SUMMARISING RUN PARAMETERS ========================== Input filename: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P07-AGTCAA-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-P07-AGTCAA-READ2-Sequences.txt.gz Running on 1 core Trimming 1 adapter with at most 10.0% errors in single-end mode ... Finished in 535.66 s (21 us/read; 2.92 M reads/minute). === Summary === Total reads processed: 26,060,601 Reads with adapters: 10,098,285 (38.7%) Reads written (passing filters): 26,060,601 (100.0%) Total basepairs processed: 2,606,060,100 bp Quality-trimmed: 11,087,610 bp (0.4%) Total written (filtered): 2,568,463,082 bp (98.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10098285 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 37.6% C: 24.2% G: 19.3% T: 18.1% none/other: 0.9% Overview of removed sequences length count expect max.err error counts 1 7082217 6515150.2 0 7082217 2 1835190 1628787.6 0 1835190 3 619784 407196.9 0 619784 4 158005 101799.2 0 158005 5 48398 25449.8 0 48398 6 23278 6362.5 0 23278 7 17688 1590.6 0 17688 8 15946 397.7 0 15946 9 15791 99.4 0 15056 735 10 15002 24.9 1 13434 1568 11 13002 6.2 1 12082 920 12 12117 1.6 1 11476 641 13 10394 0.4 1 9881 513 14 11738 0.4 1 11191 547 15 8285 0.4 1 7889 396 16 8755 0.4 1 8320 435 17 10024 0.4 1 9579 445 18 6099 0.4 1 5848 251 19 7641 0.4 1 7257 384 20 5534 0.4 1 5266 268 21 5721 0.4 1 5439 282 22 4854 0.4 1 4526 328 23 4735 0.4 1 4422 313 24 4519 0.4 1 4189 330 25 3675 0.4 1 3474 201 26 3630 0.4 1 3379 251 27 3573 0.4 1 3341 232 28 3250 0.4 1 3015 235 29 3006 0.4 1 2798 208 30 3323 0.4 1 3074 249 31 2303 0.4 1 2106 197 32 2487 0.4 1 2305 182 33 2151 0.4 1 2000 151 34 2123 0.4 1 1946 177 35 1929 0.4 1 1761 168 36 1907 0.4 1 1735 172 37 1666 0.4 1 1508 158 38 1557 0.4 1 1388 169 39 1253 0.4 1 1138 115 40 1153 0.4 1 1039 114 41 1201 0.4 1 1057 144 42 1268 0.4 1 1113 155 43 796 0.4 1 697 99 44 936 0.4 1 800 136 45 964 0.4 1 828 136 46 646 0.4 1 545 101 47 712 0.4 1 615 97 48 730 0.4 1 632 98 49 654 0.4 1 559 95 50 694 0.4 1 602 92 51 785 0.4 1 660 125 52 528 0.4 1 429 99 53 523 0.4 1 452 71 54 428 0.4 1 376 52 55 421 0.4 1 346 75 56 449 0.4 1 369 80 57 395 0.4 1 307 88 58 345 0.4 1 270 75 59 325 0.4 1 258 67 60 397 0.4 1 296 101 61 339 0.4 1 257 82 62 349 0.4 1 252 97 63 272 0.4 1 202 70 64 316 0.4 1 240 76 65 319 0.4 1 229 90 66 388 0.4 1 191 197 67 5712 0.4 1 237 5475 68 7455 0.4 1 958 6497 69 7822 0.4 1 734 7088 70 8211 0.4 1 909 7302 71 4854 0.4 1 836 4018 72 3418 0.4 1 618 2800 73 2398 0.4 1 399 1999 74 1497 0.4 1 367 1130 75 954 0.4 1 262 692 76 636 0.4 1 155 481 77 595 0.4 1 168 427 78 467 0.4 1 132 335 79 384 0.4 1 145 239 80 358 0.4 1 133 225 81 293 0.4 1 111 182 82 287 0.4 1 113 174 83 304 0.4 1 113 191 84 247 0.4 1 115 132 85 230 0.4 1 105 125 86 251 0.4 1 108 143 87 279 0.4 1 103 176 88 288 0.4 1 119 169 89 275 0.4 1 72 203 90 304 0.4 1 88 216 91 405 0.4 1 100 305 92 273 0.4 1 54 219 93 313 0.4 1 45 268 94 366 0.4 1 34 332 95 546 0.4 1 54 492 96 811 0.4 1 58 753 97 1428 0.4 1 132 1296 98 1865 0.4 1 67 1798 99 5154 0.4 1 27 5127 100 40722 0.4 1 73 40649 RUN STATISTICS FOR INPUT FILE: /mnt/data/coral_RNAseq_2017/porites/4R041-L7-P07-AGTCAA-READ2-Sequences.txt.gz ============================================= 26060601 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 26060601 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 153969 (0.59%)