SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P14-GTGGCC-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-P14-GTGGCC-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 624.32 s (20 us/read; 3.05 M reads/minute). === Summary === Total reads processed: 31,778,548 Reads with adapters: 10,990,256 (34.6%) Reads written (passing filters): 31,778,548 (100.0%) Total basepairs processed: 3,177,854,800 bp Quality-trimmed: 2,902,895 bp (0.1%) Total written (filtered): 3,153,950,683 bp (99.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10990256 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.2% C: 28.9% G: 16.7% T: 20.0% none/other: 0.2% Overview of removed sequences length count expect max.err error counts 1 8239701 7944637.0 0 8239701 2 1838601 1986159.2 0 1838601 3 511440 496539.8 0 511440 4 133720 124135.0 0 133720 5 41126 31033.7 0 41126 6 16026 7758.4 0 16026 7 12186 1939.6 0 12186 8 10453 484.9 0 10453 9 10231 121.2 0 9721 510 10 10797 30.3 1 9228 1569 11 8654 7.6 1 8035 619 12 7980 1.9 1 7663 317 13 7630 0.5 1 7326 304 14 6948 0.5 1 6657 291 15 6658 0.5 1 6384 274 16 6216 0.5 1 5991 225 17 5860 0.5 1 5602 258 18 5786 0.5 1 5570 216 19 5014 0.5 1 4806 208 20 4669 0.5 1 4440 229 21 4176 0.5 1 3998 178 22 3887 0.5 1 3699 188 23 3524 0.5 1 3357 167 24 3302 0.5 1 3166 136 25 3112 0.5 1 2964 148 26 2854 0.5 1 2714 140 27 2729 0.5 1 2598 131 28 2581 0.5 1 2459 122 29 2393 0.5 1 2267 126 30 2404 0.5 1 2292 112 31 2189 0.5 1 2107 82 32 2031 0.5 1 1933 98 33 1751 0.5 1 1664 87 34 1747 0.5 1 1670 77 35 1614 0.5 1 1547 67 36 1483 0.5 1 1405 78 37 1430 0.5 1 1350 80 38 1368 0.5 1 1267 101 39 1152 0.5 1 1096 56 40 1109 0.5 1 1047 62 41 865 0.5 1 832 33 42 878 0.5 1 817 61 43 1070 0.5 1 1015 55 44 529 0.5 1 483 46 45 635 0.5 1 589 46 46 642 0.5 1 573 69 47 679 0.5 1 633 46 48 612 0.5 1 582 30 49 616 0.5 1 579 37 50 595 0.5 1 556 39 51 543 0.5 1 491 52 52 490 0.5 1 450 40 53 483 0.5 1 444 39 54 406 0.5 1 379 27 55 410 0.5 1 383 27 56 265 0.5 1 235 30 57 324 0.5 1 282 42 58 274 0.5 1 234 40 59 274 0.5 1 232 42 60 279 0.5 1 225 54 61 274 0.5 1 245 29 62 255 0.5 1 210 45 63 236 0.5 1 202 34 64 252 0.5 1 225 27 65 241 0.5 1 205 36 66 247 0.5 1 203 44 67 270 0.5 1 233 37 68 261 0.5 1 234 27 69 257 0.5 1 208 49 70 331 0.5 1 281 50 71 300 0.5 1 251 49 72 344 0.5 1 281 63 73 386 0.5 1 289 97 74 527 0.5 1 338 189 75 3132 0.5 1 521 2611 76 5554 0.5 1 1784 3770 77 5991 0.5 1 2454 3537 78 4359 0.5 1 1685 2674 79 2845 0.5 1 1274 1571 80 1946 0.5 1 850 1096 81 1319 0.5 1 603 716 82 929 0.5 1 417 512 83 641 0.5 1 335 306 84 437 0.5 1 265 172 85 392 0.5 1 240 152 86 426 0.5 1 284 142 87 388 0.5 1 270 118 88 341 0.5 1 249 92 89 221 0.5 1 151 70 90 241 0.5 1 171 70 91 282 0.5 1 214 68 92 180 0.5 1 134 46 93 177 0.5 1 119 58 94 194 0.5 1 122 72 95 233 0.5 1 139 94 96 263 0.5 1 147 116 97 468 0.5 1 300 168 98 392 0.5 1 166 226 99 822 0.5 1 50 772 100 6501 0.5 1 80 6421 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P14-GTGGCC-READ1-Sequences.txt.gz ============================================= 31778548 sequences processed in total