for Meth1_R2_001_val_2.fq.gz Approx 30% complete for Meth1_R2_001_val_2.fq.gz Approx 35% complete for Meth1_R2_001_val_2.fq.gz Approx 40% complete for Meth1_R2_001_val_2.fq.gz Approx 45% complete for Meth1_R2_001_val_2.fq.gz Approx 50% complete for Meth1_R2_001_val_2.fq.gz Approx 55% complete for Meth1_R2_001_val_2.fq.gz Approx 60% complete for Meth1_R2_001_val_2.fq.gz Approx 65% complete for Meth1_R2_001_val_2.fq.gz Approx 70% complete for Meth1_R2_001_val_2.fq.gz Approx 75% complete for Meth1_R2_001_val_2.fq.gz Approx 80% complete for Meth1_R2_001_val_2.fq.gz Approx 85% complete for Meth1_R2_001_val_2.fq.gz Approx 90% complete for Meth1_R2_001_val_2.fq.gz Approx 95% complete for Meth1_R2_001_val_2.fq.gz Analysis complete for Meth1_R2_001_val_2.fq.gz Deleting both intermediate output files Meth1_R1_001_trimmed.fq.gz and Meth1_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth2_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth2_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2624.27 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 85,631,206 Reads with adapters: 57,282,255 (66.9%) Reads written (passing filters): 85,631,206 (100.0%) Total basepairs processed: 12,844,680,900 bp Quality-trimmed: 14,442,697 bp (0.1%) Total written (filtered): 11,233,059,088 bp (87.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 57282255 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 39.0% C: 15.8% G: 14.4% T: 30.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19795384 21407801.5 0 19795384 2 1831157 5351950.4 0 1831157 3 926757 1337987.6 0 926757 4 603821 334496.9 0 603821 5 451652 83624.2 0 451652 6 378205 20906.1 0 378205 7 403795 5226.5 0 403795 8 436443 1306.6 0 436443 9 416103 326.7 0 406757 9346 10 426363 81.7 1 402339 24024 11 446359 20.4 1 416329 30030 12 454775 5.1 1 427595 27180 13 435206 1.3 1 407389 27817 14 449362 1.3 1 417876 31486 15 445789 1.3 1 416572 29217 16 454877 1.3 1 422647 32230 17 473255 1.3 1 440704 32551 18 443621 1.3 1 416449 27172 19 436922 1.3 1 408918 28004 20 450170 1.3 1 421296 28874 21 458905 1.3 1 428441 30464 22 447990 1.3 1 420221 27769 23 462431 1.3 1 432092 30339 24 454441 1.3 1 421550 32891 25 451733 1.3 1 423558 28175 26 448476 1.3 1 420062 28414 27 463444 1.3 1 434651 28793 28 444064 1.3 1 417304 26760 29 453434 1.3 1 425031 28403 30 447516 1.3 1 422943 24573 31 443184 1.3 1 417778 25406 32 445287 1.3 1 419896 25391 33 445565 1.3 1 419104 26461 34 449132 1.3 1 422627 26505 35 451421 1.3 1 425935 25486 36 440218 1.3 1 415669 24549 37 435745 1.3 1 409391 26354 38 450619 1.3 1 425510 25109 39 429021 1.3 1 403513 25508 40 442995 1.3 1 414651 28344 41 439170 1.3 1 413432 25738 42 438474 1.3 1 413080 25394 43 435312 1.3 1 406567 28745 44 421274 1.3 1 393142 28132 45 582594 1.3 1 557420 25174 46 255962 1.3 1 237698 18264 47 411180 1.3 1 387755 23425 48 415698 1.3 1 392491 23207 49 410487 1.3 1 387646 22841 50 401224 1.3 1 376899 24325 51 421955 1.3 1 395661 26294 52 400918 1.3 1 378962 21956 53 384978 1.3 1 362919 22059 54 393480 1.3 1 369548 23932 55 397328 1.3 1 375093 22235 56 378333 1.3 1 356612 21721 57 383643 1.3 1 361758 21885 58 404139 1.3 1 381578 22561 59 350550 1.3 1 329289 21261 60 363320 1.3 1 343784 19536 61 350627 1.3 1 329853 20774 62 362636 1.3 1 341936 20700 63 360017 1.3 1 339842 20175 64 356810 1.3 1 337476 19334 65 309023 1.3 1 289593 19430 66 349962 1.3 1 329415 20547 67 384101 1.3 1 361320 22781 68 402653 1.3 1 379441 23212 69 386721 1.3 1 353320 33401 70 775481 1.3 1 747274 28207 71 54931 1.3 1 50767 4164 72 36204 1.3 1 30507 5697 73 145730 1.3 1 135258 10472 74 237568 1.3 1 223313 14255 75 262450 1.3 1 246765 15685 76 261106 1.3 1 245979 15127 77 253230 1.3 1 238354 14876 78 246727 1.3 1 232073 14654 79 241945 1.3 1 227824 14121 80 234723 1.3 1 220518 14205 81 226410 1.3 1 212580 13830 82 220415 1.3 1 206778 13637 83 212539 1.3 1 199447 13092 84 205272 1.3 1 192875 12397 85 199845 1.3 1 187200 12645 86 191977 1.3 1 179982 11995 87 186256 1.3 1 175066 11190 88 168380 1.3 1 157286 11094 89 160652 1.3 1 150136 10516 90 153355 1.3 1 143204 10151 91 147798 1.3 1 137811 9987 92 140599 1.3 1 131205 9394 93 133705 1.3 1 124506 9199 94 127557 1.3 1 118673 8884 95 119487 1.3 1 111135 8352 96 113036 1.3 1 104884 8152 97 105294 1.3 1 97714 7580 98 97352 1.3 1 90031 7321 99 90866 1.3 1 84090 6776 100 85764 1.3 1 79214 6550 101 78122 1.3 1 72042 6080 102 73307 1.3 1 67567 5740 103 66894 1.3 1 61496 5398 104 62019 1.3 1 56826 5193 105 57172 1.3 1 52392 4780 106 53365 1.3 1 48680 4685 107 47995 1.3 1 43740 4255 108 43150 1.3 1 39165 3985 109 38484 1.3 1 34589 3895 110 34526 1.3 1 31071 3455 111 30197 1.3 1 27169 3028 112 27267 1.3 1 24402 2865 113 23584 1.3 1 20947 2637 114 21658 1.3 1 19157 2501 115 19636 1.3 1 17249 2387 116 16977 1.3 1 15025 1952 117 16062 1.3 1 14069 1993 118 13357 1.3 1 11596 1761 119 11489 1.3 1 9980 1509 120 9838 1.3 1 8454 1384 121 8673 1.3 1 7392 1281 122 8237 1.3 1 6894 1343 123 7662 1.3 1 6581 1081 124 6589 1.3 1 5524 1065 125 6886 1.3 1 5892 994 126 13226 1.3 1 11580 1646 127 12563 1.3 1 10921 1642 128 6272 1.3 1 5312 960 129 4969 1.3 1 4215 754 130 7569 1.3 1 6615 954 131 13966 1.3 1 12777 1189 132 17450 1.3 1 16079 1371 133 26703 1.3 1 24688 2015 134 28492 1.3 1 26527 1965 135 8982 1.3 1 8237 745 136 2813 1.3 1 2354 459 137 1891 1.3 1 1505 386 138 1471 1.3 1 1145 326 139 676 1.3 1 490 186 140 603 1.3 1 430 173 141 222 1.3 1 134 88 142 166 1.3 1 109 57 143 147 1.3 1 104 43 144 316 1.3 1 241 75 145 1193 1.3 1 988 205 146 1174 1.3 1 937 237 147 6957 1.3 1 5785 1172 148 4324 1.3 1 3523 801 149 1611 1.3 1 1370 241 150 20493 1.3 1 17957 2536 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_R1_001.fastq.gz ============================================= 85631206 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth2_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth2_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2693.95 s (31 us/read; 1.91 M reads/minute). === Summary === Total reads processed: 85,631,206 Reads with adapters: 56,009,490 (65.4%) Reads written (passing filters): 85,631,206 (100.0%) Total basepairs processed: 12,844,680,900 bp Quality-trimmed: 167,513,930 bp (1.3%) Total written (filtered): 11,245,362,120 bp (87.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 56009490 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.9% C: 12.3% G: 18.3% T: 32.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 19526925 21407801.5 0 19526925 2 1919744 5351950.4 0 1919744 3 1000302 1337987.6 0 1000302 4 624387 334496.9 0 624387 5 454674 83624.2 0 454674 6 362196 20906.1 0 362196 7 377034 5226.5 0 377034 8 444785 1306.6 0 444785 9 388832 326.7 0 383436 5396 10 407705 81.7 1 386713 20992 11 436143 20.4 1 405334 30809 12 474952 5.1 1 446573 28379 13 399014 1.3 1 369972 29042 14 433402 1.3 1 402382 31020 15 423608 1.3 1 394967 28641 16 458900 1.3 1 424925 33975 17 450236 1.3 1 420648 29588 18 404648 1.3 1 378999 25649 19 457394 1.3 1 428403 28991 20 455617 1.3 1 427230 28387 21 416268 1.3 1 386706 29562 22 445263 1.3 1 419296 25967 23 427498 1.3 1 401454 26044 24 468136 1.3 1 438862 29274 25 539381 1.3 1 510526 28855 26 359179 1.3 1 334286 24893 27 414622 1.3 1 386523 28099 28 424441 1.3 1 404630 19811 29 439823 1.3 1 415917 23906 30 438325 1.3 1 418035 20290 31 426447 1.3 1 405301 21146 32 426641 1.3 1 407330 19311 33 437578 1.3 1 415263 22315 34 450100 1.3 1 422845 27255 35 458814 1.3 1 435678 23136 36 416993 1.3 1 398079 18914 37 480885 1.3 1 458188 22697 38 411691 1.3 1 391665 20026 39 416205 1.3 1 393247 22958 40 435739 1.3 1 408154 27585 41 457623 1.3 1 433245 24378 42 434135 1.3 1 413545 20590 43 572046 1.3 1 486118 85928 44 4439629 1.3 1 4327289 112340 45 943878 1.3 1 911234 32644 46 128272 1.3 1 113627 14645 47 649748 1.3 1 632500 17248 48 112027 1.3 1 103900 8127 49 226791 1.3 1 217697 9094 50 87315 1.3 1 81645 5670 51 160416 1.3 1 152783 7633 52 131115 1.3 1 124683 6432 53 165120 1.3 1 156944 8176 54 288967 1.3 1 279986 8981 55 127760 1.3 1 119298 8462 56 303442 1.3 1 286641 16801 57 668371 1.3 1 649676 18695 58 276318 1.3 1 265945 10373 59 152522 1.3 1 138015 14507 60 753840 1.3 1 734648 19192 61 274683 1.3 1 266406 8277 62 121713 1.3 1 112855 8858 63 377150 1.3 1 360264 16886 64 665350 1.3 1 649400 15950 65 104039 1.3 1 97711 6328 66 185040 1.3 1 178240 6800 67 116812 1.3 1 112189 4623 68 75589 1.3 1 72032 3557 69 48396 1.3 1 45577 2819 70 67820 1.3 1 64844 2976 71 48667 1.3 1 45837 2830 72 50159 1.3 1 46982 3177 73 70809 1.3 1 67074 3735 74 79735 1.3 1 75654 4081 75 87261 1.3 1 82766 4495 76 99775 1.3 1 95872 3903 77 59243 1.3 1 56439 2804 78 41631 1.3 1 39083 2548 79 62831 1.3 1 59486 3345 80 105952 1.3 1 101110 4842 81 143806 1.3 1 137879 5927 82 165444 1.3 1 158559 6885 83 182667 1.3 1 175483 7184 84 179947 1.3 1 172375 7572 85 183023 1.3 1 175727 7296 86 170339 1.3 1 163207 7132 87 160845 1.3 1 154267 6578 88 154171 1.3 1 147653 6518 89 147406 1.3 1 141317 6089 90 140259 1.3 1 134485 5774 91 132661 1.3 1 127057 5604 92 126408 1.3 1 121113 5295 93 120125 1.3 1 114920 5205 94 113174 1.3 1 108198 4976 95 105900 1.3 1 101224 4676 96 100579 1.3 1 96075 4504 97 95543 1.3 1 91403 4140 98 89238 1.3 1 85105 4133 99 84749 1.3 1 80958 3791 100 80264 1.3 1 76639 3625 101 71563 1.3 1 68287 3276 102 65843 1.3 1 62764 3079 103 59920 1.3 1 56915 3005 104 55387 1.3 1 52561 2826 105 51457 1.3 1 48888 2569 106 47709 1.3 1 45121 2588 107 43372 1.3 1 41022 2350 108 38957 1.3 1 36799 2158 109 34416 1.3 1 32322 2094 110 31685 1.3 1 29917 1768 111 28010 1.3 1 26357 1653 112 25151 1.3 1 23577 1574 113 21258 1.3 1 19851 1407 114 19115 1.3 1 17637 1478 115 17407 1.3 1 16078 1329 116 15372 1.3 1 14247 1125 117 14590 1.3 1 13440 1150 118 12148 1.3 1 11131 1017 119 10485 1.3 1 9606 879 120 8898 1.3 1 8119 779 121 7605 1.3 1 6869 736 122 7263 1.3 1 6440 823 123 6993 1.3 1 6244 749 124 5779 1.3 1 5103 676 125 6277 1.3 1 5595 682 126 11920 1.3 1 10762 1158 127 11003 1.3 1 9795 1208 128 5654 1.3 1 4913 741 129 4491 1.3 1 3966 525 130 8303 1.3 1 7551 752 131 14370 1.3 1 13513 857 132 17188 1.3 1 16250 938 133 30441 1.3 1 28534 1907 134 29014 1.3 1 27337 1677 135 8819 1.3 1 8235 584 136 2701 1.3 1 2413 288 137 1834 1.3 1 1630 204 138 1309 1.3 1 1091 218 139 635 1.3 1 515 120 140 514 1.3 1 400 114 141 238 1.3 1 153 85 142 181 1.3 1 106 75 143 179 1.3 1 128 51 144 334 1.3 1 282 52 145 1211 1.3 1 1101 110 146 966 1.3 1 827 139 147 4175 1.3 1 3631 544 148 2504 1.3 1 2101 403 149 1025 1.3 1 894 131 150 10756 1.3 1 9962 794 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth2_R2_001.fastq.gz ============================================= 85631206 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth2_R1_001_trimmed.fq.gz and Meth2_R2_001_trimmed.fq.gz file_1: Meth2_R1_001_trimmed.fq.gz, file_2: Meth2_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth2_R1_001_trimmed.fq.gz and Meth2_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth2_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth2_R2_001_val_2.fq.gz Total number of sequences analysed: 85631206 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 671988 (0.78%) >>> Now running FastQC on the validated data Meth2_R1_001_val_1.fq.gz<<< Started analysis of Meth2_R1_001_val_1.fq.gz Approx 5% complete for Meth2_R1_001_val_1.fq.gz Approx 10% complete for Meth2_R1_001_val_1.fq.gz Approx 15% complete for Meth2_R1_001_val_1.fq.gz Approx 20% complete for Meth2_R1_001_val_1.fq.gz Approx 25% complete for Meth2_R1_001_val_1.fq.gz Approx 30% complete for Meth2_R1_001_val_1.fq.gz Approx 35% complete for Meth2_R1_001_val_1.fq.gz Approx 40% complete for Meth2_R1_001_val_1.fq.gz Approx 45% complete for Meth2_R1_001_val_1.fq.gz Approx 50% complete for Meth2_R1_001_val_1.fq.gz Approx 55% complete for Meth2_R1_001_val_1.fq.gz Approx 60% complete for Meth2_R1_001_val_1.fq.gz Approx 65% complete for Meth2_R1_001_val_1.fq.gz Approx 70% complete for Meth2_R1_001_val_1.fq.gz Approx 75% complete for Meth2_R1_001_val_1.fq.gz Approx 80% complete for Meth2_R1_001_val_1.fq.gz Approx 85% complete for Meth2_R1_001_val_1.fq.gz Approx 90% complete for Meth2_R1_001_val_1.fq.gz Approx 95% complete for Meth2_R1_001_val_1.fq.gz Analysis complete for Meth2_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth2_R2_001_val_2.fq.gz<<< Started analysis of Meth2_R2_001_val_2.fq.gz Approx 5% complete for Meth2_R2_001_val_2.fq.gz Approx 10% complete for Meth2_R2_001_val_2.fq.gz Approx 15% complete for Meth2_R2_001_val_2.fq.gz Approx 20% complete for Meth2_R2_001_val_2.fq.gz Approx 25% complete for Meth2_R2_001_val_2.fq.gz Approx 30% complete for Meth2_R2_001_val_2.fq.gz Approx 35% complete for Meth2_R2_001_val_2.fq.gz Approx 40% complete for Meth2_R2_001_val_2.fq.gz Approx 45% complete for Meth2_R2_001_val_2.fq.gz Approx 50% complete for Meth2_R2_001_val_2.fq.gz Approx 55% complete for Meth2_R2_001_val_2.fq.gz Approx 60% complete for Meth2_R2_001_val_2.fq.gz Approx 65% complete for Meth2_R2_001_val_2.fq.gz Approx 70% complete for Meth2_R2_001_val_2.fq.gz Approx 75% complete for Meth2_R2_001_val_2.fq.gz Approx 80% complete for Meth2_R2_001_val_2.fq.gz Approx 85% complete for Meth2_R2_001_val_2.fq.gz Approx 90% complete for Meth2_R2_001_val_2.fq.gz Approx 95% complete for Meth2_R2_001_val_2.fq.gz Analysis complete for Meth2_R2_001_val_2.fq.gz Deleting both intermediate output files Meth2_R1_001_trimmed.fq.gz and Meth2_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth3_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth3_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2458.49 s (31 us/read; 1.91 M reads/minute). === Summary === Total reads processed: 78,207,503 Reads with adapters: 50,905,854 (65.1%) Reads written (passing filters): 78,207,503 (100.0%) Total basepairs processed: 11,731,125,450 bp Quality-trimmed: 14,629,344 bp (0.1%) Total written (filtered): 10,447,177,853 bp (89.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 50905854 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.8% C: 15.8% G: 14.6% T: 30.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18817186 19551875.8 0 18817186 2 1783364 4887968.9 0 1783364 3 892389 1221992.2 0 892389 4 569400 305498.1 0 569400 5 423376 76374.5 0 423376 6 353954 19093.6 0 353954 7 376976 4773.4 0 376976 8 404842 1193.4 0 404842 9 383998 298.3 0 374161 9837 10 398945 74.6 1 372433 26512 11 419208 18.6 1 386656 32552 12 428299 4.7 1 398529 29770 13 408665 1.2 1 378326 30339 14 420407 1.2 1 387104 33303 15 415779 1.2 1 384698 31081 16 425713 1.2 1 391243 34470 17 440543 1.2 1 405444 35099 18 417127 1.2 1 386514 30613 19 417440 1.2 1 381450 35990 20 592704 1.2 1 559369 33335 21 231658 1.2 1 208654 23004 22 415710 1.2 1 385594 30116 23 421739 1.2 1 389550 32189 24 420590 1.2 1 386019 34571 25 417350 1.2 1 386691 30659 26 413517 1.2 1 382950 30567 27 425625 1.2 1 394344 31281 28 409930 1.2 1 381716 28214 29 408321 1.2 1 378347 29974 30 409954 1.2 1 383875 26079 31 401045 1.2 1 374303 26742 32 402276 1.2 1 375995 26281 33 402045 1.2 1 373824 28221 34 414761 1.2 1 386170 28591 35 393735 1.2 1 367518 26217 36 399759 1.2 1 373763 25996 37 401927 1.2 1 374767 27160 38 388944 1.2 1 362977 25967 39 391373 1.2 1 365701 25672 40 381102 1.2 1 354682 26420 41 387443 1.2 1 361149 26294 42 381731 1.2 1 354861 26870 43 407676 1.2 1 380344 27332 44 357090 1.2 1 327702 29388 45 520315 1.2 1 494123 26192 46 210639 1.2 1 192990 17649 47 353811 1.2 1 330336 23475 48 376826 1.2 1 352451 24375 49 349095 1.2 1 326037 23058 50 342832 1.2 1 318729 24103 51 363752 1.2 1 338574 25178 52 332956 1.2 1 311367 21589 53 326829 1.2 1 305003 21826 54 337460 1.2 1 313355 24105 55 339870 1.2 1 317368 22502 56 311904 1.2 1 291006 20898 57 323083 1.2 1 301244 21839 58 324642 1.2 1 303248 21394 59 305142 1.2 1 283969 21173 60 297671 1.2 1 278735 18936 61 276080 1.2 1 256957 19123 62 299046 1.2 1 278885 20161 63 295827 1.2 1 276987 18840 64 272339 1.2 1 255033 17306 65 245991 1.2 1 227775 18216 66 288339 1.2 1 268412 19927 67 287848 1.2 1 267360 20488 68 299672 1.2 1 278833 20839 69 295519 1.2 1 266251 29268 70 570524 1.2 1 545560 24964 71 57451 1.2 1 53306 4145 72 35309 1.2 1 30622 4687 73 106668 1.2 1 97282 9386 74 176529 1.2 1 163971 12558 75 193880 1.2 1 180697 13183 76 190907 1.2 1 177555 13352 77 185648 1.2 1 172591 13057 78 178529 1.2 1 165843 12686 79 173796 1.2 1 161433 12363 80 166512 1.2 1 154297 12215 81 158669 1.2 1 147242 11427 82 152136 1.2 1 140959 11177 83 148455 1.2 1 137752 10703 84 140525 1.2 1 130109 10416 85 135307 1.2 1 125401 9906 86 129878 1.2 1 120437 9441 87 127114 1.2 1 118137 8977 88 109146 1.2 1 100293 8853 89 102693 1.2 1 94474 8219 90 99179 1.2 1 91224 7955 91 94918 1.2 1 87265 7653 92 89739 1.2 1 82767 6972 93 84019 1.2 1 77306 6713 94 80177 1.2 1 73547 6630 95 73687 1.2 1 67531 6156 96 69046 1.2 1 63301 5745 97 64353 1.2 1 58824 5529 98 59004 1.2 1 53973 5031 99 55232 1.2 1 50308 4924 100 51146 1.2 1 46429 4717 101 46745 1.2 1 42408 4337 102 43477 1.2 1 39414 4063 103 40009 1.2 1 36090 3919 104 37133 1.2 1 33555 3578 105 33471 1.2 1 29999 3472 106 31753 1.2 1 28541 3212 107 28501 1.2 1 25396 3105 108 25705 1.2 1 22845 2860 109 22666 1.2 1 20018 2648 110 20438 1.2 1 18101 2337 111 18683 1.2 1 16379 2304 112 16807 1.2 1 14757 2050 113 15324 1.2 1 13182 2142 114 14175 1.2 1 12324 1851 115 13144 1.2 1 11369 1775 116 11693 1.2 1 10123 1570 117 10822 1.2 1 9357 1465 118 9339 1.2 1 7947 1392 119 8393 1.2 1 7216 1177 120 7446 1.2 1 6375 1071 121 6919 1.2 1 5850 1069 122 6889 1.2 1 5796 1093 123 6093 1.2 1 5076 1017 124 5367 1.2 1 4593 774 125 5326 1.2 1 4452 874 126 8640 1.2 1 7514 1126 127 7616 1.2 1 6486 1130 128 5120 1.2 1 4334 786 129 4442 1.2 1 3874 568 130 6057 1.2 1 5296 761 131 8942 1.2 1 8185 757 132 9735 1.2 1 8905 830 133 14509 1.2 1 13462 1047 134 13139 1.2 1 12133 1006 135 3664 1.2 1 3222 442 136 1502 1.2 1 1202 300 137 976 1.2 1 770 206 138 828 1.2 1 590 238 139 536 1.2 1 374 162 140 515 1.2 1 348 167 141 311 1.2 1 196 115 142 248 1.2 1 135 113 143 160 1.2 1 86 74 144 179 1.2 1 130 49 145 442 1.2 1 392 50 146 544 1.2 1 463 81 147 4447 1.2 1 3941 506 148 2391 1.2 1 2095 296 149 1013 1.2 1 902 111 150 10300 1.2 1 9636 664 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_R1_001.fastq.gz ============================================= 78207503 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth3_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth3_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2483.85 s (32 us/read; 1.89 M reads/minute). === Summary === Total reads processed: 78,207,503 Reads with adapters: 49,568,577 (63.4%) Reads written (passing filters): 78,207,503 (100.0%) Total basepairs processed: 11,731,125,450 bp Quality-trimmed: 89,899,767 bp (0.8%) Total written (filtered): 10,460,935,613 bp (89.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 49568577 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.9% C: 12.8% G: 18.2% T: 32.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18539356 19551875.8 0 18539356 2 1849311 4887968.9 0 1849311 3 944620 1221992.2 0 944620 4 578894 305498.1 0 578894 5 422973 76374.5 0 422973 6 345562 19093.6 0 345562 7 358049 4773.4 0 358049 8 411077 1193.4 0 411077 9 362389 298.3 0 357124 5265 10 381564 74.6 1 361732 19832 11 409069 18.6 1 379131 29938 12 445640 4.7 1 418576 27064 13 371519 1.2 1 343726 27793 14 407030 1.2 1 377761 29269 15 394357 1.2 1 367019 27338 16 424138 1.2 1 392651 31487 17 413729 1.2 1 385841 27888 18 382883 1.2 1 357587 25296 19 418080 1.2 1 391101 26979 20 417411 1.2 1 390369 27042 21 391108 1.2 1 362638 28470 22 408757 1.2 1 383321 25436 23 393814 1.2 1 369011 24803 24 412766 1.2 1 385708 27058 25 471235 1.2 1 444153 27082 26 350024 1.2 1 325902 24122 27 397639 1.2 1 369817 27822 28 384311 1.2 1 365334 18977 29 401600 1.2 1 378414 23186 30 395236 1.2 1 376122 19114 31 394822 1.2 1 373357 21465 32 385298 1.2 1 366431 18867 33 399697 1.2 1 374939 24758 34 415117 1.2 1 391453 23664 35 384868 1.2 1 363212 21656 36 659327 1.2 1 621294 38033 37 507203 1.2 1 483879 23324 38 304492 1.2 1 288746 15746 39 296264 1.2 1 281203 15061 40 470852 1.2 1 452591 18261 41 259522 1.2 1 244158 15364 42 572654 1.2 1 552085 20569 43 222572 1.2 1 206678 15894 44 625256 1.2 1 598412 26844 45 702038 1.2 1 674299 27739 46 494705 1.2 1 475948 18757 47 250853 1.2 1 240811 10042 48 147136 1.2 1 136438 10698 49 358439 1.2 1 344038 14401 50 249649 1.2 1 238344 11305 51 199048 1.2 1 188340 10708 52 303896 1.2 1 291832 12064 53 210722 1.2 1 198585 12137 54 457860 1.2 1 443475 14385 55 120848 1.2 1 111748 9100 56 305440 1.2 1 283518 21922 57 998481 1.2 1 970374 28107 58 180329 1.2 1 171158 9171 59 116785 1.2 1 106111 10674 60 524354 1.2 1 507313 17041 61 180736 1.2 1 170243 10493 62 327554 1.2 1 310625 16929 63 506382 1.2 1 487868 18514 64 446330 1.2 1 433304 13026 65 73949 1.2 1 69257 4692 66 109192 1.2 1 102378 6814 67 214512 1.2 1 206484 8028 68 149090 1.2 1 142909 6181 69 69425 1.2 1 64744 4681 70 153867 1.2 1 147938 5929 71 80198 1.2 1 75629 4569 72 101557 1.2 1 95775 5782 73 145609 1.2 1 138466 7143 74 155465 1.2 1 147923 7542 75 159520 1.2 1 152263 7257 76 116339 1.2 1 111346 4993 77 50516 1.2 1 47090 3426 78 95348 1.2 1 90287 5061 79 140311 1.2 1 133878 6433 80 148951 1.2 1 142454 6497 81 143448 1.2 1 136993 6455 82 135865 1.2 1 129452 6413 83 135967 1.2 1 129569 6398 84 128099 1.2 1 122316 5783 85 123123 1.2 1 117414 5709 86 113136 1.2 1 107634 5502 87 107555 1.2 1 102317 5238 88 101023 1.2 1 96209 4814 89 95718 1.2 1 91053 4665 90 91400 1.2 1 87034 4366 91 85664 1.2 1 81443 4221 92 80116 1.2 1 76135 3981 93 73885 1.2 1 70135 3750 94 69022 1.2 1 65595 3427 95 64635 1.2 1 61531 3104 96 61070 1.2 1 57912 3158 97 57154 1.2 1 54105 3049 98 53409 1.2 1 50430 2979 99 50276 1.2 1 47528 2748 100 46585 1.2 1 44041 2544 101 41923 1.2 1 39432 2491 102 37986 1.2 1 35777 2209 103 34666 1.2 1 32646 2020 104 32310 1.2 1 30269 2041 105 29339 1.2 1 27528 1811 106 27580 1.2 1 25824 1756 107 24918 1.2 1 23421 1497 108 22129 1.2 1 20628 1501 109 19519 1.2 1 18111 1408 110 17761 1.2 1 16342 1419 111 15873 1.2 1 14623 1250 112 14303 1.2 1 13142 1161 113 13031 1.2 1 11936 1095 114 12305 1.2 1 11225 1080 115 11537 1.2 1 10507 1030 116 10703 1.2 1 9682 1021 117 10337 1.2 1 9413 924 118 8557 1.2 1 7670 887 119 7393 1.2 1 6592 801 120 6751 1.2 1 6045 706 121 6160 1.2 1 5454 706 122 6048 1.2 1 5311 737 123 5430 1.2 1 4751 679 124 4891 1.2 1 4280 611 125 5107 1.2 1 4385 722 126 7783 1.2 1 6987 796 127 6776 1.2 1 6046 730 128 4498 1.2 1 3916 582 129 4199 1.2 1 3731 468 130 6765 1.2 1 6171 594 131 9581 1.2 1 8922 659 132 9830 1.2 1 9217 613 133 16128 1.2 1 15146 982 134 13224 1.2 1 12384 840 135 3563 1.2 1 3260 303 136 1575 1.2 1 1333 242 137 1108 1.2 1 907 201 138 789 1.2 1 636 153 139 599 1.2 1 462 137 140 476 1.2 1 365 111 141 398 1.2 1 317 81 142 243 1.2 1 158 85 143 175 1.2 1 133 42 144 193 1.2 1 161 32 145 483 1.2 1 438 45 146 386 1.2 1 340 46 147 2094 1.2 1 1904 190 148 1128 1.2 1 1025 103 149 449 1.2 1 404 45 150 4908 1.2 1 4708 200 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth3_R2_001.fastq.gz ============================================= 78207503 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth3_R1_001_trimmed.fq.gz and Meth3_R2_001_trimmed.fq.gz file_1: Meth3_R1_001_trimmed.fq.gz, file_2: Meth3_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth3_R1_001_trimmed.fq.gz and Meth3_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth3_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth3_R2_001_val_2.fq.gz Total number of sequences analysed: 78207503 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 535230 (0.68%) >>> Now running FastQC on the validated data Meth3_R1_001_val_1.fq.gz<<< Started analysis of Meth3_R1_001_val_1.fq.gz Approx 5% complete for Meth3_R1_001_val_1.fq.gz Approx 10% complete for Meth3_R1_001_val_1.fq.gz Approx 15% complete for Meth3_R1_001_val_1.fq.gz Approx 20% complete for Meth3_R1_001_val_1.fq.gz Approx 25% complete for Meth3_R1_001_val_1.fq.gz Approx 30% complete for Meth3_R1_001_val_1.fq.gz Approx 35% complete for Meth3_R1_001_val_1.fq.gz Approx 40% complete for Meth3_R1_001_val_1.fq.gz Approx 45% complete for Meth3_R1_001_val_1.fq.gz Approx 50% complete for Meth3_R1_001_val_1.fq.gz Approx 55% complete for Meth3_R1_001_val_1.fq.gz Approx 60% complete for Meth3_R1_001_val_1.fq.gz Approx 65% complete for Meth3_R1_001_val_1.fq.gz Approx 70% complete for Meth3_R1_001_val_1.fq.gz Approx 75% complete for Meth3_R1_001_val_1.fq.gz Approx 80% complete for Meth3_R1_001_val_1.fq.gz Approx 85% complete for Meth3_R1_001_val_1.fq.gz Approx 90% complete for Meth3_R1_001_val_1.fq.gz Approx 95% complete for Meth3_R1_001_val_1.fq.gz Analysis complete for Meth3_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth3_R2_001_val_2.fq.gz<<< Started analysis of Meth3_R2_001_val_2.fq.gz Approx 5% complete for Meth3_R2_001_val_2.fq.gz Approx 10% complete for Meth3_R2_001_val_2.fq.gz Approx 15% complete for Meth3_R2_001_val_2.fq.gz Approx 20% complete for Meth3_R2_001_val_2.fq.gz Approx 25% complete for Meth3_R2_001_val_2.fq.gz Approx 30% complete for Meth3_R2_001_val_2.fq.gz Approx 35% complete for Meth3_R2_001_val_2.fq.gz Approx 40% complete for Meth3_R2_001_val_2.fq.gz Approx 45% complete for Meth3_R2_001_val_2.fq.gz Approx 50% complete for Meth3_R2_001_val_2.fq.gz Approx 55% complete for Meth3_R2_001_val_2.fq.gz Approx 60% complete for Meth3_R2_001_val_2.fq.gz Approx 65% complete for Meth3_R2_001_val_2.fq.gz Approx 70% complete for Meth3_R2_001_val_2.fq.gz Approx 75% complete for Meth3_R2_001_val_2.fq.gz Approx 80% complete for Meth3_R2_001_val_2.fq.gz Approx 85% complete for Meth3_R2_001_val_2.fq.gz Approx 90% complete for Meth3_R2_001_val_2.fq.gz Approx 95% complete for Meth3_R2_001_val_2.fq.gz Analysis complete for Meth3_R2_001_val_2.fq.gz Deleting both intermediate output files Meth3_R1_001_trimmed.fq.gz and Meth3_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth7_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth7_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_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 90000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2949.95 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 96,207,245 Reads with adapters: 66,820,598 (69.5%) Reads written (passing filters): 96,207,245 (100.0%) Total basepairs processed: 14,431,086,750 bp Quality-trimmed: 19,271,839 bp (0.1%) Total written (filtered): 12,420,465,978 bp (86.