SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P01-AGTCAA-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-P01-AGTCAA-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 516.54 s (21 us/read; 2.92 M reads/minute). === Summary === Total reads processed: 25,174,276 Reads with adapters: 9,403,896 (37.4%) Reads written (passing filters): 25,174,276 (100.0%) Total basepairs processed: 2,517,427,600 bp Quality-trimmed: 9,864,993 bp (0.4%) Total written (filtered): 2,485,657,365 bp (98.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9403896 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.6% C: 26.2% G: 18.3% T: 18.6% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 6774550 6293569.0 0 6774550 2 1577449 1573392.2 0 1577449 3 510573 393348.1 0 510573 4 141414 98337.0 0 141414 5 47461 24584.3 0 47461 6 25545 6146.1 0 25545 7 20855 1536.5 0 20855 8 18492 384.1 0 18492 9 18182 96.0 0 17551 631 10 17917 24.0 1 15405 2512 11 14804 6.0 1 13712 1092 12 13735 1.5 1 12921 814 13 12484 0.4 1 11664 820 14 13529 0.4 1 12703 826 15 10094 0.4 1 9452 642 16 10625 0.4 1 9988 637 17 11936 0.4 1 11162 774 18 7766 0.4 1 7247 519 19 9236 0.4 1 8615 621 20 6899 0.4 1 6440 459 21 6627 0.4 1 6245 382 22 5957 0.4 1 5569 388 23 5323 0.4 1 4964 359 24 5066 0.4 1 4712 354 25 4237 0.4 1 4013 224 26 4272 0.4 1 4023 249 27 4099 0.4 1 3856 243 28 3845 0.4 1 3644 201 29 3550 0.4 1 3345 205 30 3802 0.4 1 3567 235 31 2544 0.4 1 2387 157 32 2875 0.4 1 2700 175 33 2520 0.4 1 2366 154 34 2494 0.4 1 2325 169 35 2195 0.4 1 2061 134 36 2255 0.4 1 2077 178 37 1916 0.4 1 1802 114 38 1854 0.4 1 1715 139 39 1643 0.4 1 1521 122 40 1399 0.4 1 1270 129 41 1406 0.4 1 1273 133 42 1374 0.4 1 1252 122 43 948 0.4 1 873 75 44 999 0.4 1 900 99 45 1117 0.4 1 999 118 46 789 0.4 1 715 74 47 834 0.4 1 761 73 48 1002 0.4 1 893 109 49 865 0.4 1 794 71 50 824 0.4 1 739 85 51 1001 0.4 1 882 119 52 681 0.4 1 605 76 53 665 0.4 1 579 86 54 675 0.4 1 596 79 55 587 0.4 1 507 80 56 550 0.4 1 483 67 57 502 0.4 1 444 58 58 493 0.4 1 422 71 59 550 0.4 1 484 66 60 547 0.4 1 458 89 61 517 0.4 1 446 71 62 554 0.4 1 474 80 63 484 0.4 1 417 67 64 523 0.4 1 432 91 65 547 0.4 1 431 116 66 620 0.4 1 476 144 67 2545 0.4 1 474 2071 68 4972 0.4 1 2179 2793 69 4810 0.4 1 1844 2966 70 4708 0.4 1 2055 2653 71 3953 0.4 1 1963 1990 72 2652 0.4 1 1353 1299 73 1902 0.4 1 966 936 74 1332 0.4 1 765 567 75 946 0.4 1 534 412 76 655 0.4 1 369 286 77 603 0.4 1 355 248 78 462 0.4 1 294 168 79 408 0.4 1 269 139 80 442 0.4 1 284 158 81 404 0.4 1 272 132 82 422 0.4 1 283 139 83 377 0.4 1 259 118 84 380 0.4 1 261 119 85 352 0.4 1 225 127 86 396 0.4 1 254 142 87 364 0.4 1 212 152 88 314 0.4 1 183 131 89 330 0.4 1 184 146 90 334 0.4 1 165 169 91 349 0.4 1 156 193 92 208 0.4 1 71 137 93 259 0.4 1 79 180 94 219 0.4 1 41 178 95 347 0.4 1 94 253 96 432 0.4 1 66 366 97 868 0.4 1 234 634 98 732 0.4 1 61 671 99 1811 0.4 1 32 1779 100 12935 0.4 1 49 12886 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P01-AGTCAA-READ2-Sequences.txt.gz ============================================= 25174276 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 25174276 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 104393 (0.41%)