SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P09-GTGAAA-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/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-P09-GTGAAA-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 438.18 s (20 us/read; 3.03 M reads/minute). === Summary === Total reads processed: 22,109,558 Reads with adapters: 8,247,591 (37.3%) Reads written (passing filters): 22,109,558 (100.0%) Total basepairs processed: 2,210,955,800 bp Quality-trimmed: 5,902,900 bp (0.3%) Total written (filtered): 2,173,134,278 bp (98.3%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 8247591 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 33.9% C: 27.9% G: 16.5% T: 19.5% none/other: 2.1% Overview of removed sequences length count expect max.err error counts 1 5955682 5527389.5 0 5955682 2 1269050 1381847.4 0 1269050 3 390312 345461.8 0 390312 4 103756 86365.5 0 103756 5 40343 21591.4 0 40343 6 24754 5397.8 0 24754 7 20960 1349.5 0 20960 8 19145 337.4 0 19145 9 18793 84.3 0 18534 259 10 17958 21.1 1 15344 2614 11 16459 5.3 1 15671 788 12 14566 1.3 1 14025 541 13 13253 0.3 1 12704 549 14 12626 0.3 1 12078 548 15 11394 0.3 1 10934 460 16 11099 0.3 1 10633 466 17 10373 0.3 1 9936 437 18 9797 0.3 1 9389 408 19 8527 0.3 1 8195 332 20 7784 0.3 1 7511 273 21 7409 0.3 1 7093 316 22 6111 0.3 1 5861 250 23 5553 0.3 1 5308 245 24 5685 0.3 1 5428 257 25 5055 0.3 1 4867 188 26 4473 0.3 1 4286 187 27 4373 0.3 1 4163 210 28 4116 0.3 1 3929 187 29 3837 0.3 1 3640 197 30 3485 0.3 1 3336 149 31 3342 0.3 1 3181 161 32 2943 0.3 1 2802 141 33 2706 0.3 1 2576 130 34 2634 0.3 1 2481 153 35 2398 0.3 1 2282 116 36 2191 0.3 1 2088 103 37 1970 0.3 1 1870 100 38 1835 0.3 1 1739 96 39 1581 0.3 1 1497 84 40 1568 0.3 1 1479 89 41 1194 0.3 1 1134 60 42 1142 0.3 1 1094 48 43 1924 0.3 1 1844 80 44 406 0.3 1 370 36 45 590 0.3 1 540 50 46 760 0.3 1 677 83 47 773 0.3 1 713 60 48 858 0.3 1 801 57 49 762 0.3 1 706 56 50 687 0.3 1 625 62 51 722 0.3 1 661 61 52 591 0.3 1 550 41 53 554 0.3 1 514 40 54 469 0.3 1 410 59 55 420 0.3 1 384 36 56 301 0.3 1 275 26 57 293 0.3 1 274 19 58 253 0.3 1 222 31 59 266 0.3 1 225 41 60 317 0.3 1 222 95 61 276 0.3 1 191 85 62 216 0.3 1 155 61 63 191 0.3 1 150 41 64 191 0.3 1 157 34 65 202 0.3 1 149 53 66 183 0.3 1 120 63 67 205 0.3 1 157 48 68 152 0.3 1 108 44 69 245 0.3 1 188 57 70 232 0.3 1 148 84 71 202 0.3 1 145 57 72 254 0.3 1 133 121 73 448 0.3 1 196 252 74 712 0.3 1 166 546 75 11435 0.3 1 392 11043 76 14350 0.3 1 533 13817 77 12804 0.3 1 693 12111 78 11532 0.3 1 499 11033 79 7997 0.3 1 547 7450 80 6300 0.3 1 398 5902 81 4898 0.3 1 280 4618 82 3716 0.3 1 253 3463 83 2772 0.3 1 287 2485 84 2136 0.3 1 225 1911 85 1915 0.3 1 220 1695 86 1650 0.3 1 229 1421 87 1442 0.3 1 208 1234 88 1240 0.3 1 191 1049 89 1194 0.3 1 128 1066 90 1136 0.3 1 130 1006 91 1086 0.3 1 169 917 92 1039 0.3 1 127 912 93 1052 0.3 1 82 970 94 1329 0.3 1 89 1240 95 1437 0.3 1 88 1349 96 1907 0.3 1 110 1797 97 2695 0.3 1 184 2511 98 3788 0.3 1 85 3703 99 10510 0.3 1 67 10443 100 69344 0.3 1 105 69239 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P09-GTGAAA-READ1-Sequences.txt.gz ============================================= 22109558 sequences processed in total