SUMMARISING RUN PARAMETERS ========================== Input filename: /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R2.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 All Read 1 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) All Read 1 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 bp from their 3' end to avoid poor qualities or biases Running FastQC on the data once trimming has completed Running FastQC with the following extra arguments: --outdir ~/Downloads/20180411_trimgalore_10bp_Cvirginica_MBD/20180411_fastqc_trim_10bp_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 GATCGTCGGACT /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R2.fastq.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 319.52 s (18 us/read; 3.33 M reads/minute). === Summary === Total reads processed: 17,717,127 Reads with adapters: 3,640,439 (20.5%) Reads written (passing filters): 17,717,127 (100.0%) Total basepairs processed: 1,619,992,471 bp Quality-trimmed: 7,309,137 bp (0.5%) Total written (filtered): 1,605,021,321 bp (99.1%) === Adapter 1 === Sequence: GATCGTCGGACT; Type: regular 3'; Length: 12; Trimmed: 3640439 times. No. of allowed errors: 0-9 bp: 0; 10-12 bp: 1 Bases preceding removed adapters: A: 22.8% C: 14.1% G: 32.1% T: 30.8% none/other: 0.1% Overview of removed sequences length count expect max.err error counts 1 2646925 4429281.8 0 2646925 2 648480 1107320.4 0 648480 3 279757 276830.1 0 279757 4 10277 69207.5 0 10277 5 6428 17301.9 0 6428 6 2905 4325.5 0 2905 7 259 1081.4 0 259 8 192 270.3 0 192 9 207 67.6 0 48 159 10 392 16.9 1 80 312 11 202 4.2 1 90 112 12 54 1.1 1 20 34 13 116 1.1 1 59 57 14 354 1.1 1 191 163 15 65 1.1 1 26 39 16 70 1.1 1 38 32 17 209 1.1 1 127 82 18 249 1.1 1 137 112 19 201 1.1 1 110 91 20 309 1.1 1 183 126 21 369 1.1 1 231 138 22 116 1.1 1 52 64 23 96 1.1 1 46 50 24 361 1.1 1 215 146 25 490 1.1 1 312 178 26 155 1.1 1 82 73 27 428 1.1 1 283 145 28 193 1.1 1 109 84 29 297 1.1 1 182 115 30 1375 1.1 1 937 438 31 145 1.1 1 71 74 32 93 1.1 1 35 58 33 177 1.1 1 88 89 34 273 1.1 1 150 123 35 442 1.1 1 302 140 36 788 1.1 1 579 209 37 275 1.1 1 183 92 38 205 1.1 1 126 79 39 484 1.1 1 337 147 40 325 1.1 1 239 86 41 131 1.1 1 77 54 42 326 1.1 1 206 120 43 570 1.1 1 381 189 44 84 1.1 1 51 33 45 291 1.1 1 189 102 46 440 1.1 1 337 103 47 82 1.1 1 43 39 48 217 1.1 1 134 83 49 260 1.1 1 154 106 50 246 1.1 1 147 99 51 314 1.1 1 197 117 52 311 1.1 1 201 110 53 395 1.1 1 250 145 54 592 1.1 1 406 186 55 718 1.1 1 496 222 56 667 1.1 1 465 202 57 510 1.1 1 343 167 58 618 1.1 1 385 233 59 567 1.1 1 396 171 60 971 1.1 1 629 342 61 945 1.1 1 653 292 62 936 1.1 1 636 300 63 1294 1.1 1 960 334 64 2281 1.1 1 1867 414 65 1784 1.1 1 1430 354 66 1036 1.1 1 737 299 67 901 1.1 1 574 327 68 892 1.1 1 535 357 69 495 1.1 1 298 197 70 457 1.1 1 257 200 71 507 1.1 1 282 225 72 501 1.1 1 281 220 73 489 1.1 1 277 212 74 546 1.1 1 307 239 75 583 1.1 1 323 260 76 751 1.1 1 416 335 77 941 1.1 1 491 450 78 1213 1.1 1 669 544 79 1126 1.1 1 608 518 80 1054 1.1 1 575 479 81 907 1.1 1 510 397 82 521 1.1 1 278 243 83 384 1.1 1 201 183 84 335 1.1 1 193 142 85 348 1.1 1 198 150 86 415 1.1 1 234 181 87 403 1.1 1 218 185 88 335 1.1 1 170 165 89 309 1.1 1 159 150 90 324 1.1 1 179 145 91 315 1.1 1 167 148 92 258 1.1 1 146 112 93 255 1.1 1 138 117 94 282 1.1 1 143 139 95 302 1.1 1 150 152 96 305 1.1 1 143 162 97 384 1.1 1 196 188 98 449 1.1 1 236 213 99 757 1.1 1 388 369 100 1071 1.1 1 577 494 RUN STATISTICS FOR INPUT FILE: /home/sam/Downloads/zr2096/Raw_data/zr2096_10_s1_R2.fastq.gz ============================================= 17717127 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 17717127 Number of sequence pairs removed because at least one read was shorter than the length cutoff (18 bp): 268244 (1.51%)