SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P03-GTTTCG-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/montipora/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/montipora/4R041-L6-P03-GTTTCG-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 497.92 s (21 us/read; 2.91 M reads/minute). === Summary === Total reads processed: 24,131,001 Reads with adapters: 9,134,717 (37.9%) Reads written (passing filters): 24,131,001 (100.0%) Total basepairs processed: 2,413,100,100 bp Quality-trimmed: 10,631,123 bp (0.4%) Total written (filtered): 2,380,141,230 bp (98.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9134717 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.4% C: 26.3% G: 21.0% T: 16.0% none/other: 0.4% Overview of removed sequences length count expect max.err error counts 1 6322672 6032750.2 0 6322672 2 1698125 1508187.6 0 1698125 3 555519 377046.9 0 555519 4 145067 94261.7 0 145067 5 48481 23565.4 0 48481 6 26146 5891.4 0 26146 7 21373 1472.8 0 21373 8 18941 368.2 0 18941 9 18584 92.1 0 17785 799 10 18059 23.0 1 16050 2009 11 16222 5.8 1 14531 1691 12 14785 1.4 1 13725 1060 13 13177 0.4 1 12337 840 14 14510 0.4 1 13525 985 15 10042 0.4 1 9381 661 16 11001 0.4 1 10236 765 17 12440 0.4 1 11562 878 18 7385 0.4 1 6877 508 19 9520 0.4 1 8807 713 20 6776 0.4 1 6255 521 21 6738 0.4 1 6290 448 22 6287 0.4 1 5875 412 23 5645 0.4 1 5251 394 24 5600 0.4 1 5108 492 25 4515 0.4 1 4221 294 26 4486 0.4 1 4170 316 27 4246 0.4 1 3917 329 28 4160 0.4 1 3865 295 29 3579 0.4 1 3297 282 30 4225 0.4 1 3911 314 31 2655 0.4 1 2447 208 32 3016 0.4 1 2766 250 33 2692 0.4 1 2506 186 34 2583 0.4 1 2390 193 35 2254 0.4 1 2084 170 36 2313 0.4 1 2091 222 37 1949 0.4 1 1771 178 38 1822 0.4 1 1645 177 39 1607 0.4 1 1453 154 40 1458 0.4 1 1303 155 41 1353 0.4 1 1189 164 42 1364 0.4 1 1187 177 43 919 0.4 1 821 98 44 1044 0.4 1 897 147 45 1151 0.4 1 1005 146 46 750 0.4 1 656 94 47 830 0.4 1 734 96 48 977 0.4 1 834 143 49 858 0.4 1 759 99 50 851 0.4 1 736 115 51 1046 0.4 1 861 185 52 646 0.4 1 555 91 53 659 0.4 1 548 111 54 514 0.4 1 447 67 55 550 0.4 1 465 85 56 502 0.4 1 411 91 57 400 0.4 1 342 58 58 428 0.4 1 330 98 59 397 0.4 1 317 80 60 430 0.4 1 352 78 61 398 0.4 1 302 96 62 428 0.4 1 317 111 63 458 0.4 1 346 112 64 440 0.4 1 327 113 65 448 0.4 1 333 115 66 516 0.4 1 340 176 67 3037 0.4 1 315 2722 68 5109 0.4 1 1687 3422 69 4673 0.4 1 1364 3309 70 4413 0.4 1 1477 2936 71 3475 0.4 1 1348 2127 72 2357 0.4 1 948 1409 73 1717 0.4 1 721 996 74 1221 0.4 1 546 675 75 769 0.4 1 362 407 76 534 0.4 1 234 300 77 483 0.4 1 239 244 78 413 0.4 1 221 192 79 350 0.4 1 173 177 80 351 0.4 1 198 153 81 355 0.4 1 217 138 82 371 0.4 1 224 147 83 298 0.4 1 170 128 84 316 0.4 1 181 135 85 274 0.4 1 163 111 86 321 0.4 1 184 137 87 322 0.4 1 187 135 88 366 0.4 1 212 154 89 348 0.4 1 176 172 90 297 0.4 1 119 178 91 352 0.4 1 140 212 92 248 0.4 1 77 171 93 219 0.4 1 57 162 94 290 0.4 1 60 230 95 457 0.4 1 119 338 96 648 0.4 1 100 548 97 979 0.4 1 213 766 98 1004 0.4 1 124 880 99 2346 0.4 1 29 2317 100 16992 0.4 1 45 16947 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P03-GTTTCG-READ2-Sequences.txt.gz ============================================= 24131001 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 24131001 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 114490 (0.47%)