SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P08-CTTGTA-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-P08-CTTGTA-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 583.70 s (21 us/read; 2.93 M reads/minute). === Summary === Total reads processed: 28,467,375 Reads with adapters: 11,050,629 (38.8%) Reads written (passing filters): 28,467,375 (100.0%) Total basepairs processed: 2,846,737,500 bp Quality-trimmed: 12,975,319 bp (0.5%) Total written (filtered): 2,807,712,233 bp (98.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11050629 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 38.3% C: 23.6% G: 19.1% T: 18.4% none/other: 0.6% Overview of removed sequences length count expect max.err error counts 1 7843930 7116843.8 0 7843930 2 2002845 1779210.9 0 2002845 3 675101 444802.7 0 675101 4 164940 111200.7 0 164940 5 47683 27800.2 0 47683 6 20213 6950.0 0 20213 7 15510 1737.5 0 15510 8 13813 434.4 0 13813 9 13681 108.6 0 12978 703 10 13775 27.1 1 11820 1955 11 11846 6.8 1 10634 1212 12 10815 1.7 1 9950 865 13 9647 0.4 1 9143 504 14 10355 0.4 1 9718 637 15 7149 0.4 1 6720 429 16 7955 0.4 1 7504 451 17 9146 0.4 1 8552 594 18 5330 0.4 1 5003 327 19 7134 0.4 1 6689 445 20 5073 0.4 1 4773 300 21 5252 0.4 1 4971 281 22 4838 0.4 1 4482 356 23 4533 0.4 1 4113 420 24 4363 0.4 1 3970 393 25 3575 0.4 1 3321 254 26 3537 0.4 1 3247 290 27 3337 0.4 1 3080 257 28 3250 0.4 1 2969 281 29 3022 0.4 1 2734 288 30 3345 0.4 1 3031 314 31 2188 0.4 1 2002 186 32 2501 0.4 1 2254 247 33 2137 0.4 1 1902 235 34 2167 0.4 1 1926 241 35 1954 0.4 1 1732 222 36 1917 0.4 1 1679 238 37 1656 0.4 1 1476 180 38 1639 0.4 1 1364 275 39 1353 0.4 1 1180 173 40 1255 0.4 1 1105 150 41 1231 0.4 1 1056 175 42 1343 0.4 1 1146 197 43 798 0.4 1 693 105 44 971 0.4 1 811 160 45 1138 0.4 1 901 237 46 727 0.4 1 572 155 47 738 0.4 1 610 128 48 838 0.4 1 696 142 49 696 0.4 1 568 128 50 696 0.4 1 562 134 51 864 0.4 1 709 155 52 558 0.4 1 425 133 53 658 0.4 1 533 125 54 493 0.4 1 387 106 55 463 0.4 1 367 96 56 396 0.4 1 294 102 57 454 0.4 1 334 120 58 370 0.4 1 287 83 59 396 0.4 1 297 99 60 348 0.4 1 268 80 61 405 0.4 1 304 101 62 352 0.4 1 253 99 63 340 0.4 1 256 84 64 344 0.4 1 277 67 65 365 0.4 1 261 104 66 390 0.4 1 226 164 67 3662 0.4 1 286 3376 68 7361 0.4 1 936 6425 69 6755 0.4 1 1174 5581 70 5662 0.4 1 1029 4633 71 3537 0.4 1 806 2731 72 2329 0.4 1 613 1716 73 1288 0.4 1 368 920 74 791 0.4 1 216 575 75 608 0.4 1 195 413 76 362 0.4 1 135 227 77 356 0.4 1 141 215 78 314 0.4 1 124 190 79 331 0.4 1 141 190 80 290 0.4 1 118 172 81 278 0.4 1 122 156 82 264 0.4 1 126 138 83 346 0.4 1 130 216 84 257 0.4 1 113 144 85 285 0.4 1 139 146 86 267 0.4 1 122 145 87 275 0.4 1 136 139 88 304 0.4 1 172 132 89 260 0.4 1 72 188 90 264 0.4 1 74 190 91 389 0.4 1 133 256 92 341 0.4 1 100 241 93 352 0.4 1 59 293 94 453 0.4 1 51 402 95 674 0.4 1 73 601 96 1087 0.4 1 85 1002 97 1655 0.4 1 151 1504 98 2148 0.4 1 78 2070 99 5527 0.4 1 28 5499 100 31425 0.4 1 64 31361 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P08-CTTGTA-READ2-Sequences.txt.gz ============================================= 28467375 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 28467375 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 144330 (0.51%)