SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-162_S9_L002_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 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 /home/sam/data/geoduck_EPI/20180514_geoduck_trimgalore_rrbs/20180514_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/20180514_geoduck_trimgalore_rrbs/EPI-162_S9_L002_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 448.77 s (19 us/read; 3.12 M reads/minute). === Summary === Total reads processed: 23,358,871 Reads with adapters: 16,623,316 (71.2%) Reads written (passing filters): 23,358,871 (100.0%) Total basepairs processed: 2,330,642,472 bp Total written (filtered): 1,961,117,691 bp (84.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16623316 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.2% C: 23.0% G: 10.1% T: 30.3% none/other: 0.4% Overview of removed sequences length count expect max.err error counts 1 6002978 5839717.8 0 6002978 2 219993 1459929.4 0 219993 3 181974 364982.4 0 181974 4 158959 91245.6 0 158959 5 161535 22811.4 0 161535 6 164750 5702.8 0 164750 7 157609 1425.7 0 157609 8 166337 356.4 0 166337 9 160998 89.1 0 160303 695 10 163419 22.3 1 158839 4580 11 157494 5.6 1 151687 5807 12 162268 1.4 1 156624 5644 13 157642 0.3 1 152268 5374 14 171678 0.3 1 165703 5975 15 161960 0.3 1 156095 5865 16 163712 0.3 1 158056 5656 17 174302 0.3 1 168319 5983 18 157485 0.3 1 152106 5379 19 168815 0.3 1 162973 5842 20 167093 0.3 1 161264 5829 21 172080 0.3 1 165528 6552 22 175195 0.3 1 168612 6583 23 172607 0.3 1 166340 6267 24 183495 0.3 1 176628 6867 25 167319 0.3 1 161095 6224 26 171316 0.3 1 164032 7284 27 176530 0.3 1 168373 8157 28 182259 0.3 1 175593 6666 29 179715 0.3 1 172270 7445 30 195093 0.3 1 188352 6741 31 171592 0.3 1 164955 6637 32 180459 0.3 1 174627 5832 33 191657 0.3 1 184460 7197 34 198190 0.3 1 189955 8235 35 186581 0.3 1 180971 5610 36 180387 0.3 1 173816 6571 37 180094 0.3 1 173928 6166 38 162245 0.3 1 156726 5519 39 170999 0.3 1 164973 6026 40 168786 0.3 1 162986 5800 41 168588 0.3 1 163416 5172 42 167022 0.3 1 162294 4728 43 149684 0.3 1 144798 4886 44 154331 0.3 1 149540 4791 45 192478 0.3 1 187461 5017 46 148978 0.3 1 144577 4401 47 107202 0.3 1 103473 3729 48 150200 0.3 1 146349 3851 49 107936 0.3 1 104772 3164 50 113844 0.3 1 110201 3643 51 156487 0.3 1 152944 3543 52 96437 0.3 1 93318 3119 53 100043 0.3 1 96922 3121 54 89058 0.3 1 86124 2934 55 103550 0.3 1 100610 2940 56 99466 0.3 1 96364 3102 57 91001 0.3 1 88220 2781 58 88611 0.3 1 85847 2764 59 84417 0.3 1 81630 2787 60 80787 0.3 1 78214 2573 61 80428 0.3 1 77733 2695 62 80538 0.3 1 77883 2655 63 78488 0.3 1 75763 2725 64 76213 0.3 1 73595 2618 65 78832 0.3 1 76188 2644 66 83670 0.3 1 80684 2986 67 110162 0.3 1 104037 6125 68 347873 0.3 1 340674 7199 69 126664 0.3 1 123109 3555 70 60331 0.3 1 58288 2043 71 33312 0.3 1 31955 1357 72 24107 0.3 1 23038 1069 73 18359 0.3 1 17433 926 74 15230 0.3 1 14419 811 75 12912 0.3 1 12260 652 76 11396 0.3 1 10801 595 77 10184 0.3 1 9639 545 78 9241 0.3 1 8748 493 79 7740 0.3 1 7315 425 80 6748 0.3 1 6375 373 81 5905 0.3 1 5560 345 82 4889 0.3 1 4608 281 83 3970 0.3 1 3730 240 84 3371 0.3 1 3180 191 85 2583 0.3 1 2425 158 86 1937 0.3 1 1803 134 87 1820 0.3 1 1675 145 88 1385 0.3 1 1260 125 89 1439 0.3 1 1300 139 90 1791 0.3 1 1626 165 91 2322 0.3 1 2117 205 92 3405 0.3 1 3085 320 93 6857 0.3 1 6284 573 94 19646 0.3 1 18296 1350 95 34434 0.3 1 32162 2272 96 16438 0.3 1 15369 1069 97 12178 0.3 1 11305 873 98 5101 0.3 1 4753 348 99 5175 0.3 1 4802 373 100 5922 0.3 1 5506 416 101 12600 0.3 1 11553 1047 RUN STATISTICS FOR INPUT FILE: EPI-162_S9_L002_R2_001.fastq.gz ============================================= 23358871 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 3102080 (13.3%) 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 (743824) or CGA (223190) in total: 967014 (4.1%) Total number of sequences analysed for the sequence pair length validation: 23358871 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 587640 (2.52%)