SUMMARISING RUN PARAMETERS ========================== Input filename: EPI-208_S28_L004_R1_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-208_S28_L004_R1_001.fastq.gz_qual_trimmed.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 692.63 s (18 us/read; 3.38 M reads/minute). === Summary === Total reads processed: 39,075,361 Reads with adapters: 29,605,943 (75.8%) Reads written (passing filters): 39,075,361 (100.0%) Total basepairs processed: 3,802,771,903 bp Total written (filtered): 2,415,833,391 bp (63.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 29605943 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 19.9% C: 25.1% G: 21.6% T: 31.2% none/other: 2.2% Overview of removed sequences length count expect max.err error counts 1 3905176 9768840.2 0 3905176 2 1000047 2442210.1 0 1000047 3 407756 610552.5 0 407756 4 298043 152638.1 0 298043 5 185810 38159.5 0 185810 6 185999 9539.9 0 185999 7 169952 2385.0 0 169952 8 201564 596.2 0 201564 9 182423 149.1 0 180952 1471 10 170917 37.3 1 164830 6087 11 176812 9.3 1 170004 6808 12 168817 2.3 1 162384 6433 13 171322 0.6 1 164684 6638 14 182743 0.6 1 174739 8004 15 181820 0.6 1 174473 7347 16 190617 0.6 1 182124 8493 17 190084 0.6 1 181839 8245 18 179644 0.6 1 172638 7006 19 188711 0.6 1 180029 8682 20 184986 0.6 1 177709 7277 21 198182 0.6 1 189149 9033 22 188533 0.6 1 181046 7487 23 193064 0.6 1 185035 8029 24 191895 0.6 1 182986 8909 25 192154 0.6 1 184224 7930 26 199986 0.6 1 190355 9631 27 193206 0.6 1 184897 8309 28 191461 0.6 1 183234 8227 29 204488 0.6 1 195343 9145 30 201534 0.6 1 193491 8043 31 209732 0.6 1 200074 9658 32 208927 0.6 1 200175 8752 33 215983 0.6 1 206984 8999 34 208582 0.6 1 199830 8752 35 207212 0.6 1 198331 8881 36 212191 0.6 1 202529 9662 37 233518 0.6 1 222690 10828 38 212336 0.6 1 202990 9346 39 201636 0.6 1 193250 8386 40 217159 0.6 1 206814 10345 41 307511 0.6 1 295335 12176 42 180902 0.6 1 173335 7567 43 152484 0.6 1 145646 6838 44 201739 0.6 1 192929 8810 45 209653 0.6 1 200648 9005 46 204558 0.6 1 196129 8429 47 216982 0.6 1 207264 9718 48 210284 0.6 1 200973 9311 49 220087 0.6 1 210118 9969 50 205478 0.6 1 197015 8463 51 210102 0.6 1 201299 8803 52 210579 0.6 1 201586 8993 53 206116 0.6 1 197919 8197 54 208379 0.6 1 199734 8645 55 225674 0.6 1 216760 8914 56 215456 0.6 1 207101 8355 57 206910 0.6 1 198697 8213 58 213804 0.6 1 205455 8349 59 214237 0.6 1 205811 8426 60 200250 0.6 1 192359 7891 61 216246 0.6 1 207797 8449 62 223356 0.6 1 214923 8433 63 207591 0.6 1 199674 7917 64 204434 0.6 1 197092 7342 65 199357 0.6 1 191978 7379 66 192309 0.6 1 185223 7086 67 190209 0.6 1 183289 6920 68 183307 0.6 1 176647 6660 69 191334 0.6 1 184490 6844 70 184616 0.6 1 177637 6979 71 187187 0.6 1 180212 6975 72 203390 0.6 1 194088 9302 73 348864 0.6 1 315378 33486 74 1760208 0.6 1 1696001 64207 75 1974992 0.6 1 1914021 60971 76 1249958 0.6 1 1207758 42200 77 829747 0.6 1 801444 28303 78 502946 0.6 1 485890 17056 79 282727 0.6 1 272637 10090 80 178018 0.6 1 171728 6290 81 105453 0.6 1 101558 3895 82 66980 0.6 1 64289 2691 83 49470 0.6 1 47449 2021 84 40956 0.6 1 39271 1685 85 36291 0.6 1 34769 1522 86 33291 0.6 1 31839 1452 87 29503 0.6 1 28269 1234 88 27199 0.6 1 25996 1203 89 28703 0.6 1 27494 1209 90 37352 0.6 1 35828 1524 91 56242 0.6 1 53889 2353 92 89061 0.6 1 85473 3588 93 207782 0.6 1 199673 8109 94 598944 0.6 1 576422 22522 95 867012 0.6 1 834813 32199 96 358877 0.6 1 344124 14753 97 207941 0.6 1 198565 9376 98 92792 0.6 1 88462 4330 99 85417 0.6 1 81281 4136 100 93191 0.6 1 87872 5319 101 156483 0.6 1 143095 13388 RUN STATISTICS FOR INPUT FILE: EPI-208_S28_L004_R1_001.fastq.gz ============================================= 39075361 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 9807679 (25.1%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 28691654 (73.4%)