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 66820598 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.6% C: 16.4% G: 16.1% T: 30.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18893415 24051811.2 0 18893415 2 2075402 6012952.8 0 2075402 3 1074832 1503238.2 0 1074832 4 730565 375809.6 0 730565 5 580700 93952.4 0 580700 6 491843 23488.1 0 491843 7 522550 5872.0 0 522550 8 574535 1468.0 0 574535 9 523760 367.0 0 511010 12750 10 551855 91.8 1 517158 34697 11 582007 22.9 1 539163 42844 12 586589 5.7 1 548044 38545 13 567003 1.4 1 527337 39666 14 586004 1.4 1 542029 43975 15 586147 1.4 1 543616 42531 16 593848 1.4 1 549250 44598 17 620099 1.4 1 573194 46905 18 588658 1.4 1 548830 39828 19 579962 1.4 1 539737 40225 20 594745 1.4 1 553187 41558 21 607750 1.4 1 564289 43461 22 598226 1.4 1 557033 41193 23 635604 1.4 1 590527 45077 24 586555 1.4 1 539603 46952 25 605497 1.4 1 563591 41906 26 593682 1.4 1 552487 41195 27 612737 1.4 1 570472 42265 28 603319 1.4 1 562873 40446 29 601801 1.4 1 560787 41014 30 597397 1.4 1 560562 36835 31 589632 1.4 1 552154 37478 32 599864 1.4 1 562538 37326 33 600972 1.4 1 561842 39130 34 609415 1.4 1 570334 39081 35 596730 1.4 1 557997 38733 36 621741 1.4 1 581719 40022 37 598406 1.4 1 554479 43927 38 587255 1.4 1 552033 35222 39 606528 1.4 1 564104 42424 40 764827 1.4 1 726986 37841 41 404975 1.4 1 371970 33005 42 576453 1.4 1 541025 35428 43 612011 1.4 1 571195 40816 44 570091 1.4 1 527482 42609 45 797978 1.4 1 760167 37811 46 331195 1.4 1 305285 25910 47 554541 1.4 1 520335 34206 48 566789 1.4 1 531638 35151 49 558560 1.4 1 524333 34227 50 538884 1.4 1 503131 35753 51 560715 1.4 1 522963 37752 52 539256 1.4 1 506364 32892 53 524054 1.4 1 491032 33022 54 528681 1.4 1 494411 34270 55 534643 1.4 1 500987 33656 56 507072 1.4 1 475525 31547 57 515673 1.4 1 483351 32322 58 533527 1.4 1 501349 32178 59 459223 1.4 1 429002 30221 60 487148 1.4 1 457924 29224 61 460611 1.4 1 431426 29185 62 478646 1.4 1 448702 29944 63 469042 1.4 1 439966 29076 64 466395 1.4 1 438681 27714 65 397730 1.4 1 370996 26734 66 453532 1.4 1 423943 29589 67 508141 1.4 1 475422 32719 68 528689 1.4 1 495643 33046 69 491943 1.4 1 448180 43763 70 935459 1.4 1 897026 38433 71 66887 1.4 1 61349 5538 72 47925 1.4 1 40567 7358 73 198195 1.4 1 183494 14701 74 302845 1.4 1 283180 19665 75 326283 1.4 1 305671 20612 76 322166 1.4 1 301376 20790 77 312601 1.4 1 292445 20156 78 301088 1.4 1 281054 20034 79 294019 1.4 1 274810 19209 80 282610 1.4 1 263801 18809 81 270475 1.4 1 252551 17924 82 261004 1.4 1 243724 17280 83 251344 1.4 1 234576 16768 84 240432 1.4 1 224432 16000 85 232334 1.4 1 216933 15401 86 221499 1.4 1 206669 14830 87 215211 1.4 1 200849 14362 88 189862 1.4 1 176031 13831 89 178105 1.4 1 164999 13106 90 172068 1.4 1 159584 12484 91 166119 1.4 1 154162 11957 92 157287 1.4 1 146104 11183 93 146262 1.4 1 135496 10766 94 138741 1.4 1 128833 9908 95 129089 1.4 1 119561 9528 96 120481 1.4 1 111443 9038 97 110869 1.4 1 102513 8356 98 102578 1.4 1 94496 8082 99 94646 1.4 1 87244 7402 100 89245 1.4 1 82113 7132 101 81358 1.4 1 74573 6785 102 74918 1.4 1 68660 6258 103 68945 1.4 1 63064 5881 104 63207 1.4 1 57686 5521 105 57242 1.4 1 52246 4996 106 52314 1.4 1 47521 4793 107 47066 1.4 1 42551 4515 108 42246 1.4 1 38201 4045 109 38600 1.4 1 34623 3977 110 33927 1.4 1 30387 3540 111 30596 1.4 1 27273 3323 112 27117 1.4 1 24103 3014 113 24611 1.4 1 21688 2923 114 21494 1.4 1 18841 2653 115 19212 1.4 1 16899 2313 116 17131 1.4 1 14849 2282 117 15036 1.4 1 13033 2003 118 13359 1.4 1 11542 1817 119 11717 1.4 1 10030 1687 120 10232 1.4 1 8719 1513 121 9285 1.4 1 7764 1521 122 8582 1.4 1 7202 1380 123 7857 1.4 1 6556 1301 124 7039 1.4 1 5809 1230 125 6765 1.4 1 5698 1067 126 8112 1.4 1 6897 1215 127 7797 1.4 1 6701 1096 128 6069 1.4 1 5118 951 129 5321 1.4 1 4563 758 130 5103 1.4 1 4363 740 131 6000 1.4 1 5279 721 132 5773 1.4 1 5003 770 133 7617 1.4 1 6735 882 134 6688 1.4 1 5947 741 135 2292 1.4 1 1834 458 136 1048 1.4 1 766 282 137 826 1.4 1 531 295 138 753 1.4 1 528 225 139 505 1.4 1 270 235 140 421 1.4 1 268 153 141 292 1.4 1 159 133 142 235 1.4 1 136 99 143 174 1.4 1 110 64 144 168 1.4 1 104 64 145 287 1.4 1 221 66 146 324 1.4 1 266 58 147 2001 1.4 1 1767 234 148 1053 1.4 1 933 120 149 368 1.4 1 330 38 150 5131 1.4 1 4735 396 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_R1_001.fastq.gz ============================================= 96207245 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth7_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth7_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_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 90000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2940.87 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 96,207,245 Reads with adapters: 65,385,386 (68.0%) Reads written (passing filters): 96,207,245 (100.0%) Total basepairs processed: 14,431,086,750 bp Quality-trimmed: 141,077,461 bp (1.0%) Total written (filtered): 12,438,890,323 bp (86.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 65385386 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.7% C: 13.4% G: 20.1% T: 31.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18976422 24051811.2 0 18976422 2 2084710 6012952.8 0 2084710 3 1114269 1503238.2 0 1114269 4 725430 375809.6 0 725430 5 575667 93952.4 0 575667 6 479732 23488.1 0 479732 7 490148 5872.0 0 490148 8 553113 1468.0 0 553113 9 522583 367.0 0 515106 7477 10 526865 91.8 1 500542 26323 11 574255 22.9 1 532022 42233 12 618664 5.7 1 582766 35898 13 515306 1.4 1 477436 37870 14 567248 1.4 1 527150 40098 15 556525 1.4 1 517670 38855 16 600683 1.4 1 556105 44578 17 578663 1.4 1 539848 38815 18 551760 1.4 1 515289 36471 19 591009 1.4 1 552541 38468 20 614368 1.4 1 574530 39838 21 559014 1.4 1 518297 40717 22 590914 1.4 1 555307 35607 23 567898 1.4 1 532224 35674 24 602977 1.4 1 563732 39245 25 687263 1.4 1 647776 39487 26 511894 1.4 1 475420 36474 27 582949 1.4 1 540349 42600 28 566240 1.4 1 538534 27706 29 593508 1.4 1 558042 35466 30 585073 1.4 1 555540 29533 31 575808 1.4 1 543989 31819 32 578263 1.4 1 549329 28934 33 596984 1.4 1 560950 36034 34 620394 1.4 1 585134 35260 35 598011 1.4 1 552996 45015 36 2015543 1.4 1 1933590 81953 37 377082 1.4 1 353958 23124 38 347407 1.4 1 324143 23264 39 592172 1.4 1 565324 26848 40 453726 1.4 1 432610 21116 41 515119 1.4 1 487693 27426 42 638286 1.4 1 611756 26530 43 557445 1.4 1 526316 31129 44 839063 1.4 1 799731 39332 45 1205982 1.4 1 1158564 47418 46 532775 1.4 1 506220 26555 47 499256 1.4 1 482014 17242 48 162667 1.4 1 148284 14383 49 507253 1.4 1 485193 22060 50 346329 1.4 1 330530 15799 51 325411 1.4 1 307710 17701 52 434741 1.4 1 415955 18786 53 413056 1.4 1 391459 21597 54 756415 1.4 1 732185 24230 55 184485 1.4 1 169529 14956 56 514428 1.4 1 474010 40418 57 1816126 1.4 1 1765396 50730 58 293380 1.4 1 278459 14921 59 165112 1.4 1 146129 18983 60 974101 1.4 1 943492 30609 61 262487 1.4 1 248279 14208 62 339380 1.4 1 314753 24627 63 956017 1.4 1 919696 36321 64 966391 1.4 1 939647 26744 65 107259 1.4 1 99996 7263 66 175124 1.4 1 164258 10866 67 315204 1.4 1 303712 11492 68 190116 1.4 1 181736 8380 69 118894 1.4 1 111249 7645 70 224215 1.4 1 215523 8692 71 108384 1.4 1 102740 5644 72 119228 1.4 1 111869 7359 73 174139 1.4 1 165297 8842 74 183694 1.4 1 174810 8884 75 177881 1.4 1 168820 9061 76 164876 1.4 1 157771 7105 77 92427 1.4 1 86556 5871 78 176116 1.4 1 167530 8586 79 239174 1.4 1 228659 10515 80 256644 1.4 1 245471 11173 81 247199 1.4 1 236188 11011 82 234648 1.4 1 223875 10773 83 230736 1.4 1 220108 10628 84 220072 1.4 1 210112 9960 85 211986 1.4 1 202424 9562 86 195550 1.4 1 186387 9163 87 186259 1.4 1 177344 8915 88 176228 1.4 1 167985 8243 89 165856 1.4 1 157863 7993 90 159561 1.4 1 152195 7366 91 150635 1.4 1 143456 7179 92 141718 1.4 1 134942 6776 93 131393 1.4 1 125103 6290 94 122509 1.4 1 116488 6021 95 115329 1.4 1 109506 5823 96 108643 1.4 1 103045 5598 97 101748 1.4 1 96544 5204 98 94490 1.4 1 89763 4727 99 88228 1.4 1 83723 4505 100 83051 1.4 1 78528 4523 101 73833 1.4 1 69876 3957 102 66993 1.4 1 63319 3674 103 61193 1.4 1 57721 3472 104 56064 1.4 1 52809 3255 105 51256 1.4 1 48227 3029 106 46630 1.4 1 43636 2994 107 42299 1.4 1 39691 2608 108 37454 1.4 1 34998 2456 109 34020 1.4 1 31730 2290 110 29847 1.4 1 27644 2203 111 26771 1.4 1 24802 1969 112 23873 1.4 1 21997 1876 113 21652 1.4 1 19956 1696 114 18856 1.4 1 17302 1554 115 17153 1.4 1 15560 1593 116 15048 1.4 1 13714 1334 117 13387 1.4 1 12104 1283 118 12135 1.4 1 10704 1431 119 10592 1.4 1 9417 1175 120 8981 1.4 1 7894 1087 121 8107 1.4 1 6968 1139 122 7560 1.4 1 6604 956 123 6944 1.4 1 6036 908 124 6306 1.4 1 5395 911 125 6083 1.4 1 5205 878 126 7074 1.4 1 6206 868 127 6690 1.4 1 5839 851 128 4997 1.4 1 4326 671 129 4362 1.4 1 3742 620 130 4971 1.4 1 4334 637 131 5873 1.4 1 5304 569 132 5609 1.4 1 5003 606 133 8463 1.4 1 7578 885 134 6910 1.4 1 6215 695 135 2272 1.4 1 1910 362 136 1123 1.4 1 853 270 137 913 1.4 1 728 185 138 758 1.4 1 574 184 139 509 1.4 1 376 133 140 481 1.4 1 365 116 141 337 1.4 1 222 115 142 257 1.4 1 149 108 143 215 1.4 1 134 81 144 181 1.4 1 116 65 145 328 1.4 1 286 42 146 249 1.4 1 186 63 147 1151 1.4 1 1038 113 148 538 1.4 1 472 66 149 193 1.4 1 176 17 150 2436 1.4 1 2285 151 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth7_R2_001.fastq.gz ============================================= 96207245 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth7_R1_001_trimmed.fq.gz and Meth7_R2_001_trimmed.fq.gz file_1: Meth7_R1_001_trimmed.fq.gz, file_2: Meth7_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth7_R1_001_trimmed.fq.gz and Meth7_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth7_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth7_R2_001_val_2.fq.gz Total number of sequences analysed: 96207245 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 669920 (0.70%) >>> Now running FastQC on the validated data Meth7_R1_001_val_1.fq.gz<<< Started analysis of Meth7_R1_001_val_1.fq.gz Approx 5% complete for Meth7_R1_001_val_1.fq.gz Approx 10% complete for Meth7_R1_001_val_1.fq.gz Approx 15% complete for Meth7_R1_001_val_1.fq.gz Approx 20% complete for Meth7_R1_001_val_1.fq.gz Approx 25% complete for Meth7_R1_001_val_1.fq.gz Approx 30% complete for Meth7_R1_001_val_1.fq.gz Approx 35% complete for Meth7_R1_001_val_1.fq.gz Approx 40% complete for Meth7_R1_001_val_1.fq.gz Approx 45% complete for Meth7_R1_001_val_1.fq.gz Approx 50% complete for Meth7_R1_001_val_1.fq.gz Approx 55% complete for Meth7_R1_001_val_1.fq.gz Approx 60% complete for Meth7_R1_001_val_1.fq.gz Approx 65% complete for Meth7_R1_001_val_1.fq.gz Approx 70% complete for Meth7_R1_001_val_1.fq.gz Approx 75% complete for Meth7_R1_001_val_1.fq.gz Approx 80% complete for Meth7_R1_001_val_1.fq.gz Approx 85% complete for Meth7_R1_001_val_1.fq.gz Approx 90% complete for Meth7_R1_001_val_1.fq.gz Approx 95% complete for Meth7_R1_001_val_1.fq.gz Analysis complete for Meth7_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth7_R2_001_val_2.fq.gz<<< Started analysis of Meth7_R2_001_val_2.fq.gz Approx 5% complete for Meth7_R2_001_val_2.fq.gz Approx 10% complete for Meth7_R2_001_val_2.fq.gz Approx 15% complete for Meth7_R2_001_val_2.fq.gz Approx 20% complete for Meth7_R2_001_val_2.fq.gz Approx 25% complete for Meth7_R2_001_val_2.fq.gz Approx 30% complete for Meth7_R2_001_val_2.fq.gz Approx 35% complete for Meth7_R2_001_val_2.fq.gz Approx 40% complete for Meth7_R2_001_val_2.fq.gz Approx 45% complete for Meth7_R2_001_val_2.fq.gz Approx 50% complete for Meth7_R2_001_val_2.fq.gz Approx 55% complete for Meth7_R2_001_val_2.fq.gz Approx 60% complete for Meth7_R2_001_val_2.fq.gz Approx 65% complete for Meth7_R2_001_val_2.fq.gz Approx 70% complete for Meth7_R2_001_val_2.fq.gz Approx 75% complete for Meth7_R2_001_val_2.fq.gz Approx 80% complete for Meth7_R2_001_val_2.fq.gz Approx 85% complete for Meth7_R2_001_val_2.fq.gz Approx 90% complete for Meth7_R2_001_val_2.fq.gz Approx 95% complete for Meth7_R2_001_val_2.fq.gz Analysis complete for Meth7_R2_001_val_2.fq.gz Deleting both intermediate output files Meth7_R1_001_trimmed.fq.gz and Meth7_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth8_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth8_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2608.31 s (30 us/read; 1.98 M reads/minute). === Summary === Total reads processed: 86,019,978 Reads with adapters: 58,906,572 (68.5%) Reads written (passing filters): 86,019,978 (100.0%) Total basepairs processed: 12,902,996,700 bp Quality-trimmed: 72,570,856 bp (0.6%) Total written (filtered): 11,013,524,647 bp (85.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 58906572 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.0% C: 17.3% G: 16.8% T: 30.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16528924 21504994.5 0 16528924 2 1852713 5376248.6 0 1852713 3 902077 1344062.2 0 902077 4 603529 336015.5 0 603529 5 468971 84003.9 0 468971 6 408734 21001.0 0 408734 7 429921 5250.2 0 429921 8 464410 1312.6 0 464410 9 429657 328.1 0 419930 9727 10 455273 82.0 1 427521 27752 11 474161 20.5 1 440146 34015 12 481402 5.1 1 450977 30425 13 467127 1.3 1 435837 31290 14 483123 1.3 1 448049 35074 15 479400 1.3 1 446160 33240 16 486536 1.3 1 450447 36089 17 504765 1.3 1 467752 37013 18 483633 1.3 1 452185 31448 19 480864 1.3 1 448016 32848 20 489046 1.3 1 456461 32585 21 498117 1.3 1 464266 33851 22 490208 1.3 1 457667 32541 23 504406 1.3 1 469231 35175 24 499630 1.3 1 461451 38179 25 498584 1.3 1 465317 33267 26 491535 1.3 1 459758 31777 27 507136 1.3 1 474063 33073 28 492573 1.3 1 461740 30833 29 497576 1.3 1 465602 31974 30 493742 1.3 1 466072 27670 31 489033 1.3 1 460652 28381 32 498868 1.3 1 471076 27792 33 490983 1.3 1 461542 29441 34 503013 1.3 1 472964 30049 35 491984 1.3 1 463819 28165 36 495957 1.3 1 468056 27901 37 493873 1.3 1 465789 28084 38 497920 1.3 1 467409 30511 39 496904 1.3 1 467419 29485 40 507826 1.3 1 479097 28729 41 483843 1.3 1 455669 28174 42 538087 1.3 1 507648 30439 43 479845 1.3 1 440795 39050 44 505837 1.3 1 469329 36508 45 687694 1.3 1 654361 33333 46 316234 1.3 1 291496 24738 47 581107 1.3 1 487049 94058 48 3294957 1.3 1 3168271 126686 49 594387 1.3 1 565016 29371 50 247543 1.3 1 214064 33479 51 1136150 1.3 1 1089965 46185 52 356228 1.3 1 339424 16804 53 122866 1.3 1 104004 18862 54 677671 1.3 1 645294 32377 55 493584 1.3 1 474002 19582 56 163879 1.3 1 153295 10584 57 240847 1.3 1 231045 9802 58 120478 1.3 1 107622 12856 59 416596 1.3 1 401656 14940 60 83853 1.3 1 78143 5710 61 126254 1.3 1 114871 11383 62 339648 1.3 1 325408 14240 63 158472 1.3 1 151491 6981 64 112244 1.3 1 103689 8555 65 339639 1.3 1 323770 15869 66 322079 1.3 1 309328 12751 67 103591 1.3 1 94260 9331 68 291022 1.3 1 274365 16657 69 337994 1.3 1 311452 26542 70 632946 1.3 1 603667 29279 71 316247 1.3 1 301938 14309 72 117180 1.3 1 110904 6276 73 42755 1.3 1 37435 5320 74 146711 1.3 1 135823 10888 75 255699 1.3 1 239816 15883 76 297589 1.3 1 280478 17111 77 287906 1.3 1 270462 17444 78 289192 1.3 1 271745 17447 79 286225 1.3 1 269110 17115 80 274745 1.3 1 258074 16671 81 267028 1.3 1 250429 16599 82 267287 1.3 1 251466 15821 83 254363 1.3 1 238757 15606 84 242273 1.3 1 227034 15239 85 240149 1.3 1 225429 14720 86 232423 1.3 1 218170 14253 87 229302 1.3 1 215535 13767 88 212996 1.3 1 199905 13091 89 193416 1.3 1 180844 12572 90 183933 1.3 1 171557 12376 91 178230 1.3 1 166332 11898 92 172236 1.3 1 160982 11254 93 164837 1.3 1 153859 10978 94 157453 1.3 1 146982 10471 95 147480 1.3 1 137660 9820 96 139337 1.3 1 129883 9454 97 132238 1.3 1 123217 9021 98 123215 1.3 1 114629 8586 99 114660 1.3 1 106699 7961 100 107074 1.3 1 99402 7672 101 99938 1.3 1 92696 7242 102 92431 1.3 1 85529 6902 103 86595 1.3 1 80059 6536 104 79827 1.3 1 73546 6281 105 73802 1.3 1 67892 5910 106 68924 1.3 1 63381 5543 107 61984 1.3 1 56946 5038 108 56820 1.3 1 52008 4812 109 51537 1.3 1 46930 4607 110 46426 1.3 1 42196 4230 111 42265 1.3 1 38340 3925 112 38430 1.3 1 34744 3686 113 35302 1.3 1 31711 3591 114 31474 1.3 1 28195 3279 115 28532 1.3 1 25602 2930 116 25617 1.3 1 22983 2634 117 23248 1.3 1 20662 2586 118 20564 1.3 1 18229 2335 119 18261 1.3 1 16029 2232 120 16410 1.3 1 14423 1987 121 14549 1.3 1 12577 1972 122 13654 1.3 1 11892 1762 123 13135 1.3 1 11303 1832 124 11428 1.3 1 9780 1648 125 11031 1.3 1 9440 1591 126 13859 1.3 1 12104 1755 127 12255 1.3 1 10790 1465 128 8719 1.3 1 7528 1191 129 8525 1.3 1 7544 981 130 9508 1.3 1 8385 1123 131 14036 1.3 1 12924 1112 132 13809 1.3 1 12664 1145 133 18443 1.3 1 17138 1305 134 16329 1.3 1 15153 1176 135 4723 1.3 1 4181 542 136 2040 1.3 1 1646 394 137 1375 1.3 1 1036 339 138 1127 1.3 1 848 279 139 650 1.3 1 480 170 140 555 1.3 1 365 190 141 346 1.3 1 202 144 142 282 1.3 1 159 123 143 241 1.3 1 130 111 144 198 1.3 1 132 66 145 439 1.3 1 367 72 146 865 1.3 1 776 89 147 6317 1.3 1 5747 570 148 3369 1.3 1 3017 352 149 787 1.3 1 712 75 150 11703 1.3 1 10957 746 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_R1_001.fastq.gz ============================================= 86019978 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth8_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth8_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2638.98 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 86,019,978 Reads with adapters: 57,885,033 (67.3%) Reads written (passing filters): 86,019,978 (100.0%) Total basepairs processed: 12,902,996,700 bp Quality-trimmed: 120,161,263 bp (0.9%) Total written (filtered): 11,046,493,995 bp (85.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 57885033 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.1% C: 14.8% G: 20.5% T: 30.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16820582 21504994.5 0 16820582 2 1862286 5376248.6 0 1862286 3 936466 1344062.2 0 936466 4 605592 336015.5 0 605592 5 475487 84003.9 0 475487 6 398105 21001.0 0 398105 7 408347 5250.2 0 408347 8 471707 1312.6 0 471707 9 407942 328.1 0 401353 6589 10 439530 82.0 1 415296 24234 11 467816 20.5 1 432957 34859 12 520643 5.1 1 488863 31780 13 415938 1.3 1 383469 32469 14 466905 1.3 1 434195 32710 15 458557 1.3 1 427008 31549 16 492516 1.3 1 456792 35724 17 477379 1.3 1 445152 32227 18 451182 1.3 1 421421 29761 19 500424 1.3 1 468212 32212 20 494705 1.3 1 462934 31771 21 455003 1.3 1 422802 32201 22 486051 1.3 1 456395 29656 23 469019 1.3 1 439069 29950 24 503598 1.3 1 470321 33277 25 565563 1.3 1 533711 31852 26 409431 1.3 1 381032 28399 27 479240 1.3 1 447524 31716 28 466152 1.3 1 443935 22217 29 489845 1.3 1 463159 26686 30 479751 1.3 1 457328 22423 31 476875 1.3 1 453177 23698 32 478041 1.3 1 456431 21610 33 482644 1.3 1 458872 23772 34 507689 1.3 1 481041 26648 35 469306 1.3 1 444560 24746 36 496338 1.3 1 468972 27366 37 513606 1.3 1 488338 25268 38 451239 1.3 1 430247 20992 39 566543 1.3 1 542086 24457 40 405070 1.3 1 379663 25407 41 537051 1.3 1 504559 32492 42 499931 1.3 1 477755 22176 43 507165 1.3 1 466642 40523 44 1941183 1.3 1 1876477 64706 45 935552 1.3 1 897820 37732 46 501780 1.3 1 479910 21870 47 398760 1.3 1 384907 13853 48 175976 1.3 1 163182 12794 49 438207 1.3 1 420436 17771 50 323829 1.3 1 309651 14178 51 276691 1.3 1 262719 13972 52 411424 1.3 1 395723 15701 53 279200 1.3 1 264119 15081 54 563836 1.3 1 546949 16887 55 164834 1.3 1 153087 11747 56 444528 1.3 1 413264 31264 57 1514464 1.3 1 1474243 40221 58 279899 1.3 1 266737 13162 59 160998 1.3 1 145677 15321 60 809693 1.3 1 784650 25043 61 301140 1.3 1 286569 14571 62 445501 1.3 1 423540 21961 63 715056 1.3 1 689734 25322 64 656664 1.3 1 637998 18666 65 113751 1.3 1 107241 6510 66 146000 1.3 1 137093 8907 67 299921 1.3 1 289150 10771 68 208678 1.3 1 200605 8073 69 94632 1.3 1 88579 6053 70 187195 1.3 1 180159 7036 71 119160 1.3 1 113174 5986 72 141554 1.3 1 133747 7807 73 209527 1.3 1 199874 9653 74 230261 1.3 1 219752 10509 75 245790 1.3 1 234882 10908 76 197447 1.3 1 189638 7809 77 82092 1.3 1 77338 4754 78 119203 1.3 1 112733 6470 79 204760 1.3 1 195984 8776 80 243731 1.3 1 233374 10357 81 246576 1.3 1 236316 10260 82 240303 1.3 1 229689 10614 83 242699 1.3 1 232273 10426 84 232354 1.3 1 222463 9891 85 227598 1.3 1 217577 10021 86 209159 1.3 1 200090 9069 87 198649 1.3 1 190030 8619 88 191699 1.3 1 183327 8372 89 182515 1.3 1 174595 7920 90 178321 1.3 1 170410 7911 91 168801 1.3 1 161150 7651 92 158966 1.3 1 151850 7116 93 148659 1.3 1 141828 6831 94 138882 1.3 1 132247 6635 95 130280 1.3 1 123994 6286 96 124412 1.3 1 118631 5781 97 120129 1.3 1 114339 5790 98 113295 1.3 1 107862 5433 99 106685 1.3 1 101638 5047 100 99370 1.3 1 94497 4873 101 91066 1.3 1 86557 4509 102 82461 1.3 1 78359 4102 103 76536 1.3 1 72612 3924 104 69662 1.3 1 66047 3615 105 65495 1.3 1 61854 3641 106 61148 1.3 1 57699 3449 107 54909 1.3 1 51731 3178 108 49804 1.3 1 46602 3202 109 45055 1.3 1 42356 2699 110 40566 1.3 1 37953 2613 111 36910 1.3 1 34503 2407 112 33589 1.3 1 31217 2372 113 30757 1.3 1 28545 2212 114 27661 1.3 1 25585 2076 115 25344 1.3 1 23309 2035 116 23323 1.3 1 21399 1924 117 21198 1.3 1 19322 1876 118 18450 1.3 1 16795 1655 119 15973 1.3 1 14451 1522 120 14417 1.3 1 13027 1390 121 12683 1.3 1 11377 1306 122 11909 1.3 1 10563 1346 123 11431 1.3 1 10210 1221 124 9711 1.3 1 8589 1122 125 9421 1.3 1 8294 1127 126 12127 1.3 1 10879 1248 127 10697 1.3 1 9511 1186 128 7739 1.3 1 6747 992 129 7480 1.3 1 6576 904 130 10033 1.3 1 9013 1020 131 14306 1.3 1 13318 988 132 13444 1.3 1 12483 961 133 20433 1.3 1 19047 1386 134 15714 1.3 1 14483 1231 135 4673 1.3 1 4142 531 136 1959 1.3 1 1698 261 137 1427 1.3 1 1187 240 138 1111 1.3 1 894 217 139 717 1.3 1 579 138 140 701 1.3 1 507 194 141 455 1.3 1 310 145 142 292 1.3 1 214 78 143 267 1.3 1 195 72 144 243 1.3 1 175 68 145 514 1.3 1 451 63 146 575 1.3 1 514 61 147 3653 1.3 1 3383 270 148 1777 1.3 1 1589 188 149 436 1.3 1 389 47 150 5252 1.3 1 5061 191 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth8_R2_001.fastq.gz ============================================= 86019978 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth8_R1_001_trimmed.fq.gz and Meth8_R2_001_trimmed.fq.gz file_1: Meth8_R1_001_trimmed.fq.gz, file_2: Meth8_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth8_R1_001_trimmed.fq.gz and Meth8_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth8_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth8_R2_001_val_2.fq.gz Total number of sequences analysed: 86019978 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 845678 (0.98%) >>> Now running FastQC on the validated data Meth8_R1_001_val_1.fq.gz<<< Started analysis of Meth8_R1_001_val_1.fq.gz Approx 5% complete for Meth8_R1_001_val_1.fq.gz Approx 10% complete for Meth8_R1_001_val_1.fq.gz Approx 15% complete for Meth8_R1_001_val_1.fq.gz Approx 20% complete for Meth8_R1_001_val_1.fq.gz Approx 25% complete for Meth8_R1_001_val_1.fq.gz Approx 30% complete for Meth8_R1_001_val_1.fq.gz Approx 35% complete for Meth8_R1_001_val_1.fq.gz Approx 40% complete for Meth8_R1_001_val_1.fq.gz Approx 45% complete for Meth8_R1_001_val_1.fq.gz Approx 50% complete for Meth8_R1_001_val_1.fq.gz Approx 55% complete for Meth8_R1_001_val_1.fq.gz Approx 60% complete for Meth8_R1_001_val_1.fq.gz Approx 65% complete for Meth8_R1_001_val_1.fq.gz Approx 70% complete for Meth8_R1_001_val_1.fq.gz Approx 75% complete for Meth8_R1_001_val_1.fq.gz Approx 80% complete for Meth8_R1_001_val_1.fq.gz Approx 85% complete for Meth8_R1_001_val_1.fq.gz Approx 90% complete for Meth8_R1_001_val_1.fq.gz Approx 95% complete for Meth8_R1_001_val_1.fq.gz Analysis complete for Meth8_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth8_R2_001_val_2.fq.gz<<< Started analysis of Meth8_R2_001_val_2.fq.gz Approx 5% complete for Meth8_R2_001_val_2.fq.gz Approx 10% complete for Meth8_R2_001_val_2.fq.gz Approx 15% complete for Meth8_R2_001_val_2.fq.gz Approx 20% complete for Meth8_R2_001_val_2.fq.gz Approx 25% complete for Meth8_R2_001_val_2.fq.gz Approx 30% complete for Meth8_R2_001_val_2.fq.gz Approx 35% complete for Meth8_R2_001_val_2.fq.gz Approx 40% complete for Meth8_R2_001_val_2.fq.gz Approx 45% complete for Meth8_R2_001_val_2.fq.gz Approx 50% complete for Meth8_R2_001_val_2.fq.gz Approx 55% complete for Meth8_R2_001_val_2.fq.gz Approx 60% complete for Meth8_R2_001_val_2.fq.gz Approx 65% complete for Meth8_R2_001_val_2.fq.gz Approx 70% complete for Meth8_R2_001_val_2.fq.gz Approx 75% complete for Meth8_R2_001_val_2.fq.gz Approx 80% complete for Meth8_R2_001_val_2.fq.gz Approx 85% complete for Meth8_R2_001_val_2.fq.gz Approx 90% complete for Meth8_R2_001_val_2.fq.gz Approx 95% complete for Meth8_R2_001_val_2.fq.gz Analysis complete for Meth8_R2_001_val_2.fq.gz Deleting both intermediate output files Meth8_R1_001_trimmed.fq.gz and Meth8_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth9_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth9_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2604.91 s (30 us/read; 2.02 M reads/minute). === Summary === Total reads processed: 87,891,647 Reads with adapters: 61,760,471 (70.3%) Reads written (passing filters): 87,891,647 (100.0%) Total basepairs processed: 13,183,747,050 bp Quality-trimmed: 20,211,428 bp (0.2%) Total written (filtered): 11,221,722,276 bp (85.