SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P08-CTTGTA-READ1-Sequences.txt.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: '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 All Read 1 sequences will be trimmed by 15 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 15 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 4 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 4 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 /mnt/data/coral_RNAseq_2017/porites/20180415_trimmed/fastqc --threads 24 Output file will be GZIP compressed This is cutadapt 1.16 with Python 3.6.4 Command line parameters: -f fastq -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P08-CTTGTA-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 565.91 s (20 us/read; 3.02 M reads/minute). === Summary === Total reads processed: 28,467,375 Reads with adapters: 10,107,610 (35.5%) Reads written (passing filters): 28,467,375 (100.0%) Total basepairs processed: 2,846,737,500 bp Quality-trimmed: 4,562,072 bp (0.2%) Total written (filtered): 2,818,843,445 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10107610 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.8% C: 28.5% G: 16.1% T: 19.9% none/other: 0.7% Overview of removed sequences length count expect max.err error counts 1 7493128 7116843.8 0 7493128 2 1672176 1779210.9 0 1672176 3 480110 444802.7 0 480110 4 121401 111200.7 0 121401 5 40846 27800.2 0 40846 6 18726 6950.0 0 18726 7 14938 1737.5 0 14938 8 13611 434.4 0 13611 9 13651 108.6 0 12419 1232 10 15021 27.1 1 11648 3373 11 11089 6.8 1 10406 683 12 10093 1.7 1 9595 498 13 9673 0.4 1 9249 424 14 8627 0.4 1 8234 393 15 8223 0.4 1 7806 417 16 7765 0.4 1 7419 346 17 7265 0.4 1 6932 333 18 6794 0.4 1 6475 319 19 6101 0.4 1 5852 249 20 5601 0.4 1 5368 233 21 5216 0.4 1 4963 253 22 4642 0.4 1 4408 234 23 4113 0.4 1 3874 239 24 3798 0.4 1 3596 202 25 3586 0.4 1 3402 184 26 3218 0.4 1 3060 158 27 3041 0.4 1 2890 151 28 2953 0.4 1 2788 165 29 2755 0.4 1 2596 159 30 2542 0.4 1 2387 155 31 2423 0.4 1 2311 112 32 2206 0.4 1 2061 145 33 1936 0.4 1 1834 102 34 1877 0.4 1 1758 119 35 1763 0.4 1 1652 111 36 1566 0.4 1 1490 76 37 1396 0.4 1 1317 79 38 1279 0.4 1 1205 74 39 1191 0.4 1 1100 91 40 1074 0.4 1 1010 64 41 1301 0.4 1 1227 74 42 615 0.4 1 552 63 43 712 0.4 1 668 44 44 680 0.4 1 634 46 45 625 0.4 1 579 46 46 603 0.4 1 556 47 47 626 0.4 1 553 73 48 593 0.4 1 535 58 49 572 0.4 1 518 54 50 541 0.4 1 502 39 51 454 0.4 1 412 42 52 407 0.4 1 377 30 53 503 0.4 1 463 40 54 296 0.4 1 253 43 55 308 0.4 1 284 24 56 228 0.4 1 203 25 57 278 0.4 1 244 34 58 224 0.4 1 193 31 59 219 0.4 1 183 36 60 196 0.4 1 171 25 61 218 0.4 1 191 27 62 171 0.4 1 156 15 63 194 0.4 1 160 34 64 217 0.4 1 187 30 65 184 0.4 1 161 23 66 183 0.4 1 152 31 67 197 0.4 1 175 22 68 226 0.4 1 184 42 69 226 0.4 1 171 55 70 278 0.4 1 185 93 71 302 0.4 1 171 131 72 592 0.4 1 196 396 73 6813 0.4 1 272 6541 74 11687 0.4 1 1162 10525 75 11397 0.4 1 1538 9859 76 7342 0.4 1 1303 6039 77 5260 0.4 1 1050 4210 78 3546 0.4 1 672 2874 79 2244 0.4 1 488 1756 80 1583 0.4 1 336 1247 81 1158 0.4 1 253 905 82 759 0.4 1 185 574 83 686 0.4 1 213 473 84 515 0.4 1 176 339 85 428 0.4 1 170 258 86 355 0.4 1 164 191 87 339 0.4 1 175 164 88 292 0.4 1 163 129 89 240 0.4 1 121 119 90 214 0.4 1 102 112 91 255 0.4 1 147 108 92 229 0.4 1 114 115 93 192 0.4 1 68 124 94 271 0.4 1 89 182 95 296 0.4 1 106 190 96 377 0.4 1 105 272 97 556 0.4 1 189 367 98 674 0.4 1 128 546 99 2000 0.4 1 52 1948 100 17519 0.4 1 59 17460 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P08-CTTGTA-READ1-Sequences.txt.gz ============================================= 28467375 sequences processed in total