SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-168_S11_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 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-168_S11_L002_R2_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 449.24 s (19 us/read; 3.11 M reads/minute). === Summary === Total reads processed: 23,309,550 Reads with adapters: 14,831,532 (63.6%) Reads written (passing filters): 23,309,550 (100.0%) Total basepairs processed: 2,327,911,552 bp Total written (filtered): 2,101,242,697 bp (90.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 14831532 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.7% C: 21.0% G: 8.4% T: 31.5% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 7583919 5827387.5 0 7583919 2 223517 1456846.9 0 223517 3 183031 364211.7 0 183031 4 156302 91052.9 0 156302 5 154711 22763.2 0 154711 6 154811 5690.8 0 154811 7 150647 1422.7 0 150647 8 157653 355.7 0 157653 9 151098 88.9 0 150440 658 10 152350 22.2 1 148081 4269 11 144052 5.6 1 138938 5114 12 145607 1.4 1 140520 5087 13 139846 0.3 1 135073 4773 14 150651 0.3 1 145263 5388 15 139350 0.3 1 134403 4947 16 139866 0.3 1 135132 4734 17 144652 0.3 1 139515 5137 18 129100 0.3 1 124628 4472 19 135628 0.3 1 130982 4646 20 133510 0.3 1 128681 4829 21 135801 0.3 1 130757 5044 22 136246 0.3 1 131071 5175 23 129145 0.3 1 124449 4696 24 135368 0.3 1 130427 4941 25 120250 0.3 1 115927 4323 26 120845 0.3 1 115907 4938 27 122835 0.3 1 117497 5338 28 125245 0.3 1 120676 4569 29 121116 0.3 1 116029 5087 30 128907 0.3 1 124404 4503 31 110668 0.3 1 106423 4245 32 113951 0.3 1 110147 3804 33 119618 0.3 1 115023 4595 34 120015 0.3 1 115235 4780 35 110648 0.3 1 107273 3375 36 104861 0.3 1 100986 3875 37 105327 0.3 1 101628 3699 38 92099 0.3 1 88831 3268 39 96476 0.3 1 93023 3453 40 92483 0.3 1 89365 3118 41 91820 0.3 1 88928 2892 42 88778 0.3 1 86315 2463 43 77771 0.3 1 75122 2649 44 78690 0.3 1 76152 2538 45 96085 0.3 1 93476 2609 46 73404 0.3 1 71193 2211 47 52629 0.3 1 50769 1860 48 72522 0.3 1 70666 1856 49 51474 0.3 1 49813 1661 50 53172 0.3 1 51459 1713 51 71497 0.3 1 69784 1713 52 43367 0.3 1 41868 1499 53 44275 0.3 1 42823 1452 54 38647 0.3 1 37384 1263 55 45065 0.3 1 43724 1341 56 42461 0.3 1 41057 1404 57 38339 0.3 1 37077 1262 58 36203 0.3 1 35100 1103 59 34428 0.3 1 33259 1169 60 32228 0.3 1 31092 1136 61 31345 0.3 1 30234 1111 62 31690 0.3 1 30583 1107 63 30820 0.3 1 29717 1103 64 30760 0.3 1 29634 1126 65 32199 0.3 1 30982 1217 66 36629 0.3 1 35098 1531 67 58789 0.3 1 54373 4416 68 228605 0.3 1 223011 5594 69 83986 0.3 1 81290 2696 70 43727 0.3 1 42232 1495 71 22370 0.3 1 21457 913 72 15197 0.3 1 14510 687 73 10426 0.3 1 9920 506 74 8022 0.3 1 7615 407 75 6444 0.3 1 6083 361 76 5373 0.3 1 5078 295 77 4777 0.3 1 4497 280 78 4242 0.3 1 4016 226 79 3666 0.3 1 3445 221 80 3129 0.3 1 2931 198 81 2729 0.3 1 2555 174 82 2343 0.3 1 2190 153 83 2056 0.3 1 1914 142 84 1942 0.3 1 1794 148 85 1544 0.3 1 1414 130 86 1501 0.3 1 1392 109 87 1421 0.3 1 1281 140 88 1346 0.3 1 1222 124 89 1563 0.3 1 1412 151 90 1867 0.3 1 1719 148 91 2658 0.3 1 2434 224 92 3823 0.3 1 3494 329 93 8577 0.3 1 7935 642 94 25579 0.3 1 23862 1717 95 44797 0.3 1 41943 2854 96 20239 0.3 1 18963 1276 97 13862 0.3 1 12915 947 98 5459 0.3 1 5093 366 99 5587 0.3 1 5214 373 100 5325 0.3 1 4949 376 101 10058 0.3 1 9182 876 RUN STATISTICS FOR INPUT FILE: EPI-168_S11_L002_R2_001.fastq.gz ============================================= 23309550 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2534681 (10.9%) 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: 23309550 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 621083 (2.66%)