SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P07-ATGTCA-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/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-P07-ATGTCA-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 598.43 s (21 us/read; 2.92 M reads/minute). === Summary === Total reads processed: 29,165,404 Reads with adapters: 11,128,889 (38.2%) Reads written (passing filters): 29,165,404 (100.0%) Total basepairs processed: 2,916,540,400 bp Quality-trimmed: 11,398,778 bp (0.4%) Total written (filtered): 2,879,912,003 bp (98.7%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11128889 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 36.8% C: 25.9% G: 20.4% T: 16.6% none/other: 0.3% Overview of removed sequences length count expect max.err error counts 1 7793155 7291351.0 0 7793155 2 2046903 1822837.8 0 2046903 3 674975 455709.4 0 674975 4 172783 113927.4 0 172783 5 53579 28481.8 0 53579 6 27651 7120.5 0 27651 7 22354 1780.1 0 22354 8 19418 445.0 0 19418 9 19528 111.3 0 18596 932 10 18769 27.8 1 16680 2089 11 16751 7.0 1 15204 1547 12 15902 1.7 1 14816 1086 13 13640 0.4 1 12781 859 14 15332 0.4 1 14317 1015 15 10814 0.4 1 10082 732 16 11500 0.4 1 10772 728 17 13543 0.4 1 12644 899 18 8085 0.4 1 7518 567 19 10624 0.4 1 9896 728 20 7594 0.4 1 7044 550 21 7659 0.4 1 7220 439 22 7113 0.4 1 6673 440 23 6427 0.4 1 5978 449 24 6384 0.4 1 5901 483 25 5114 0.4 1 4772 342 26 5178 0.4 1 4824 354 27 5041 0.4 1 4709 332 28 4675 0.4 1 4353 322 29 4337 0.4 1 4069 268 30 4950 0.4 1 4604 346 31 3315 0.4 1 3101 214 32 3718 0.4 1 3449 269 33 3113 0.4 1 2882 231 34 3015 0.4 1 2805 210 35 2669 0.4 1 2486 183 36 2662 0.4 1 2449 213 37 2276 0.4 1 2082 194 38 2163 0.4 1 1972 191 39 1964 0.4 1 1813 151 40 1730 0.4 1 1565 165 41 1720 0.4 1 1512 208 42 1639 0.4 1 1462 177 43 1184 0.4 1 1065 119 44 1298 0.4 1 1137 161 45 1361 0.4 1 1195 166 46 910 0.4 1 795 115 47 977 0.4 1 861 116 48 1157 0.4 1 995 162 49 969 0.4 1 865 104 50 995 0.4 1 861 134 51 1174 0.4 1 993 181 52 751 0.4 1 641 110 53 784 0.4 1 640 144 54 589 0.4 1 497 92 55 553 0.4 1 417 136 56 567 0.4 1 466 101 57 508 0.4 1 417 91 58 397 0.4 1 318 79 59 476 0.4 1 392 84 60 459 0.4 1 356 103 61 428 0.4 1 334 94 62 436 0.4 1 311 125 63 413 0.4 1 302 111 64 425 0.4 1 297 128 65 400 0.4 1 291 109 66 483 0.4 1 305 178 67 2404 0.4 1 322 2082 68 4434 0.4 1 1684 2750 69 4295 0.4 1 1326 2969 70 4156 0.4 1 1489 2667 71 3589 0.4 1 1487 2102 72 2454 0.4 1 1056 1398 73 1818 0.4 1 842 976 74 1258 0.4 1 632 626 75 864 0.4 1 428 436 76 520 0.4 1 254 266 77 524 0.4 1 278 246 78 415 0.4 1 224 191 79 362 0.4 1 191 171 80 337 0.4 1 197 140 81 412 0.4 1 230 182 82 353 0.4 1 228 125 83 345 0.4 1 219 126 84 316 0.4 1 197 119 85 339 0.4 1 187 152 86 335 0.4 1 204 131 87 365 0.4 1 203 162 88 410 0.4 1 246 164 89 336 0.4 1 184 152 90 323 0.4 1 134 189 91 354 0.4 1 138 216 92 221 0.4 1 81 140 93 251 0.4 1 65 186 94 277 0.4 1 66 211 95 466 0.4 1 132 334 96 599 0.4 1 120 479 97 970 0.4 1 232 738 98 940 0.4 1 139 801 99 1946 0.4 1 42 1904 100 14445 0.4 1 65 14380 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/montipora/4R041-L6-P07-ATGTCA-READ2-Sequences.txt.gz ============================================= 29165404 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 29165404 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 109175 (0.37%)