SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P05-GAGTGG-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-P05-GAGTGG-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 533.51 s (20 us/read; 3.01 M reads/minute). === Summary === Total reads processed: 26,724,234 Reads with adapters: 10,856,043 (40.6%) Reads written (passing filters): 26,724,234 (100.0%) Total basepairs processed: 2,672,423,400 bp Quality-trimmed: 19,068,208 bp (0.7%) Total written (filtered): 2,583,146,968 bp (96.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10856043 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.6% C: 22.6% G: 17.3% T: 17.6% none/other: 5.0% Overview of removed sequences length count expect max.err error counts 1 7352268 6681058.5 0 7352268 2 1715986 1670264.6 0 1715986 3 593328 417566.2 0 593328 4 158365 104391.5 0 158365 5 54056 26097.9 0 54056 6 30719 6524.5 0 30719 7 26333 1631.1 0 26333 8 23750 407.8 0 23750 9 22939 101.9 0 22352 587 10 22299 25.5 1 20522 1777 11 19878 6.4 1 18686 1192 12 18171 1.6 1 17221 950 13 16628 0.4 1 15827 801 14 17823 0.4 1 16927 896 15 13425 0.4 1 12798 627 16 14117 0.4 1 13472 645 17 16127 0.4 1 15368 759 18 10739 0.4 1 10227 512 19 13260 0.4 1 12624 636 20 9850 0.4 1 9397 453 21 9747 0.4 1 9267 480 22 9093 0.4 1 8507 586 23 8678 0.4 1 8106 572 24 8056 0.4 1 7583 473 25 6705 0.4 1 6342 363 26 6990 0.4 1 6571 419 27 6651 0.4 1 6241 410 28 6412 0.4 1 6051 361 29 5743 0.4 1 5414 329 30 6255 0.4 1 5885 370 31 4587 0.4 1 4351 236 32 4987 0.4 1 4662 325 33 4544 0.4 1 4260 284 34 4419 0.4 1 4109 310 35 4036 0.4 1 3796 240 36 3908 0.4 1 3686 222 37 3692 0.4 1 3460 232 38 3402 0.4 1 3155 247 39 3092 0.4 1 2903 189 40 2741 0.4 1 2587 154 41 2501 0.4 1 2300 201 42 2608 0.4 1 2402 206 43 1907 0.4 1 1760 147 44 1969 0.4 1 1821 148 45 2295 0.4 1 2130 165 46 1609 0.4 1 1458 151 47 1913 0.4 1 1775 138 48 1954 0.4 1 1831 123 49 1949 0.4 1 1784 165 50 1831 0.4 1 1710 121 51 2235 0.4 1 2058 177 52 1551 0.4 1 1422 129 53 1573 0.4 1 1447 126 54 1307 0.4 1 1217 90 55 1192 0.4 1 1116 76 56 1051 0.4 1 962 89 57 1052 0.4 1 915 137 58 975 0.4 1 859 116 59 875 0.4 1 773 102 60 766 0.4 1 676 90 61 806 0.4 1 710 96 62 670 0.4 1 549 121 63 676 0.4 1 565 111 64 768 0.4 1 628 140 65 747 0.4 1 511 236 66 1185 0.4 1 507 678 67 32523 0.4 1 596 31927 68 39196 0.4 1 1933 37263 69 40116 0.4 1 1608 38508 70 41527 0.4 1 1839 39688 71 23648 0.4 1 1649 21999 72 17110 0.4 1 1164 15946 73 12063 0.4 1 877 11186 74 7075 0.4 1 675 6400 75 4034 0.4 1 492 3542 76 2841 0.4 1 307 2534 77 2392 0.4 1 300 2092 78 1761 0.4 1 211 1550 79 1333 0.4 1 223 1110 80 1382 0.4 1 199 1183 81 1053 0.4 1 208 845 82 1008 0.4 1 218 790 83 991 0.4 1 235 756 84 778 0.4 1 198 580 85 716 0.4 1 150 566 86 782 0.4 1 154 628 87 813 0.4 1 172 641 88 835 0.4 1 182 653 89 829 0.4 1 109 720 90 958 0.4 1 142 816 91 1184 0.4 1 168 1016 92 1208 0.4 1 65 1143 93 1306 0.4 1 55 1251 94 1837 0.4 1 58 1779 95 2748 0.4 1 79 2669 96 4252 0.4 1 80 4172 97 7341 0.4 1 149 7192 98 11424 0.4 1 101 11323 99 32808 0.4 1 212 32596 100 254407 0.4 1 788 253619 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P05-GAGTGG-READ2-Sequences.txt.gz ============================================= 26724234 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 26724234 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 633493 (2.37%)