SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P04-ATCACG-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-P04-ATCACG-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 493.79 s (21 us/read; 2.91 M reads/minute). === Summary === Total reads processed: 23,947,263 Reads with adapters: 9,600,288 (40.1%) Reads written (passing filters): 23,947,263 (100.0%) Total basepairs processed: 2,394,726,300 bp Quality-trimmed: 20,428,613 bp (0.9%) Total written (filtered): 2,326,298,351 bp (97.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 9600288 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.4% C: 24.1% G: 19.0% T: 15.8% none/other: 3.7% Overview of removed sequences length count expect max.err error counts 1 6605020 5986815.8 0 6605020 2 1623662 1496703.9 0 1623662 3 556328 374176.0 0 556328 4 138925 93544.0 0 138925 5 42522 23386.0 0 42522 6 21794 5846.5 0 21794 7 17790 1461.6 0 17790 8 15169 365.4 0 15169 9 15458 91.4 0 14633 825 10 15088 22.8 1 13065 2023 11 13317 5.7 1 11879 1438 12 12389 1.4 1 11350 1039 13 10798 0.4 1 9839 959 14 12135 0.4 1 11078 1057 15 8309 0.4 1 7615 694 16 9072 0.4 1 8368 704 17 10831 0.4 1 9888 943 18 6506 0.4 1 5965 541 19 8390 0.4 1 7673 717 20 5565 0.4 1 5055 510 21 6103 0.4 1 5650 453 22 5544 0.4 1 5093 451 23 5044 0.4 1 4599 445 24 4787 0.4 1 4358 429 25 4074 0.4 1 3719 355 26 4172 0.4 1 3801 371 27 3874 0.4 1 3584 290 28 3820 0.4 1 3512 308 29 3453 0.4 1 3204 249 30 3743 0.4 1 3427 316 31 2463 0.4 1 2264 199 32 2804 0.4 1 2564 240 33 2479 0.4 1 2261 218 34 2541 0.4 1 2325 216 35 2257 0.4 1 2071 186 36 2174 0.4 1 1956 218 37 2044 0.4 1 1868 176 38 1868 0.4 1 1694 174 39 1579 0.4 1 1432 147 40 1494 0.4 1 1346 148 41 1376 0.4 1 1219 157 42 1341 0.4 1 1176 165 43 933 0.4 1 829 104 44 1017 0.4 1 881 136 45 1125 0.4 1 1002 123 46 831 0.4 1 731 100 47 894 0.4 1 814 80 48 946 0.4 1 809 137 49 937 0.4 1 848 89 50 862 0.4 1 734 128 51 959 0.4 1 835 124 52 632 0.4 1 562 70 53 713 0.4 1 612 101 54 601 0.4 1 510 91 55 515 0.4 1 427 88 56 458 0.4 1 384 74 57 460 0.4 1 383 77 58 432 0.4 1 349 83 59 400 0.4 1 328 72 60 366 0.4 1 304 62 61 373 0.4 1 306 67 62 392 0.4 1 289 103 63 396 0.4 1 311 85 64 420 0.4 1 292 128 65 520 0.4 1 274 246 66 1076 0.4 1 296 780 67 25644 0.4 1 290 25354 68 44457 0.4 1 1192 43265 69 38569 0.4 1 1534 37035 70 26494 0.4 1 1404 25090 71 19139 0.4 1 1049 18090 72 10992 0.4 1 792 10200 73 6188 0.4 1 568 5620 74 4001 0.4 1 363 3638 75 2628 0.4 1 285 2343 76 1808 0.4 1 216 1592 77 1676 0.4 1 184 1492 78 1504 0.4 1 163 1341 79 1260 0.4 1 162 1098 80 1104 0.4 1 192 912 81 998 0.4 1 188 810 82 862 0.4 1 177 685 83 764 0.4 1 165 599 84 761 0.4 1 178 583 85 717 0.4 1 169 548 86 678 0.4 1 187 491 87 668 0.4 1 141 527 88 718 0.4 1 187 531 89 718 0.4 1 119 599 90 743 0.4 1 106 637 91 906 0.4 1 142 764 92 895 0.4 1 80 815 93 1077 0.4 1 52 1025 94 1542 0.4 1 36 1506 95 2276 0.4 1 72 2204 96 3483 0.4 1 69 3414 97 5092 0.4 1 148 4944 98 7001 0.4 1 72 6929 99 19430 0.4 1 46 19384 100 131135 0.4 1 69 131066 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P04-ATCACG-READ2-Sequences.txt.gz ============================================= 23947263 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 23947263 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 450862 (1.88%)