SUMMARISING RUN PARAMETERS ========================== Input filename: R1.fastq Trimming mode: paired-end Trim Galore version: 0.4.0 Cutadapt version: 1.8.1 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 Length cut-off for read 1: 35 bp (default) Length cut-off for read 2: 35 bp (default) This is cutadapt 1.8.1 with Python 2.7.10 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC R1.fastq Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 9037.77 s (10 us/read; 6.22 M reads/minute). === Summary === Total reads processed: 937,202,899 Reads with adapters: 356,174,188 (38.0%) Reads written (passing filters): 937,202,899 (100.0%) Total basepairs processed: 41,779,239,564 bp Quality-trimmed: 502,915,432 bp (1.2%) Total written (filtered): 39,929,247,810 bp (95.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 356174188 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.5% C: 23.1% G: 16.2% T: 19.9% none/other: 6.3% Overview of removed sequences length count expect max.err error counts 1 249507875 234300724.8 0 249507875 2 58883142 58575181.2 0 58883142 3 19933903 14643795.3 0 19933903 4 3778621 3660948.8 0 3778621 5 743808 915237.2 0 743808 6 131344 228809.3 0 131344 7 48311 57202.3 0 48311 8 30192 14300.6 0 30192 9 40008 3575.1 0 24061 15947 10 55041 893.8 1 20668 34373 11 29846 223.4 1 19306 10540 12 24334 55.9 1 21249 3085 13 20384 14.0 1 19179 1205 14 21444 14.0 1 20299 1145 15 26283 14.0 1 25097 1186 16 22743 14.0 1 21176 1567 17 25032 14.0 1 23211 1821 18 21713 14.0 1 19592 2121 19 22269 14.0 1 20676 1593 20 23144 14.0 1 21160 1984 21 21224 14.0 1 18722 2502 22 19033 14.0 1 16162 2871 23 19364 14.0 1 14880 4484 24 29779 14.0 1 23219 6560 25 24577 14.0 1 15978 8599 26 28556 14.0 1 17050 11506 27 44849 14.0 1 21356 23493 28 37623 14.0 1 17962 19661 29 44052 14.0 1 20142 23910 30 35155 14.0 1 19537 15618 31 38982 14.0 1 17713 21269 32 48313 14.0 1 17604 30709 33 121837 14.0 1 35492 86345 34 233078 14.0 1 56258 176820 35 707048 14.0 1 297133 409915 36 18199291 14.0 1 4774264 13425027 37 24248 14.0 1 5779 18469 38 29759 14.0 1 7077 22682 39 38372 14.0 1 7309 31063 40 49968 14.0 1 10540 39428 41 34797 14.0 1 13808 20989 42 38698 14.0 1 9281 29417 43 27563 14.0 1 13132 14431 44 38729 14.0 1 6563 32166 45 42853 14.0 1 12030 30823 46 30309 14.0 1 10213 20096 47 27693 14.0 1 7937 19756 48 30221 14.0 1 7209 23012 49 29430 14.0 1 7957 21473 50 28966 14.0 1 7287 21679 51 69734 14.0 1 7286 62448 52 92152 14.0 1 17407 74745 53 41276 14.0 1 19721 21555 54 36134 14.0 1 7428 28706 55 31643 14.0 1 9177 22466 56 48430 14.0 1 7663 40767 57 48431 14.0 1 10921 37510 58 78974 14.0 1 10519 68455 59 52248 14.0 1 17284 34964 60 55257 14.0 1 9701 45556 61 76855 14.0 1 12860 63995 62 175186 14.0 1 17609 157577 63 197887 14.0 1 39008 158879 64 122848 14.0 1 38522 84326 65 85413 14.0 1 22646 62767 66 116361 14.0 1 19925 96436 67 163900 14.0 1 25021 138879 68 271961 14.0 1 37785 234176 69 365011 14.0 1 58318 306693 70 241610 14.0 1 76299 165311 71 145508 14.0 1 38669 106839 72 74901 14.0 1 27598 47303 73 19037 14.0 1 7591 11446 74 13889 14.0 1 4672 9217 75 5707 14.0 1 1628 4079 76 30031 14.0 1 10128 19903 RUN STATISTICS FOR INPUT FILE: R1.fastq ============================================= 937202899 sequences processed in total