SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P14-GTGGCC-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-P14-GTGGCC-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 668.44 s (21 us/read; 2.85 M reads/minute). === Summary === Total reads processed: 31,778,548 Reads with adapters: 12,209,152 (38.4%) Reads written (passing filters): 31,778,548 (100.0%) Total basepairs processed: 3,177,854,800 bp Quality-trimmed: 15,060,724 bp (0.5%) Total written (filtered): 3,138,823,875 bp (98.8%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12209152 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.8% C: 24.8% G: 19.3% T: 17.9% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 8724358 7944637.0 0 8724358 2 2259557 1986159.2 0 2259557 3 752730 496539.8 0 752730 4 177780 124135.0 0 177780 5 46891 31033.7 0 46891 6 18028 7758.4 0 18028 7 12788 1939.6 0 12788 8 10845 484.9 0 10845 9 11251 121.2 0 10156 1095 10 11414 30.3 1 9512 1902 11 9461 7.6 1 8318 1143 12 8806 1.9 1 8032 774 13 7715 0.5 1 7228 487 14 8638 0.5 1 8061 577 15 5911 0.5 1 5552 359 16 6552 0.5 1 6177 375 17 7620 0.5 1 7079 541 18 4543 0.5 1 4267 276 19 6100 0.5 1 5714 386 20 4265 0.5 1 3974 291 21 4365 0.5 1 4097 268 22 4188 0.5 1 3837 351 23 3943 0.5 1 3564 379 24 3939 0.5 1 3564 375 25 3240 0.5 1 2968 272 26 3225 0.5 1 2921 304 27 3089 0.5 1 2783 306 28 2978 0.5 1 2663 315 29 2698 0.5 1 2427 271 30 3236 0.5 1 2889 347 31 2048 0.5 1 1851 197 32 2417 0.5 1 2130 287 33 1979 0.5 1 1781 198 34 2079 0.5 1 1822 257 35 1879 0.5 1 1650 229 36 1847 0.5 1 1602 245 37 1708 0.5 1 1484 224 38 1594 0.5 1 1324 270 39 1358 0.5 1 1184 174 40 1243 0.5 1 1084 159 41 1200 0.5 1 1006 194 42 1383 0.5 1 1147 236 43 851 0.5 1 736 115 44 1015 0.5 1 847 168 45 1248 0.5 1 1036 212 46 740 0.5 1 596 144 47 797 0.5 1 675 122 48 904 0.5 1 774 130 49 811 0.5 1 653 158 50 825 0.5 1 681 144 51 1045 0.5 1 814 231 52 639 0.5 1 492 147 53 640 0.5 1 514 126 54 551 0.5 1 444 107 55 512 0.5 1 409 103 56 500 0.5 1 386 114 57 491 0.5 1 367 124 58 430 0.5 1 334 96 59 421 0.5 1 314 107 60 441 0.5 1 335 106 61 525 0.5 1 417 108 62 445 0.5 1 304 141 63 440 0.5 1 323 117 64 423 0.5 1 313 110 65 440 0.5 1 313 127 66 395 0.5 1 264 131 67 2087 0.5 1 342 1745 68 3800 0.5 1 1539 2261 69 3538 0.5 1 1222 2316 70 3501 0.5 1 1269 2232 71 2701 0.5 1 1204 1497 72 1899 0.5 1 878 1021 73 1379 0.5 1 671 708 74 1004 0.5 1 532 472 75 708 0.5 1 365 343 76 477 0.5 1 262 215 77 436 0.5 1 223 213 78 323 0.5 1 173 150 79 314 0.5 1 183 131 80 323 0.5 1 184 139 81 307 0.5 1 203 104 82 282 0.5 1 180 102 83 297 0.5 1 172 125 84 244 0.5 1 141 103 85 273 0.5 1 158 115 86 312 0.5 1 188 124 87 365 0.5 1 209 156 88 301 0.5 1 180 121 89 263 0.5 1 111 152 90 288 0.5 1 127 161 91 351 0.5 1 170 181 92 229 0.5 1 81 148 93 228 0.5 1 58 170 94 263 0.5 1 58 205 95 347 0.5 1 80 267 96 430 0.5 1 102 328 97 795 0.5 1 209 586 98 761 0.5 1 105 656 99 1681 0.5 1 20 1661 100 12227 0.5 1 48 12179 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P14-GTGGCC-READ2-Sequences.txt.gz ============================================= 31778548 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 31778548 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 121684 (0.38%)