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 61760471 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.2% C: 16.1% G: 17.1% T: 30.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16847785 21972911.8 0 16847785 2 1852562 5493227.9 0 1852562 3 940028 1373307.0 0 940028 4 636787 343326.7 0 636787 5 505072 85831.7 0 505072 6 434729 21457.9 0 434729 7 460541 5364.5 0 460541 8 507040 1341.1 0 507040 9 463907 335.3 0 452561 11346 10 490189 83.8 1 457837 32352 11 515269 21.0 1 476503 38766 12 523939 5.2 1 487963 35976 13 512531 1.3 1 475591 36940 14 524954 1.3 1 484361 40593 15 529048 1.3 1 489326 39722 16 528686 1.3 1 487936 40750 17 548705 1.3 1 505772 42933 18 525659 1.3 1 488883 36776 19 523246 1.3 1 484396 38850 20 536154 1.3 1 496531 39623 21 545243 1.3 1 504803 40440 22 534326 1.3 1 496047 38279 23 555291 1.3 1 514115 41176 24 544462 1.3 1 500084 44378 25 546278 1.3 1 507108 39170 26 542570 1.3 1 503738 38832 27 555912 1.3 1 516527 39385 28 541268 1.3 1 504927 36341 29 546883 1.3 1 510031 36852 30 543315 1.3 1 510810 32505 31 537576 1.3 1 503361 34215 32 543453 1.3 1 510494 32959 33 546960 1.3 1 511676 35284 34 547479 1.3 1 513822 33657 35 550355 1.3 1 513234 37121 36 547515 1.3 1 515057 32458 37 540863 1.3 1 506710 34153 38 545596 1.3 1 510749 34847 39 540110 1.3 1 507658 32452 40 543877 1.3 1 508430 35447 41 545948 1.3 1 511311 34637 42 538597 1.3 1 504629 33968 43 562723 1.3 1 525641 37082 44 527782 1.3 1 487958 39824 45 756131 1.3 1 720753 35378 46 293956 1.3 1 270790 23166 47 517489 1.3 1 485516 31973 48 555461 1.3 1 521925 33536 49 511675 1.3 1 480648 31027 50 495780 1.3 1 462655 33125 51 570245 1.3 1 534387 35858 52 482901 1.3 1 454046 28855 53 469185 1.3 1 440224 28961 54 507197 1.3 1 473672 33525 55 526725 1.3 1 495537 31188 56 468306 1.3 1 438797 29509 57 500587 1.3 1 470500 30087 58 489270 1.3 1 459200 30070 59 498438 1.3 1 468391 30047 60 437109 1.3 1 412409 24700 61 407719 1.3 1 381105 26614 62 482806 1.3 1 453063 29743 63 476252 1.3 1 448835 27417 64 403709 1.3 1 379697 24012 65 393985 1.3 1 366634 27351 66 486105 1.3 1 457155 28950 67 431735 1.3 1 403752 27983 68 472253 1.3 1 442031 30222 69 479947 1.3 1 437169 42778 70 905596 1.3 1 867697 37899 71 105233 1.3 1 98613 6620 72 64790 1.3 1 58098 6692 73 171445 1.3 1 157897 13548 74 293933 1.3 1 274796 19137 75 324541 1.3 1 303670 20871 76 322566 1.3 1 302046 20520 77 313353 1.3 1 293456 19897 78 301758 1.3 1 281871 19887 79 297598 1.3 1 278030 19568 80 287535 1.3 1 268721 18814 81 275059 1.3 1 256731 18328 82 267723 1.3 1 250149 17574 83 259659 1.3 1 242580 17079 84 248441 1.3 1 231791 16650 85 238711 1.3 1 222540 16171 86 234946 1.3 1 219137 15809 87 231444 1.3 1 216073 15371 88 192125 1.3 1 177715 14410 89 181724 1.3 1 167883 13841 90 179345 1.3 1 166288 13057 91 172807 1.3 1 160339 12468 92 164676 1.3 1 152659 12017 93 156315 1.3 1 144837 11478 94 148546 1.3 1 137273 11273 95 139633 1.3 1 129011 10622 96 131843 1.3 1 121808 10035 97 121878 1.3 1 112431 9447 98 113756 1.3 1 104673 9083 99 104871 1.3 1 96377 8494 100 98118 1.3 1 89912 8206 101 90616 1.3 1 83130 7486 102 83900 1.3 1 76596 7304 103 77645 1.3 1 70800 6845 104 72293 1.3 1 65576 6717 105 65800 1.3 1 59654 6146 106 60961 1.3 1 55290 5671 107 55557 1.3 1 50083 5474 108 50267 1.3 1 45252 5015 109 45409 1.3 1 40909 4500 110 41515 1.3 1 37237 4278 111 37359 1.3 1 33325 4034 112 34320 1.3 1 30438 3882 113 30858 1.3 1 27139 3719 114 27871 1.3 1 24445 3426 115 25839 1.3 1 22610 3229 116 23384 1.3 1 20352 3032 117 21732 1.3 1 18973 2759 118 19394 1.3 1 16726 2668 119 16607 1.3 1 14241 2366 120 14783 1.3 1 12829 1954 121 13033 1.3 1 11141 1892 122 12794 1.3 1 10895 1899 123 12514 1.3 1 10634 1880 124 11058 1.3 1 9266 1792 125 10738 1.3 1 9138 1600 126 13732 1.3 1 11811 1921 127 12336 1.3 1 10669 1667 128 8970 1.3 1 7699 1271 129 8909 1.3 1 7781 1128 130 10326 1.3 1 9071 1255 131 15906 1.3 1 14501 1405 132 15199 1.3 1 13819 1380 133 20022 1.3 1 18443 1579 134 18471 1.3 1 17024 1447 135 5387 1.3 1 4684 703 136 2162 1.3 1 1694 468 137 1478 1.3 1 1098 380 138 1120 1.3 1 826 294 139 703 1.3 1 461 242 140 647 1.3 1 427 220 141 424 1.3 1 241 183 142 283 1.3 1 156 127 143 189 1.3 1 128 61 144 187 1.3 1 114 73 145 307 1.3 1 229 78 146 767 1.3 1 633 134 147 5340 1.3 1 4694 646 148 3158 1.3 1 2707 451 149 736 1.3 1 638 98 150 11318 1.3 1 10443 875 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_R1_001.fastq.gz ============================================= 87891647 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth9_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth9_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2657.61 s (30 us/read; 1.98 M reads/minute). === Summary === Total reads processed: 87,891,647 Reads with adapters: 60,091,932 (68.4%) Reads written (passing filters): 87,891,647 (100.0%) Total basepairs processed: 13,183,747,050 bp Quality-trimmed: 102,987,221 bp (0.8%) Total written (filtered): 11,269,063,168 bp (85.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 60091932 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.9% C: 14.0% G: 20.8% T: 31.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16863866 21972911.8 0 16863866 2 1852658 5493227.9 0 1852658 3 977867 1373307.0 0 977867 4 639712 343326.7 0 639712 5 514286 85831.7 0 514286 6 425910 21457.9 0 425910 7 440303 5364.5 0 440303 8 531132 1341.1 0 531132 9 421023 335.3 0 414358 6665 10 473612 83.8 1 443457 30155 11 503048 21.0 1 463047 40001 12 538489 5.2 1 499991 38498 13 477709 1.3 1 436900 40809 14 514614 1.3 1 472741 41873 15 499528 1.3 1 462169 37359 16 533681 1.3 1 490320 43361 17 536141 1.3 1 495121 41020 18 477513 1.3 1 443644 33869 19 540324 1.3 1 501090 39234 20 540333 1.3 1 501060 39273 21 499777 1.3 1 461229 38548 22 529211 1.3 1 493145 36066 23 513863 1.3 1 478576 35287 24 548989 1.3 1 508901 40088 25 618339 1.3 1 579119 39220 26 472131 1.3 1 438173 33958 27 510995 1.3 1 474482 36513 28 516235 1.3 1 489118 27117 29 531926 1.3 1 501713 30213 30 537338 1.3 1 509401 27937 31 514166 1.3 1 486556 27610 32 549655 1.3 1 521505 28150 33 535265 1.3 1 506879 28386 34 516983 1.3 1 488239 28744 35 529970 1.3 1 503823 26147 36 525560 1.3 1 497685 27875 37 555810 1.3 1 527476 28334 38 539527 1.3 1 511066 28461 39 504000 1.3 1 475682 28318 40 510954 1.3 1 486703 24251 41 513428 1.3 1 486306 27122 42 642433 1.3 1 608269 34164 43 449405 1.3 1 422113 27292 44 887164 1.3 1 845889 41275 45 706281 1.3 1 671104 35177 46 456874 1.3 1 429976 26898 47 804981 1.3 1 778258 26723 48 164303 1.3 1 152308 11995 49 411518 1.3 1 391507 20011 50 426878 1.3 1 409568 17310 51 309958 1.3 1 293861 16097 52 418002 1.3 1 398925 19077 53 458565 1.3 1 434668 23897 54 757643 1.3 1 730811 26832 55 192405 1.3 1 178438 13967 56 493727 1.3 1 458732 34995 57 1620116 1.3 1 1569153 50963 58 235380 1.3 1 220684 14696 59 215900 1.3 1 197773 18127 60 897185 1.3 1 865130 32055 61 273893 1.3 1 260569 13324 62 306206 1.3 1 279460 26746 63 1283571 1.3 1 1240821 42750 64 798128 1.3 1 771242 26886 65 118897 1.3 1 111299 7598 66 192185 1.3 1 179490 12695 67 423318 1.3 1 408525 14793 68 211686 1.3 1 201863 9823 69 183174 1.3 1 173135 10039 70 291566 1.3 1 280726 10840 71 141818 1.3 1 134980 6838 72 139518 1.3 1 131687 7831 73 191727 1.3 1 183017 8710 74 186722 1.3 1 178387 8335 75 160604 1.3 1 152691 7913 76 142460 1.3 1 135492 6968 77 147016 1.3 1 139131 7885 78 231621 1.3 1 221287 10334 79 260377 1.3 1 248742 11635 80 275092 1.3 1 263128 11964 81 252094 1.3 1 240762 11332 82 235967 1.3 1 225042 10925 83 232988 1.3 1 221903 11085 84 223995 1.3 1 213699 10296 85 210974 1.3 1 201328 9646 86 199512 1.3 1 190102 9410 87 189886 1.3 1 180736 9150 88 177954 1.3 1 169537 8417 89 169290 1.3 1 161278 8012 90 166003 1.3 1 158270 7733 91 152653 1.3 1 145358 7295 92 142895 1.3 1 135742 7153 93 135571 1.3 1 128727 6844 94 127887 1.3 1 121344 6543 95 122022 1.3 1 115812 6210 96 115619 1.3 1 109893 5726 97 107721 1.3 1 102250 5471 98 101041 1.3 1 95920 5121 99 93942 1.3 1 89108 4834 100 87563 1.3 1 82808 4755 101 79137 1.3 1 74821 4316 102 72144 1.3 1 68020 4124 103 65976 1.3 1 62262 3714 104 60961 1.3 1 57381 3580 105 56651 1.3 1 53309 3342 106 52401 1.3 1 49030 3371 107 47820 1.3 1 44780 3040 108 42625 1.3 1 39713 2912 109 38430 1.3 1 35835 2595 110 34910 1.3 1 32479 2431 111 31398 1.3 1 29062 2336 112 28817 1.3 1 26615 2202 113 25795 1.3 1 23692 2103 114 24181 1.3 1 22109 2072 115 22343 1.3 1 20459 1884 116 21556 1.3 1 19696 1860 117 20108 1.3 1 18334 1774 118 17683 1.3 1 15918 1765 119 14350 1.3 1 12875 1475 120 13126 1.3 1 11696 1430 121 11540 1.3 1 10344 1196 122 11128 1.3 1 9768 1360 123 10509 1.3 1 9247 1262 124 9408 1.3 1 8162 1246 125 9376 1.3 1 8148 1228 126 11877 1.3 1 10640 1237 127 10540 1.3 1 9382 1158 128 8027 1.3 1 7055 972 129 8292 1.3 1 7260 1032 130 10884 1.3 1 9769 1115 131 15854 1.3 1 14666 1188 132 14466 1.3 1 13377 1089 133 21448 1.3 1 19943 1505 134 17180 1.3 1 15932 1248 135 4967 1.3 1 4407 560 136 2064 1.3 1 1692 372 137 1436 1.3 1 1144 292 138 1215 1.3 1 910 305 139 895 1.3 1 649 246 140 807 1.3 1 630 177 141 516 1.3 1 367 149 142 363 1.3 1 241 122 143 296 1.3 1 175 121 144 188 1.3 1 141 47 145 341 1.3 1 290 51 146 373 1.3 1 300 73 147 2047 1.3 1 1820 227 148 1227 1.3 1 1069 158 149 331 1.3 1 275 56 150 4180 1.3 1 3958 222 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth9_R2_001.fastq.gz ============================================= 87891647 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth9_R1_001_trimmed.fq.gz and Meth9_R2_001_trimmed.fq.gz file_1: Meth9_R1_001_trimmed.fq.gz, file_2: Meth9_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth9_R1_001_trimmed.fq.gz and Meth9_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth9_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth9_R2_001_val_2.fq.gz Total number of sequences analysed: 87891647 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 857936 (0.98%) >>> Now running FastQC on the validated data Meth9_R1_001_val_1.fq.gz<<< Started analysis of Meth9_R1_001_val_1.fq.gz Approx 5% complete for Meth9_R1_001_val_1.fq.gz Approx 10% complete for Meth9_R1_001_val_1.fq.gz Approx 15% complete for Meth9_R1_001_val_1.fq.gz Approx 20% complete for Meth9_R1_001_val_1.fq.gz Approx 25% complete for Meth9_R1_001_val_1.fq.gz Approx 30% complete for Meth9_R1_001_val_1.fq.gz Approx 35% complete for Meth9_R1_001_val_1.fq.gz Approx 40% complete for Meth9_R1_001_val_1.fq.gz Approx 45% complete for Meth9_R1_001_val_1.fq.gz Approx 50% complete for Meth9_R1_001_val_1.fq.gz Approx 55% complete for Meth9_R1_001_val_1.fq.gz Approx 60% complete for Meth9_R1_001_val_1.fq.gz Approx 65% complete for Meth9_R1_001_val_1.fq.gz Approx 70% complete for Meth9_R1_001_val_1.fq.gz Approx 75% complete for Meth9_R1_001_val_1.fq.gz Approx 80% complete for Meth9_R1_001_val_1.fq.gz Approx 85% complete for Meth9_R1_001_val_1.fq.gz Approx 90% complete for Meth9_R1_001_val_1.fq.gz Approx 95% complete for Meth9_R1_001_val_1.fq.gz Analysis complete for Meth9_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth9_R2_001_val_2.fq.gz<<< Started analysis of Meth9_R2_001_val_2.fq.gz Approx 5% complete for Meth9_R2_001_val_2.fq.gz Approx 10% complete for Meth9_R2_001_val_2.fq.gz Approx 15% complete for Meth9_R2_001_val_2.fq.gz Approx 20% complete for Meth9_R2_001_val_2.fq.gz Approx 25% complete for Meth9_R2_001_val_2.fq.gz Approx 30% complete for Meth9_R2_001_val_2.fq.gz Approx 35% complete for Meth9_R2_001_val_2.fq.gz Approx 40% complete for Meth9_R2_001_val_2.fq.gz Approx 45% complete for Meth9_R2_001_val_2.fq.gz Approx 50% complete for Meth9_R2_001_val_2.fq.gz Approx 55% complete for Meth9_R2_001_val_2.fq.gz Approx 60% complete for Meth9_R2_001_val_2.fq.gz Approx 65% complete for Meth9_R2_001_val_2.fq.gz Approx 70% complete for Meth9_R2_001_val_2.fq.gz Approx 75% complete for Meth9_R2_001_val_2.fq.gz Approx 80% complete for Meth9_R2_001_val_2.fq.gz Approx 85% complete for Meth9_R2_001_val_2.fq.gz Approx 90% complete for Meth9_R2_001_val_2.fq.gz Approx 95% complete for Meth9_R2_001_val_2.fq.gz Analysis complete for Meth9_R2_001_val_2.fq.gz Deleting both intermediate output files Meth9_R1_001_trimmed.fq.gz and Meth9_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth16_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth16_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2293.21 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 74,853,767 Reads with adapters: 48,037,292 (64.2%) Reads written (passing filters): 74,853,767 (100.0%) Total basepairs processed: 11,228,065,050 bp Quality-trimmed: 36,053,773 bp (0.3%) Total written (filtered): 9,837,986,914 bp (87.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 48037292 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.2% C: 18.3% G: 15.5% T: 30.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17313868 18713441.8 0 17313868 2 1583328 4678360.4 0 1583328 3 734995 1169590.1 0 734995 4 484487 292397.5 0 484487 5 365747 73099.4 0 365747 6 306052 18274.8 0 306052 7 326825 4568.7 0 326825 8 355821 1142.2 0 355821 9 329077 285.5 0 318768 10309 10 350603 71.4 1 323517 27086 11 363844 17.8 1 332511 31333 12 370191 4.5 1 340171 30020 13 360136 1.1 1 329053 31083 14 364817 1.1 1 332231 32586 15 363063 1.1 1 331453 31610 16 367140 1.1 1 334097 33043 17 377091 1.1 1 343906 33185 18 369893 1.1 1 339507 30386 19 355969 1.1 1 326336 29633 20 368159 1.1 1 336773 31386 21 367387 1.1 1 336304 31083 22 368597 1.1 1 337612 30985 23 374460 1.1 1 342564 31896 24 360467 1.1 1 327479 32988 25 365354 1.1 1 334690 30664 26 358786 1.1 1 328491 30295 27 368523 1.1 1 338620 29903 28 354139 1.1 1 325824 28315 29 361461 1.1 1 333316 28145 30 357984 1.1 1 332552 25432 31 350548 1.1 1 325225 25323 32 352088 1.1 1 326296 25792 33 353494 1.1 1 326851 26643 34 357245 1.1 1 330047 27198 35 388681 1.1 1 361266 27415 36 323469 1.1 1 295859 27610 37 349230 1.1 1 323398 25832 38 356217 1.1 1 330275 25942 39 340660 1.1 1 314720 25940 40 344816 1.1 1 319567 25249 41 345993 1.1 1 317927 28066 42 432513 1.1 1 404984 27529 43 269958 1.1 1 241567 28391 44 341755 1.1 1 311467 30288 45 470912 1.1 1 442075 28837 46 207165 1.1 1 186995 20170 47 370164 1.1 1 317931 52233 48 1092468 1.1 1 1030000 62468 49 338111 1.1 1 314927 23184 50 250889 1.1 1 218205 32684 51 693389 1.1 1 655996 37393 52 216232 1.1 1 201252 14980 53 149513 1.1 1 127675 21838 54 515579 1.1 1 479477 36102 55 434588 1.1 1 409565 25023 56 195335 1.1 1 178481 16854 57 277121 1.1 1 261646 15475 58 150426 1.1 1 132871 17555 59 370147 1.1 1 351761 18386 60 96297 1.1 1 88498 7799 61 124619 1.1 1 110743 13876 62 295323 1.1 1 276486 18837 63 201374 1.1 1 190618 10756 64 97923 1.1 1 87928 9995 65 236194 1.1 1 218487 17707 66 263554 1.1 1 248715 14839 67 112345 1.1 1 101331 11014 68 218261 1.1 1 201501 16760 69 240572 1.1 1 213510 27062 70 463476 1.1 1 436848 26628 71 175158 1.1 1 165372 9786 72 66039 1.1 1 61303 4736 73 46538 1.1 1 40240 6298 74 127225 1.1 1 115404 11821 75 178458 1.1 1 163549 14909 76 195988 1.1 1 180316 15672 77 184658 1.1 1 169056 15602 78 182029 1.1 1 166775 15254 79 183405 1.1 1 168575 14830 80 172253 1.1 1 157933 14320 81 168491 1.1 1 154027 14464 82 172525 1.1 1 158471 14054 83 165173 1.1 1 151286 13887 84 155803 1.1 1 142247 13556 85 153354 1.1 1 139663 13691 86 147524 1.1 1 135117 12407 87 145467 1.1 1 133330 12137 88 130493 1.1 1 118765 11728 89 118194 1.1 1 106908 11286 90 113080 1.1 1 102483 10597 91 112244 1.1 1 101690 10554 92 109435 1.1 1 99380 10055 93 103795 1.1 1 94108 9687 94 102631 1.1 1 92932 9699 95 97961 1.1 1 88897 9064 96 91876 1.1 1 83190 8686 97 86589 1.1 1 78224 8365 98 80136 1.1 1 72237 7899 99 75024 1.1 1 67446 7578 100 71637 1.1 1 64122 7515 101 70871 1.1 1 63555 7316 102 64137 1.1 1 57054 7083 103 59036 1.1 1 52880 6156 104 62022 1.1 1 55212 6810 105 58151 1.1 1 51491 6660 106 58726 1.1 1 52266 6460 107 54282 1.1 1 47901 6381 108 46819 1.1 1 41236 5583 109 41970 1.1 1 36717 5253 110 39692 1.1 1 34953 4739 111 35311 1.1 1 30880 4431 112 33592 1.1 1 29203 4389 113 34643 1.1 1 30384 4259 114 32144 1.1 1 28069 4075 115 31532 1.1 1 27473 4059 116 33589 1.1 1 29399 4190 117 34762 1.1 1 30672 4090 118 29062 1.1 1 25800 3262 119 24079 1.1 1 21370 2709 120 22610 1.1 1 19799 2811 121 20137 1.1 1 17519 2618 122 21585 1.1 1 19057 2528 123 22643 1.1 1 19986 2657 124 18961 1.1 1 16765 2196 125 19089 1.1 1 16946 2143 126 36041 1.1 1 31917 4124 127 29177 1.1 1 25594 3583 128 16168 1.1 1 14106 2062 129 17006 1.1 1 15017 1989 130 38957 1.1 1 35348 3609 131 73329 1.1 1 69245 4084 132 72500 1.1 1 67887 4613 133 108649 1.1 1 101987 6662 134 103526 1.1 1 97141 6385 135 26937 1.1 1 24874 2063 136 7964 1.1 1 6962 1002 137 5443 1.1 1 4749 694 138 4256 1.1 1 3541 715 139 2400 1.1 1 1838 562 140 1986 1.1 1 1524 462 141 774 1.1 1 515 259 142 538 1.1 1 348 190 143 454 1.1 1 307 147 144 763 1.1 1 623 140 145 2455 1.1 1 2152 303 146 5761 1.1 1 5162 599 147 49520 1.1 1 44674 4846 148 26470 1.1 1 23282 3188 149 6519 1.1 1 5725 794 150 80163 1.1 1 74408 5755 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_R1_001.fastq.gz ============================================= 74853767 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth16_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth16_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2419.39 s (32 us/read; 1.86 M reads/minute). === Summary === Total reads processed: 74,853,767 Reads with adapters: 46,193,449 (61.7%) Reads written (passing filters): 74,853,767 (100.0%) Total basepairs processed: 11,228,065,050 bp Quality-trimmed: 92,500,615 bp (0.8%) Total written (filtered): 9,861,964,532 bp (87.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 46193449 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.2% C: 15.8% G: 18.5% T: 31.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16857444 18713441.8 0 16857444 2 1622265 4678360.4 0 1622265 3 776299 1169590.1 0 776299 4 493224 292397.5 0 493224 5 376158 73099.4 0 376158 6 296744 18274.8 0 296744 7 304967 4568.7 0 304967 8 369889 1142.2 0 369889 9 291515 285.5 0 286266 5249 10 331876 71.4 1 306820 25056 11 350023 17.8 1 317258 32765 12 383350 4.5 1 351569 31781 13 324899 1.1 1 293300 31599 14 353376 1.1 1 320030 33346 15 336985 1.1 1 307559 29426 16 368024 1.1 1 333022 35002 17 364381 1.1 1 331961 32420 18 323535 1.1 1 296706 26829 19 373153 1.1 1 342021 31132 20 362128 1.1 1 332288 29840 21 329167 1.1 1 299498 29669 22 361779 1.1 1 332770 29009 23 339307 1.1 1 312167 27140 24 357156 1.1 1 327333 29823 25 395068 1.1 1 365255 29813 26 306523 1.1 1 280923 25600 27 344334 1.1 1 316340 27994 28 332517 1.1 1 311683 20834 29 349643 1.1 1 326127 23516 30 343761 1.1 1 322652 21109 31 334410 1.1 1 313201 21209 32 333602 1.1 1 314043 19559 33 349550 1.1 1 327508 22042 34 347733 1.1 1 326392 21341 35 337882 1.1 1 313701 24181 36 341720 1.1 1 320203 21517 37 336767 1.1 1 315521 21246 38 345512 1.1 1 324065 21447 39 355935 1.1 1 335261 20674 40 289540 1.1 1 270519 19021 41 332171 1.1 1 313453 18718 42 340348 1.1 1 321277 19071 43 290012 1.1 1 272885 17127 44 360524 1.1 1 339659 20865 45 352868 1.1 1 332322 20546 46 290741 1.1 1 269895 20846 47 576533 1.1 1 551382 25151 48 185048 1.1 1 173744 11304 49 208224 1.1 1 194376 13848 50 307512 1.1 1 291995 15517 51 229463 1.1 1 214990 14473 52 282228 1.1 1 266076 16152 53 295164 1.1 1 277413 17751 54 409855 1.1 1 390576 19279 55 160564 1.1 1 148869 11695 56 301533 1.1 1 279491 22042 57 735948 1.1 1 704821 31127 58 151820 1.1 1 140872 10948 59 184867 1.1 1 170409 14458 60 523855 1.1 1 500022 23833 61 226970 1.1 1 214990 11980 62 165682 1.1 1 145373 20309 63 891407 1.1 1 856221 35186 64 292436 1.1 1 277290 15146 65 120691 1.1 1 113231 7460 66 120334 1.1 1 109477 10857 67 330872 1.1 1 316328 14544 68 157121 1.1 1 148039 9082 69 152687 1.1 1 143285 9402 70 186526 1.1 1 176575 9951 71 141762 1.1 1 134210 7552 72 95641 1.1 1 89155 6486 73 118673 1.1 1 111775 6898 74 103410 1.1 1 97126 6284 75 96060 1.1 1 89990 6070 76 86625 1.1 1 80634 5991 77 128061 1.1 1 120564 7497 78 149888 1.1 1 141351 8537 79 161524 1.1 1 152386 9138 80 168715 1.1 1 159693 9022 81 155231 1.1 1 146238 8993 82 152479 1.1 1 143566 8913 83 152323 1.1 1 143205 9118 84 146819 1.1 1 138296 8523 85 139114 1.1 1 130844 8270 86 128439 1.1 1 120886 7553 87 121266 1.1 1 114042 7224 88 115683 1.1 1 108677 7006 89 108535 1.1 1 101855 6680 90 106053 1.1 1 99659 6394 91 100638 1.1 1 94355 6283 92 95316 1.1 1 89239 6077 93 90370 1.1 1 84573 5797 94 89220 1.1 1 83422 5798 95 85775 1.1 1 80191 5584 96 81111 1.1 1 75808 5303 97 77518 1.1 1 72310 5208 98 72019 1.1 1 67119 4900 99 69206 1.1 1 64373 4833 100 65518 1.1 1 60840 4678 101 63416 1.1 1 58906 4510 102 55728 1.1 1 51605 4123 103 51631 1.1 1 47853 3778 104 53436 1.1 1 49417 4019 105 51115 1.1 1 47170 3945 106 52357 1.1 1 48203 4154 107 48910 1.1 1 44872 4038 108 41602 1.1 1 38286 3316 109 36896 1.1 1 33830 3066 110 35806 1.1 1 32728 3078 111 31185 1.1 1 28405 2780 112 29571 1.1 1 26831 2740 113 33046 1.1 1 29885 3161 114 32401 1.1 1 29445 2956 115 32639 1.1 1 29662 2977 116 39577 1.1 1 36305 3272 117 41766 1.1 1 38288 3478 118 33002 1.1 1 30170 2832 119 24880 1.1 1 22606 2274 120 22503 1.1 1 20446 2057 121 19739 1.1 1 17779 1960 122 19765 1.1 1 17879 1886 123 20347 1.1 1 18294 2053 124 17414 1.1 1 15558 1856 125 17667 1.1 1 15775 1892 126 32306 1.1 1 29360 2946 127 25114 1.1 1 22492 2622 128 15143 1.1 1 13567 1576 129 17373 1.1 1 15782 1591 130 48340 1.1 1 44582 3758 131 79909 1.1 1 74813 5096 132 71856 1.1 1 67349 4507 133 118930 1.1 1 111564 7366 134 98719 1.1 1 92294 6425 135 24161 1.1 1 22481 1680 136 7285 1.1 1 6641 644 137 5044 1.1 1 4491 553 138 3415 1.1 1 2921 494 139 1813 1.1 1 1542 271 140 1565 1.1 1 1302 263 141 768 1.1 1 620 148 142 524 1.1 1 369 155 143 442 1.1 1 324 118 144 848 1.1 1 726 122 145 2194 1.1 1 2052 142 146 2965 1.1 1 2682 283 147 20914 1.1 1 19232 1682 148 10587 1.1 1 9552 1035 149 2856 1.1 1 2604 252 150 34842 1.1 1 33103 1739 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth16_R2_001.fastq.gz ============================================= 74853767 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth16_R1_001_trimmed.fq.gz and Meth16_R2_001_trimmed.fq.gz file_1: Meth16_R1_001_trimmed.fq.gz, file_2: Meth16_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth16_R1_001_trimmed.fq.gz and Meth16_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth16_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth16_R2_001_val_2.fq.gz Total number of sequences analysed: 74853767 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1580710 (2.11%) >>> Now running FastQC on the validated data Meth16_R1_001_val_1.fq.gz<<< Started analysis of Meth16_R1_001_val_1.fq.gz Approx 5% complete for Meth16_R1_001_val_1.fq.gz Approx 10% complete for Meth16_R1_001_val_1.fq.gz Approx 15% complete for Meth16_R1_001_val_1.fq.gz Approx 20% complete for Meth16_R1_001_val_1.fq.gz Approx 25% complete for Meth16_R1_001_val_1.fq.gz Approx 30% complete for Meth16_R1_001_val_1.fq.gz Approx 35% complete for Meth16_R1_001_val_1.fq.gz Approx 40% complete for Meth16_R1_001_val_1.fq.gz Approx 45% complete for Meth16_R1_001_val_1.fq.gz Approx 50% complete for Meth16_R1_001_val_1.fq.gz Approx 55% complete for Meth16_R1_001_val_1.fq.gz Approx 60% complete for Meth16_R1_001_val_1.fq.gz Approx 65% complete for Meth16_R1_001_val_1.fq.gz Approx 70% complete for Meth16_R1_001_val_1.fq.gz Approx 75% complete for Meth16_R1_001_val_1.fq.gz Approx 80% complete for Meth16_R1_001_val_1.fq.gz Approx 85% complete for Meth16_R1_001_val_1.fq.gz Approx 90% complete for Meth16_R1_001_val_1.fq.gz Approx 95% complete for Meth16_R1_001_val_1.fq.gz Analysis complete for Meth16_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth16_R2_001_val_2.fq.gz<<< Started analysis of Meth16_R2_001_val_2.fq.gz Approx 5% complete for Meth16_R2_001_val_2.fq.gz Approx 10% complete for Meth16_R2_001_val_2.fq.gz Approx 15% complete for Meth16_R2_001_val_2.fq.gz Approx 20% complete for Meth16_R2_001_val_2.fq.gz Approx 25% complete for Meth16_R2_001_val_2.fq.gz Approx 30% complete for Meth16_R2_001_val_2.fq.gz Approx 35% complete for Meth16_R2_001_val_2.fq.gz Approx 40% complete for Meth16_R2_001_val_2.fq.gz Approx 45% complete for Meth16_R2_001_val_2.fq.gz Approx 50% complete for Meth16_R2_001_val_2.fq.gz Approx 55% complete for Meth16_R2_001_val_2.fq.gz Approx 60% complete for Meth16_R2_001_val_2.fq.gz Approx 65% complete for Meth16_R2_001_val_2.fq.gz Approx 70% complete for Meth16_R2_001_val_2.fq.gz Approx 75% complete for Meth16_R2_001_val_2.fq.gz Approx 80% complete for Meth16_R2_001_val_2.fq.gz Approx 85% complete for Meth16_R2_001_val_2.fq.gz Approx 90% complete for Meth16_R2_001_val_2.fq.gz Approx 95% complete for Meth16_R2_001_val_2.fq.gz Analysis complete for Meth16_R2_001_val_2.fq.gz Deleting both intermediate output files Meth16_R1_001_trimmed.fq.gz and Meth16_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth17_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth17_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2515.36 s (30 us/read; 2.01 M reads/minute). === Summary === Total reads processed: 84,066,692 Reads with adapters: 53,982,918 (64.2%) Reads written (passing filters): 84,066,692 (100.0%) Total basepairs processed: 12,610,003,800 bp Quality-trimmed: 20,918,384 bp (0.2%) Total written (filtered): 10,867,974,302 bp (86.