SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P15-GTTTCG-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-P15-GTTTCG-READ1-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 686.87 s (20 us/read; 3.05 M reads/minute). === Summary === Total reads processed: 34,898,106 Reads with adapters: 12,716,168 (36.4%) Reads written (passing filters): 34,898,106 (100.0%) Total basepairs processed: 3,489,810,600 bp Quality-trimmed: 9,506,829 bp (0.3%) Total written (filtered): 3,432,271,892 bp (98.4%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 12716168 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 34.3% C: 27.7% G: 16.4% T: 19.4% none/other: 2.2% Overview of removed sequences length count expect max.err error counts 1 9152187 8724526.5 0 9152187 2 2045192 2181131.6 0 2045192 3 594999 545282.9 0 594999 4 157439 136320.7 0 157439 5 59760 34080.2 0 59760 6 33489 8520.0 0 33489 7 28495 2130.0 0 28495 8 25135 532.5 0 25135 9 23862 133.1 0 23449 413 10 25782 33.3 1 21743 4039 11 20460 8.3 1 19179 1281 12 19150 2.1 1 18423 727 13 17756 0.5 1 17052 704 14 16358 0.5 1 15721 637 15 16051 0.5 1 15446 605 16 14490 0.5 1 13912 578 17 13798 0.5 1 13262 536 18 13173 0.5 1 12597 576 19 11672 0.5 1 11211 461 20 10894 0.5 1 10474 420 21 9789 0.5 1 9403 386 22 8813 0.5 1 8443 370 23 7723 0.5 1 7422 301 24 7264 0.5 1 6977 287 25 6412 0.5 1 6156 256 26 6195 0.5 1 5945 250 27 5920 0.5 1 5676 244 28 5710 0.5 1 5446 264 29 5064 0.5 1 4836 228 30 4875 0.5 1 4646 229 31 4428 0.5 1 4237 191 32 4325 0.5 1 4126 199 33 3860 0.5 1 3682 178 34 3658 0.5 1 3468 190 35 3504 0.5 1 3356 148 36 3061 0.5 1 2918 143 37 2800 0.5 1 2656 144 38 2518 0.5 1 2383 135 39 2216 0.5 1 2097 119 40 2134 0.5 1 1999 135 41 1928 0.5 1 1807 121 42 1555 0.5 1 1453 102 43 2100 0.5 1 1983 117 44 803 0.5 1 754 49 45 1082 0.5 1 1024 58 46 1135 0.5 1 1067 68 47 1135 0.5 1 1060 75 48 1230 0.5 1 1152 78 49 1138 0.5 1 1064 74 50 1041 0.5 1 975 66 51 1106 0.5 1 1017 89 52 912 0.5 1 848 64 53 825 0.5 1 770 55 54 778 0.5 1 680 98 55 702 0.5 1 627 75 56 448 0.5 1 415 33 57 506 0.5 1 452 54 58 424 0.5 1 388 36 59 371 0.5 1 336 35 60 330 0.5 1 293 37 61 288 0.5 1 263 25 62 294 0.5 1 247 47 63 271 0.5 1 236 35 64 278 0.5 1 247 31 65 284 0.5 1 221 63 66 291 0.5 1 238 53 67 290 0.5 1 241 49 68 288 0.5 1 231 57 69 381 0.5 1 285 96 70 324 0.5 1 213 111 71 384 0.5 1 236 148 72 510 0.5 1 245 265 73 810 0.5 1 275 535 74 1884 0.5 1 307 1577 75 29888 0.5 1 525 29363 76 38886 0.5 1 1519 37367 77 39150 0.5 1 1810 37340 78 32701 0.5 1 1461 31240 79 19239 0.5 1 1130 18109 80 13041 0.5 1 753 12288 81 8717 0.5 1 491 8226 82 5762 0.5 1 333 5429 83 3553 0.5 1 328 3225 84 2277 0.5 1 247 2030 85 2037 0.5 1 256 1781 86 1468 0.5 1 190 1278 87 1165 0.5 1 217 948 88 969 0.5 1 182 787 89 860 0.5 1 164 696 90 720 0.5 1 130 590 91 730 0.5 1 201 529 92 628 0.5 1 112 516 93 687 0.5 1 85 602 94 792 0.5 1 94 698 95 931 0.5 1 106 825 96 1274 0.5 1 140 1134 97 1766 0.5 1 218 1548 98 2381 0.5 1 118 2263 99 8437 0.5 1 77 8360 100 71572 0.5 1 119 71453 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P15-GTTTCG-READ1-Sequences.txt.gz ============================================= 34898106 sequences processed in total