SUMMARISING RUN PARAMETERS ========================== Input filename: HMEC_NOMe-Seq-GSM1383850.end2.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4 Cutadapt version: 1.16 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 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.13 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC HMEC_NOMe-Seq-GSM1383850.end2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 10074.06 s (38 us/read; 1.57 M reads/minute). === Summary === Total reads processed: 263,607,668 Reads with adapters: 128,087,368 (48.6%) Reads written (passing filters): 263,607,668 (100.0%) Total basepairs processed: 19,527,098,950 bp Quality-trimmed: 581,346,094 bp (3.0%) Total written (filtered): 18,813,904,449 bp (96.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 128087368 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 56.0% C: 14.3% G: 0.4% T: 29.2% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 127303491 65901917.0 0 127303491 2 584499 16475479.2 0 584499 3 72642 4118869.8 0 72642 4 30401 1029717.5 0 30401 5 8007 257429.4 0 8007 6 1890 64357.3 0 1890 7 836 16089.3 0 836 8 988 4022.3 0 988 9 2399 1005.6 0 2314 85 10 1230 251.4 1 1003 227 11 2122 62.8 1 1843 279 12 1025 15.7 1 884 141 13 1725 3.9 1 1474 251 14 1340 3.9 1 1193 147 15 893 3.9 1 705 188 16 2172 3.9 1 1766 406 17 1828 3.9 1 1616 212 18 1204 3.9 1 1017 187 19 1292 3.9 1 1143 149 20 1338 3.9 1 1110 228 21 1626 3.9 1 1408 218 22 761 3.9 1 661 100 23 9796 3.9 1 8918 878 24 766 3.9 1 686 80 25 458 3.9 1 340 118 26 1506 3.9 1 500 1006 27 2190 3.9 1 1783 407 28 1589 3.9 1 1321 268 29 2670 3.9 1 2149 521 30 5252 3.9 1 5023 229 31 8075 3.9 1 7587 488 32 196 3.9 1 160 36 33 201 3.9 1 123 78 34 240 3.9 1 180 60 35 189 3.9 1 86 103 36 378 3.9 1 305 73 37 272 3.9 1 158 114 38 230 3.9 1 87 143 39 722 3.9 1 357 365 40 1420 3.9 1 1158 262 41 756 3.9 1 144 612 42 321 3.9 1 109 212 43 397 3.9 1 242 155 44 748 3.9 1 121 627 45 100 3.9 1 68 32 46 208 3.9 1 61 147 47 268 3.9 1 117 151 48 78 3.9 1 30 48 49 356 3.9 1 31 325 50 3698 3.9 1 154 3544 51 57 3.9 1 52 5 52 53 3.9 1 49 4 53 21 3.9 1 17 4 54 144 3.9 1 128 16 55 97 3.9 1 86 11 56 82 3.9 1 75 7 57 180 3.9 1 115 65 58 1289 3.9 1 1169 120 59 461 3.9 1 395 66 60 493 3.9 1 408 85 61 779 3.9 1 629 150 62 1507 3.9 1 1170 337 63 4104 3.9 1 3362 742 64 4197 3.9 1 2972 1225 65 4992 3.9 1 3988 1004 66 1499 3.9 1 1395 104 67 257 3.9 1 228 29 68 61 3.9 1 51 10 69 55 3.9 1 46 9 70 43 3.9 1 36 7 71 27 3.9 1 25 2 72 24 3.9 1 21 3 73 26 3.9 1 23 3 74 13 3.9 1 12 1 75 12 3.9 1 12 76 4 3.9 1 4 77 5 3.9 1 4 1 78 12 3.9 1 12 79 13 3.9 1 12 1 80 15 3.9 1 11 4 81 47 3.9 1 41 6 82 1 3.9 1 1 85 1 3.9 1 0 1 86 1 3.9 1 1 89 2 3.9 1 1 1 90 1 3.9 1 1 93 1 3.9 1 0 1 95 1 3.9 1 0 1 98 1 3.9 1 0 1 100 1 3.9 1 0 1 RUN STATISTICS FOR INPUT FILE: HMEC_NOMe-Seq-GSM1383850.end2.fastq.gz ============================================= 263607668 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 263607668 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1464446 (0.56%)