SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P12-GCCAAT-READ1-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-P12-GCCAAT-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 839.36 s (20 us/read; 3.07 M reads/minute). === Summary === Total reads processed: 42,977,789 Reads with adapters: 15,864,330 (36.9%) Reads written (passing filters): 42,977,789 (100.0%) Total basepairs processed: 4,297,778,900 bp Quality-trimmed: 8,480,142 bp (0.2%) Total written (filtered): 4,241,922,600 bp (98.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15864330 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 35.5% C: 28.0% G: 16.6% T: 18.5% none/other: 1.4% Overview of removed sequences length count expect max.err error counts 1 11634682 10744447.2 0 11634682 2 2493333 2686111.8 0 2493333 3 759492 671528.0 0 759492 4 206437 167882.0 0 206437 5 74858 41970.5 0 74858 6 39759 10492.6 0 39759 7 33633 2623.2 0 33633 8 28835 655.8 0 28835 9 28381 163.9 0 27602 779 10 34176 41.0 1 25209 8967 11 23142 10.2 1 21999 1143 12 21922 2.6 1 20972 950 13 19959 0.6 1 19141 818 14 18556 0.6 1 17796 760 15 17506 0.6 1 16688 818 16 16913 0.6 1 16161 752 17 15156 0.6 1 14420 736 18 15178 0.6 1 14489 689 19 12575 0.6 1 12012 563 20 11867 0.6 1 11404 463 21 10335 0.6 1 9835 500 22 9377 0.6 1 8933 444 23 8464 0.6 1 8115 349 24 7548 0.6 1 7215 333 25 7172 0.6 1 6895 277 26 6482 0.6 1 6203 279 27 6156 0.6 1 5913 243 28 5900 0.6 1 5662 238 29 5376 0.6 1 5166 210 30 4974 0.6 1 4768 206 31 4739 0.6 1 4554 185 32 4400 0.6 1 4180 220 33 3803 0.6 1 3638 165 34 3690 0.6 1 3521 169 35 3238 0.6 1 3094 144 36 3009 0.6 1 2860 149 37 2880 0.6 1 2755 125 38 2506 0.6 1 2390 116 39 2325 0.6 1 2203 122 40 1904 0.6 1 1780 124 41 2341 0.6 1 2247 94 42 998 0.6 1 939 59 43 1259 0.6 1 1186 73 44 1186 0.6 1 1099 87 45 1136 0.6 1 1077 59 46 1152 0.6 1 1086 66 47 1136 0.6 1 1046 90 48 1119 0.6 1 1033 86 49 1055 0.6 1 999 56 50 935 0.6 1 854 81 51 792 0.6 1 731 61 52 813 0.6 1 732 81 53 817 0.6 1 760 57 54 513 0.6 1 460 53 55 528 0.6 1 473 55 56 401 0.6 1 376 25 57 376 0.6 1 340 36 58 362 0.6 1 312 50 59 359 0.6 1 300 59 60 340 0.6 1 285 55 61 273 0.6 1 230 43 62 319 0.6 1 282 37 63 260 0.6 1 195 65 64 254 0.6 1 194 60 65 264 0.6 1 213 51 66 212 0.6 1 174 38 67 264 0.6 1 187 77 68 267 0.6 1 174 93 69 339 0.6 1 207 132 70 436 0.6 1 221 215 71 646 0.6 1 201 445 72 1418 0.6 1 221 1197 73 19654 0.6 1 269 19385 74 36046 0.6 1 1012 35034 75 30358 0.6 1 1457 28901 76 21393 0.6 1 1201 20192 77 15112 0.6 1 935 14177 78 9849 0.6 1 623 9226 79 7075 0.6 1 463 6612 80 5135 0.6 1 321 4814 81 3269 0.6 1 255 3014 82 2255 0.6 1 210 2045 83 1799 0.6 1 185 1614 84 1465 0.6 1 188 1277 85 1004 0.6 1 174 830 86 904 0.6 1 163 741 87 791 0.6 1 139 652 88 705 0.6 1 175 530 89 552 0.6 1 102 450 90 463 0.6 1 86 377 91 538 0.6 1 138 400 92 462 0.6 1 67 395 93 512 0.6 1 78 434 94 636 0.6 1 65 571 95 745 0.6 1 97 648 96 1038 0.6 1 139 899 97 1476 0.6 1 157 1319 98 2024 0.6 1 99 1925 99 6470 0.6 1 61 6409 100 59392 0.6 1 74 59318 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P12-GCCAAT-READ1-Sequences.txt.gz ============================================= 42977789 sequences processed in total