SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/zr2096_10_s1_R1.fastq.gz Trimming mode: paired-end Trim Galore version: 0.4.4_dev Cutadapt version: 1.16 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Adapter sequence: 'TGGAATTCTCGG' (Illumina small RNA adapter; auto-detected) Maximum trimming error rate: 0.1 (default) Optional adapter 2 sequence (only used for read 2 of paired-end files): 'GATCGTCGGACT' Minimum required adapter overlap (stringency): 1 bp Minimum required sequence length for both reads before a sequence pair gets removed: 18 bp Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir /home/sam/20180409_trimgalore_autotrim_Cvirginica_MBD/20180409_fastqc_trimgalore_autotrim_Cvirginica_MBD --threads 18 Output file will be GZIP compressed This is cutadapt 1.16 with Python 2.7.12 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a TGGAATTCTCGG /mnt/owl/nightingales/C_virginica/zr2096_10_s1_R1.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 342.62 s (19 us/read; 3.10 M reads/minute). === Summary === Total reads processed: 17,717,127 Reads with adapters: 8,066,766 (45.5%) Reads written (passing filters): 17,717,127 (100.0%) Total basepairs processed: 1,619,391,518 bp Quality-trimmed: 7,953,221 bp (0.5%) Total written (filtered): 1,596,548,832 bp (98.6%) === Adapter 1 === Sequence: TGGAATTCTCGG; Type: regular 3'; Length: 12; Trimmed: 8066766 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 26.9% C: 6.0% G: 21.7% T: 45.2% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 6836099 4429281.8 0 6836099 2 785279 1107320.4 0 785279 3 280553 276830.1 0 280553 4 50900 69207.5 0 50900 5 19406 17301.9 0 19406 6 6096 4325.5 0 6096 7 3109 1081.4 0 3109 8 231 270.3 0 231 9 424 67.6 0 390 34 10 319 16.9 1 160 159 11 279 4.2 1 160 119 12 156 1.1 1 71 85 13 298 1.1 1 157 141 14 152 1.1 1 49 103 15 245 1.1 1 136 109 16 179 1.1 1 109 70 17 230 1.1 1 155 75 18 561 1.1 1 381 180 19 507 1.1 1 378 129 20 136 1.1 1 65 71 21 137 1.1 1 67 70 22 415 1.1 1 272 143 23 452 1.1 1 283 169 24 430 1.1 1 316 114 25 576 1.1 1 414 162 26 538 1.1 1 376 162 27 893 1.1 1 688 205 28 353 1.1 1 240 113 29 464 1.1 1 321 143 30 610 1.1 1 397 213 31 556 1.1 1 388 168 32 820 1.1 1 565 255 33 603 1.1 1 449 154 34 728 1.1 1 555 173 35 741 1.1 1 564 177 36 882 1.1 1 684 198 37 1416 1.1 1 1143 273 38 513 1.1 1 363 150 39 535 1.1 1 379 156 40 590 1.1 1 415 175 41 417 1.1 1 285 132 42 360 1.1 1 255 105 43 639 1.1 1 492 147 44 378 1.1 1 289 89 45 552 1.1 1 415 137 46 974 1.1 1 695 279 47 1020 1.1 1 707 313 48 623 1.1 1 398 225 49 689 1.1 1 509 180 50 675 1.1 1 507 168 51 395 1.1 1 290 105 52 745 1.1 1 569 176 53 945 1.1 1 704 241 54 1060 1.1 1 844 216 55 1798 1.1 1 1454 344 56 1255 1.1 1 990 265 57 878 1.1 1 668 210 58 614 1.1 1 449 165 59 856 1.1 1 668 188 60 1283 1.1 1 1030 253 61 1817 1.1 1 1389 428 62 429 1.1 1 314 115 63 552 1.1 1 432 120 64 1073 1.1 1 826 247 65 1173 1.1 1 884 289 66 1534 1.1 1 1164 370 67 2018 1.1 1 1575 443 68 3376 1.1 1 2743 633 69 1972 1.1 1 1592 380 70 2167 1.1 1 1814 353 71 3104 1.1 1 2698 406 72 4968 1.1 1 4397 571 73 4402 1.1 1 3871 531 74 2816 1.1 1 2417 399 75 1918 1.1 1 1560 358 76 1595 1.1 1 1177 418 77 1719 1.1 1 1226 493 78 1925 1.1 1 1302 623 79 1864 1.1 1 1265 599 80 1778 1.1 1 1246 532 81 1534 1.1 1 1090 444 82 852 1.1 1 582 270 83 513 1.1 1 345 168 84 478 1.1 1 324 154 85 536 1.1 1 347 189 86 545 1.1 1 354 191 87 476 1.1 1 293 183 88 436 1.1 1 284 152 89 404 1.1 1 261 143 90 409 1.1 1 267 142 91 440 1.1 1 283 157 92 414 1.1 1 257 157 93 357 1.1 1 250 107 94 408 1.1 1 262 146 95 365 1.1 1 243 122 96 385 1.1 1 237 148 97 479 1.1 1 307 172 98 462 1.1 1 298 164 99 664 1.1 1 428 236 100 842 1.1 1 560 282 RUN STATISTICS FOR INPUT FILE: /mnt/owl/nightingales/C_virginica/zr2096_10_s1_R1.fastq.gz ============================================= 17717127 sequences processed in total