SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P06-GCCAAT-READ2-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-P06-GCCAAT-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 376.38 s (20 us/read; 2.96 M reads/minute). === Summary === Total reads processed: 18,561,500 Reads with adapters: 7,037,876 (37.9%) Reads written (passing filters): 18,561,500 (100.0%) Total basepairs processed: 1,856,150,000 bp Quality-trimmed: 10,302,737 bp (0.6%) Total written (filtered): 1,822,120,138 bp (98.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 7037876 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.6% C: 23.7% G: 17.7% T: 19.0% none/other: 2.0% Overview of removed sequences length count expect max.err error counts 1 5044369 4640375.0 0 5044369 2 1212187 1160093.8 0 1212187 3 396210 290023.4 0 396210 4 100150 72505.9 0 100150 5 26983 18126.5 0 26983 6 11393 4531.6 0 11393 7 8012 1132.9 0 8012 8 6949 283.2 0 6949 9 7096 70.8 0 6734 362 10 6851 17.7 1 5772 1079 11 5870 4.4 1 5312 558 12 5325 1.1 1 5015 310 13 4640 0.3 1 4382 258 14 5078 0.3 1 4770 308 15 3487 0.3 1 3291 196 16 3681 0.3 1 3479 202 17 4133 0.3 1 3902 231 18 2545 0.3 1 2404 141 19 3195 0.3 1 3027 168 20 2374 0.3 1 2266 108 21 2319 0.3 1 2180 139 22 2126 0.3 1 1970 156 23 1960 0.3 1 1779 181 24 1833 0.3 1 1661 172 25 1508 0.3 1 1374 134 26 1488 0.3 1 1389 99 27 1376 0.3 1 1280 96 28 1382 0.3 1 1255 127 29 1289 0.3 1 1193 96 30 1401 0.3 1 1269 132 31 893 0.3 1 803 90 32 1038 0.3 1 940 98 33 911 0.3 1 809 102 34 929 0.3 1 832 97 35 862 0.3 1 745 117 36 813 0.3 1 724 89 37 777 0.3 1 693 84 38 650 0.3 1 560 90 39 586 0.3 1 511 75 40 540 0.3 1 478 62 41 504 0.3 1 419 85 42 601 0.3 1 503 98 43 352 0.3 1 309 43 44 402 0.3 1 342 60 45 483 0.3 1 399 84 46 318 0.3 1 255 63 47 300 0.3 1 256 44 48 429 0.3 1 364 65 49 331 0.3 1 282 49 50 356 0.3 1 307 49 51 398 0.3 1 333 65 52 306 0.3 1 237 69 53 304 0.3 1 254 50 54 270 0.3 1 228 42 55 254 0.3 1 192 62 56 224 0.3 1 183 41 57 208 0.3 1 164 44 58 198 0.3 1 161 37 59 236 0.3 1 184 52 60 213 0.3 1 158 55 61 202 0.3 1 165 37 62 200 0.3 1 145 55 63 179 0.3 1 135 44 64 185 0.3 1 147 38 65 199 0.3 1 119 80 66 335 0.3 1 125 210 67 8406 0.3 1 172 8234 68 14840 0.3 1 481 14359 69 12417 0.3 1 601 11816 70 9851 0.3 1 539 9312 71 5930 0.3 1 431 5499 72 3693 0.3 1 308 3385 73 2087 0.3 1 232 1855 74 1201 0.3 1 127 1074 75 849 0.3 1 133 716 76 504 0.3 1 83 421 77 458 0.3 1 70 388 78 433 0.3 1 63 370 79 357 0.3 1 67 290 80 322 0.3 1 53 269 81 251 0.3 1 44 207 82 240 0.3 1 44 196 83 308 0.3 1 70 238 84 255 0.3 1 51 204 85 243 0.3 1 76 167 86 226 0.3 1 47 179 87 226 0.3 1 42 184 88 255 0.3 1 52 203 89 252 0.3 1 28 224 90 273 0.3 1 22 251 91 356 0.3 1 36 320 92 351 0.3 1 27 324 93 430 0.3 1 26 404 94 630 0.3 1 16 614 95 976 0.3 1 19 957 96 1528 0.3 1 16 1512 97 2474 0.3 1 41 2433 98 3637 0.3 1 26 3611 99 9531 0.3 1 11 9520 100 60890 0.3 1 30 60860 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P06-GCCAAT-READ2-Sequences.txt.gz ============================================= 18561500 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 18561500 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 194532 (1.05%)