SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P06-AGTTCC-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-P06-AGTTCC-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 839.93 s (21 us/read; 2.88 M reads/minute). === Summary === Total reads processed: 40,368,134 Reads with adapters: 15,413,049 (38.2%) Reads written (passing filters): 40,368,134 (100.0%) Total basepairs processed: 4,036,813,400 bp Quality-trimmed: 20,888,496 bp (0.5%) Total written (filtered): 3,980,556,203 bp (98.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15413049 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.9% C: 25.2% G: 19.6% T: 16.7% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 10992279 10092033.5 0 10992279 2 2797836 2523008.4 0 2797836 3 916087 630752.1 0 916087 4 226475 157688.0 0 226475 5 63278 39422.0 0 63278 6 27192 9855.5 0 27192 7 20610 2463.9 0 20610 8 17368 616.0 0 17368 9 18207 154.0 0 16860 1347 10 17899 38.5 1 14902 2997 11 15613 9.6 1 13407 2206 12 14538 2.4 1 13036 1502 13 12237 0.6 1 11098 1139 14 13906 0.6 1 12612 1294 15 9718 0.6 1 8789 929 16 10326 0.6 1 9347 979 17 12150 0.6 1 10960 1190 18 7167 0.6 1 6417 750 19 9292 0.6 1 8378 914 20 6760 0.6 1 6109 651 21 6794 0.6 1 6152 642 22 6233 0.6 1 5643 590 23 5773 0.6 1 5141 632 24 5531 0.6 1 4906 625 25 4519 0.6 1 4016 503 26 4583 0.6 1 4104 479 27 4360 0.6 1 3891 469 28 4169 0.6 1 3743 426 29 3581 0.6 1 3217 364 30 4371 0.6 1 3810 561 31 2931 0.6 1 2643 288 32 3219 0.6 1 2857 362 33 2759 0.6 1 2450 309 34 2648 0.6 1 2341 307 35 2487 0.6 1 2177 310 36 2473 0.6 1 2143 330 37 2034 0.6 1 1776 258 38 1980 0.6 1 1709 271 39 1755 0.6 1 1531 224 40 1594 0.6 1 1369 225 41 1663 0.6 1 1389 274 42 1675 0.6 1 1394 281 43 1057 0.6 1 885 172 44 1236 0.6 1 954 282 45 1379 0.6 1 1116 263 46 922 0.6 1 743 179 47 988 0.6 1 819 169 48 1147 0.6 1 948 199 49 992 0.6 1 811 181 50 891 0.6 1 730 161 51 1186 0.6 1 906 280 52 782 0.6 1 632 150 53 724 0.6 1 584 140 54 644 0.6 1 509 135 55 626 0.6 1 463 163 56 621 0.6 1 461 160 57 566 0.6 1 443 123 58 586 0.6 1 431 155 59 556 0.6 1 387 169 60 563 0.6 1 390 173 61 510 0.6 1 353 157 62 546 0.6 1 367 179 63 554 0.6 1 395 159 64 528 0.6 1 372 156 65 629 0.6 1 422 207 66 730 0.6 1 396 334 67 6152 0.6 1 356 5796 68 9441 0.6 1 2054 7387 69 8735 0.6 1 1596 7139 70 8203 0.6 1 1661 6542 71 6198 0.6 1 1764 4434 72 4121 0.6 1 1215 2906 73 2948 0.6 1 862 2086 74 2014 0.6 1 717 1297 75 1210 0.6 1 412 798 76 864 0.6 1 321 543 77 735 0.6 1 301 434 78 614 0.6 1 264 350 79 527 0.6 1 260 267 80 528 0.6 1 242 286 81 524 0.6 1 286 238 82 467 0.6 1 248 219 83 460 0.6 1 256 204 84 466 0.6 1 260 206 85 445 0.6 1 228 217 86 443 0.6 1 251 192 87 513 0.6 1 248 265 88 471 0.6 1 241 230 89 423 0.6 1 208 215 90 446 0.6 1 157 289 91 524 0.6 1 186 338 92 369 0.6 1 104 265 93 389 0.6 1 89 300 94 482 0.6 1 79 403 95 766 0.6 1 145 621 96 1125 0.6 1 139 986 97 1720 0.6 1 246 1474 98 1986 0.6 1 105 1881 99 5216 0.6 1 36 5180 100 38491 0.6 1 78 38413 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P06-AGTTCC-READ2-Sequences.txt.gz ============================================= 40368134 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 40368134 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 221320 (0.55%)