SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P11-ACTTGA-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-P11-ACTTGA-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 434.79 s (20 us/read; 3.05 M reads/minute). === Summary === Total reads processed: 22,073,550 Reads with adapters: 7,747,847 (35.1%) Reads written (passing filters): 22,073,550 (100.0%) Total basepairs processed: 2,207,355,000 bp Quality-trimmed: 3,920,662 bp (0.2%) Total written (filtered): 2,184,786,544 bp (99.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7747847 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.3% C: 28.7% G: 16.4% T: 19.8% none/other: 0.8% Overview of removed sequences length count expect max.err error counts 1 5746935 5518387.5 0 5746935 2 1286626 1379596.9 0 1286626 3 363956 344899.2 0 363956 4 92834 86224.8 0 92834 5 29866 21556.2 0 29866 6 13220 5389.1 0 13220 7 10584 1347.3 0 10584 8 9189 336.8 0 9189 9 8925 84.2 0 8619 306 10 10456 21.1 1 8152 2304 11 7407 5.3 1 6977 430 12 7077 1.3 1 6748 329 13 6533 0.3 1 6239 294 14 5931 0.3 1 5674 257 15 5824 0.3 1 5588 236 16 5318 0.3 1 5081 237 17 5056 0.3 1 4821 235 18 4675 0.3 1 4462 213 19 4210 0.3 1 4015 195 20 3955 0.3 1 3753 202 21 3693 0.3 1 3498 195 22 3252 0.3 1 3083 169 23 2866 0.3 1 2740 126 24 2744 0.3 1 2612 132 25 2471 0.3 1 2346 125 26 2315 0.3 1 2186 129 27 2210 0.3 1 2099 111 28 2111 0.3 1 2005 106 29 1970 0.3 1 1856 114 30 1842 0.3 1 1756 86 31 1707 0.3 1 1625 82 32 1584 0.3 1 1496 88 33 1421 0.3 1 1338 83 34 1447 0.3 1 1341 106 35 1226 0.3 1 1166 60 36 1274 0.3 1 1185 89 37 1149 0.3 1 1085 64 38 1011 0.3 1 938 73 39 977 0.3 1 895 82 40 835 0.3 1 778 57 41 1075 0.3 1 1011 64 42 447 0.3 1 414 33 43 575 0.3 1 538 37 44 573 0.3 1 530 43 45 554 0.3 1 506 48 46 589 0.3 1 545 44 47 545 0.3 1 499 46 48 533 0.3 1 463 70 49 499 0.3 1 456 43 50 417 0.3 1 381 36 51 471 0.3 1 423 48 52 410 0.3 1 372 38 53 420 0.3 1 377 43 54 319 0.3 1 281 38 55 265 0.3 1 235 30 56 249 0.3 1 225 24 57 243 0.3 1 211 32 58 208 0.3 1 188 20 59 178 0.3 1 167 11 60 186 0.3 1 161 25 61 220 0.3 1 195 25 62 172 0.3 1 146 26 63 174 0.3 1 145 29 64 237 0.3 1 214 23 65 161 0.3 1 146 15 66 201 0.3 1 176 25 67 204 0.3 1 178 26 68 206 0.3 1 163 43 69 241 0.3 1 189 52 70 293 0.3 1 204 89 71 301 0.3 1 165 136 72 548 0.3 1 194 354 73 6284 0.3 1 272 6012 74 10360 0.3 1 982 9378 75 9987 0.3 1 1283 8704 76 6503 0.3 1 1011 5492 77 4613 0.3 1 786 3827 78 3146 0.3 1 548 2598 79 1972 0.3 1 386 1586 80 1499 0.3 1 276 1223 81 976 0.3 1 215 761 82 678 0.3 1 164 514 83 581 0.3 1 173 408 84 478 0.3 1 147 331 85 380 0.3 1 164 216 86 326 0.3 1 133 193 87 333 0.3 1 165 168 88 248 0.3 1 113 135 89 206 0.3 1 83 123 90 200 0.3 1 96 104 91 231 0.3 1 126 105 92 172 0.3 1 72 100 93 172 0.3 1 54 118 94 222 0.3 1 65 157 95 256 0.3 1 80 176 96 287 0.3 1 70 217 97 516 0.3 1 151 365 98 576 0.3 1 77 499 99 1859 0.3 1 28 1831 100 16390 0.3 1 71 16319 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P11-ACTTGA-READ1-Sequences.txt.gz ============================================= 22073550 sequences processed in total