SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-104_S28_L005_R2_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.9.1 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 All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/20180516_geoduck_trimmed_fastqc --threads 16 Output file will be GZIP compressed This is cutadapt 1.9.1 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -O 1 -a AGATCGGAAGAGC /home/sam/data/geoduck_EPI/20180516_geoduck_trimgalore_rrbs/EPI-104_S28_L005_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 587.06 s (19 us/read; 3.08 M reads/minute). === Summary === Total reads processed: 30,166,064 Reads with adapters: 18,579,315 (61.6%) Reads written (passing filters): 30,166,064 (100.0%) Total basepairs processed: 3,020,280,908 bp Total written (filtered): 2,779,371,441 bp (92.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 18579315 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.6% C: 23.9% G: 7.8% T: 29.7% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 10411506 7541516.0 0 10411506 2 263932 1885379.0 0 263932 3 238755 471344.8 0 238755 4 182681 117836.2 0 182681 5 187793 29459.0 0 187793 6 189004 7364.8 0 189004 7 176526 1841.2 0 176526 8 222611 460.3 0 222611 9 170428 115.1 0 169731 697 10 165129 28.8 1 158560 6569 11 165007 7.2 1 155955 9052 12 162064 1.8 1 154299 7765 13 155836 0.4 1 148056 7780 14 170631 0.4 1 162318 8313 15 155641 0.4 1 147638 8003 16 158001 0.4 1 149952 8049 17 167504 0.4 1 159572 7932 18 141489 0.4 1 134461 7028 19 149796 0.4 1 142900 6896 20 146024 0.4 1 138442 7582 21 153742 0.4 1 144981 8761 22 153126 0.4 1 145234 7892 23 145391 0.4 1 138037 7354 24 151354 0.4 1 143916 7438 25 132068 0.4 1 125284 6784 26 139458 0.4 1 131361 8097 27 146699 0.4 1 136915 9784 28 143020 0.4 1 136043 6977 29 142118 0.4 1 133265 8853 30 150089 0.4 1 143290 6799 31 126079 0.4 1 119047 7032 32 128494 0.4 1 123147 5347 33 137417 0.4 1 129913 7504 34 145705 0.4 1 137301 8404 35 124479 0.4 1 119332 5147 36 121941 0.4 1 115277 6664 37 114212 0.4 1 108136 6076 38 105067 0.4 1 99668 5399 39 108646 0.4 1 102790 5856 40 109849 0.4 1 103977 5872 41 104665 0.4 1 100001 4664 42 110586 0.4 1 106446 4140 43 86079 0.4 1 81457 4622 44 95055 0.4 1 90599 4456 45 137097 0.4 1 132383 4714 46 84278 0.4 1 80267 4011 47 58040 0.4 1 54633 3407 48 91664 0.4 1 88232 3432 49 55414 0.4 1 52815 2599 50 62088 0.4 1 58871 3217 51 94873 0.4 1 91739 3134 52 48196 0.4 1 45653 2543 53 54309 0.4 1 51485 2824 54 46471 0.4 1 43950 2521 55 61959 0.4 1 59197 2762 56 58705 0.4 1 55699 3006 57 52859 0.4 1 50345 2514 58 51796 0.4 1 49396 2400 59 48904 0.4 1 46388 2516 60 49575 0.4 1 46957 2618 61 50162 0.4 1 47526 2636 62 52438 0.4 1 49720 2718 63 53340 0.4 1 50642 2698 64 53450 0.4 1 50767 2683 65 55378 0.4 1 52598 2780 66 57877 0.4 1 55084 2793 67 65879 0.4 1 62242 3637 68 132920 0.4 1 129333 3587 69 43214 0.4 1 41254 1960 70 21566 0.4 1 20285 1281 71 13788 0.4 1 12811 977 72 10567 0.4 1 9695 872 73 8891 0.4 1 8194 697 74 7411 0.4 1 6862 549 75 6147 0.4 1 5685 462 76 5392 0.4 1 4961 431 77 4505 0.4 1 4195 310 78 3680 0.4 1 3404 276 79 3060 0.4 1 2846 214 80 2222 0.4 1 2041 181 81 1705 0.4 1 1562 143 82 1186 0.4 1 1092 94 83 859 0.4 1 784 75 84 533 0.4 1 483 50 85 368 0.4 1 334 34 86 232 0.4 1 209 23 87 155 0.4 1 133 22 88 134 0.4 1 119 15 89 139 0.4 1 121 18 90 199 0.4 1 178 21 91 242 0.4 1 215 27 92 389 0.4 1 346 43 93 668 0.4 1 591 77 94 1501 0.4 1 1328 173 95 2365 0.4 1 2134 231 96 1417 0.4 1 1285 132 97 879 0.4 1 794 85 98 297 0.4 1 259 38 99 240 0.4 1 203 37 100 492 0.4 1 431 61 101 1503 0.4 1 1292 211 RUN STATISTICS FOR INPUT FILE: EPI-104_S28_L005_R2_001.fastq.gz ============================================= 30166064 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3674423 (12.2%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 30166064 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 150803 (0.50%)