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 53982918 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.6% C: 19.5% G: 16.0% T: 28.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18241553 21016673.0 0 18241553 2 1862687 5254168.2 0 1862687 3 833046 1313542.1 0 833046 4 516579 328385.5 0 516579 5 391725 82096.4 0 391725 6 321578 20524.1 0 321578 7 339416 5131.0 0 339416 8 364811 1282.8 0 364811 9 342163 320.7 0 331139 11024 10 366956 80.2 1 336869 30087 11 386092 20.0 1 350781 35311 12 388598 5.0 1 355892 32706 13 372333 1.3 1 339080 33253 14 379847 1.3 1 343961 35886 15 380756 1.3 1 346533 34223 16 389402 1.3 1 353476 35926 17 397244 1.3 1 360847 36397 18 378093 1.3 1 345267 32826 19 373706 1.3 1 339971 33735 20 384835 1.3 1 350873 33962 21 389517 1.3 1 354181 35336 22 385354 1.3 1 351056 34298 23 394576 1.3 1 359374 35202 24 383165 1.3 1 346880 36285 25 389063 1.3 1 355061 34002 26 386488 1.3 1 352699 33789 27 394205 1.3 1 359008 35197 28 387219 1.3 1 354631 32588 29 386534 1.3 1 353495 33039 30 385582 1.3 1 354878 30704 31 378741 1.3 1 348477 30264 32 381496 1.3 1 350881 30615 33 380078 1.3 1 348170 31908 34 386598 1.3 1 353100 33498 35 437824 1.3 1 406428 31396 36 319589 1.3 1 291939 27650 37 386294 1.3 1 354201 32093 38 387420 1.3 1 357234 30186 39 377276 1.3 1 344190 33086 40 380004 1.3 1 349514 30490 41 378400 1.3 1 346411 31989 42 368715 1.3 1 339028 29687 43 393263 1.3 1 359333 33930 44 371321 1.3 1 337007 34314 45 492350 1.3 1 459797 32553 46 247208 1.3 1 223670 23538 47 360607 1.3 1 331388 29219 48 371474 1.3 1 341636 29838 49 364728 1.3 1 335604 29124 50 356549 1.3 1 326287 30262 51 376963 1.3 1 345079 31884 52 356425 1.3 1 328020 28405 53 338455 1.3 1 310191 28264 54 350556 1.3 1 321230 29326 55 357130 1.3 1 328622 28508 56 339762 1.3 1 311807 27955 57 348990 1.3 1 319578 29412 58 363847 1.3 1 334763 29084 59 321036 1.3 1 292991 28045 60 330539 1.3 1 304298 26241 61 316332 1.3 1 289897 26435 62 330822 1.3 1 303274 27548 63 336876 1.3 1 309013 27863 64 323007 1.3 1 297091 25916 65 285363 1.3 1 258734 26629 66 337137 1.3 1 307329 29808 67 354167 1.3 1 322051 32116 68 376537 1.3 1 344529 32008 69 366041 1.3 1 322871 43170 70 685429 1.3 1 647559 37870 71 58912 1.3 1 53673 5239 72 41160 1.3 1 34454 6706 73 142719 1.3 1 127267 15452 74 228335 1.3 1 207761 20574 75 248506 1.3 1 226185 22321 76 250348 1.3 1 228177 22171 77 246047 1.3 1 224038 22009 78 241776 1.3 1 219577 22199 79 240909 1.3 1 219225 21684 80 230041 1.3 1 209163 20878 81 227283 1.3 1 206367 20916 82 224775 1.3 1 203770 21005 83 219042 1.3 1 199636 19406 84 211949 1.3 1 193324 18625 85 206705 1.3 1 187417 19288 86 198070 1.3 1 179511 18559 87 196394 1.3 1 178172 18222 88 172375 1.3 1 155263 17112 89 164349 1.3 1 147287 17062 90 161509 1.3 1 144701 16808 91 159887 1.3 1 143250 16637 92 152138 1.3 1 136692 15446 93 144742 1.3 1 129919 14823 94 143351 1.3 1 128852 14499 95 137554 1.3 1 123193 14361 96 128515 1.3 1 115058 13457 97 123948 1.3 1 110847 13101 98 113273 1.3 1 100799 12474 99 107803 1.3 1 95518 12285 100 103457 1.3 1 91768 11689 101 102113 1.3 1 90487 11626 102 91930 1.3 1 80734 11196 103 88109 1.3 1 77683 10426 104 91171 1.3 1 80503 10668 105 87463 1.3 1 76891 10572 106 87859 1.3 1 77315 10544 107 81281 1.3 1 71246 10035 108 70347 1.3 1 61624 8723 109 61615 1.3 1 53343 8272 110 58115 1.3 1 50285 7830 111 53031 1.3 1 45317 7714 112 49720 1.3 1 42849 6871 113 49878 1.3 1 43367 6511 114 47224 1.3 1 41140 6084 115 45098 1.3 1 39294 5804 116 46676 1.3 1 40888 5788 117 48959 1.3 1 43067 5892 118 41255 1.3 1 36147 5108 119 35910 1.3 1 31626 4284 120 32932 1.3 1 28993 3939 121 28575 1.3 1 24860 3715 122 33533 1.3 1 29452 4081 123 33378 1.3 1 29388 3990 124 28827 1.3 1 25348 3479 125 28718 1.3 1 24934 3784 126 56698 1.3 1 49735 6963 127 45176 1.3 1 39337 5839 128 23455 1.3 1 20403 3052 129 25227 1.3 1 22368 2859 130 61584 1.3 1 56091 5493 131 122842 1.3 1 115925 6917 132 131126 1.3 1 122965 8161 133 213119 1.3 1 200231 12888 134 221596 1.3 1 207188 14408 135 55160 1.3 1 50811 4349 136 14830 1.3 1 12995 1835 137 9504 1.3 1 8070 1434 138 7082 1.3 1 5656 1426 139 3894 1.3 1 2975 919 140 3420 1.3 1 2419 1001 141 1329 1.3 1 915 414 142 970 1.3 1 580 390 143 793 1.3 1 605 188 144 1547 1.3 1 1288 259 145 5321 1.3 1 4709 612 146 9538 1.3 1 8221 1317 147 81394 1.3 1 70126 11268 148 44121 1.3 1 36994 7127 149 12986 1.3 1 11079 1907 150 172145 1.3 1 154799 17346 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_R1_001.fastq.gz ============================================= 84066692 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth17_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth17_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_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 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2572.46 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 84,066,692 Reads with adapters: 51,628,964 (61.4%) Reads written (passing filters): 84,066,692 (100.0%) Total basepairs processed: 12,610,003,800 bp Quality-trimmed: 119,212,960 bp (0.9%) Total written (filtered): 10,895,096,635 bp (86.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 51628964 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.4% C: 16.5% G: 19.6% T: 30.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17596614 21016673.0 0 17596614 2 1876603 5254168.2 0 1876603 3 848089 1313542.1 0 848089 4 522037 328385.5 0 522037 5 390819 82096.4 0 390819 6 312330 20524.1 0 312330 7 323086 5131.0 0 323086 8 384719 1282.8 0 384719 9 304627 320.7 0 299432 5195 10 346691 80.2 1 322847 23844 11 370811 20.0 1 339969 30842 12 398407 5.0 1 368415 29992 13 336693 1.3 1 306493 30200 14 362589 1.3 1 331980 30609 15 357043 1.3 1 328991 28052 16 384496 1.3 1 352384 32112 17 377909 1.3 1 348350 29559 18 340317 1.3 1 314345 25972 19 385242 1.3 1 356518 28724 20 381087 1.3 1 352543 28544 21 346065 1.3 1 317243 28822 22 374572 1.3 1 347570 27002 23 358215 1.3 1 332551 25664 24 385711 1.3 1 356265 29446 25 445897 1.3 1 416193 29704 26 315169 1.3 1 290542 24627 27 347318 1.3 1 321297 26021 28 364911 1.3 1 343974 20937 29 372169 1.3 1 348834 23335 30 373789 1.3 1 352206 21583 31 355313 1.3 1 334448 20865 32 362329 1.3 1 342152 20177 33 362347 1.3 1 340897 21450 34 365197 1.3 1 344929 20268 35 365653 1.3 1 343806 21847 36 404456 1.3 1 380334 24122 37 421614 1.3 1 398328 23286 38 328632 1.3 1 308282 20350 39 368820 1.3 1 348244 20576 40 345256 1.3 1 326285 18971 41 333822 1.3 1 314094 19728 42 375664 1.3 1 357113 18551 43 325895 1.3 1 306952 18943 44 397677 1.3 1 376990 20687 45 412905 1.3 1 389790 23115 46 323571 1.3 1 301249 22322 47 662220 1.3 1 635126 27094 48 186131 1.3 1 175107 11024 49 242071 1.3 1 226983 15088 50 337981 1.3 1 322379 15602 51 254512 1.3 1 239559 14953 52 317286 1.3 1 300612 16674 53 334133 1.3 1 315176 18957 54 481387 1.3 1 460504 20883 55 171783 1.3 1 159671 12112 56 351691 1.3 1 325142 26549 57 1049962 1.3 1 1009065 40897 58 162928 1.3 1 151562 11366 59 191403 1.3 1 175847 15556 60 657588 1.3 1 629906 27682 61 240014 1.3 1 227808 12206 62 180294 1.3 1 158394 21900 63 1090354 1.3 1 1049491 40863 64 371407 1.3 1 353763 17644 65 121749 1.3 1 114357 7392 66 137669 1.3 1 126158 11511 67 386046 1.3 1 370046 16000 68 169521 1.3 1 159924 9597 69 175643 1.3 1 165266 10377 70 229207 1.3 1 218045 11162 71 153671 1.3 1 145986 7685 72 105674 1.3 1 99091 6583 73 135749 1.3 1 128411 7338 74 119862 1.3 1 113003 6859 75 113631 1.3 1 106722 6909 76 102562 1.3 1 95696 6866 77 158583 1.3 1 149993 8590 78 195568 1.3 1 185175 10393 79 210630 1.3 1 199653 10977 80 217624 1.3 1 206053 11571 81 202701 1.3 1 191804 10897 82 198674 1.3 1 187247 11427 83 198721 1.3 1 187336 11385 84 194231 1.3 1 183303 10928 85 185583 1.3 1 174855 10728 86 172860 1.3 1 162855 10005 87 166823 1.3 1 157228 9595 88 159356 1.3 1 150511 8845 89 151109 1.3 1 142788 8321 90 147078 1.3 1 138515 8563 91 141921 1.3 1 133402 8519 92 133838 1.3 1 125675 8163 93 127909 1.3 1 120415 7494 94 126574 1.3 1 118664 7910 95 121930 1.3 1 114589 7341 96 114793 1.3 1 107748 7045 97 111404 1.3 1 104365 7039 98 102307 1.3 1 95914 6393 99 98993 1.3 1 92344 6649 100 95094 1.3 1 88961 6133 101 92056 1.3 1 85876 6180 102 81668 1.3 1 76175 5493 103 77292 1.3 1 72021 5271 104 80472 1.3 1 74852 5620 105 77771 1.3 1 72360 5411 106 78781 1.3 1 72914 5867 107 72848 1.3 1 67770 5078 108 62794 1.3 1 58284 4510 109 54674 1.3 1 50325 4349 110 52500 1.3 1 48537 3963 111 47592 1.3 1 43699 3893 112 43337 1.3 1 39662 3675 113 47630 1.3 1 43516 4114 114 45743 1.3 1 41822 3921 115 44781 1.3 1 40993 3788 116 52207 1.3 1 48070 4137 117 57587 1.3 1 53150 4437 118 45114 1.3 1 41658 3456 119 37140 1.3 1 34085 3055 120 32976 1.3 1 30215 2761 121 28006 1.3 1 25649 2357 122 31197 1.3 1 28425 2772 123 30475 1.3 1 27646 2829 124 26611 1.3 1 24233 2378 125 26522 1.3 1 24060 2462 126 52087 1.3 1 47255 4832 127 40055 1.3 1 35874 4181 128 22200 1.3 1 20009 2191 129 26333 1.3 1 24293 2040 130 78462 1.3 1 73222 5240 131 135081 1.3 1 127507 7574 132 132315 1.3 1 124593 7722 133 246060 1.3 1 231560 14500 134 222036 1.3 1 208328 13708 135 53528 1.3 1 49894 3634 136 14149 1.3 1 12838 1311 137 9467 1.3 1 8436 1031 138 5758 1.3 1 4958 800 139 3211 1.3 1 2701 510 140 2670 1.3 1 2284 386 141 1106 1.3 1 931 175 142 724 1.3 1 614 110 143 728 1.3 1 585 143 144 1567 1.3 1 1317 250 145 5038 1.3 1 4675 363 146 5433 1.3 1 4752 681 147 37204 1.3 1 33274 3930 148 19138 1.3 1 16850 2288 149 6176 1.3 1 5472 704 150 79055 1.3 1 74226 4829 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth17_R2_001.fastq.gz ============================================= 84066692 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth17_R1_001_trimmed.fq.gz and Meth17_R2_001_trimmed.fq.gz file_1: Meth17_R1_001_trimmed.fq.gz, file_2: Meth17_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth17_R1_001_trimmed.fq.gz and Meth17_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth17_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth17_R2_001_val_2.fq.gz Total number of sequences analysed: 84066692 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 2457196 (2.92%) >>> Now running FastQC on the validated data Meth17_R1_001_val_1.fq.gz<<< Started analysis of Meth17_R1_001_val_1.fq.gz Approx 5% complete for Meth17_R1_001_val_1.fq.gz Approx 10% complete for Meth17_R1_001_val_1.fq.gz Approx 15% complete for Meth17_R1_001_val_1.fq.gz Approx 20% complete for Meth17_R1_001_val_1.fq.gz Approx 25% complete for Meth17_R1_001_val_1.fq.gz Approx 30% complete for Meth17_R1_001_val_1.fq.gz Approx 35% complete for Meth17_R1_001_val_1.fq.gz Approx 40% complete for Meth17_R1_001_val_1.fq.gz Approx 45% complete for Meth17_R1_001_val_1.fq.gz Approx 50% complete for Meth17_R1_001_val_1.fq.gz Approx 55% complete for Meth17_R1_001_val_1.fq.gz Approx 60% complete for Meth17_R1_001_val_1.fq.gz Approx 65% complete for Meth17_R1_001_val_1.fq.gz Approx 70% complete for Meth17_R1_001_val_1.fq.gz Approx 75% complete for Meth17_R1_001_val_1.fq.gz Approx 80% complete for Meth17_R1_001_val_1.fq.gz Approx 85% complete for Meth17_R1_001_val_1.fq.gz Approx 90% complete for Meth17_R1_001_val_1.fq.gz Approx 95% complete for Meth17_R1_001_val_1.fq.gz Analysis complete for Meth17_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth17_R2_001_val_2.fq.gz<<< Started analysis of Meth17_R2_001_val_2.fq.gz Approx 5% complete for Meth17_R2_001_val_2.fq.gz Approx 10% complete for Meth17_R2_001_val_2.fq.gz Approx 15% complete for Meth17_R2_001_val_2.fq.gz Approx 20% complete for Meth17_R2_001_val_2.fq.gz Approx 25% complete for Meth17_R2_001_val_2.fq.gz Approx 30% complete for Meth17_R2_001_val_2.fq.gz Approx 35% complete for Meth17_R2_001_val_2.fq.gz Approx 40% complete for Meth17_R2_001_val_2.fq.gz Approx 45% complete for Meth17_R2_001_val_2.fq.gz Approx 50% complete for Meth17_R2_001_val_2.fq.gz Approx 55% complete for Meth17_R2_001_val_2.fq.gz Approx 60% complete for Meth17_R2_001_val_2.fq.gz Approx 65% complete for Meth17_R2_001_val_2.fq.gz Approx 70% complete for Meth17_R2_001_val_2.fq.gz Approx 75% complete for Meth17_R2_001_val_2.fq.gz Approx 80% complete for Meth17_R2_001_val_2.fq.gz Approx 85% complete for Meth17_R2_001_val_2.fq.gz Approx 90% complete for Meth17_R2_001_val_2.fq.gz Approx 95% complete for Meth17_R2_001_val_2.fq.gz Analysis complete for Meth17_R2_001_val_2.fq.gz Deleting both intermediate output files Meth17_R1_001_trimmed.fq.gz and Meth17_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth18_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth18_R1_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R1_001.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 1915.67 s (31 us/read; 1.96 M reads/minute). === Summary === Total reads processed: 62,709,665 Reads with adapters: 40,276,846 (64.2%) Reads written (passing filters): 62,709,665 (100.0%) Total basepairs processed: 9,406,449,750 bp Quality-trimmed: 13,181,420 bp (0.1%) Total written (filtered): 8,278,807,374 bp (88.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 40276846 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.4% C: 19.3% G: 14.9% T: 29.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 14603394 15677416.2 0 14603394 2 1307142 3919354.1 0 1307142 3 620947 979838.5 0 620947 4 414208 244959.6 0 414208 5 316368 61239.9 0 316368 6 270939 15310.0 0 270939 7 287587 3827.5 0 287587 8 307571 956.9 0 307571 9 291943 239.2 0 282290 9653 10 307212 59.8 1 282437 24775 11 324430 15.0 1 295685 28745 12 324931 3.7 1 297576 27355 13 310057 0.9 1 281854 28203 14 319835 0.9 1 290105 29730 15 316897 0.9 1 288199 28698 16 320152 0.9 1 289773 30379 17 331126 0.9 1 300877 30249 18 316149 0.9 1 288328 27821 19 309858 0.9 1 281474 28384 20 317463 0.9 1 289824 27639 21 322446 0.9 1 292983 29463 22 315246 0.9 1 287741 27505 23 318776 0.9 1 290279 28497 24 317130 0.9 1 287444 29686 25 316748 0.9 1 288506 28242 26 312623 0.9 1 284985 27638 27 315963 0.9 1 289143 26820 28 308124 0.9 1 282067 26057 29 313104 0.9 1 286542 26562 30 305952 0.9 1 281690 24262 31 304134 0.9 1 279368 24766 32 303558 0.9 1 279370 24188 33 303893 0.9 1 278900 24993 34 309218 0.9 1 284210 25008 35 297568 0.9 1 272333 25235 36 298995 0.9 1 275445 23550 37 294671 0.9 1 271449 23222 38 297407 0.9 1 272901 24506 39 293165 0.9 1 269627 23538 40 289296 0.9 1 265392 23904 41 291360 0.9 1 265470 25890 42 355817 0.9 1 330018 25799 43 228920 0.9 1 205404 23516 44 283541 0.9 1 256980 26561 45 382574 0.9 1 357752 24822 46 170015 0.9 1 153114 16901 47 274307 0.9 1 251167 23140 48 288981 0.9 1 266366 22615 49 267341 0.9 1 246164 21177 50 262545 0.9 1 238827 23718 51 309854 0.9 1 285611 24243 52 234312 0.9 1 214802 19510 53 239120 0.9 1 218787 20333 54 265265 0.9 1 242029 23236 55 267428 0.9 1 245787 21641 56 237662 0.9 1 217530 20132 57 261343 0.9 1 239988 21355 58 250492 0.9 1 229315 21177 59 255887 0.9 1 235257 20630 60 216508 0.9 1 199315 17193 61 201088 0.9 1 182910 18178 62 241115 0.9 1 220874 20241 63 251346 0.9 1 232213 19133 64 197045 0.9 1 180407 16638 65 201530 0.9 1 182837 18693 66 237722 0.9 1 218444 19278 67 209414 0.9 1 190744 18670 68 230710 0.9 1 210503 20207 69 240393 0.9 1 211428 28965 70 474752 0.9 1 447253 27499 71 70131 0.9 1 64871 5260 72 34318 0.9 1 30099 4219 73 73975 0.9 1 65127 8848 74 141387 0.9 1 128289 13098 75 159757 0.9 1 145916 13841 76 161791 0.9 1 147865 13926 77 155984 0.9 1 142301 13683 78 151988 0.9 1 137458 14530 79 148788 0.9 1 135487 13301 80 143094 0.9 1 129829 13265 81 138762 0.9 1 125718 13044 82 139690 0.9 1 126839 12851 83 134840 0.9 1 122736 12104 84 130580 0.9 1 118601 11979 85 123383 0.9 1 111910 11473 86 117432 0.9 1 106943 10489 87 116497 0.9 1 105948 10549 88 102840 0.9 1 93024 9816 89 96936 0.9 1 87251 9685 90 92329 0.9 1 82936 9393 91 92315 0.9 1 82931 9384 92 85579 0.9 1 77148 8431 93 81824 0.9 1 73594 8230 94 80538 0.9 1 72344 8194 95 76259 0.9 1 68343 7916 96 71614 0.9 1 63843 7771 97 68904 0.9 1 61350 7554 98 62679 0.9 1 55862 6817 99 58401 0.9 1 51652 6749 100 56028 0.9 1 49611 6417 101 55872 0.9 1 49522 6350 102 49325 0.9 1 43305 6020 103 46128 0.9 1 40440 5688 104 49109 0.9 1 43181 5928 105 45999 0.9 1 40385 5614 106 47857 0.9 1 41726 6131 107 43913 0.9 1 38515 5398 108 37490 0.9 1 32533 4957 109 31238 0.9 1 27191 4047 110 29474 0.9 1 25395 4079 111 26769 0.9 1 22915 3854 112 25120 0.9 1 21522 3598 113 25299 0.9 1 21691 3608 114 24400 0.9 1 21060 3340 115 23839 0.9 1 20669 3170 116 23656 0.9 1 20243 3413 117 24613 0.9 1 21161 3452 118 20639 0.9 1 17969 2670 119 17306 0.9 1 14902 2404 120 16945 0.9 1 14510 2435 121 14466 0.9 1 12437 2029 122 15550 0.9 1 13404 2146 123 16818 0.9 1 14662 2156 124 13836 0.9 1 11819 2017 125 13708 0.9 1 11782 1926 126 23751 0.9 1 20650 3101 127 19283 0.9 1 16602 2681 128 11956 0.9 1 10235 1721 129 12417 0.9 1 10865 1552 130 24411 0.9 1 21918 2493 131 44236 0.9 1 41265 2971 132 46490 0.9 1 43176 3314 133 74517 0.9 1 69869 4648 134 82144 0.9 1 76941 5203 135 20244 0.9 1 18592 1652 136 5533 0.9 1 4741 792 137 3702 0.9 1 3172 530 138 3027 0.9 1 2388 639 139 1479 0.9 1 1075 404 140 1311 0.9 1 959 352 141 530 0.9 1 342 188 142 344 0.9 1 214 130 143 337 0.9 1 246 91 144 611 0.9 1 484 127 145 2283 0.9 1 2061 222 146 3252 0.9 1 2855 397 147 25656 0.9 1 22355 3301 148 13908 0.9 1 11832 2076 149 4146 0.9 1 3549 597 150 58653 0.9 1 53591 5062 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R1_001.fastq.gz ============================================= 62709665 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/Meth18_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; user defined) 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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC --threads 28' Output file(s) will be GZIP compressed Writing final adapter and quality trimmed output to Meth18_R2_001_trimmed.fq.gz >>> Now performing quality (cutoff 20) and adapter trimming in a single pass for the adapter sequence: 'AGATCGGAAGAGC' from file /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R2_001.fastq.gz <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 1945.42 s (31 us/read; 1.93 M reads/minute). === Summary === Total reads processed: 62,709,665 Reads with adapters: 38,470,962 (61.3%) Reads written (passing filters): 62,709,665 (100.0%) Total basepairs processed: 9,406,449,750 bp Quality-trimmed: 123,266,483 bp (1.3%) Total written (filtered): 8,293,089,887 bp (88.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 38470962 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.9% C: 15.7% G: 18.8% T: 31.