SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P09-GTGAAA-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-P09-GTGAAA-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 446.53 s (20 us/read; 2.97 M reads/minute). === Summary === Total reads processed: 22,109,558 Reads with adapters: 8,720,472 (39.4%) Reads written (passing filters): 22,109,558 (100.0%) Total basepairs processed: 2,210,955,800 bp Quality-trimmed: 10,968,521 bp (0.5%) Total written (filtered): 2,167,546,551 bp (98.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8720472 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.2% C: 23.0% G: 19.2% T: 18.6% none/other: 2.0% Overview of removed sequences length count expect max.err error counts 1 6033527 5527389.5 0 6033527 2 1496891 1381847.4 0 1496891 3 514242 345461.8 0 514242 4 137411 86365.5 0 137411 5 45561 21591.4 0 45561 6 26223 5397.8 0 26223 7 21556 1349.5 0 21556 8 19173 337.4 0 19173 9 18870 84.3 0 18396 474 10 17347 21.1 1 15989 1358 11 16326 5.3 1 15386 940 12 15165 1.3 1 14436 729 13 13007 0.3 1 12441 566 14 14407 0.3 1 13708 699 15 10069 0.3 1 9608 461 16 10830 0.3 1 10332 498 17 12602 0.3 1 12011 591 18 7503 0.3 1 7150 353 19 9755 0.3 1 9294 461 20 6860 0.3 1 6555 305 21 7240 0.3 1 6940 300 22 6341 0.3 1 5929 412 23 5711 0.3 1 5322 389 24 5786 0.3 1 5444 342 25 4898 0.3 1 4616 282 26 4588 0.3 1 4327 261 27 4606 0.3 1 4347 259 28 4236 0.3 1 4009 227 29 3802 0.3 1 3569 233 30 4204 0.3 1 3967 237 31 2815 0.3 1 2670 145 32 3081 0.3 1 2910 171 33 2700 0.3 1 2491 209 34 2767 0.3 1 2581 186 35 2436 0.3 1 2289 147 36 2329 0.3 1 2163 166 37 2086 0.3 1 1944 142 38 1940 0.3 1 1774 166 39 1643 0.3 1 1506 137 40 1564 0.3 1 1454 110 41 1277 0.3 1 1167 110 42 1323 0.3 1 1219 104 43 962 0.3 1 893 69 44 1071 0.3 1 966 105 45 1069 0.3 1 955 114 46 795 0.3 1 696 99 47 787 0.3 1 694 93 48 988 0.3 1 893 95 49 825 0.3 1 739 86 50 728 0.3 1 647 81 51 924 0.3 1 822 102 52 568 0.3 1 471 97 53 627 0.3 1 563 64 54 490 0.3 1 421 69 55 429 0.3 1 390 39 56 394 0.3 1 344 50 57 357 0.3 1 306 51 58 313 0.3 1 265 48 59 317 0.3 1 254 63 60 298 0.3 1 250 48 61 311 0.3 1 246 65 62 270 0.3 1 204 66 63 252 0.3 1 197 55 64 269 0.3 1 200 69 65 296 0.3 1 202 94 66 387 0.3 1 135 252 67 10607 0.3 1 192 10415 68 14194 0.3 1 703 13491 69 16021 0.3 1 713 15308 70 14402 0.3 1 695 13707 71 8379 0.3 1 602 7777 72 5973 0.3 1 434 5539 73 4243 0.3 1 324 3919 74 2390 0.3 1 272 2118 75 1632 0.3 1 222 1410 76 1106 0.3 1 147 959 77 963 0.3 1 125 838 78 795 0.3 1 103 692 79 693 0.3 1 137 556 80 602 0.3 1 103 499 81 468 0.3 1 85 383 82 370 0.3 1 74 296 83 505 0.3 1 101 404 84 363 0.3 1 91 272 85 342 0.3 1 75 267 86 317 0.3 1 89 228 87 354 0.3 1 95 259 88 361 0.3 1 73 288 89 331 0.3 1 45 286 90 356 0.3 1 59 297 91 428 0.3 1 71 357 92 394 0.3 1 38 356 93 453 0.3 1 15 438 94 630 0.3 1 26 604 95 931 0.3 1 32 899 96 1428 0.3 1 33 1395 97 2262 0.3 1 73 2189 98 3409 0.3 1 26 3383 99 9367 0.3 1 23 9344 100 76978 0.3 1 77 76901 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P09-GTGAAA-READ2-Sequences.txt.gz ============================================= 22109558 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 22109558 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 227225 (1.03%)