SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P09-GGCTAC-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-P09-GGCTAC-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 658.81 s (20 us/read; 3.07 M reads/minute). === Summary === Total reads processed: 33,663,894 Reads with adapters: 12,083,383 (35.9%) Reads written (passing filters): 33,663,894 (100.0%) Total basepairs processed: 3,366,389,400 bp Quality-trimmed: 9,426,123 bp (0.3%) Total written (filtered): 3,318,435,852 bp (98.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12083383 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.7% C: 29.3% G: 16.9% T: 17.5% none/other: 1.6% Overview of removed sequences length count expect max.err error counts 1 8823005 8415973.5 0 8823005 2 1935482 2103993.4 0 1935482 3 560164 525998.3 0 560164 4 155471 131499.6 0 155471 5 55612 32874.9 0 55612 6 28472 8218.7 0 28472 7 23563 2054.7 0 23563 8 20676 513.7 0 20676 9 20063 128.4 0 19618 445 10 24491 32.1 1 17671 6820 11 17011 8.0 1 15815 1196 12 15801 2.0 1 14923 878 13 14619 0.5 1 13704 915 14 13589 0.5 1 12824 765 15 12866 0.5 1 12125 741 16 12144 0.5 1 11425 719 17 11491 0.5 1 10772 719 18 11197 0.5 1 10430 767 19 9377 0.5 1 8848 529 20 8950 0.5 1 8419 531 21 8200 0.5 1 7732 468 22 7504 0.5 1 7027 477 23 6672 0.5 1 6247 425 24 6154 0.5 1 5784 370 25 5735 0.5 1 5379 356 26 5188 0.5 1 4946 242 27 5059 0.5 1 4814 245 28 4775 0.5 1 4510 265 29 4313 0.5 1 4097 216 30 4261 0.5 1 4052 209 31 4039 0.5 1 3824 215 32 3617 0.5 1 3369 248 33 3095 0.5 1 2899 196 34 3114 0.5 1 2915 199 35 2796 0.5 1 2631 165 36 2751 0.5 1 2564 187 37 2489 0.5 1 2345 144 38 2320 0.5 1 2166 154 39 2046 0.5 1 1894 152 40 1929 0.5 1 1789 140 41 2127 0.5 1 2007 120 42 914 0.5 1 835 79 43 1112 0.5 1 1034 78 44 1092 0.5 1 1014 78 45 1103 0.5 1 1015 88 46 1010 0.5 1 943 67 47 1108 0.5 1 1032 76 48 1077 0.5 1 1009 68 49 1070 0.5 1 975 95 50 936 0.5 1 874 62 51 872 0.5 1 794 78 52 770 0.5 1 684 86 53 746 0.5 1 677 69 54 515 0.5 1 474 41 55 485 0.5 1 430 55 56 420 0.5 1 359 61 57 361 0.5 1 309 52 58 332 0.5 1 286 46 59 285 0.5 1 245 40 60 295 0.5 1 236 59 61 253 0.5 1 216 37 62 221 0.5 1 184 37 63 209 0.5 1 166 43 64 173 0.5 1 130 43 65 175 0.5 1 138 37 66 163 0.5 1 111 52 67 178 0.5 1 110 68 68 165 0.5 1 92 73 69 233 0.5 1 123 110 70 324 0.5 1 121 203 71 477 0.5 1 125 352 72 1126 0.5 1 138 988 73 17040 0.5 1 194 16846 74 32474 0.5 1 691 31783 75 26520 0.5 1 1042 25478 76 18551 0.5 1 796 17755 77 13125 0.5 1 615 12510 78 8612 0.5 1 422 8190 79 6065 0.5 1 266 5799 80 4411 0.5 1 209 4202 81 2933 0.5 1 173 2760 82 1986 0.5 1 136 1850 83 1549 0.5 1 120 1429 84 1255 0.5 1 132 1123 85 959 0.5 1 123 836 86 749 0.5 1 98 651 87 641 0.5 1 109 532 88 510 0.5 1 106 404 89 443 0.5 1 86 357 90 428 0.5 1 66 362 91 493 0.5 1 89 404 92 408 0.5 1 59 349 93 424 0.5 1 52 372 94 481 0.5 1 46 435 95 743 0.5 1 63 680 96 832 0.5 1 99 733 97 1320 0.5 1 115 1205 98 1751 0.5 1 79 1672 99 5815 0.5 1 38 5777 100 52437 0.5 1 64 52373 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P09-GGCTAC-READ1-Sequences.txt.gz ============================================= 33663894 sequences processed in total