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 13938102 15677416.2 0 13938102 2 1359085 3919354.1 0 1359085 3 655707 979838.5 0 655707 4 424350 244959.6 0 424350 5 319726 61239.9 0 319726 6 262112 15310.0 0 262112 7 271385 3827.5 0 271385 8 308619 956.9 0 308619 9 274806 239.2 0 270909 3897 10 289786 59.8 1 272669 17117 11 313346 15.0 1 288947 24399 12 342477 3.7 1 319651 22826 13 271931 0.9 1 249417 22514 14 304901 0.9 1 280810 24091 15 296605 0.9 1 274390 22215 16 317217 0.9 1 291435 25782 17 310223 0.9 1 287370 22853 18 285260 0.9 1 265121 20139 19 316262 0.9 1 293234 23028 20 313717 0.9 1 291447 22270 21 292460 0.9 1 269393 23067 22 306848 0.9 1 285978 20870 23 292904 0.9 1 272708 20196 24 305824 0.9 1 284026 21798 25 347412 0.9 1 324914 22498 26 260991 0.9 1 241945 19046 27 295345 0.9 1 274519 20826 28 289282 0.9 1 273557 15725 29 300009 0.9 1 282102 17907 30 291390 0.9 1 275828 15562 31 291938 0.9 1 275449 16489 32 285292 0.9 1 270572 14720 33 296526 0.9 1 280520 16006 34 290373 0.9 1 273385 16988 35 275373 0.9 1 261229 14144 36 309222 0.9 1 286985 22237 37 303293 0.9 1 287295 15998 38 263075 0.9 1 249446 13629 39 277927 0.9 1 261674 16253 40 281344 0.9 1 266350 14994 41 314164 0.9 1 285346 28818 42 859329 0.9 1 821915 37414 43 214873 0.9 1 177493 37380 44 2127916 0.9 1 2053251 74665 45 656389 0.9 1 629255 27134 46 95251 0.9 1 86718 8533 47 272611 0.9 1 261799 10812 48 64446 0.9 1 59424 5022 49 131431 0.9 1 124864 6567 50 74671 0.9 1 70255 4416 51 88881 0.9 1 83627 5254 52 108893 0.9 1 103315 5578 53 96814 0.9 1 90928 5886 54 181867 0.9 1 174468 7399 55 91933 0.9 1 85542 6391 56 202134 0.9 1 189063 13071 57 485918 0.9 1 467361 18557 58 222943 0.9 1 212802 10141 59 108710 0.9 1 98168 10542 60 533815 0.9 1 514315 19500 61 175316 0.9 1 168033 7283 62 110774 0.9 1 104147 6627 63 173022 0.9 1 162763 10259 64 302922 0.9 1 291617 11305 65 58519 0.9 1 54470 4049 66 76865 0.9 1 72536 4329 67 74982 0.9 1 70890 4092 68 67096 0.9 1 63594 3502 69 29767 0.9 1 27509 2258 70 42075 0.9 1 39471 2604 71 38108 0.9 1 35538 2570 72 45987 0.9 1 42773 3214 73 68951 0.9 1 64906 4045 74 80469 0.9 1 75872 4597 75 90238 0.9 1 84880 5358 76 95749 0.9 1 91000 4749 77 54195 0.9 1 51219 2976 78 32377 0.9 1 29925 2452 79 48931 0.9 1 45613 3318 80 77168 0.9 1 72494 4674 81 98659 0.9 1 93220 5439 82 110484 0.9 1 104341 6143 83 116379 0.9 1 110222 6157 84 113064 0.9 1 106708 6356 85 111232 0.9 1 105095 6137 86 100271 0.9 1 94615 5656 87 95678 0.9 1 90055 5623 88 92558 0.9 1 87256 5302 89 87143 0.9 1 82148 4995 90 83107 0.9 1 78387 4720 91 81141 0.9 1 76375 4766 92 75016 0.9 1 70683 4333 93 71384 0.9 1 67152 4232 94 68641 0.9 1 64479 4162 95 64919 0.9 1 60813 4106 96 61201 0.9 1 57219 3982 97 60034 0.9 1 55999 4035 98 55725 0.9 1 52200 3525 99 52598 0.9 1 49023 3575 100 50269 0.9 1 46953 3316 101 49968 0.9 1 46553 3415 102 43032 0.9 1 40044 2988 103 39766 0.9 1 36758 3008 104 42804 0.9 1 39652 3152 105 40656 0.9 1 37618 3038 106 42333 0.9 1 39247 3086 107 39304 0.9 1 36432 2872 108 33100 0.9 1 30480 2620 109 28032 0.9 1 25648 2384 110 25918 0.9 1 23678 2240 111 23406 0.9 1 21343 2063 112 22518 0.9 1 20530 1988 113 22972 0.9 1 20783 2189 114 22593 0.9 1 20364 2229 115 23108 0.9 1 21018 2090 116 25370 0.9 1 23152 2218 117 27684 0.9 1 25351 2333 118 21699 0.9 1 19859 1840 119 17433 0.9 1 15678 1755 120 16264 0.9 1 14745 1519 121 14027 0.9 1 12711 1316 122 14518 0.9 1 13046 1472 123 14995 0.9 1 13343 1652 124 12332 0.9 1 11021 1311 125 13155 0.9 1 11793 1362 126 21866 0.9 1 19754 2112 127 17451 0.9 1 15442 2009 128 11229 0.9 1 9967 1262 129 12020 0.9 1 10880 1140 130 29273 0.9 1 27237 2036 131 46913 0.9 1 44236 2677 132 45943 0.9 1 43119 2824 133 85100 0.9 1 80107 4993 134 80390 0.9 1 75630 4760 135 19109 0.9 1 17816 1293 136 5201 0.9 1 4669 532 137 3737 0.9 1 3340 397 138 2522 0.9 1 2120 402 139 1322 0.9 1 1011 311 140 1264 0.9 1 1049 215 141 542 0.9 1 422 120 142 433 0.9 1 261 172 143 414 0.9 1 288 126 144 602 0.9 1 523 79 145 2117 0.9 1 1982 135 146 1897 0.9 1 1712 185 147 11623 0.9 1 10545 1078 148 6005 0.9 1 5257 748 149 2018 0.9 1 1806 212 150 26536 0.9 1 25134 1402 RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth18_R2_001.fastq.gz ============================================= 62709665 sequences processed in total The length threshold of paired-end sequences gets evaluated later on (in the validation step) Validate paired-end files Meth18_R1_001_trimmed.fq.gz and Meth18_R2_001_trimmed.fq.gz file_1: Meth18_R1_001_trimmed.fq.gz, file_2: Meth18_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth18_R1_001_trimmed.fq.gz and Meth18_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth18_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth18_R2_001_val_2.fq.gz Total number of sequences analysed: 62709665 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1124265 (1.79%) >>> Now running FastQC on the validated data Meth18_R1_001_val_1.fq.gz<<< Started analysis of Meth18_R1_001_val_1.fq.gz Approx 5% complete for Meth18_R1_001_val_1.fq.gz Approx 10% complete for Meth18_R1_001_val_1.fq.gz Approx 15% complete for Meth18_R1_001_val_1.fq.gz Approx 20% complete for Meth18_R1_001_val_1.fq.gz Approx 25% complete for Meth18_R1_001_val_1.fq.gz Approx 30% complete for Meth18_R1_001_val_1.fq.gz Approx 35% complete for Meth18_R1_001_val_1.fq.gz Approx 40% complete for Meth18_R1_001_val_1.fq.gz Approx 45% complete for Meth18_R1_001_val_1.fq.gz Approx 50% complete for Meth18_R1_001_val_1.fq.gz Approx 55% complete for Meth18_R1_001_val_1.fq.gz Approx 60% complete for Meth18_R1_001_val_1.fq.gz Approx 65% complete for Meth18_R1_001_val_1.fq.gz Approx 70% complete for Meth18_R1_001_val_1.fq.gz Approx 75% complete for Meth18_R1_001_val_1.fq.gz Approx 80% complete for Meth18_R1_001_val_1.fq.gz Approx 85% complete for Meth18_R1_001_val_1.fq.gz Approx 90% complete for Meth18_R1_001_val_1.fq.gz Approx 95% complete for Meth18_R1_001_val_1.fq.gz Analysis complete for Meth18_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth18_R2_001_val_2.fq.gz<<< Started analysis of Meth18_R2_001_val_2.fq.gz Approx 5% complete for Meth18_R2_001_val_2.fq.gz Approx 10% complete for Meth18_R2_001_val_2.fq.gz Approx 15% complete for Meth18_R2_001_val_2.fq.gz Approx 20% complete for Meth18_R2_001_val_2.fq.gz Approx 25% complete for Meth18_R2_001_val_2.fq.gz Approx 30% complete for Meth18_R2_001_val_2.fq.gz Approx 35% complete for Meth18_R2_001_val_2.fq.gz Approx 40% complete for Meth18_R2_001_val_2.fq.gz Approx 45% complete for Meth18_R2_001_val_2.fq.gz Approx 50% complete for Meth18_R2_001_val_2.fq.gz Approx 55% complete for Meth18_R2_001_val_2.fq.gz Approx 60% complete for Meth18_R2_001_val_2.fq.gz Approx 65% complete for Meth18_R2_001_val_2.fq.gz Approx 70% complete for Meth18_R2_001_val_2.fq.gz Approx 75% complete for Meth18_R2_001_val_2.fq.gz Approx 80% complete for Meth18_R2_001_val_2.fq.gz Approx 85% complete for Meth18_R2_001_val_2.fq.gz Approx 90% complete for Meth18_R2_001_val_2.fq.gz Approx 95% complete for Meth18_R2_001_val_2.fq.gz Analysis complete for Meth18_R2_001_val_2.fq.gz Deleting both intermediate output files Meth18_R1_001_trimmed.fq.gz and Meth18_R2_001_trimmed.fq.gz ==================================================================================================== No quality encoding type selected. Assuming that the data provided uses Sanger encoded Phred scores (default) Path to Cutadapt set as: '/gscratch/srlab/programs/miniconda3/bin/cutadapt' (user defined) 2.4 Cutadapt seems to be working fine (tested command '/gscratch/srlab/programs/miniconda3/bin/cutadapt --version') AUTO-DETECTING ADAPTER TYPE =========================== Attempting to auto-detect adapter type from the first 1 million sequences of the first file (>> /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth13_R1_001.fastq.gz <<) Found perfect matches for the following adapter sequences: Adapter type Count Sequence Sequences analysed Percentage Illumina 457885 AGATCGGAAGAGC 1000000 45.79 smallRNA 0 TGGAATTCTCGG 1000000 0.00 Nextera 0 CTGTCTCTTATA 1000000 0.00 Using Illumina adapter for trimming (count: 457885). Second best hit was smallRNA (count: 0) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth13_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth13_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth13_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed Finished in 990.17 s (10 us/read; 6.12 M reads/minute). === Summary === Total reads processed: 100,994,125 Reads with adapters: 0 (0.0%) Reads written (passing filters): 100,994,125 (100.0%) Total basepairs processed: 15,149,118,750 bp Quality-trimmed: 15,277,665 bp (0.1%) Total written (filtered): 15,133,841,085 bp (99.9%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 100994125 sequences processed in total Writing final adapter and quality trimmed output to Meth13_R1_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth13_R1_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth13_R1_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2603.60 s (26 us/read; 2.33 M reads/minute). === Summary === Total reads processed: 100,994,125 Reads with adapters: 75,452,441 (74.7%) Reads written (passing filters): 100,994,125 (100.0%) Total basepairs processed: 15,133,841,085 bp Total written (filtered): 11,286,581,533 bp (74.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 75452441 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.8% C: 3.5% G: 42.0% T: 7.8% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16889854 25248531.2 0 16889854 2 1387092 6312132.8 0 1387092 3 993122 1578033.2 0 993122 4 431060 394508.3 0 431060 5 275682 98627.1 0 275682 6 233401 24656.8 0 233401 7 293154 6164.2 0 293154 8 291627 1541.0 0 291627 9 282078 385.3 0 278508 3570 10 329147 96.3 1 300652 28495 11 581523 24.1 1 522909 58614 12 349882 6.0 1 315325 34557 13 313904 1.5 1 280320 33584 14 311573 1.5 1 277270 34303 15 260519 1.5 1 232317 28202 16 280060 1.5 1 248629 31431 17 309633 1.5 1 275006 34627 18 299523 1.5 1 268511 31012 19 308381 1.5 1 275762 32619 20 319544 1.5 1 285436 34108 21 307838 1.5 1 274585 33253 22 346274 1.5 1 309836 36438 23 436976 1.5 1 390674 46302 24 385479 1.5 1 342645 42834 25 336519 1.5 1 300157 36362 26 286169 1.5 1 255735 30434 27 302039 1.5 1 269115 32924 28 505249 1.5 1 451790 53459 29 356797 1.5 1 316417 40380 30 333714 1.5 1 298431 35283 31 348698 1.5 1 311129 37569 32 367127 1.5 1 327760 39367 33 317415 1.5 1 282607 34808 34 352429 1.5 1 314640 37789 35 326336 1.5 1 290643 35693 36 339179 1.5 1 301577 37602 37 481410 1.5 1 429087 52323 38 448729 1.5 1 395717 53012 39 414453 1.5 1 370021 44432 40 544488 1.5 1 486617 57871 41 545768 1.5 1 486251 59517 42 474348 1.5 1 425187 49161 43 335612 1.5 1 295805 39807 44 363737 1.5 1 321199 42538 45 612969 1.5 1 550568 62401 46 236931 1.5 1 210315 26616 47 340836 1.5 1 303534 37302 48 428571 1.5 1 381101 47470 49 789485 1.5 1 705703 83782 50 421164 1.5 1 373382 47782 51 489216 1.5 1 432238 56978 52 533011 1.5 1 475013 57998 53 470642 1.5 1 418275 52367 54 823609 1.5 1 732350 91259 55 528241 1.5 1 470022 58219 56 413780 1.5 1 367680 46100 57 485033 1.5 1 430576 54457 58 739339 1.5 1 657723 81616 59 419372 1.5 1 371464 47908 60 857360 1.5 1 765572 91788 61 470376 1.5 1 417741 52635 62 433854 1.5 1 384546 49308 63 401851 1.5 1 356696 45155 64 433832 1.5 1 385879 47953 65 358350 1.5 1 317317 41033 66 444050 1.5 1 393209 50841 67 582832 1.5 1 515092 67740 68 746325 1.5 1 660769 85556 69 670332 1.5 1 580864 89468 70 2073202 1.5 1 1871175 202027 71 121451 1.5 1 105945 15506 72 52792 1.5 1 43475 9317 73 538152 1.5 1 472151 66001 74 1756813 1.5 1 1560951 195862 75 441617 1.5 1 389006 52611 76 504090 1.5 1 445913 58177 77 565547 1.5 1 500475 65072 78 426572 1.5 1 377709 48863 79 456994 1.5 1 404267 52727 80 462729 1.5 1 408983 53746 81 405931 1.5 1 358406 47525 82 437959 1.5 1 387478 50481 83 408216 1.5 1 360003 48213 84 562518 1.5 1 497661 64857 85 514509 1.5 1 454185 60324 86 424696 1.5 1 374471 50225 87 445051 1.5 1 391943 53108 88 443537 1.5 1 390586 52951 89 546419 1.5 1 481197 65222 90 499277 1.5 1 439779 59498 91 566915 1.5 1 498750 68165 92 375931 1.5 1 329894 46037 93 500854 1.5 1 440092 60762 94 547235 1.5 1 480575 66660 95 391331 1.5 1 343323 48008 96 422734 1.5 1 370502 52232 97 536091 1.5 1 469971 66120 98 532528 1.5 1 466445 66083 99 488932 1.5 1 428065 60867 100 500021 1.5 1 436747 63274 101 389481 1.5 1 340084 49397 102 384198 1.5 1 336082 48116 103 467887 1.5 1 408747 59140 104 410457 1.5 1 357935 52522 105 398892 1.5 1 347934 50958 106 628657 1.5 1 548475 80182 107 497594 1.5 1 432357 65237 108 499014 1.5 1 433694 65320 109 553229 1.5 1 481173 72056 110 382989 1.5 1 332050 50939 111 364439 1.5 1 316458 47981 112 405699 1.5 1 351377 54322 113 356009 1.5 1 308400 47609 114 619887 1.5 1 538428 81459 115 1146598 1.5 1 996001 150597 116 330227 1.5 1 283825 46402 117 447731 1.5 1 387042 60689 118 395667 1.5 1 341652 54015 119 446331 1.5 1 385057 61274 120 254368 1.5 1 218804 35564 121 257448 1.5 1 221667 35781 122 238783 1.5 1 205563 33220 123 250549 1.5 1 215898 34651 124 240416 1.5 1 206474 33942 125 321804 1.5 1 276819 44985 126 183366 1.5 1 157670 25696 127 148680 1.5 1 127230 21450 128 93397 1.5 1 80218 13179 129 76162 1.5 1 65344 10818 130 57264 1.5 1 49107 8157 131 74918 1.5 1 64528 10390 132 32450 1.5 1 27800 4650 133 11091 1.5 1 9620 1471 134 4995 1.5 1 4285 710 135 1217 1.5 1 1029 188 136 490 1.5 1 426 64 137 53 1.5 1 49 4 138 8 1.5 1 7 1 139 9 1.5 1 9 140 9 1.5 1 6 3 141 6 1.5 1 4 2 142 1 1.5 1 1 145 1 1.5 1 1 146 1 1.5 1 0 1 147 2 1.5 1 0 2 148 86 1.5 1 67 19 149 7 1.5 1 6 1 150 327 1.5 1 286 41 Successfully deleted temporary file Meth13_R1_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth13_R1_001.fastq.gz ============================================= 100994125 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 5451098 (5.4%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 36165151 (35.8%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1139376) or CGA (49790870) in total: 50930246 (50.4%) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth13_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth13_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth13_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed Finished in 969.66 s (10 us/read; 6.25 M reads/minute). === Summary === Total reads processed: 100,994,125 Reads with adapters: 0 (0.0%) Reads written (passing filters): 100,994,125 (100.0%) Total basepairs processed: 15,149,118,750 bp Quality-trimmed: 116,375,081 bp (0.8%) Total written (filtered): 15,032,743,669 bp (99.2%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 100994125 sequences processed in total Writing final adapter and quality trimmed output to Meth13_R2_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth13_R2_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth13_R2_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2674.42 s (26 us/read; 2.27 M reads/minute). === Summary === Total reads processed: 100,994,125 Reads with adapters: 74,282,317 (73.6%) Reads written (passing filters): 100,994,125 (100.0%) Total basepairs processed: 15,032,743,669 bp Total written (filtered): 11,294,465,516 bp (75.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 74282317 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.4% C: 3.1% G: 42.4% T: 8.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 16858905 25248531.2 0 16858905 2 1409178 6312132.8 0 1409178 3 1022247 1578033.2 0 1022247 4 449685 394508.3 0 449685 5 282584 98627.1 0 282584 6 231575 24656.8 0 231575 7 275852 6164.2 0 275852 8 305134 1541.0 0 305134 9 261671 385.3 0 259774 1897 10 318513 96.3 1 293638 24875 11 567085 24.1 1 515255 51830 12 364336 6.0 1 330294 34042 13 290786 1.5 1 258428 32358 14 303138 1.5 1 270634 32504 15 246093 1.5 1 220948 25145 16 285123 1.5 1 253722 31401 17 284664 1.5 1 255137 29527 18 286469 1.5 1 258114 28355 19 308210 1.5 1 277962 30248 20 324953 1.5 1 291571 33382 21 303171 1.5 1 270805 32366 22 350374 1.5 1 316862 33512 23 396907 1.5 1 358066 38841 24 381124 1.5 1 343563 37561 25 381056 1.5 1 343740 37316 26 245479 1.5 1 220057 25422 27 291422 1.5 1 259208 32214 28 487231 1.5 1 443161 44070 29 347094 1.5 1 312544 34550 30 331761 1.5 1 300206 31555 31 338587 1.5 1 306037 32550 32 358592 1.5 1 324285 34307 33 314593 1.5 1 283789 30804 34 342874 1.5 1 309361 33513 35 336170 1.5 1 304544 31626 36 344386 1.5 1 308783 35603 37 415065 1.5 1 375228 39837 38 459882 1.5 1 415569 44313 39 404887 1.5 1 365056 39831 40 571974 1.5 1 518878 53096 41 505738 1.5 1 457619 48119 42 365004 1.5 1 331197 33807 43 413898 1.5 1 374763 39135 44 357178 1.5 1 323405 33773 45 457513 1.5 1 412411 45102 46 435158 1.5 1 391388 43770 47 457055 1.5 1 415593 41462 48 395224 1.5 1 357064 38160 49 674244 1.5 1 611485 62759 50 434007 1.5 1 393088 40919 51 427500 1.5 1 385958 41542 52 527271 1.5 1 477474 49797 53 471108 1.5 1 426085 45023 54 923952 1.5 1 841152 82800 55 367371 1.5 1 332096 35275 56 430114 1.5 1 387358 42756 57 935761 1.5 1 849893 85868 58 412305 1.5 1 370915 41390 59 386265 1.5 1 348305 37960 60 1040895 1.5 1 947342 93553 61 455365 1.5 1 412374 42991 62 358198 1.5 1 316355 41843 63 1602264 1.5 1 1461599 140665 64 380614 1.5 1 342988 37626 65 211938 1.5 1 190908 21030 66 250630 1.5 1 223979 26651 67 816496 1.5 1 742960 73536 68 606413 1.5 1 549483 56930 69 513297 1.5 1 464468 48829 70 778232 1.5 1 706072 72160 71 638686 1.5 1 578942 59744 72 481606 1.5 1 435034 46572 73 985078 1.5 1 894565 90513 74 1294627 1.5 1 1176076 118551 75 402361 1.5 1 363629 38732 76 367554 1.5 1 332914 34640 77 298809 1.5 1 267530 31279 78 347369 1.5 1 313518 33851 79 412815 1.5 1 372637 40178 80 429933 1.5 1 387774 42159 81 384917 1.5 1 347266 37651 82 421423 1.5 1 380392 41031 83 424394 1.5 1 382335 42059 84 551836 1.5 1 497555 54281 85 529303 1.5 1 476883 52420 86 424156 1.5 1 381288 42868 87 432689 1.5 1 389037 43652 88 428451 1.5 1 385513 42938 89 518280 1.5 1 466734 51546 90 480143 1.5 1 432447 47696 91 534963 1.5 1 481319 53644 92 359938 1.5 1 323524 36414 93 478512 1.5 1 430743 47769 94 513875 1.5 1 462209 51666 95 371059 1.5 1 333246 37813 96 402062 1.5 1 361080 40982 97 514433 1.5 1 461861 52572 98 516253 1.5 1 463634 52619 99 484360 1.5 1 434891 49469 100 492619 1.5 1 440850 51769 101 379216 1.5 1 339118 40098 102 367605 1.5 1 329106 38499 103 441408 1.5 1 394943 46465 104 386261 1.5 1 345006 41255 105 380001 1.5 1 339706 40295 106 591703 1.5 1 528612 63091 107 472566 1.5 1 421694 50872 108 474327 1.5 1 422729 51598 109 522002 1.5 1 466969 55033 110 362933 1.5 1 323370 39563 111 347657 1.5 1 309474 38183 112 388527 1.5 1 345990 42537 113 339670 1.5 1 302340 37330 114 591254 1.5 1 526319 64935 115 1088418 1.5 1 968434 119984 116 319102 1.5 1 283133 35969 117 434552 1.5 1 386087 48465 118 390585 1.5 1 345582 45003 119 434222 1.5 1 384929 49293 120 249611 1.5 1 221221 28390 121 250773 1.5 1 222295 28478 122 229186 1.5 1 202720 26466 123 241833 1.5 1 213756 28077 124 232011 1.5 1 205157 26854 125 312472 1.5 1 276186 36286 126 178172 1.5 1 157076 21096 127 143853 1.5 1 126656 17197 128 91075 1.5 1 80088 10987 129 73099 1.5 1 64502 8597 130 55464 1.5 1 48732 6732 131 71783 1.5 1 63274 8509 132 30986 1.5 1 27253 3733 133 10709 1.5 1 9385 1324 134 4811 1.5 1 4208 603 135 1166 1.5 1 1010 156 136 476 1.5 1 425 51 137 53 1.5 1 50 3 138 11 1.5 1 8 3 139 8 1.5 1 8 140 6 1.5 1 6 141 6 1.5 1 5 1 142 1 1.5 1 1 143 1 1.5 1 1 145 1 1.5 1 1 146 1 1.5 1 1 148 83 1.5 1 78 5 149 11 1.5 1 10 1 150 304 1.5 1 276 28 Successfully deleted temporary file Meth13_R2_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth13_R2_001.fastq.gz ============================================= 100994125 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 11269639 (11.2%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1082919) or CGA (46567288) in total: 47650207 (47.2%) Validate paired-end files Meth13_R1_001_trimmed.fq.gz and Meth13_R2_001_trimmed.fq.gz file_1: Meth13_R1_001_trimmed.fq.gz, file_2: Meth13_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth13_R1_001_trimmed.fq.gz and Meth13_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth13_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth13_R2_001_val_2.fq.gz Total number of sequences analysed: 100994125 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 386198 (0.38%) >>> Now running FastQC on the validated data Meth13_R1_001_val_1.fq.gz<<< Started analysis of Meth13_R1_001_val_1.fq.gz Approx 5% complete for Meth13_R1_001_val_1.fq.gz Approx 10% complete for Meth13_R1_001_val_1.fq.gz Approx 15% complete for Meth13_R1_001_val_1.fq.gz Approx 20% complete for Meth13_R1_001_val_1.fq.gz Approx 25% complete for Meth13_R1_001_val_1.fq.gz Approx 30% complete for Meth13_R1_001_val_1.fq.gz Approx 35% complete for Meth13_R1_001_val_1.fq.gz Approx 40% complete for Meth13_R1_001_val_1.fq.gz Approx 45% complete for Meth13_R1_001_val_1.fq.gz Approx 50% complete for Meth13_R1_001_val_1.fq.gz Approx 55% complete for Meth13_R1_001_val_1.fq.gz Approx 60% complete for Meth13_R1_001_val_1.fq.gz Approx 65% complete for Meth13_R1_001_val_1.fq.gz Approx 70% complete for Meth13_R1_001_val_1.fq.gz Approx 75% complete for Meth13_R1_001_val_1.fq.gz Approx 80% complete for Meth13_R1_001_val_1.fq.gz Approx 85% complete for Meth13_R1_001_val_1.fq.gz Approx 90% complete for Meth13_R1_001_val_1.fq.gz Approx 95% complete for Meth13_R1_001_val_1.fq.gz Analysis complete for Meth13_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth13_R2_001_val_2.fq.gz<<< Started analysis of Meth13_R2_001_val_2.fq.gz Approx 5% complete for Meth13_R2_001_val_2.fq.gz Approx 10% complete for Meth13_R2_001_val_2.fq.gz Approx 15% complete for Meth13_R2_001_val_2.fq.gz Approx 20% complete for Meth13_R2_001_val_2.fq.gz Approx 25% complete for Meth13_R2_001_val_2.fq.gz Approx 30% complete for Meth13_R2_001_val_2.fq.gz Approx 35% complete for Meth13_R2_001_val_2.fq.gz Approx 40% complete for Meth13_R2_001_val_2.fq.gz Approx 45% complete for Meth13_R2_001_val_2.fq.gz Approx 50% complete for Meth13_R2_001_val_2.fq.gz Approx 55% complete for Meth13_R2_001_val_2.fq.gz Approx 60% complete for Meth13_R2_001_val_2.fq.gz Approx 65% complete for Meth13_R2_001_val_2.fq.gz Approx 70% complete for Meth13_R2_001_val_2.fq.gz Approx 75% complete for Meth13_R2_001_val_2.fq.gz Approx 80% complete for Meth13_R2_001_val_2.fq.gz Approx 85% complete for Meth13_R2_001_val_2.fq.gz Approx 90% complete for Meth13_R2_001_val_2.fq.gz Approx 95% complete for Meth13_R2_001_val_2.fq.gz Analysis complete for Meth13_R2_001_val_2.fq.gz Deleting both intermediate output files Meth13_R1_001_trimmed.fq.gz and Meth13_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth14_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed Finished in 638.24 s (9 us/read; 6.53 M reads/minute). === Summary === Total reads processed: 69,473,196 Reads with adapters: 0 (0.0%) Reads written (passing filters): 69,473,196 (100.0%) Total basepairs processed: 10,420,979,400 bp Quality-trimmed: 11,201,680 bp (0.1%) Total written (filtered): 10,409,777,720 bp (99.9%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 69473196 sequences processed in total Writing final adapter and quality trimmed output to Meth14_R1_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth14_R1_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth14_R1_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 1651.33 s (24 us/read; 2.52 M reads/minute). === Summary === Total reads processed: 69,473,196 Reads with adapters: 55,400,990 (79.7%) Reads written (passing filters): 69,473,196 (100.0%) Total basepairs processed: 10,409,777,720 bp Total written (filtered): 7,291,489,780 bp (70.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 55400990 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 40.9% C: 2.5% G: 51.1% T: 5.5% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 8782866 17368299.0 0 8782866 2 857608 4342074.8 0 857608 3 658045 1085518.7 0 658045 4 300067 271379.7 0 300067 5 207375 67844.9 0 207375 6 181801 16961.2 0 181801 7 219369 4240.3 0 219369 8 219799 1060.1 0 219799 9 205689 265.0 0 202777 2912 10 246677 66.3 1 226049 20628 11 418235 16.6 1 378095 40140 12 254220 4.1 1 229651 24569 13 229447 1.0 1 205325 24122 14 231819 1.0 1 206513 25306 15 197934 1.0 1 176411 21523 16 207582 1.0 1 184590 22992 17 239494 1.0 1 213264 26230 18 227732 1.0 1 204314 23418 19 240456 1.0 1 215059 25397 20 243286 1.0 1 218005 25281 21 270542 1.0 1 241962 28580 22 261114 1.0 1 233681 27433 23 324289 1.0 1 290172 34117 24 304424 1.0 1 270683 33741 25 268262 1.0 1 239785 28477 26 230253 1.0 1 205804 24449 27 266605 1.0 1 238152 28453 28 422673 1.0 1 378173 44500 29 273666 1.0 1 242704 30962 30 258507 1.0 1 230975 27532 31 260642 1.0 1 232758 27884 32 282796 1.0 1 252895 29901 33 251359 1.0 1 223613 27746 34 270491 1.0 1 241227 29264 35 261946 1.0 1 233346 28600 36 264319 1.0 1 234923 29396 37 363860 1.0 1 324492 39368 38 330615 1.0 1 294792 35823 39 317729 1.0 1 281947 35782 40 443709 1.0 1 396553 47156 41 439031 1.0 1 392495 46536 42 293226 1.0 1 261246 31980 43 349316 1.0 1 310324 38992 44 278944 1.0 1 247166 31778 45 430265 1.0 1 386344 43921 46 209795 1.0 1 186554 23241 47 270492 1.0 1 241475 29017 48 338914 1.0 1 301468 37446 49 608396 1.0 1 543874 64522 50 345036 1.0 1 305958 39078 51 393371 1.0 1 346977 46394 52 434189 1.0 1 387030 47159 53 375166 1.0 1 333040 42126 54 677937 1.0 1 602728 75209 55 438277 1.0 1 389961 48316 56 336391 1.0 1 299219 37172 57 381521 1.0 1 338996 42525 58 578958 1.0 1 514594 64364 59 348832 1.0 1 309050 39782 60 690597 1.0 1 616628 73969 61 378363 1.0 1 335286 43077 62 371312 1.0 1 328574 42738 63 325780 1.0 1 288761 37019 64 360043 1.0 1 320109 39934 65 299565 1.0 1 265521 34044 66 351273 1.0 1 310428 40845 67 446381 1.0 1 393754 52627 68 581169 1.0 1 513322 67847 69 555370 1.0 1 477063 78307 70 1821958 1.0 1 1645415 176543 71 159722 1.0 1 141530 18192 72 66696 1.0 1 57291 9405 73 388987 1.0 1 339110 49877 74 1374358 1.0 1 1216794 157564 75 332841 1.0 1 292206 40635 76 416417 1.0 1 367866 48551 77 460145 1.0 1 406050 54095 78 331342 1.0 1 291983 39359 79 366128 1.0 1 323010 43118 80 382456 1.0 1 336936 45520 81 326902 1.0 1 287716 39186 82 348100 1.0 1 306813 41287 83 332056 1.0 1 292244 39812 84 475457 1.0 1 419007 56450 85 420225 1.0 1 369669 50556 86 345642 1.0 1 303706 41936 87 426380 1.0 1 375165 51215 88 363082 1.0 1 318909 44173 89 441663 1.0 1 388095 53568 90 420556 1.0 1 368610 51946 91 461064 1.0 1 404128 56936 92 336462 1.0 1 294241 42221 93 393138 1.0 1 344342 48796 94 443807 1.0 1 388607 55200 95 316764 1.0 1 276823 39941 96 338920 1.0 1 295107 43813 97 449770 1.0 1 391931 57839 98 424585 1.0 1 369668 54917 99 375734 1.0 1 327187 48547 100 399744 1.0 1 347485 52259 101 306235 1.0 1 266586 39649 102 303444 1.0 1 263487 39957 103 381845 1.0 1 331309 50536 104 325653 1.0 1 282316 43337 105 312837 1.0 1 271156 41681 106 518166 1.0 1 449072 69094 107 394290 1.0 1 340403 53887 108 400937 1.0 1 346365 54572 109 457671 1.0 1 394132 63539 110 296032 1.0 1 255379 40653 111 290983 1.0 1 250446 40537 112 324856 1.0 1 279357 45499 113 280038 1.0 1 240483 39555 114 482507 1.0 1 414788 67719 115 943892 1.0 1 812500 131392 116 271430 1.0 1 232083 39347 117 382741 1.0 1 327790 54951 118 350788 1.0 1 300238 50550 119 368835 1.0 1 315411 53424 120 207719 1.0 1 177597 30122 121 211750 1.0 1 180751 30999 122 191203 1.0 1 162999 28204 123 206942 1.0 1 176595 30347 124 200886 1.0 1 171101 29785 125 263147 1.0 1 224479 38668 126 157461 1.0 1 133795 23666 127 132546 1.0 1 112871 19675 128 82021 1.0 1 69657 12364 129 66010 1.0 1 56158 9852 130 47701 1.0 1 40590 7111 131 65077 1.0 1 55570 9507 132 29191 1.0 1 24701 4490 133 10959 1.0 1 9307 1652 134 6055 1.0 1 5140 915 135 1656 1.0 1 1395 261 136 705 1.0 1 608 97 137 41 1.0 1 32 9 138 10 1.0 1 10 139 6 1.0 1 6 140 9 1.0 1 9 141 6 1.0 1 4 2 142 2 1.0 1 2 144 1 1.0 1 0 1 145 2 1.0 1 1 1 148 59 1.0 1 52 7 149 26 1.0 1 17 9 150 306 1.0 1 266 40 Successfully deleted temporary file Meth14_R1_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_R1_001.fastq.gz ============================================= 69473196 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3888847 (5.6%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 30667943 (44.1%) RRBS reads trimmed by 2 bp at the start when read started with CAA (641373) or CGA (30028291) in total: 30669664 (44.1%) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth14_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed Finished in 642.50 s (9 us/read; 6.49 M reads/minute). === Summary === Total reads processed: 69,473,196 Reads with adapters: 0 (0.0%) Reads written (passing filters): 69,473,196 (100.0%) Total basepairs processed: 10,420,979,400 bp Quality-trimmed: 78,623,751 bp (0.8%) Total written (filtered): 10,342,355,649 bp (99.2%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 69473196 sequences processed in total Writing final adapter and quality trimmed output to Meth14_R2_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth14_R2_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth14_R2_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 1689.49 s (24 us/read; 2.47 M reads/minute). === Summary === Total reads processed: 69,473,196 Reads with adapters: 54,757,002 (78.8%) Reads written (passing filters): 69,473,196 (100.0%) Total basepairs processed: 10,342,355,649 bp Total written (filtered): 7,306,131,783 bp (70.