SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P11-GAGTGG-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-P11-GAGTGG-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 868.13 s (20 us/read; 3.01 M reads/minute). === Summary === Total reads processed: 43,493,444 Reads with adapters: 16,896,044 (38.8%) Reads written (passing filters): 43,493,444 (100.0%) Total basepairs processed: 4,349,344,400 bp Quality-trimmed: 17,521,483 bp (0.4%) Total written (filtered): 4,252,103,759 bp (97.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16896044 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.3% C: 25.5% G: 17.6% T: 17.5% none/other: 3.2% Overview of removed sequences length count expect max.err error counts 1 11830295 10873361.0 0 11830295 2 2725990 2718340.2 0 2725990 3 876296 679585.1 0 876296 4 243559 169896.3 0 243559 5 82882 42474.1 0 82882 6 44480 10618.5 0 44480 7 36912 2654.6 0 36912 8 33011 663.7 0 33011 9 31482 165.9 0 30418 1064 10 34474 41.5 1 28061 6413 11 27071 10.4 1 25104 1967 12 25327 2.6 1 23917 1410 13 23491 0.6 1 22278 1213 14 21624 0.6 1 20466 1158 15 21071 0.6 1 19891 1180 16 19142 0.6 1 18057 1085 17 18461 0.6 1 17460 1001 18 17398 0.6 1 16390 1008 19 15821 0.6 1 14886 935 20 14590 0.6 1 13802 788 21 13565 0.6 1 12806 759 22 12033 0.6 1 11335 698 23 11048 0.6 1 10439 609 24 10067 0.6 1 9432 635 25 9388 0.6 1 8907 481 26 8791 0.6 1 8349 442 27 8313 0.6 1 7835 478 28 7798 0.6 1 7354 444 29 7260 0.6 1 6842 418 30 7002 0.6 1 6625 377 31 6574 0.6 1 6221 353 32 6207 0.6 1 5857 350 33 5464 0.6 1 5165 299 34 5408 0.6 1 5063 345 35 5302 0.6 1 5001 301 36 4847 0.6 1 4465 382 37 5124 0.6 1 4484 640 38 4208 0.6 1 3949 259 39 3686 0.6 1 3427 259 40 3484 0.6 1 3226 258 41 3348 0.6 1 3102 246 42 2652 0.6 1 2447 205 43 3564 0.6 1 3338 226 44 1373 0.6 1 1262 111 45 2117 0.6 1 1974 143 46 2187 0.6 1 2031 156 47 2271 0.6 1 2096 175 48 2347 0.6 1 2170 177 49 2229 0.6 1 2083 146 50 2125 0.6 1 1956 169 51 2176 0.6 1 2019 157 52 1953 0.6 1 1799 154 53 1842 0.6 1 1679 163 54 1683 0.6 1 1510 173 55 1700 0.6 1 1527 173 56 1234 0.6 1 1099 135 57 1180 0.6 1 1076 104 58 1085 0.6 1 967 118 59 1060 0.6 1 950 110 60 971 0.6 1 897 74 61 874 0.6 1 792 82 62 918 0.6 1 803 115 63 769 0.6 1 664 105 64 785 0.6 1 656 129 65 922 0.6 1 674 248 66 753 0.6 1 612 141 67 702 0.6 1 578 124 68 813 0.6 1 662 151 69 827 0.6 1 673 154 70 870 0.6 1 661 209 71 944 0.6 1 641 303 72 1120 0.6 1 608 512 73 1799 0.6 1 713 1086 74 3883 0.6 1 748 3135 75 48006 0.6 1 916 47090 76 80426 0.6 1 2421 78005 77 74744 0.6 1 3327 71417 78 56889 0.6 1 2622 54267 79 37949 0.6 1 1941 36008 80 25623 0.6 1 1342 24281 81 16392 0.6 1 985 15407 82 11313 0.6 1 688 10625 83 6786 0.6 1 560 6226 84 4646 0.6 1 405 4241 85 3842 0.6 1 432 3410 86 3050 0.6 1 371 2679 87 2372 0.6 1 345 2027 88 1952 0.6 1 299 1653 89 1596 0.6 1 282 1314 90 1383 0.6 1 205 1178 91 1349 0.6 1 261 1088 92 1259 0.6 1 160 1099 93 1302 0.6 1 148 1154 94 1383 0.6 1 126 1257 95 1813 0.6 1 148 1665 96 2385 0.6 1 144 2241 97 3541 0.6 1 287 3254 98 4648 0.6 1 131 4517 99 16578 0.6 1 194 16384 100 140795 0.6 1 251 140544 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P11-GAGTGG-READ1-Sequences.txt.gz ============================================= 43493444 sequences processed in total