SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P02-ACAGTG-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-P02-ACAGTG-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 496.21 s (21 us/read; 2.92 M reads/minute). === Summary === Total reads processed: 24,157,901 Reads with adapters: 9,235,435 (38.2%) Reads written (passing filters): 24,157,901 (100.0%) Total basepairs processed: 2,415,790,100 bp Quality-trimmed: 13,197,068 bp (0.5%) Total written (filtered): 2,365,044,184 bp (97.9%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9235435 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.3% C: 25.2% G: 17.1% T: 19.0% none/other: 2.4% Overview of removed sequences length count expect max.err error counts 1 6501476 6039475.2 0 6501476 2 1512450 1509868.8 0 1512450 3 487981 377467.2 0 487981 4 130644 94366.8 0 130644 5 47785 23591.7 0 47785 6 27089 5897.9 0 27089 7 22597 1474.5 0 22597 8 20394 368.6 0 20394 9 19602 92.2 0 19185 417 10 19926 23.0 1 16882 3044 11 15858 5.8 1 14779 1079 12 15498 1.4 1 14554 944 13 13371 0.4 1 12576 795 14 15079 0.4 1 14157 922 15 10995 0.4 1 10362 633 16 11511 0.4 1 10804 707 17 13445 0.4 1 12656 789 18 8538 0.4 1 8047 491 19 10528 0.4 1 9855 673 20 7617 0.4 1 7119 498 21 7447 0.4 1 6986 461 22 6767 0.4 1 6268 499 23 6050 0.4 1 5595 455 24 5793 0.4 1 5317 476 25 4781 0.4 1 4476 305 26 4588 0.4 1 4240 348 27 4427 0.4 1 4101 326 28 4422 0.4 1 4128 294 29 3765 0.4 1 3461 304 30 4287 0.4 1 3955 332 31 2920 0.4 1 2693 227 32 3335 0.4 1 3065 270 33 2824 0.4 1 2597 227 34 2875 0.4 1 2612 263 35 2433 0.4 1 2191 242 36 2389 0.4 1 2210 179 37 2308 0.4 1 2096 212 38 2002 0.4 1 1806 196 39 1822 0.4 1 1679 143 40 1492 0.4 1 1354 138 41 1454 0.4 1 1292 162 42 1482 0.4 1 1313 169 43 924 0.4 1 820 104 44 921 0.4 1 789 132 45 1215 0.4 1 1084 131 46 825 0.4 1 715 110 47 949 0.4 1 833 116 48 925 0.4 1 828 97 49 909 0.4 1 813 96 50 882 0.4 1 763 119 51 891 0.4 1 767 124 52 575 0.4 1 477 98 53 710 0.4 1 619 91 54 564 0.4 1 484 80 55 541 0.4 1 475 66 56 426 0.4 1 375 51 57 425 0.4 1 356 69 58 434 0.4 1 377 57 59 405 0.4 1 335 70 60 381 0.4 1 304 77 61 447 0.4 1 369 78 62 331 0.4 1 272 59 63 338 0.4 1 261 77 64 346 0.4 1 269 77 65 416 0.4 1 306 110 66 643 0.4 1 302 341 67 11749 0.4 1 332 11417 68 23402 0.4 1 1082 22320 69 16935 0.4 1 1393 15542 70 13577 0.4 1 1047 12530 71 8307 0.4 1 743 7564 72 4773 0.4 1 544 4229 73 2361 0.4 1 318 2043 74 1505 0.4 1 192 1313 75 958 0.4 1 173 785 76 644 0.4 1 132 512 77 563 0.4 1 138 425 78 525 0.4 1 108 417 79 468 0.4 1 132 336 80 477 0.4 1 136 341 81 440 0.4 1 95 345 82 362 0.4 1 117 245 83 358 0.4 1 117 241 84 295 0.4 1 92 203 85 342 0.4 1 113 229 86 362 0.4 1 111 251 87 359 0.4 1 108 251 88 371 0.4 1 118 253 89 377 0.4 1 56 321 90 376 0.4 1 38 338 91 546 0.4 1 92 454 92 514 0.4 1 54 460 93 678 0.4 1 28 650 94 1215 0.4 1 19 1196 95 1779 0.4 1 33 1746 96 2795 0.4 1 34 2761 97 4522 0.4 1 71 4451 98 6593 0.4 1 33 6560 99 18937 0.4 1 24 18913 100 100500 0.4 1 61 100439 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P02-ACAGTG-READ2-Sequences.txt.gz ============================================= 24157901 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 24157901 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 293514 (1.21%)