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 54757002 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 52.5% C: 2.6% G: 39.4% T: 5.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 9197747 17368299.0 0 9197747 2 791126 4342074.8 0 791126 3 650060 1085518.7 0 650060 4 300051 271379.7 0 300051 5 207094 67844.9 0 207094 6 183231 16961.2 0 183231 7 206636 4240.3 0 206636 8 226217 1060.1 0 226217 9 194194 265.0 0 192768 1426 10 239058 66.3 1 221959 17099 11 408625 16.6 1 373369 35256 12 262789 4.1 1 239771 23018 13 214488 1.0 1 191823 22665 14 227214 1.0 1 204150 23064 15 186533 1.0 1 168602 17931 16 210213 1.0 1 188151 22062 17 224535 1.0 1 202585 21950 18 215457 1.0 1 195058 20399 19 241405 1.0 1 218468 22937 20 243924 1.0 1 220366 23558 21 264163 1.0 1 237649 26514 22 264559 1.0 1 239756 24803 23 297505 1.0 1 269472 28033 24 302339 1.0 1 273883 28456 25 298219 1.0 1 270303 27916 26 200126 1.0 1 179911 20215 27 255485 1.0 1 228796 26689 28 406873 1.0 1 371566 35307 29 269701 1.0 1 243338 26363 30 252209 1.0 1 229366 22843 31 259037 1.0 1 234311 24726 32 273918 1.0 1 248477 25441 33 248703 1.0 1 224614 24089 34 260017 1.0 1 236461 23556 35 257033 1.0 1 232060 24973 36 268162 1.0 1 243710 24452 37 339901 1.0 1 308266 31635 38 334547 1.0 1 303634 30913 39 314407 1.0 1 284548 29859 40 443344 1.0 1 403840 39504 41 422616 1.0 1 382612 40004 42 288615 1.0 1 262857 25758 43 319929 1.0 1 290681 29248 44 277603 1.0 1 252069 25534 45 317264 1.0 1 287321 29943 46 342879 1.0 1 309141 33738 47 299956 1.0 1 273661 26295 48 336404 1.0 1 305257 31147 49 553560 1.0 1 503398 50162 50 348651 1.0 1 316232 32419 51 349468 1.0 1 316200 33268 52 436733 1.0 1 395379 41354 53 379569 1.0 1 344088 35481 54 721200 1.0 1 657042 64158 55 342173 1.0 1 309916 32257 56 347373 1.0 1 314411 32962 57 608317 1.0 1 552920 55397 58 367949 1.0 1 332225 35724 59 324979 1.0 1 294257 30722 60 740386 1.0 1 674689 65697 61 382326 1.0 1 346166 36160 62 332142 1.0 1 295077 37065 63 951147 1.0 1 867402 83745 64 272348 1.0 1 245701 26647 65 198937 1.0 1 179459 19478 66 215348 1.0 1 193519 21829 67 572565 1.0 1 521252 51313 68 542463 1.0 1 491631 50832 69 427048 1.0 1 386599 40449 70 618005 1.0 1 560912 57093 71 569054 1.0 1 515913 53141 72 462342 1.0 1 417497 44845 73 941079 1.0 1 855358 85721 74 1301136 1.0 1 1181408 119728 75 406521 1.0 1 367659 38862 76 338564 1.0 1 306385 32179 77 230982 1.0 1 206795 24187 78 267339 1.0 1 241279 26060 79 331027 1.0 1 298842 32185 80 355168 1.0 1 319944 35224 81 309160 1.0 1 278700 30460 82 335140 1.0 1 302340 32800 83 345577 1.0 1 311091 34486 84 464235 1.0 1 418098 46137 85 430740 1.0 1 387769 42971 86 344274 1.0 1 309038 35236 87 409694 1.0 1 368415 41279 88 347765 1.0 1 312880 34885 89 419319 1.0 1 376833 42486 90 402929 1.0 1 362455 40474 91 435170 1.0 1 390938 44232 92 321501 1.0 1 288699 32802 93 375027 1.0 1 336301 38726 94 417103 1.0 1 374154 42949 95 299840 1.0 1 268676 31164 96 322439 1.0 1 288700 33739 97 430709 1.0 1 385800 44909 98 410208 1.0 1 367535 42673 99 371684 1.0 1 332048 39636 100 391758 1.0 1 349967 41791 101 297443 1.0 1 265087 32356 102 290284 1.0 1 258921 31363 103 359954 1.0 1 321158 38796 104 306323 1.0 1 272755 33568 105 298940 1.0 1 266054 32886 106 486818 1.0 1 433188 53630 107 373478 1.0 1 331629 41849 108 383489 1.0 1 341083 42406 109 430389 1.0 1 382372 48017 110 284755 1.0 1 252983 31772 111 284268 1.0 1 252483 31785 112 320100 1.0 1 283685 36415 113 283802 1.0 1 251693 32109 114 472995 1.0 1 418840 54155 115 891460 1.0 1 789541 101919 116 259122 1.0 1 228258 30864 117 361635 1.0 1 318519 43116 118 335624 1.0 1 295770 39854 119 352655 1.0 1 310802 41853 120 201209 1.0 1 176857 24352 121 204289 1.0 1 179728 24561 122 183152 1.0 1 160739 22413 123 199205 1.0 1 174646 24559 124 193647 1.0 1 169805 23842 125 255331 1.0 1 223703 31628 126 153044 1.0 1 133926 19118 127 128172 1.0 1 112200 15972 128 79879 1.0 1 69697 10182 129 63552 1.0 1 55540 8012 130 46254 1.0 1 40233 6021 131 62315 1.0 1 54565 7750 132 28013 1.0 1 24322 3691 133 10585 1.0 1 9135 1450 134 5808 1.0 1 4947 861 135 1598 1.0 1 1368 230 136 684 1.0 1 601 83 137 36 1.0 1 33 3 138 11 1.0 1 10 1 139 7 1.0 1 6 1 140 8 1.0 1 8 141 8 1.0 1 6 2 142 2 1.0 1 1 1 144 2 1.0 1 1 1 145 2 1.0 1 2 147 2 1.0 1 2 148 58 1.0 1 51 7 149 24 1.0 1 20 4 150 289 1.0 1 264 25 Successfully deleted temporary file Meth14_R2_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth14_R2_001.fastq.gz ============================================= 69473196 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 7124230 (10.3%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (771107) or CGA (36511320) in total: 37282427 (53.7%) Validate paired-end files Meth14_R1_001_trimmed.fq.gz and Meth14_R2_001_trimmed.fq.gz file_1: Meth14_R1_001_trimmed.fq.gz, file_2: Meth14_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth14_R1_001_trimmed.fq.gz and Meth14_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth14_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth14_R2_001_val_2.fq.gz Total number of sequences analysed: 69473196 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 313337 (0.45%) >>> Now running FastQC on the validated data Meth14_R1_001_val_1.fq.gz<<< Started analysis of Meth14_R1_001_val_1.fq.gz Approx 5% complete for Meth14_R1_001_val_1.fq.gz Approx 10% complete for Meth14_R1_001_val_1.fq.gz Approx 15% complete for Meth14_R1_001_val_1.fq.gz Approx 20% complete for Meth14_R1_001_val_1.fq.gz Approx 25% complete for Meth14_R1_001_val_1.fq.gz Approx 30% complete for Meth14_R1_001_val_1.fq.gz Approx 35% complete for Meth14_R1_001_val_1.fq.gz Approx 40% complete for Meth14_R1_001_val_1.fq.gz Approx 45% complete for Meth14_R1_001_val_1.fq.gz Approx 50% complete for Meth14_R1_001_val_1.fq.gz Approx 55% complete for Meth14_R1_001_val_1.fq.gz Approx 60% complete for Meth14_R1_001_val_1.fq.gz Approx 65% complete for Meth14_R1_001_val_1.fq.gz Approx 70% complete for Meth14_R1_001_val_1.fq.gz Approx 75% complete for Meth14_R1_001_val_1.fq.gz Approx 80% complete for Meth14_R1_001_val_1.fq.gz Approx 85% complete for Meth14_R1_001_val_1.fq.gz Approx 90% complete for Meth14_R1_001_val_1.fq.gz Approx 95% complete for Meth14_R1_001_val_1.fq.gz Analysis complete for Meth14_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth14_R2_001_val_2.fq.gz<<< Started analysis of Meth14_R2_001_val_2.fq.gz Approx 5% complete for Meth14_R2_001_val_2.fq.gz Approx 10% complete for Meth14_R2_001_val_2.fq.gz Approx 15% complete for Meth14_R2_001_val_2.fq.gz Approx 20% complete for Meth14_R2_001_val_2.fq.gz Approx 25% complete for Meth14_R2_001_val_2.fq.gz Approx 30% complete for Meth14_R2_001_val_2.fq.gz Approx 35% complete for Meth14_R2_001_val_2.fq.gz Approx 40% complete for Meth14_R2_001_val_2.fq.gz Approx 45% complete for Meth14_R2_001_val_2.fq.gz Approx 50% complete for Meth14_R2_001_val_2.fq.gz Approx 55% complete for Meth14_R2_001_val_2.fq.gz Approx 60% complete for Meth14_R2_001_val_2.fq.gz Approx 65% complete for Meth14_R2_001_val_2.fq.gz Approx 70% complete for Meth14_R2_001_val_2.fq.gz Approx 75% complete for Meth14_R2_001_val_2.fq.gz Approx 80% complete for Meth14_R2_001_val_2.fq.gz Approx 85% complete for Meth14_R2_001_val_2.fq.gz Approx 90% complete for Meth14_R2_001_val_2.fq.gz Approx 95% complete for Meth14_R2_001_val_2.fq.gz Analysis complete for Meth14_R2_001_val_2.fq.gz Deleting both intermediate output files Meth14_R1_001_trimmed.fq.gz and Meth14_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth15_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth15_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth15_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed Finished in 1014.11 s (9 us/read; 6.48 M reads/minute). === Summary === Total reads processed: 109,570,006 Reads with adapters: 0 (0.0%) Reads written (passing filters): 109,570,006 (100.0%) Total basepairs processed: 16,435,500,900 bp Quality-trimmed: 17,058,606 bp (0.1%) Total written (filtered): 16,418,442,294 bp (99.9%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 109570006 sequences processed in total Writing final adapter and quality trimmed output to Meth15_R1_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth15_R1_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth15_R1_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2660.07 s (24 us/read; 2.47 M reads/minute). === Summary === Total reads processed: 109,570,006 Reads with adapters: 85,450,494 (78.0%) Reads written (passing filters): 109,570,006 (100.0%) Total basepairs processed: 16,418,442,294 bp Total written (filtered): 11,708,570,940 bp (71.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 85450494 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.5% C: 3.1% G: 43.1% T: 6.4% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15881685 27392501.5 0 15881685 2 1326314 6848125.4 0 1326314 3 987908 1712031.3 0 987908 4 479892 428007.8 0 479892 5 315963 107002.0 0 315963 6 284231 26750.5 0 284231 7 332502 6687.6 0 332502 8 336661 1671.9 0 336661 9 319375 418.0 0 315014 4361 10 376078 104.5 1 343524 32554 11 652211 26.1 1 584608 67603 12 385526 6.5 1 346589 38937 13 367125 1.6 1 327068 40057 14 345421 1.6 1 306617 38804 15 308922 1.6 1 274813 34109 16 325782 1.6 1 288166 37616 17 343774 1.6 1 304581 39193 18 351421 1.6 1 313771 37650 19 366477 1.6 1 326737 39740 20 357719 1.6 1 318838 38881 21 355737 1.6 1 316455 39282 22 396415 1.6 1 353903 42512 23 534508 1.6 1 476805 57703 24 438039 1.6 1 388134 49905 25 392153 1.6 1 349639 42514 26 326147 1.6 1 290198 35949 27 367964 1.6 1 326870 41094 28 589600 1.6 1 526234 63366 29 392793 1.6 1 347702 45091 30 371448 1.6 1 331148 40300 31 385679 1.6 1 343409 42270 32 413960 1.6 1 368784 45176 33 380206 1.6 1 337064 43142 34 433647 1.6 1 385023 48624 35 384518 1.6 1 341965 42553 36 393763 1.6 1 350251 43512 37 524656 1.6 1 465666 58990 38 548952 1.6 1 487732 61220 39 538971 1.6 1 481224 57747 40 575079 1.6 1 510147 64932 41 629906 1.6 1 558113 71793 42 406006 1.6 1 361276 44730 43 509761 1.6 1 450931 58830 44 418557 1.6 1 367831 50726 45 657598 1.6 1 588206 69392 46 301467 1.6 1 266028 35439 47 384563 1.6 1 341752 42811 48 479560 1.6 1 424891 54669 49 919153 1.6 1 819152 100001 50 482536 1.6 1 425678 56858 51 565122 1.6 1 496604 68518 52 646514 1.6 1 574128 72386 53 520868 1.6 1 461228 59640 54 954083 1.6 1 846167 107916 55 621495 1.6 1 550973 70522 56 475172 1.6 1 421258 53914 57 568249 1.6 1 502917 65332 58 866998 1.6 1 768288 98710 59 472499 1.6 1 416890 55609 60 1000128 1.6 1 890090 110038 61 558077 1.6 1 493433 64644 62 505737 1.6 1 447064 58673 63 455947 1.6 1 403334 52613 64 520537 1.6 1 461227 59310 65 422608 1.6 1 372821 49787 66 506601 1.6 1 446321 60280 67 681931 1.6 1 600525 81406 68 844668 1.6 1 744047 100621 69 797831 1.6 1 685016 112815 70 2455220 1.6 1 2209337 245883 71 165028 1.6 1 143638 21390 72 75859 1.6 1 63042 12817 73 627173 1.6 1 547548 79625 74 2053322 1.6 1 1816689 236633 75 504092 1.6 1 440997 63095 76 600709 1.6 1 529073 71636 77 637126 1.6 1 560130 76996 78 494842 1.6 1 435516 59326 79 522272 1.6 1 459493 62779 80 543212 1.6 1 477983 65229 81 465519 1.6 1 409098 56421 82 504755 1.6 1 443375 61380 83 475264 1.6 1 417280 57984 84 699035 1.6 1 614950 84085 85 611586 1.6 1 536803 74783 86 490097 1.6 1 429187 60910 87 577172 1.6 1 506192 70980 88 521333 1.6 1 456853 64480 89 634181 1.6 1 555529 78652 90 593188 1.6 1 519930 73258 91 679111 1.6 1 594973 84138 92 471265 1.6 1 412028 59237 93 583880 1.6 1 510091 73789 94 660442 1.6 1 577533 82909 95 454088 1.6 1 395746 58342 96 489013 1.6 1 425639 63374 97 636451 1.6 1 554620 81831 98 619482 1.6 1 539222 80260 99 550951 1.6 1 478829 72122 100 611930 1.6 1 531343 80587 101 477720 1.6 1 414868 62852 102 469210 1.6 1 406380 62830 103 559469 1.6 1 485715 73754 104 496435 1.6 1 429327 67108 105 478535 1.6 1 413559 64976 106 774275 1.6 1 669839 104436 107 617133 1.6 1 532627 84506 108 613075 1.6 1 527738 85337 109 696205 1.6 1 600909 95296 110 467767 1.6 1 403306 64461 111 444303 1.6 1 381719 62584 112 518609 1.6 1 446790 71819 113 446848 1.6 1 383017 63831 114 756680 1.6 1 650302 106378 115 1428651 1.6 1 1230013 198638 116 451175 1.6 1 384952 66223 117 589655 1.6 1 504024 85631 118 583890 1.6 1 498851 85039 119 633978 1.6 1 541847 92131 120 357006 1.6 1 304026 52980 121 371769 1.6 1 316182 55587 122 339599 1.6 1 289245 50354 123 378713 1.6 1 322408 56305 124 381818 1.6 1 324294 57524 125 491769 1.6 1 417384 74385 126 304155 1.6 1 257227 46928 127 265411 1.6 1 224767 40644 128 173625 1.6 1 147409 26216 129 144139 1.6 1 121958 22181 130 106601 1.6 1 90012 16589 131 141712 1.6 1 119681 22031 132 71531 1.6 1 60372 11159 133 26436 1.6 1 22268 4168 134 14419 1.6 1 12179 2240 135 4404 1.6 1 3659 745 136 1873 1.6 1 1614 259 137 111 1.6 1 91 20 138 30 1.6 1 24 6 139 10 1.6 1 9 1 140 4 1.6 1 4 141 3 1.6 1 2 1 142 1 1.6 1 1 144 6 1.6 1 2 4 147 8 1.6 1 4 4 148 147 1.6 1 126 21 149 29 1.6 1 26 3 150 560 1.6 1 491 69 Successfully deleted temporary file Meth15_R1_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth15_R1_001.fastq.gz ============================================= 109570006 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 5866846 (5.4%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 41006195 (37.4%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1231660) or CGA (54436579) in total: 55668239 (50.8%) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth15_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth15_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth15_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed Finished in 1032.28 s (9 us/read; 6.37 M reads/minute). === Summary === Total reads processed: 109,570,006 Reads with adapters: 0 (0.0%) Reads written (passing filters): 109,570,006 (100.0%) Total basepairs processed: 16,435,500,900 bp Quality-trimmed: 157,545,324 bp (1.0%) Total written (filtered): 16,277,955,576 bp (99.0%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 109570006 sequences processed in total Writing final adapter and quality trimmed output to Meth15_R2_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth15_R2_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth15_R2_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 2732.35 s (25 us/read; 2.41 M reads/minute). === Summary === Total reads processed: 109,570,006 Reads with adapters: 83,811,500 (76.5%) Reads written (passing filters): 109,570,006 (100.0%) Total basepairs processed: 16,277,955,576 bp Total written (filtered): 11,729,149,239 bp (72.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 83811500 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.2% C: 2.6% G: 44.4% T: 6.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15643604 27392501.5 0 15643604 2 1404461 6848125.4 0 1404461 3 1032068 1712031.3 0 1032068 4 495162 428007.8 0 495162 5 315265 107002.0 0 315265 6 281806 26750.5 0 281806 7 315056 6687.6 0 315056 8 343362 1671.9 0 343362 9 303966 418.0 0 301786 2180 10 364458 104.5 1 337350 27108 11 636950 26.1 1 577475 59475 12 415500 6.5 1 378195 37305 13 327101 1.6 1 291246 35855 14 334728 1.6 1 300065 34663 15 293162 1.6 1 262741 30421 16 333254 1.6 1 297273 35981 17 328131 1.6 1 295009 33122 18 321080 1.6 1 289708 31372 19 382369 1.6 1 344782 37587 20 357602 1.6 1 321903 35699 21 333890 1.6 1 299589 34301 22 403737 1.6 1 364438 39299 23 495561 1.6 1 447621 47940 24 430568 1.6 1 388613 41955 25 435718 1.6 1 393815 41903 26 279865 1.6 1 251513 28352 27 353301 1.6 1 315930 37371 28 569412 1.6 1 518365 51047 29 386976 1.6 1 347737 39239 30 361508 1.6 1 327534 33974 31 384181 1.6 1 345906 38275 32 398982 1.6 1 361474 37508 33 378366 1.6 1 340059 38307 34 422614 1.6 1 382314 40300 35 367792 1.6 1 332596 35196 36 403291 1.6 1 361515 41776 37 529705 1.6 1 478848 50857 38 528089 1.6 1 472928 55161 39 511744 1.6 1 457170 54574 40 641148 1.6 1 582863 58285 41 597201 1.6 1 539426 57775 42 443261 1.6 1 402607 40654 43 432281 1.6 1 390543 41738 44 452376 1.6 1 409941 42435 45 537153 1.6 1 484438 52715 46 510405 1.6 1 458984 51421 47 700998 1.6 1 639352 61646 48 312850 1.6 1 281030 31820 49 724516 1.6 1 656801 67715 50 504634 1.6 1 457939 46695 51 433338 1.6 1 390768 42570 52 619613 1.6 1 560502 59111 53 524596 1.6 1 472405 52191 54 1164400 1.6 1 1061414 102986 55 336683 1.6 1 302509 34174 56 506802 1.6 1 452593 54209 57 1713467 1.6 1 1562674 150793 58 380124 1.6 1 339541 40583 59 350769 1.6 1 312681 38088 60 1486641 1.6 1 1353823 132818 61 474221 1.6 1 428726 45495 62 389291 1.6 1 339128 50163 63 2403019 1.6 1 2192515 210504 64 664617 1.6 1 603401 61216 65 209309 1.6 1 187984 21325 66 259805 1.6 1 230002 29803 67 1021196 1.6 1 929011 92185 68 556813 1.6 1 502779 54034 69 498388 1.6 1 449011 49377 70 799861 1.6 1 725414 74447 71 549560 1.6 1 496408 53152 72 431189 1.6 1 387803 43386 73 912672 1.6 1 825986 86686 74 1215964 1.6 1 1101520 114444 75 387223 1.6 1 348654 38569 76 439150 1.6 1 397016 42134 77 308592 1.6 1 275729 32863 78 390003 1.6 1 351604 38399 79 465817 1.6 1 419820 45997 80 500520 1.6 1 450662 49858 81 439923 1.6 1 395631 44292 82 486249 1.6 1 437371 48878 83 499883 1.6 1 449436 50447 84 685820 1.6 1 616711 69109 85 633416 1.6 1 568645 64771 86 491581 1.6 1 440530 51051 87 556922 1.6 1 499982 56940 88 500754 1.6 1 450100 50654 89 600638 1.6 1 539777 60861 90 567327 1.6 1 509781 57546 91 639615 1.6 1 574511 65104 92 449676 1.6 1 403204 46472 93 555974 1.6 1 499491 56483 94 618669 1.6 1 555245 63424 95 428774 1.6 1 383862 44912 96 464401 1.6 1 416024 48377 97 609349 1.6 1 545451 63898 98 599249 1.6 1 536342 62907 99 546292 1.6 1 488390 57902 100 600200 1.6 1 535861 64339 101 463544 1.6 1 413256 50288 102 447382 1.6 1 398994 48388 103 527840 1.6 1 471266 56574 104 466116 1.6 1 415619 50497 105 457490 1.6 1 407507 49983 106 729732 1.6 1 649934 79798 107 586569 1.6 1 521881 64688 108 585355 1.6 1 520142 65213 109 655586 1.6 1 582992 72594 110 445079 1.6 1 395391 49688 111 423064 1.6 1 375407 47657 112 491877 1.6 1 436210 55667 113 426838 1.6 1 377878 48960 114 718856 1.6 1 636056 82800 115 1343866 1.6 1 1190996 152870 116 433588 1.6 1 383499 50089 117 562583 1.6 1 496034 66549 118 564042 1.6 1 497114 66928 119 608898 1.6 1 537036 71862 120 345174 1.6 1 303547 41627 121 358548 1.6 1 315632 42916 122 324348 1.6 1 284899 39449 123 363526 1.6 1 319323 44203 124 366908 1.6 1 322053 44855 125 475676 1.6 1 416659 59017 126 294723 1.6 1 258353 36370 127 256017 1.6 1 224163 31854 128 168906 1.6 1 147377 21529 129 138126 1.6 1 120620 17506 130 102655 1.6 1 89603 13052 131 134692 1.6 1 117223 17469 132 68185 1.6 1 59411 8774 133 25423 1.6 1 21912 3511 134 13817 1.6 1 11938 1879 135 4221 1.6 1 3660 561 136 1815 1.6 1 1547 268 137 97 1.6 1 82 15 138 26 1.6 1 25 1 139 9 1.6 1 8 1 140 6 1.6 1 6 141 3 1.6 1 3 142 3 1.6 1 0 3 144 6 1.6 1 2 4 145 1 1.6 1 0 1 146 1 1.6 1 0 1 147 3 1.6 1 3 148 145 1.6 1 129 16 149 30 1.6 1 21 9 150 542 1.6 1 498 44 Successfully deleted temporary file Meth15_R2_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth15_R2_001.fastq.gz ============================================= 109570006 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 14718642 (13.4%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1128168) or CGA (49375162) in total: 50503330 (46.1%) Validate paired-end files Meth15_R1_001_trimmed.fq.gz and Meth15_R2_001_trimmed.fq.gz file_1: Meth15_R1_001_trimmed.fq.gz, file_2: Meth15_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth15_R1_001_trimmed.fq.gz and Meth15_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth15_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth15_R2_001_val_2.fq.gz Total number of sequences analysed: 109570006 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 658759 (0.60%) >>> Now running FastQC on the validated data Meth15_R1_001_val_1.fq.gz<<< Started analysis of Meth15_R1_001_val_1.fq.gz Approx 5% complete for Meth15_R1_001_val_1.fq.gz Approx 10% complete for Meth15_R1_001_val_1.fq.gz Approx 15% complete for Meth15_R1_001_val_1.fq.gz Approx 20% complete for Meth15_R1_001_val_1.fq.gz Approx 25% complete for Meth15_R1_001_val_1.fq.gz Approx 30% complete for Meth15_R1_001_val_1.fq.gz Approx 35% complete for Meth15_R1_001_val_1.fq.gz Approx 40% complete for Meth15_R1_001_val_1.fq.gz Approx 45% complete for Meth15_R1_001_val_1.fq.gz Approx 50% complete for Meth15_R1_001_val_1.fq.gz Approx 55% complete for Meth15_R1_001_val_1.fq.gz Approx 60% complete for Meth15_R1_001_val_1.fq.gz Approx 65% complete for Meth15_R1_001_val_1.fq.gz Approx 70% complete for Meth15_R1_001_val_1.fq.gz Approx 75% complete for Meth15_R1_001_val_1.fq.gz Approx 80% complete for Meth15_R1_001_val_1.fq.gz Approx 85% complete for Meth15_R1_001_val_1.fq.gz Approx 90% complete for Meth15_R1_001_val_1.fq.gz Approx 95% complete for Meth15_R1_001_val_1.fq.gz Analysis complete for Meth15_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth15_R2_001_val_2.fq.gz<<< Started analysis of Meth15_R2_001_val_2.fq.gz Approx 5% complete for Meth15_R2_001_val_2.fq.gz Approx 10% complete for Meth15_R2_001_val_2.fq.gz Approx 15% complete for Meth15_R2_001_val_2.fq.gz Approx 20% complete for Meth15_R2_001_val_2.fq.gz Approx 25% complete for Meth15_R2_001_val_2.fq.gz Approx 30% complete for Meth15_R2_001_val_2.fq.gz Approx 35% complete for Meth15_R2_001_val_2.fq.gz Approx 40% complete for Meth15_R2_001_val_2.fq.gz Approx 45% complete for Meth15_R2_001_val_2.fq.gz Approx 50% complete for Meth15_R2_001_val_2.fq.gz Approx 55% complete for Meth15_R2_001_val_2.fq.gz Approx 60% complete for Meth15_R2_001_val_2.fq.gz Approx 65% complete for Meth15_R2_001_val_2.fq.gz Approx 70% complete for Meth15_R2_001_val_2.fq.gz Approx 75% complete for Meth15_R2_001_val_2.fq.gz Approx 80% complete for Meth15_R2_001_val_2.fq.gz Approx 85% complete for Meth15_R2_001_val_2.fq.gz Approx 90% complete for Meth15_R2_001_val_2.fq.gz Approx 95% complete for Meth15_R2_001_val_2.fq.gz Analysis complete for Meth15_R2_001_val_2.fq.gz Deleting both intermediate output files Meth15_R1_001_trimmed.fq.gz and Meth15_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth4_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth4_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth4_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed Finished in 1431.02 s (10 us/read; 6.32 M reads/minute). === Summary === Total reads processed: 150,624,528 Reads with adapters: 0 (0.0%) Reads written (passing filters): 150,624,528 (100.0%) Total basepairs processed: 22,593,679,200 bp Quality-trimmed: 28,858,391 bp (0.1%) Total written (filtered): 22,564,820,809 bp (99.9%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 150624528 sequences processed in total Writing final adapter and quality trimmed output to Meth4_R1_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth4_R1_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth4_R1_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 3618.83 s (24 us/read; 2.50 M reads/minute). === Summary === Total reads processed: 150,624,528 Reads with adapters: 123,278,388 (81.8%) Reads written (passing filters): 150,624,528 (100.0%) Total basepairs processed: 22,564,820,809 bp Total written (filtered): 15,728,080,367 bp (69.