SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/owl/nightingales/C_virginica/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 14 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 14 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/20180410_trimgalore_trim14bp_Cvirginica_MBD/20180410_fastqc_trimgalore_trim14bp_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 /mnt/owl/nightingales/C_virginica/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 342.15 s (19 us/read; 3.11 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: /mnt/owl/nightingales/C_virginica/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): 181256 (1.02%)