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 123278388 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 47.3% C: 2.9% G: 44.7% T: 5.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17926941 37656132.0 0 17926941 2 1629060 9414033.0 0 1629060 3 1127081 2353508.2 0 1127081 4 4408237 588377.1 0 4408237 5 507349 147094.3 0 507349 6 409510 36773.6 0 409510 7 436136 9193.4 0 436136 8 402372 2298.3 0 402372 9 371021 574.6 0 365110 5911 10 559431 143.6 1 513570 45861 11 488616 35.9 1 442071 46545 12 503385 9.0 1 455371 48014 13 526794 2.2 1 470871 55923 14 552304 2.2 1 491787 60517 15 674521 2.2 1 603250 71271 16 763387 2.2 1 676764 86623 17 524698 2.2 1 465066 59632 18 549959 2.2 1 492758 57201 19 534333 2.2 1 477885 56448 20 930236 2.2 1 832975 97261 21 563541 2.2 1 501928 61613 22 747074 2.2 1 669031 78043 23 550154 2.2 1 490338 59816 24 573693 2.2 1 507658 66035 25 1011625 2.2 1 904878 106747 26 551110 2.2 1 490832 60278 27 761201 2.2 1 677236 83965 28 2074838 2.2 1 1858685 216153 29 698868 2.2 1 619185 79683 30 634708 2.2 1 567752 66956 31 697946 2.2 1 623660 74286 32 911986 2.2 1 815557 96429 33 620881 2.2 1 551932 68949 34 710617 2.2 1 633940 76677 35 656720 2.2 1 584849 71871 36 604486 2.2 1 534170 70316 37 649973 2.2 1 581767 68206 38 970085 2.2 1 867378 102707 39 737457 2.2 1 657190 80267 40 901784 2.2 1 805308 96476 41 1224543 2.2 1 1092982 131561 42 704106 2.2 1 623714 80392 43 994656 2.2 1 871526 123130 44 952359 2.2 1 841944 110415 45 1141074 2.2 1 1021530 119544 46 543061 2.2 1 480898 62163 47 595940 2.2 1 527957 67983 48 744798 2.2 1 661862 82936 49 805957 2.2 1 718270 87687 50 581810 2.2 1 510966 70844 51 955412 2.2 1 855088 100324 52 643803 2.2 1 568882 74921 53 561556 2.2 1 496265 65291 54 844459 2.2 1 749828 94631 55 985435 2.2 1 875588 109847 56 729733 2.2 1 647451 82282 57 940576 2.2 1 837633 102943 58 1047851 2.2 1 926197 121654 59 1255922 2.2 1 1123839 132083 60 925301 2.2 1 823105 102196 61 835208 2.2 1 740018 95190 62 787102 2.2 1 695244 91858 63 925875 2.2 1 827116 98759 64 750734 2.2 1 665032 85702 65 752704 2.2 1 667155 85549 66 947743 2.2 1 836316 111427 67 776177 2.2 1 686068 90109 68 732667 2.2 1 646315 86352 69 834630 2.2 1 720687 113943 70 2073402 2.2 1 1865772 207630 71 346381 2.2 1 309848 36533 72 88612 2.2 1 76012 12600 73 189138 2.2 1 160288 28850 74 527145 2.2 1 462450 64695 75 706430 2.2 1 624059 82371 76 1099520 2.2 1 971235 128285 77 744676 2.2 1 655670 89006 78 592279 2.2 1 521339 70940 79 808120 2.2 1 712479 95641 80 730827 2.2 1 642344 88483 81 720896 2.2 1 634443 86453 82 951089 2.2 1 836563 114526 83 762900 2.2 1 670404 92496 84 905291 2.2 1 795140 110151 85 933124 2.2 1 816240 116884 86 788744 2.2 1 687756 100988 87 835429 2.2 1 731643 103786 88 1058598 2.2 1 927737 130861 89 961249 2.2 1 841738 119511 90 1105458 2.2 1 968895 136563 91 1119746 2.2 1 980263 139483 92 1016580 2.2 1 888416 128164 93 1014188 2.2 1 885659 128529 94 1175409 2.2 1 1024452 150957 95 826076 2.2 1 718798 107278 96 1292670 2.2 1 1128212 164458 97 1142779 2.2 1 995220 147559 98 1104950 2.2 1 961366 143584 99 955719 2.2 1 830972 124747 100 1014295 2.2 1 881529 132766 101 787403 2.2 1 682689 104714 102 722257 2.2 1 626532 95725 103 951202 2.2 1 825115 126087 104 814717 2.2 1 704603 110114 105 769224 2.2 1 665301 103923 106 948544 2.2 1 820515 128029 107 686527 2.2 1 591875 94652 108 798243 2.2 1 687617 110626 109 870079 2.2 1 747453 122626 110 765858 2.2 1 658273 107585 111 743948 2.2 1 638808 105140 112 1170274 2.2 1 1005227 165047 113 712644 2.2 1 609774 102870 114 913331 2.2 1 781221 132110 115 1064364 2.2 1 911825 152539 116 685707 2.2 1 585330 100377 117 706162 2.2 1 602201 103961 118 1015924 2.2 1 866717 149207 119 1238461 2.2 1 1055942 182519 120 615046 2.2 1 522969 92077 121 672403 2.2 1 571120 101283 122 593766 2.2 1 504215 89551 123 627170 2.2 1 532776 94394 124 711539 2.2 1 604566 106973 125 365643 2.2 1 309999 55644 126 399539 2.2 1 338517 61022 127 548562 2.2 1 465380 83182 128 223311 2.2 1 188582 34729 129 168704 2.2 1 142915 25789 130 149921 2.2 1 126976 22945 131 151895 2.2 1 128658 23237 132 76747 2.2 1 64877 11870 133 29756 2.2 1 25187 4569 134 5398 2.2 1 4590 808 135 1162 2.2 1 939 223 136 1058 2.2 1 881 177 137 83 2.2 1 68 15 138 38 2.2 1 30 8 139 24 2.2 1 23 1 140 16 2.2 1 15 1 141 12 2.2 1 10 2 142 5 2.2 1 3 2 143 3 2.2 1 1 2 144 2 2.2 1 1 1 145 3 2.2 1 3 146 5 2.2 1 5 147 14 2.2 1 9 5 148 211 2.2 1 171 40 149 306 2.2 1 260 46 150 4147 2.2 1 3579 568 Successfully deleted temporary file Meth4_R1_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth4_R1_001.fastq.gz ============================================= 150624528 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 9496390 (6.3%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 61328973 (40.7%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1764891) or CGA (72831693) in total: 74596584 (49.5%) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth4_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth4_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth4_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed Finished in 1397.04 s (9 us/read; 6.47 M reads/minute). === Summary === Total reads processed: 150,624,528 Reads with adapters: 0 (0.0%) Reads written (passing filters): 150,624,528 (100.0%) Total basepairs processed: 22,593,679,200 bp Quality-trimmed: 196,540,406 bp (0.9%) Total written (filtered): 22,397,138,794 bp (99.1%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 150624528 sequences processed in total Writing final adapter and quality trimmed output to Meth4_R2_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth4_R2_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth4_R2_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 3676.96 s (24 us/read; 2.46 M reads/minute). === Summary === Total reads processed: 150,624,528 Reads with adapters: 120,971,047 (80.3%) Reads written (passing filters): 150,624,528 (100.0%) Total basepairs processed: 22,397,138,794 bp Total written (filtered): 15,763,645,799 bp (70.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 120971047 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 46.9% C: 2.4% G: 45.1% T: 5.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17704778 37656132.0 0 17704778 2 1751103 9414033.0 0 1751103 3 1263294 2353508.2 0 1263294 4 4365421 588377.1 0 4365421 5 508068 147094.3 0 508068 6 402402 36773.6 0 402402 7 410156 9193.4 0 410156 8 410374 2298.3 0 410374 9 353798 574.6 0 350726 3072 10 539760 143.6 1 503994 35766 11 477668 35.9 1 436982 40686 12 532131 9.0 1 487671 44460 13 486822 2.2 1 436506 50316 14 539545 2.2 1 484419 55126 15 639200 2.2 1 577264 61936 16 761846 2.2 1 679999 81847 17 495288 2.2 1 446356 48932 18 507725 2.2 1 461048 46677 19 565907 2.2 1 512127 53780 20 916493 2.2 1 830102 86391 21 526657 2.2 1 474040 52617 22 738304 2.2 1 672767 65537 23 504904 2.2 1 458802 46102 24 563879 2.2 1 510652 53227 25 1056223 2.2 1 961389 94834 26 497243 2.2 1 448937 48306 27 788720 2.2 1 700456 88264 28 1960766 2.2 1 1792799 167967 29 686529 2.2 1 621548 64981 30 617053 2.2 1 563016 54037 31 693488 2.2 1 629748 63740 32 875248 2.2 1 798864 76384 33 612393 2.2 1 554151 58242 34 716742 2.2 1 648612 68130 35 627810 2.2 1 566068 61742 36 583703 2.2 1 530958 52745 37 648382 2.2 1 589829 58553 38 1010711 2.2 1 920975 89736 39 752123 2.2 1 683221 68902 40 845533 2.2 1 772514 73019 41 1180412 2.2 1 1073473 106939 42 682186 2.2 1 622808 59378 43 912325 2.2 1 831696 80629 44 924149 2.2 1 844398 79751 45 912963 2.2 1 829264 83699 46 823104 2.2 1 747224 75880 47 847707 2.2 1 777784 69923 48 475945 2.2 1 432201 43744 49 675107 2.2 1 613943 61164 50 553917 2.2 1 505794 48123 51 507775 2.2 1 460521 47254 52 892849 2.2 1 814507 78342 53 649067 2.2 1 591115 57952 54 935579 2.2 1 856816 78763 55 601790 2.2 1 545633 56157 56 820426 2.2 1 743091 77335 57 1857360 2.2 1 1700456 156904 58 621978 2.2 1 560827 61151 59 708920 2.2 1 641179 67741 60 1741444 2.2 1 1594528 146916 61 967071 2.2 1 881412 85659 62 563156 2.2 1 497672 65484 63 3045739 2.2 1 2793845 251894 64 811007 2.2 1 736692 74315 65 342532 2.2 1 310142 32390 66 439834 2.2 1 392775 47059 67 1275204 2.2 1 1165564 109640 68 579467 2.2 1 526231 53236 69 548629 2.2 1 497301 51328 70 787077 2.2 1 717268 69809 71 582894 2.2 1 530001 52893 72 397882 2.2 1 360012 37870 73 556894 2.2 1 506122 50772 74 464822 2.2 1 420788 44034 75 551862 2.2 1 499878 51984 76 625742 2.2 1 566750 58992 77 442317 2.2 1 400503 41814 78 500512 2.2 1 453768 46744 79 728733 2.2 1 661483 67250 80 679047 2.2 1 614607 64440 81 687573 2.2 1 623341 64232 82 908445 2.2 1 821639 86806 83 788613 2.2 1 711731 76882 84 893243 2.2 1 806888 86355 85 964196 2.2 1 867348 96848 86 784286 2.2 1 702026 82260 87 809792 2.2 1 730495 79297 88 1004633 2.2 1 907807 96826 89 912131 2.2 1 823742 88389 90 1051789 2.2 1 951255 100534 91 1056348 2.2 1 953368 102980 92 961691 2.2 1 867792 93899 93 963799 2.2 1 870026 93773 94 1101267 2.2 1 990532 110735 95 785924 2.2 1 707576 78348 96 1220856 2.2 1 1100359 120497 97 1090480 2.2 1 981335 109145 98 1066093 2.2 1 960124 105969 99 942920 2.2 1 848644 94276 100 990754 2.2 1 890669 100085 101 756926 2.2 1 679074 77852 102 686249 2.2 1 615696 70553 103 893629 2.2 1 802176 91453 104 761610 2.2 1 682225 79385 105 729367 2.2 1 652853 76514 106 892685 2.2 1 799804 92881 107 653036 2.2 1 584237 68799 108 761204 2.2 1 680292 80912 109 819521 2.2 1 730935 88586 110 726323 2.2 1 647765 78558 111 723001 2.2 1 644213 78788 112 1128978 2.2 1 1005814 123164 113 707572 2.2 1 629023 78549 114 895709 2.2 1 795691 100018 115 1014650 2.2 1 901547 113103 116 660820 2.2 1 586918 73902 117 679832 2.2 1 602661 77171 118 986966 2.2 1 874932 112034 119 1188741 2.2 1 1053713 135028 120 596497 2.2 1 527773 68724 121 649928 2.2 1 575276 74652 122 567927 2.2 1 501179 66748 123 604361 2.2 1 534320 70041 124 683263 2.2 1 603279 79984 125 358064 2.2 1 316245 41819 126 391821 2.2 1 345278 46543 127 528991 2.2 1 466161 62830 128 217432 2.2 1 191228 26204 129 162497 2.2 1 142759 19738 130 145048 2.2 1 127349 17699 131 145578 2.2 1 127871 17707 132 73729 2.2 1 64689 9040 133 28631 2.2 1 25101 3530 134 5200 2.2 1 4565 635 135 1120 2.2 1 966 154 136 1060 2.2 1 904 156 137 74 2.2 1 69 5 138 34 2.2 1 33 1 139 24 2.2 1 17 7 140 19 2.2 1 18 1 141 13 2.2 1 7 6 142 9 2.2 1 5 4 143 1 2.2 1 1 144 2 2.2 1 0 2 145 3 2.2 1 3 146 7 2.2 1 4 3 147 13 2.2 1 9 4 148 193 2.2 1 164 29 149 311 2.2 1 266 45 150 3931 2.2 1 3534 397 Successfully deleted temporary file Meth4_R2_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth4_R2_001.fastq.gz ============================================= 150624528 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 17381248 (11.5%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1609237) or CGA (67354262) in total: 68963499 (45.8%) Validate paired-end files Meth4_R1_001_trimmed.fq.gz and Meth4_R2_001_trimmed.fq.gz file_1: Meth4_R1_001_trimmed.fq.gz, file_2: Meth4_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth4_R1_001_trimmed.fq.gz and Meth4_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth4_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth4_R2_001_val_2.fq.gz Total number of sequences analysed: 150624528 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 795739 (0.53%) >>> Now running FastQC on the validated data Meth4_R1_001_val_1.fq.gz<<< Started analysis of Meth4_R1_001_val_1.fq.gz Approx 5% complete for Meth4_R1_001_val_1.fq.gz Approx 10% complete for Meth4_R1_001_val_1.fq.gz Approx 15% complete for Meth4_R1_001_val_1.fq.gz Approx 20% complete for Meth4_R1_001_val_1.fq.gz Approx 25% complete for Meth4_R1_001_val_1.fq.gz Approx 30% complete for Meth4_R1_001_val_1.fq.gz Approx 35% complete for Meth4_R1_001_val_1.fq.gz Approx 40% complete for Meth4_R1_001_val_1.fq.gz Approx 45% complete for Meth4_R1_001_val_1.fq.gz Approx 50% complete for Meth4_R1_001_val_1.fq.gz Approx 55% complete for Meth4_R1_001_val_1.fq.gz Approx 60% complete for Meth4_R1_001_val_1.fq.gz Approx 65% complete for Meth4_R1_001_val_1.fq.gz Approx 70% complete for Meth4_R1_001_val_1.fq.gz Approx 75% complete for Meth4_R1_001_val_1.fq.gz Approx 80% complete for Meth4_R1_001_val_1.fq.gz Approx 85% complete for Meth4_R1_001_val_1.fq.gz Approx 90% complete for Meth4_R1_001_val_1.fq.gz Approx 95% complete for Meth4_R1_001_val_1.fq.gz Analysis complete for Meth4_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth4_R2_001_val_2.fq.gz<<< Started analysis of Meth4_R2_001_val_2.fq.gz Approx 5% complete for Meth4_R2_001_val_2.fq.gz Approx 10% complete for Meth4_R2_001_val_2.fq.gz Approx 15% complete for Meth4_R2_001_val_2.fq.gz Approx 20% complete for Meth4_R2_001_val_2.fq.gz Approx 25% complete for Meth4_R2_001_val_2.fq.gz Approx 30% complete for Meth4_R2_001_val_2.fq.gz Approx 35% complete for Meth4_R2_001_val_2.fq.gz Approx 40% complete for Meth4_R2_001_val_2.fq.gz Approx 45% complete for Meth4_R2_001_val_2.fq.gz Approx 50% complete for Meth4_R2_001_val_2.fq.gz Approx 55% complete for Meth4_R2_001_val_2.fq.gz Approx 60% complete for Meth4_R2_001_val_2.fq.gz Approx 65% complete for Meth4_R2_001_val_2.fq.gz Approx 70% complete for Meth4_R2_001_val_2.fq.gz Approx 75% complete for Meth4_R2_001_val_2.fq.gz Approx 80% complete for Meth4_R2_001_val_2.fq.gz Approx 85% complete for Meth4_R2_001_val_2.fq.gz Approx 90% complete for Meth4_R2_001_val_2.fq.gz Approx 95% complete for Meth4_R2_001_val_2.fq.gz Analysis complete for Meth4_R2_001_val_2.fq.gz Deleting both intermediate output files Meth4_R1_001_trimmed.fq.gz and Meth4_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth5_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed 200000000 sequences processed 210000000 sequences processed 220000000 sequences processed 230000000 sequences processed 240000000 sequences processed 250000000 sequences processed 260000000 sequences processed 270000000 sequences processed 280000000 sequences processed Finished in 2667.76 s (9 us/read; 6.42 M reads/minute). === Summary === Total reads processed: 285,607,307 Reads with adapters: 0 (0.0%) Reads written (passing filters): 285,607,307 (100.0%) Total basepairs processed: 42,841,096,050 bp Quality-trimmed: 42,177,750 bp (0.1%) Total written (filtered): 42,798,918,300 bp (99.9%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 285607307 sequences processed in total Writing final adapter and quality trimmed output to Meth5_R1_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth5_R1_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed 200000000 sequences processed 210000000 sequences processed 220000000 sequences processed 230000000 sequences processed 240000000 sequences processed 250000000 sequences processed 260000000 sequences processed 270000000 sequences processed 280000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth5_R1_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 6887.26 s (24 us/read; 2.49 M reads/minute). === Summary === Total reads processed: 285,607,307 Reads with adapters: 229,365,416 (80.3%) Reads written (passing filters): 285,607,307 (100.0%) Total basepairs processed: 42,798,918,300 bp Total written (filtered): 30,082,664,292 bp (70.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 229365416 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.5% C: 2.8% G: 43.1% T: 5.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 37615404 71401826.8 0 37615404 2 3823272 17850456.7 0 3823272 3 1929705 4462614.2 0 1929705 4 8216086 1115653.5 0 8216086 5 874551 278913.4 0 874551 6 729732 69728.3 0 729732 7 719271 17432.1 0 719271 8 636616 4358.0 0 636616 9 610015 1089.5 0 601088 8927 10 897943 272.4 1 826202 71741 11 835081 68.1 1 758841 76240 12 732250 17.0 1 664625 67625 13 855682 4.3 1 768432 87250 14 934838 4.3 1 833256 101582 15 1237634 4.3 1 1110781 126853 16 1385243 4.3 1 1230937 154306 17 877314 4.3 1 779091 98223 18 908164 4.3 1 816927 91237 19 831362 4.3 1 745063 86299 20 1555687 4.3 1 1398148 157539 21 2741198 4.3 1 2465529 275669 22 1820876 4.3 1 1637482 183394 23 899390 4.3 1 803614 95776 24 918471 4.3 1 814304 104167 25 1671292 4.3 1 1502852 168440 26 867775 4.3 1 775720 92055 27 1324017 4.3 1 1180731 143286 28 4561981 4.3 1 4104006 457975 29 1146671 4.3 1 1017804 128867 30 1027972 4.3 1 924415 103557 31 1085728 4.3 1 972859 112869 32 1611448 4.3 1 1448791 162657 33 886562 4.3 1 789986 96576 34 1119780 4.3 1 1003394 116386 35 1031703 4.3 1 919280 112423 36 943899 4.3 1 846420 97479 37 1021879 4.3 1 914638 107241 38 1703806 4.3 1 1531207 172599 39 1123930 4.3 1 1003160 120770 40 1482557 4.3 1 1327082 155475 41 1692413 4.3 1 1520244 172169 42 1153325 4.3 1 1033386 119939 43 1672983 4.3 1 1496297 176686 44 1714346 4.3 1 1528267 186079 45 1935829 4.3 1 1747015 188814 46 768909 4.3 1 685312 83597 47 896871 4.3 1 802485 94386 48 1053398 4.3 1 944221 109177 49 1302932 4.3 1 1168808 134124 50 885825 4.3 1 788797 97028 51 1010152 4.3 1 899387 110765 52 1404553 4.3 1 1260893 143660 53 930746 4.3 1 831140 99606 54 1129444 4.3 1 1007089 122355 55 1433735 4.3 1 1282800 150935 56 1194201 4.3 1 1067503 126698 57 1324099 4.3 1 1183222 140877 58 2002838 4.3 1 1793889 208949 59 1371764 4.3 1 1224247 147517 60 2124403 4.3 1 1907764 216639 61 2020633 4.3 1 1811014 209619 62 1081769 4.3 1 965189 116580 63 1231632 4.3 1 1101342 130290 64 1763384 4.3 1 1582772 180612 65 1092017 4.3 1 973871 118146 66 1470910 4.3 1 1313554 157356 67 1593438 4.3 1 1422138 171300 68 1348060 4.3 1 1201756 146304 69 1376068 4.3 1 1200593 175475 70 3341550 4.3 1 3030992 310558 71 249878 4.3 1 218574 31304 72 104243 4.3 1 85095 19148 73 534650 4.3 1 469177 65473 74 1018477 4.3 1 907342 111135 75 1252802 4.3 1 1117960 134842 76 2034078 4.3 1 1819042 215036 77 1298399 4.3 1 1156782 141617 78 1009250 4.3 1 898957 110293 79 1326076 4.3 1 1182564 143512 80 1241862 4.3 1 1105651 136211 81 1246431 4.3 1 1107915 138516 82 1860293 4.3 1 1632119 228174 83 1544206 4.3 1 1361468 182738 84 1473965 4.3 1 1309253 164712 85 1514414 4.3 1 1347322 167092 86 1131141 4.3 1 1004718 126423 87 1457872 4.3 1 1296908 160964 88 1729833 4.3 1 1539759 190074 89 1706854 4.3 1 1517143 189711 90 2084838 4.3 1 1854550 230288 91 1887471 4.3 1 1675495 211976 92 2101576 4.3 1 1863429 238147 93 2084969 4.3 1 1849308 235661 94 2336410 4.3 1 2066675 269735 95 1590695 4.3 1 1407361 183334 96 2684007 4.3 1 2384074 299933 97 2256733 4.3 1 1998241 258492 98 2219956 4.3 1 1964200 255756 99 1737602 4.3 1 1536908 200694 100 1881866 4.3 1 1664340 217526 101 1686004 4.3 1 1489669 196335 102 1364518 4.3 1 1204809 159709 103 2414501 4.3 1 2136096 278405 104 1521021 4.3 1 1339449 181572 105 1471000 4.3 1 1296875 174125 106 1849669 4.3 1 1632079 217590 107 1356605 4.3 1 1193999 162606 108 2158876 4.3 1 1902708 256168 109 1684151 4.3 1 1477712 206439 110 1457010 4.3 1 1280244 176766 111 1398943 4.3 1 1228355 170588 112 2115042 4.3 1 1858382 256660 113 1446018 4.3 1 1267467 178551 114 2191531 4.3 1 1920127 271404 115 2230740 4.3 1 1957130 273610 116 1344965 4.3 1 1176649 168316 117 1386741 4.3 1 1214186 172555 118 1947265 4.3 1 1704881 242384 119 2807501 4.3 1 2458055 349446 120 1145668 4.3 1 999495 146173 121 1344777 4.3 1 1174737 170040 122 1151281 4.3 1 1004528 146753 123 1360292 4.3 1 1188619 171673 124 1273651 4.3 1 1112417 161234 125 736748 4.3 1 642212 94536 126 739344 4.3 1 644508 94836 127 1094512 4.3 1 954291 140221 128 424513 4.3 1 369000 55513 129 295771 4.3 1 257526 38245 130 264580 4.3 1 230384 34196 131 367593 4.3 1 319865 47728 132 135721 4.3 1 117681 18040 133 54134 4.3 1 47126 7008 134 10091 4.3 1 8754 1337 135 2902 4.3 1 2533 369 136 7458 4.3 1 6469 989 137 264 4.3 1 206 58 138 56 4.3 1 39 17 139 40 4.3 1 36 4 140 24 4.3 1 16 8 141 18 4.3 1 16 2 142 15 4.3 1 7 8 143 2 4.3 1 2 144 10 4.3 1 3 7 145 3 4.3 1 2 1 146 1 4.3 1 1 147 8 4.3 1 5 3 148 193 4.3 1 164 29 149 207 4.3 1 190 17 150 3579 4.3 1 3140 439 Successfully deleted temporary file Meth5_R1_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_R1_001.fastq.gz ============================================= 285607307 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 12455645 (4.4%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 108911143 (38.1%) RRBS reads trimmed by 2 bp at the start when read started with CAA (3181836) or CGA (143429518) in total: 146611354 (51.3%) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth5_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed 200000000 sequences processed 210000000 sequences processed 220000000 sequences processed 230000000 sequences processed 240000000 sequences processed 250000000 sequences processed 260000000 sequences processed 270000000 sequences processed 280000000 sequences processed Finished in 2628.95 s (9 us/read; 6.52 M reads/minute). === Summary === Total reads processed: 285,607,307 Reads with adapters: 0 (0.0%) Reads written (passing filters): 285,607,307 (100.0%) Total basepairs processed: 42,841,096,050 bp Quality-trimmed: 324,449,136 bp (0.8%) Total written (filtered): 42,516,646,914 bp (99.2%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 285607307 sequences processed in total Writing final adapter and quality trimmed output to Meth5_R2_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth5_R2_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed 150000000 sequences processed 160000000 sequences processed 170000000 sequences processed 180000000 sequences processed 190000000 sequences processed 200000000 sequences processed 210000000 sequences processed 220000000 sequences processed 230000000 sequences processed 240000000 sequences processed 250000000 sequences processed 260000000 sequences processed 270000000 sequences processed 280000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth5_R2_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 7144.92 s (25 us/read; 2.40 M reads/minute). === Summary === Total reads processed: 285,607,307 Reads with adapters: 225,585,200 (79.0%) Reads written (passing filters): 285,607,307 (100.0%) Total basepairs processed: 42,516,646,914 bp Total written (filtered): 30,155,326,446 bp (70.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 225585200 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 2.4% G: 45.8% T: 6.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 37550958 71401826.8 0 37550958 2 3999282 17850456.7 0 3999282 3 2189402 4462614.2 0 2189402 4 8119262 1115653.5 0 8119262 5 873671 278913.4 0 873671 6 709476 69728.3 0 709476 7 656407 17432.1 0 656407 8 637060 4358.0 0 637060 9 590881 1089.5 0 586446 4435 10 862637 272.4 1 804753 57884 11 824942 68.1 1 751663 73279 12 800616 17.0 1 733556 67060 13 776504 4.3 1 694301 82203 14 914479 4.3 1 818113 96366 15 1168832 4.3 1 1050977 117855 16 1375438 4.3 1 1219584 155854 17 821395 4.3 1 736617 84778 18 836446 4.3 1 756621 79825 19 883523 4.3 1 796330 87193 20 1661465 4.3 1 1500619 160846 21 2530193 4.3 1 2289437 240756 22 1790993 4.3 1 1630887 160106 23 816304 4.3 1 739867 76437 24 910457 4.3 1 821999 88458 25 1742369 4.3 1 1582488 159881 26 775650 4.3 1 695991 79659 27 1392418 4.3 1 1223561 168857 28 4306874 4.3 1 3932359 374515 29 1126540 4.3 1 1016211 110329 30 998742 4.3 1 909760 88982 31 1089490 4.3 1 985790 103700 32 1541836 4.3 1 1407132 134704 33 886377 4.3 1 802233 84144 34 1142805 4.3 1 1028498 114307 35 1013539 4.3 1 920862 92677 36 873015 4.3 1 797615 75400 37 1020651 4.3 1 927408 93243 38 1610806 4.3 1 1464903 145903 39 1178072 4.3 1 1067170 110902 40 1452147 4.3 1 1315194 136953 41 1658733 4.3 1 1514018 144715 42 1128479 4.3 1 1028781 99698 43 1542277 4.3 1 1405387 136890 44 1725407 4.3 1 1575400 150007 45 1474146 4.3 1 1339373 134773 46 1343257 4.3 1 1217202 126055 47 1088504 4.3 1 998241 90263 48 902566 4.3 1 820574 81992 49 1156175 4.3 1 1052588 103587 50 904523 4.3 1 824983 79540 51 844725 4.3 1 767457 77268 52 1414166 4.3 1 1290004 124162 53 932731 4.3 1 850233 82498 54 1439177 4.3 1 1317857 121320 55 962029 4.3 1 873407 88622 56 1249213 4.3 1 1129428 119785 57 2495058 4.3 1 2280619 214439 58 1082649 4.3 1 978738 103911 59 1196960 4.3 1 1086582 110378 60 2655580 4.3 1 2434981 220599 61 1878629 4.3 1 1715325 163304 62 955590 4.3 1 850632 104958 63 4125480 4.3 1 3793647 331833 64 1156038 4.3 1 1052382 103656 65 633976 4.3 1 576567 57409 66 827307 4.3 1 747215 80092 67 2040729 4.3 1 1870475 170254 68 1138467 4.3 1 1037794 100673 69 953600 4.3 1 868744 84856 70 1330080 4.3 1 1216756 113324 71 1065370 4.3 1 973142 92228 72 910235 4.3 1 828615 81620 73 1301346 4.3 1 1187735 113611 74 1212881 4.3 1 1103622 109259 75 1426499 4.3 1 1299462 127037 76 1442267 4.3 1 1318503 123764 77 616653 4.3 1 556610 60043 78 796348 4.3 1 724140 72208 79 1173497 4.3 1 1069659 103838 80 1147825 4.3 1 1043683 104142 81 1190242 4.3 1 1078511 111731 82 1766597 4.3 1 1579901 186696 83 1596348 4.3 1 1436533 159815 84 1469557 4.3 1 1333989 135568 85 1611221 4.3 1 1464960 146261 86 1178902 4.3 1 1070210 108692 87 1436923 4.3 1 1305971 130952 88 1674824 4.3 1 1523974 150850 89 1637483 4.3 1 1488217 149266 90 1988478 4.3 1 1809837 178641 91 1795727 4.3 1 1630997 164730 92 1986686 4.3 1 1803966 182720 93 1981772 4.3 1 1800991 180781 94 2188078 4.3 1 1982590 205488 95 1515832 4.3 1 1374456 141376 96 2527317 4.3 1 2299131 228186 97 2154423 4.3 1 1958347 196076 98 2140234 4.3 1 1945322 194912 99 1721542 4.3 1 1563192 158350 100 1854808 4.3 1 1684175 170633 101 1626385 4.3 1 1475357 151028 102 1311137 4.3 1 1188590 122547 103 2263843 4.3 1 2054809 209034 104 1424019 4.3 1 1289898 134121 105 1393582 4.3 1 1262542 131040 106 1734960 4.3 1 1571195 163765 107 1291706 4.3 1 1169023 122683 108 2035934 4.3 1 1842451 193483 109 1576095 4.3 1 1422638 153457 110 1373934 4.3 1 1241688 132246 111 1325579 4.3 1 1196575 129004 112 2004815 4.3 1 1811963 192852 113 1416896 4.3 1 1279101 137795 114 2124004 4.3 1 1916759 207245 115 2170659 4.3 1 1958563 212096 116 1324252 4.3 1 1193624 130628 117 1343993 4.3 1 1211034 132959 118 1904040 4.3 1 1716333 187707 119 2690112 4.3 1 2423928 266184 120 1115731 4.3 1 1003786 111945 121 1300134 4.3 1 1169857 130277 122 1101233 4.3 1 990008 111225 123 1307813 4.3 1 1176141 131672 124 1219643 4.3 1 1097092 122551 125 720809 4.3 1 648163 72646 126 725237 4.3 1 651779 73458 127 1052435 4.3 1 944640 107795 128 411841 4.3 1 369359 42482 129 284093 4.3 1 255062 29031 130 256111 4.3 1 229972 26139 131 350724 4.3 1 314098 36626 132 129417 4.3 1 116452 12965 133 51882 4.3 1 46490 5392 134 9690 4.3 1 8650 1040 135 2831 4.3 1 2512 319 136 7300 4.3 1 6487 813 137 246 4.3 1 222 24 138 52 4.3 1 47 5 139 39 4.3 1 34 5 140 20 4.3 1 19 1 141 19 4.3 1 14 5 142 13 4.3 1 9 4 143 9 4.3 1 3 6 144 13 4.3 1 5 8 145 3 4.3 1 2 1 146 2 4.3 1 0 2 147 12 4.3 1 9 3 148 189 4.3 1 163 26 149 221 4.3 1 197 24 150 3373 4.3 1 3088 285 Successfully deleted temporary file Meth5_R2_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth5_R2_001.fastq.gz ============================================= 285607307 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 29966360 (10.5%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (2851016) or CGA (127749902) in total: 130600918 (45.7%) Validate paired-end files Meth5_R1_001_trimmed.fq.gz and Meth5_R2_001_trimmed.fq.gz file_1: Meth5_R1_001_trimmed.fq.gz, file_2: Meth5_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth5_R1_001_trimmed.fq.gz and Meth5_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth5_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth5_R2_001_val_2.fq.gz Total number of sequences analysed: 285607307 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1490937 (0.52%) >>> Now running FastQC on the validated data Meth5_R1_001_val_1.fq.gz<<< Started analysis of Meth5_R1_001_val_1.fq.gz Approx 5% complete for Meth5_R1_001_val_1.fq.gz Approx 10% complete for Meth5_R1_001_val_1.fq.gz Approx 15% complete for Meth5_R1_001_val_1.fq.gz Approx 20% complete for Meth5_R1_001_val_1.fq.gz Approx 25% complete for Meth5_R1_001_val_1.fq.gz Approx 30% complete for Meth5_R1_001_val_1.fq.gz Approx 35% complete for Meth5_R1_001_val_1.fq.gz Approx 40% complete for Meth5_R1_001_val_1.fq.gz Approx 45% complete for Meth5_R1_001_val_1.fq.gz Approx 50% complete for Meth5_R1_001_val_1.fq.gz Approx 55% complete for Meth5_R1_001_val_1.fq.gz Approx 60% complete for Meth5_R1_001_val_1.fq.gz Approx 65% complete for Meth5_R1_001_val_1.fq.gz Approx 70% complete for Meth5_R1_001_val_1.fq.gz Approx 75% complete for Meth5_R1_001_val_1.fq.gz Approx 80% complete for Meth5_R1_001_val_1.fq.gz Approx 85% complete for Meth5_R1_001_val_1.fq.gz Approx 90% complete for Meth5_R1_001_val_1.fq.gz Approx 95% complete for Meth5_R1_001_val_1.fq.gz Analysis complete for Meth5_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth5_R2_001_val_2.fq.gz<<< Started analysis of Meth5_R2_001_val_2.fq.gz Approx 5% complete for Meth5_R2_001_val_2.fq.gz Approx 10% complete for Meth5_R2_001_val_2.fq.gz Approx 15% complete for Meth5_R2_001_val_2.fq.gz Approx 20% complete for Meth5_R2_001_val_2.fq.gz Approx 25% complete for Meth5_R2_001_val_2.fq.gz Approx 30% complete for Meth5_R2_001_val_2.fq.gz Approx 35% complete for Meth5_R2_001_val_2.fq.gz Approx 40% complete for Meth5_R2_001_val_2.fq.gz Approx 45% complete for Meth5_R2_001_val_2.fq.gz Approx 50% complete for Meth5_R2_001_val_2.fq.gz Approx 55% complete for Meth5_R2_001_val_2.fq.gz Approx 60% complete for Meth5_R2_001_val_2.fq.gz Approx 65% complete for Meth5_R2_001_val_2.fq.gz Approx 70% complete for Meth5_R2_001_val_2.fq.gz Approx 75% complete for Meth5_R2_001_val_2.fq.gz Approx 80% complete for Meth5_R2_001_val_2.fq.gz Approx 85% complete for Meth5_R2_001_val_2.fq.gz Approx 90% complete for Meth5_R2_001_val_2.fq.gz Approx 95% complete for Meth5_R2_001_val_2.fq.gz Analysis complete for Meth5_R2_001_val_2.fq.gz Deleting both intermediate output files Meth5_R1_001_trimmed.fq.gz and Meth5_R2_001_trimmed.fq.gz ==================================================================================================== Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth6_R1_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth6_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth6_R1_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed Finished in 1500.63 s (11 us/read; 5.64 M reads/minute). === Summary === Total reads processed: 141,156,454 Reads with adapters: 0 (0.0%) Reads written (passing filters): 141,156,454 (100.0%) Total basepairs processed: 21,173,468,100 bp Quality-trimmed: 20,236,937 bp (0.1%) Total written (filtered): 21,153,231,163 bp (99.9%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 141156454 sequences processed in total Writing final adapter and quality trimmed output to Meth6_R1_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth6_R1_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth6_R1_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 3425.33 s (24 us/read; 2.47 M reads/minute). === Summary === Total reads processed: 141,156,454 Reads with adapters: 113,837,190 (80.6%) Reads written (passing filters): 141,156,454 (100.0%) Total basepairs processed: 21,153,231,163 bp Total written (filtered): 14,777,295,273 bp (69.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 113837190 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 48.0% C: 2.9% G: 43.5% T: 5.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 18114339 35289113.5 0 18114339 2 1574373 8822278.4 0 1574373 3 1007754 2205569.6 0 1007754 4 4250018 551392.4 0 4250018 5 442302 137848.1 0 442302 6 347762 34462.0 0 347762 7 365334 8615.5 0 365334 8 340357 2153.9 0 340357 9 315482 538.5 0 310640 4842 10 471633 134.6 1 433478 38155 11 421663 33.7 1 382044 39619 12 434916 8.4 1 394292 40624 13 438923 2.1 1 393185 45738 14 471028 2.1 1 419073 51955 15 588334 2.1 1 527038 61296 16 659216 2.1 1 584462 74754 17 442242 2.1 1 392690 49552 18 464738 2.1 1 417189 47549 19 447764 2.1 1 401135 46629 20 789970 2.1 1 708475 81495 21 480558 2.1 1 429131 51427 22 635929 2.1 1 571408 64521 23 458058 2.1 1 409657 48401 24 482611 2.1 1 427382 55229 25 876414 2.1 1 785434 90980 26 460939 2.1 1 412215 48724 27 658626 2.1 1 587078 71548 28 1799758 2.1 1 1615498 184260 29 585850 2.1 1 520236 65614 30 529463 2.1 1 475005 54458 31 585282 2.1 1 523720 61562 32 791339 2.1 1 709838 81501 33 523884 2.1 1 464846 59038 34 614228 2.1 1 548103 66125 35 503259 2.1 1 451141 52118 36 518785 2.1 1 462642 56143 37 577418 2.1 1 516472 60946 38 829171 2.1 1 742766 86405 39 598228 2.1 1 536212 62016 40 771221 2.1 1 689855 81366 41 1007719 2.1 1 902199 105520 42 651096 2.1 1 579895 71201 43 810589 2.1 1 718318 92271 44 815704 2.1 1 726364 89340 45 873113 2.1 1 783105 90008 46 555823 2.1 1 496558 59265 47 497466 2.1 1 443750 53716 48 536018 2.1 1 478412 57606 49 706414 2.1 1 631817 74597 50 462296 2.1 1 409859 52437 51 553201 2.1 1 492675 60526 52 747148 2.1 1 667860 79288 53 584687 2.1 1 520990 63697 54 594976 2.1 1 528661 66315 55 807010 2.1 1 720703 86307 56 617385 2.1 1 549783 67602 57 664943 2.1 1 592087 72856 58 1049360 2.1 1 936792 112568 59 788797 2.1 1 701914 86883 60 1032253 2.1 1 923344 108909 61 924201 2.1 1 825200 99001 62 665287 2.1 1 592754 72533 63 646590 2.1 1 576969 69621 64 904196 2.1 1 807939 96257 65 600971 2.1 1 533159 67812 66 804852 2.1 1 713102 91750 67 834196 2.1 1 740599 93597 68 704606 2.1 1 624292 80314 69 737201 2.1 1 639979 97222 70 1835471 2.1 1 1659177 176294 71 146239 2.1 1 128480 17759 72 51812 2.1 1 42369 9443 73 266751 2.1 1 231764 34987 74 527827 2.1 1 467912 59915 75 640957 2.1 1 568727 72230 76 991456 2.1 1 881059 110397 77 661610 2.1 1 587359 74251 78 524422 2.1 1 463885 60537 79 724671 2.1 1 642981 81690 80 665056 2.1 1 587670 77386 81 651505 2.1 1 577184 74321 82 848683 2.1 1 750901 97782 83 700372 2.1 1 618164 82208 84 837584 2.1 1 740385 97199 85 867679 2.1 1 761382 106297 86 716477 2.1 1 627596 88881 87 757725 2.1 1 668461 89264 88 966584 2.1 1 853364 113220 89 886376 2.1 1 781501 104875 90 1083017 2.1 1 956205 126812 91 1029811 2.1 1 908183 121628 92 969446 2.1 1 853993 115453 93 946417 2.1 1 832660 113757 94 1108732 2.1 1 973513 135219 95 788984 2.1 1 693000 95984 96 1236749 2.1 1 1088116 148633 97 1103594 2.1 1 969080 134514 98 1044148 2.1 1 916235 127913 99 893180 2.1 1 783603 109577 100 949568 2.1 1 832494 117074 101 757207 2.1 1 661462 95745 102 683926 2.1 1 597480 86446 103 951775 2.1 1 834069 117706 104 782437 2.1 1 683548 98889 105 739176 2.1 1 646051 93125 106 906327 2.1 1 791325 115002 107 662894 2.1 1 576957 85937 108 785037 2.1 1 683425 101612 109 844550 2.1 1 733461 111089 110 744513 2.1 1 646804 97709 111 723492 2.1 1 627629 95863 112 1135938 2.1 1 987053 148885 113 702661 2.1 1 607906 94755 114 912212 2.1 1 789279 122933 115 1072461 2.1 1 929016 143445 116 695792 2.1 1 600051 95741 117 707423 2.1 1 610644 96779 118 1029503 2.1 1 889552 139951 119 1348020 2.1 1 1163691 184329 120 649575 2.1 1 558317 91258 121 663434 2.1 1 570732 92702 122 594253 2.1 1 511395 82858 123 644630 2.1 1 555455 89175 124 698142 2.1 1 600164 97978 125 361771 2.1 1 310176 51595 126 400106 2.1 1 343199 56907 127 566043 2.1 1 485840 80203 128 223004 2.1 1 191159 31845 129 163989 2.1 1 140469 23520 130 146798 2.1 1 125751 21047 131 152862 2.1 1 130878 21984 132 76554 2.1 1 65612 10942 133 28647 2.1 1 24708 3939 134 5546 2.1 1 4770 776 135 1233 2.1 1 1031 202 136 1363 2.1 1 1190 173 137 103 2.1 1 90 13 138 27 2.1 1 22 5 139 26 2.1 1 22 4 140 14 2.1 1 3 11 141 5 2.1 1 5 142 5 2.1 1 3 2 143 4 2.1 1 4 144 6 2.1 1 6 145 1 2.1 1 0 1 146 5 2.1 1 3 2 147 4 2.1 1 2 2 148 134 2.1 1 111 23 149 204 2.1 1 172 32 150 3188 2.1 1 2733 455 Successfully deleted temporary file Meth6_R1_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth6_R1_001.fastq.gz ============================================= 141156454 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 6247628 (4.4%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 55045586 (39.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1680815) or CGA (69814672) in total: 71495487 (50.6%) Writing report to '/gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth6_R2_001.fastq.gz_trimming_report.txt' SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth6_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 2.4 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'AGATCGGAAGAGC' (Illumina TruSeq, Sanger iPCR; 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction File was specified to be a non-directional MspI-digested RRBS sample. Sequences starting with either 'CAA' or 'CGA' will have the first 2 bp trimmed off to remove potential methylation-biased bases from the end-repair reaction Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: '--outdir /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC --threads 28' Output file(s) will be GZIP compressed >>> Now performing adaptive quality trimming with a Phred-score cutoff of: 20 <<< This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -q 20 -a X /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth6_R2_001.fastq.gz WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed Finished in 1305.84 s (9 us/read; 6.49 M reads/minute). === Summary === Total reads processed: 141,156,454 Reads with adapters: 0 (0.0%) Reads written (passing filters): 141,156,454 (100.0%) Total basepairs processed: 21,173,468,100 bp Quality-trimmed: 194,044,876 bp (0.9%) Total written (filtered): 20,979,423,224 bp (99.1%) === Adapter 1 === Sequence: X; Type: regular 3'; Length: 1; Trimmed: 0 times. >>> Quality trimming completed <<< 141156454 sequences processed in total Writing final adapter and quality trimmed output to Meth6_R2_001_trimmed.fq.gz >>> Now performing adapter trimming for the adapter sequence: 'AGATCGGAAGAGC' from file Meth6_R2_001.fastq.gz_qual_trimmed.fastq <<< 10000000 sequences processed 20000000 sequences processed 30000000 sequences processed 40000000 sequences processed 50000000 sequences processed 60000000 sequences processed 70000000 sequences processed 80000000 sequences processed 90000000 sequences processed 100000000 sequences processed 110000000 sequences processed 120000000 sequences processed 130000000 sequences processed 140000000 sequences processed This is cutadapt 2.4 with Python 3.7.3 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /gscratch/scrubbed/strigg/analyses/20200311/RRBS/Meth6_R2_001.fastq.gz_qual_trimmed.fastq WARNING: Option --format is deprecated and ignored because the input file format is always auto-detected Processing reads on 1 core in single-end mode ... Finished in 3476.60 s (25 us/read; 2.44 M reads/minute). === Summary === Total reads processed: 141,156,454 Reads with adapters: 111,733,219 (79.2%) Reads written (passing filters): 141,156,454 (100.0%) Total basepairs processed: 20,979,423,224 bp Total written (filtered): 14,812,856,951 bp (70.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 111733219 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 45.7% C: 2.4% G: 45.9% T: 6.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 17858932 35289113.5 0 17858932 2 1685175 8822278.4 0 1685175 3 1124401 2205569.6 0 1124401 4 4220919 551392.4 0 4220919 5 443848 137848.1 0 443848 6 341360 34462.0 0 341360 7 342952 8615.5 0 342952 8 356623 2153.9 0 356623 9 290110 538.5 0 287583 2527 10 454777 134.6 1 421576 33201 11 413253 33.7 1 375286 37967 12 456190 8.4 1 415576 40614 13 408256 2.1 1 363113 45143 14 459736 2.1 1 409896 49840 15 559389 2.1 1 503284 56105 16 655958 2.1 1 582534 73424 17 421067 2.1 1 377065 44002 18 425463 2.1 1 384800 40663 19 482623 2.1 1 434178 48445 20 779305 2.1 1 703755 75550 21 440291 2.1 1 394388 45903 22 627676 2.1 1 569224 58452 23 422073 2.1 1 382010 40063 24 503775 2.1 1 452738 51037 25 937725 2.1 1 851371 86354 26 402134 2.1 1 360990 41144 27 624215 2.1 1 552281 71934 28 1731891 2.1 1 1578669 153222 29 570079 2.1 1 514473 55606 30 530485 2.1 1 481756 48729 31 567254 2.1 1 514197 53057 32 776163 2.1 1 705291 70872 33 504872 2.1 1 455882 48990 34 592287 2.1 1 537595 54692 35 561574 2.1 1 509203 52371 36 482695 2.1 1 437276 45419 37 522907 2.1 1 471859 51048 38 828973 2.1 1 754521 74452 39 642886 2.1 1 583250 59636 40 721153 2.1 1 650973 70180 41 991611 2.1 1 902072 89539 42 605436 2.1 1 550101 55335 43 791018 2.1 1 716693 74325 44 1159234 2.1 1 1054627 104607 45 898926 2.1 1 814064 84862 46 699793 2.1 1 634958 64835 47 684835 2.1 1 626890 57945 48 243094 2.1 1 217758 25336 49 630998 2.1 1 574754 56244 50 425578 2.1 1 387204 38374 51 404356 2.1 1 366658 37698 52 727803 2.1 1 663712 64091 53 543965 2.1 1 494058 49907 54 953452 2.1 1 874691 78761 55 373643 2.1 1 336354 37289 56 661450 2.1 1 593000 68450 57 2364263 2.1 1 2168267 195996 58 478801 2.1 1 430071 48730 59 458217 2.1 1 411353 46864 60 1717820 2.1 1 1572953 144867 61 696246 2.1 1 633874 62372 62 560955 2.1 1 498886 62069 63 2435828 2.1 1 2234061 201767 64 1034971 2.1 1 943304 91667 65 226288 2.1 1 203628 22660 66 376835 2.1 1 337545 39290 67 954911 2.1 1 873694 81217 68 412791 2.1 1 375565 37226 69 325391 2.1 1 294251 31140 70 591408 2.1 1 540495 50913 71 335944 2.1 1 305764 30180 72 308894 2.1 1 279852 29042 73 480128 2.1 1 436832 43296 74 476667 2.1 1 432947 43720 75 570273 2.1 1 518524 51749 76 628946 2.1 1 574175 54771 77 244084 2.1 1 219063 25021 78 379810 2.1 1 344178 35632 79 624782 2.1 1 566778 58004 80 610404 2.1 1 551758 58646 81 620049 2.1 1 561932 58117 82 815011 2.1 1 737990 77021 83 738729 2.1 1 667051 71678 84 834801 2.1 1 754060 80741 85 915295 2.1 1 822073 93222 86 727156 2.1 1 650738 76418 87 743126 2.1 1 670270 72856 88 928181 2.1 1 839185 88996 89 847306 2.1 1 767044 80262 90 1031875 2.1 1 933919 97956 91 973712 2.1 1 879276 94436 92 918932 2.1 1 831550 87382 93 902762 2.1 1 816499 86263 94 1040450 2.1 1 937478 102972 95 752249 2.1 1 679003 73246 96 1168688 2.1 1 1055805 112883 97 1054965 2.1 1 953091 101874 98 1007282 2.1 1 909349 97933 99 883508 2.1 1 796332 87176 100 929808 2.1 1 838918 90890 101 730503 2.1 1 657472 73031 102 652090 2.1 1 587111 64979 103 895396 2.1 1 807211 88185 104 732440 2.1 1 658599 73841 105 701726 2.1 1 630831 70895 106 853741 2.1 1 767751 85990 107 631935 2.1 1 567318 64617 108 751248 2.1 1 674879 76369 109 803270 2.1 1 719722 83548 110 715468 2.1 1 641478 73990 111 703844 2.1 1 630306 73538 112 1085719 2.1 1 972938 112781 113 669719 2.1 1 598176 71543 114 865811 2.1 1 773438 92373 115 1006313 2.1 1 899665 106648 116 663558 2.1 1 592333 71225 117 680402 2.1 1 606877 73525 118 999647 2.1 1 892258 107389 119 1296038 2.1 1 1155443 140595 120 630947 2.1 1 562461 68486 121 642203 2.1 1 572254 69949 122 568797 2.1 1 505376 63421 123 621348 2.1 1 552761 68587 124 669349 2.1 1 595229 74120 125 354144 2.1 1 314752 39392 126 392385 2.1 1 348863 43522 127 545238 2.1 1 484293 60945 128 216795 2.1 1 192329 24466 129 157673 2.1 1 139757 17916 130 141932 2.1 1 126177 15755 131 146108 2.1 1 129591 16517 132 73370 2.1 1 65100 8270 133 27488 2.1 1 24402 3086 134 5301 2.1 1 4663 638 135 1186 2.1 1 1031 155 136 1359 2.1 1 1160 199 137 100 2.1 1 93 7 138 27 2.1 1 25 2 139 25 2.1 1 22 3 140 18 2.1 1 17 1 141 7 2.1 1 7 142 6 2.1 1 4 2 143 4 2.1 1 4 144 4 2.1 1 4 146 8 2.1 1 6 2 147 5 2.1 1 4 1 148 138 2.1 1 115 23 149 205 2.1 1 188 17 150 3002 2.1 1 2719 283 Successfully deleted temporary file Meth6_R2_001.fastq.gz_qual_trimmed.fastq RUN STATISTICS FOR INPUT FILE: /gscratch/scrubbed/sr320/froger-raw/00_fastq/Meth6_R2_001.fastq.gz ============================================= 141156454 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 18064917 (12.8%) The length threshold of paired-end sequences gets evaluated later on (in the validation step) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) RRBS reads trimmed by 2 bp at the start when read started with CAA (1486804) or CGA (62519750) in total: 64006554 (45.3%) Validate paired-end files Meth6_R1_001_trimmed.fq.gz and Meth6_R2_001_trimmed.fq.gz file_1: Meth6_R1_001_trimmed.fq.gz, file_2: Meth6_R2_001_trimmed.fq.gz >>>>> Now validing the length of the 2 paired-end infiles: Meth6_R1_001_trimmed.fq.gz and Meth6_R2_001_trimmed.fq.gz <<<<< Writing validated paired-end read 1 reads to Meth6_R1_001_val_1.fq.gz Writing validated paired-end read 2 reads to Meth6_R2_001_val_2.fq.gz Total number of sequences analysed: 141156454 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 774349 (0.55%) >>> Now running FastQC on the validated data Meth6_R1_001_val_1.fq.gz<<< Started analysis of Meth6_R1_001_val_1.fq.gz Approx 5% complete for Meth6_R1_001_val_1.fq.gz Approx 10% complete for Meth6_R1_001_val_1.fq.gz Approx 15% complete for Meth6_R1_001_val_1.fq.gz Approx 20% complete for Meth6_R1_001_val_1.fq.gz Approx 25% complete for Meth6_R1_001_val_1.fq.gz Approx 30% complete for Meth6_R1_001_val_1.fq.gz Approx 35% complete for Meth6_R1_001_val_1.fq.gz Approx 40% complete for Meth6_R1_001_val_1.fq.gz Approx 45% complete for Meth6_R1_001_val_1.fq.gz Approx 50% complete for Meth6_R1_001_val_1.fq.gz Approx 55% complete for Meth6_R1_001_val_1.fq.gz Approx 60% complete for Meth6_R1_001_val_1.fq.gz Approx 65% complete for Meth6_R1_001_val_1.fq.gz Approx 70% complete for Meth6_R1_001_val_1.fq.gz Approx 75% complete for Meth6_R1_001_val_1.fq.gz Approx 80% complete for Meth6_R1_001_val_1.fq.gz Approx 85% complete for Meth6_R1_001_val_1.fq.gz Approx 90% complete for Meth6_R1_001_val_1.fq.gz Approx 95% complete for Meth6_R1_001_val_1.fq.gz Analysis complete for Meth6_R1_001_val_1.fq.gz >>> Now running FastQC on the validated data Meth6_R2_001_val_2.fq.gz<<< Started analysis of Meth6_R2_001_val_2.fq.gz Approx 5% complete for Meth6_R2_001_val_2.fq.gz Approx 10% complete for Meth6_R2_001_val_2.fq.gz Approx 15% complete for Meth6_R2_001_val_2.fq.gz Approx 20% complete for Meth6_R2_001_val_2.fq.gz Approx 25% complete for Meth6_R2_001_val_2.fq.gz Approx 30% complete for Meth6_R2_001_val_2.fq.gz Approx 35% complete for Meth6_R2_001_val_2.fq.gz Approx 40% complete for Meth6_R2_001_val_2.fq.gz Approx 45% complete for Meth6_R2_001_val_2.fq.gz Approx 50% complete for Meth6_R2_001_val_2.fq.gz Approx 55% complete for Meth6_R2_001_val_2.fq.gz Approx 60% complete for Meth6_R2_001_val_2.fq.gz Approx 65% complete for Meth6_R2_001_val_2.fq.gz Approx 70% complete for Meth6_R2_001_val_2.fq.gz Approx 75% complete for Meth6_R2_001_val_2.fq.gz Approx 80% complete for Meth6_R2_001_val_2.fq.gz Approx 85% complete for Meth6_R2_001_val_2.fq.gz Approx 90% complete for Meth6_R2_001_val_2.fq.gz Approx 95% complete for Meth6_R2_001_val_2.fq.gz Analysis complete for Meth6_R2_001_val_2.fq.gz Deleting both intermediate output files Meth6_R1_001_trimmed.fq.gz and Meth6_R2_001_trimmed.fq.gz ==================================================================================================== [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/strigg/analyses/20200311/WGBS_MBD/FASTQC [INFO ] fastqc : Found 24 reports [INFO ] multiqc : Compressing plot data [INFO ] multiqc : Report : multiqc_report.html [INFO ] multiqc : Data : multiqc_data [INFO ] multiqc : MultiQC complete [INFO ] multiqc : This is MultiQC v1.8 [INFO ] multiqc : Template : default [INFO ] multiqc : Searching : /gscratch/scrubbed/strigg/analyses/20200311/RRBS/FASTQC [INFO ] fastqc : Found 12 reports [INFO ] multiqc : Compressing plot data [WARNING] multiqc : Previous MultiQC output found! Adjusting filenames.. [WARNING] multiqc : Use -f or --force to overwrite existing reports instead [INFO ] multiqc : Report : multiqc_report_1.html [INFO ] multiqc : Data : multiqc_data_1 [INFO ] multiqc : MultiQC complete