SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2//RRBS21T000231_val_2.fq.gz Trimming mode: paired-end Trim Galore version: 0.6.2 Cutadapt version: 2.6 Number of cores used for trimming: 1 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 File was specified to be an MspI-digested RRBS sample. Read 1 sequences with adapter contamination will be trimmed a further 2 bp from their 3' end, and Read 2 sequences will be trimmed by 2 bp from their 5' end to remove potential methylation-biased bases from the end-repair reaction All Read 2 sequences will be trimmed by 2 bp from their 5' end to avoid poor qualities or biases (e.g. M-bias for BS-Seq applications) Output file will be GZIP compressed This is cutadapt 2.6 with Python 3.6.7 Command line parameters: -j 1 -e 0.1 -O 1 -a AGATCGGAAGAGC /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/test_analysis_2/tmp/429dfac2-e7c4-11eb-b765-6c92bfc39756/trimmed/RRBS21T000231_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 828.42 s (19 us/read; 3.22 M reads/minute). === Summary === Total reads processed: 44,418,673 Reads with adapters: 23,286,452 (52.4%) Reads written (passing filters): 44,418,673 (100.0%) Total basepairs processed: 3,926,937,738 bp Total written (filtered): 3,770,216,257 bp (96.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 23286452 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 4.9% C: 93.7% G: 0.2% T: 1.2% none/other: 0.0% WARNING: The adapter is preceded by "C" extremely often. The provided adapter sequence could be incomplete at its 3' end. Overview of removed sequences length count expect max.err error counts 1 22207229 11104668.2 0 22207229 2 38302 2776167.1 0 38302 3 10598 694041.8 0 10598 4 9853 173510.4 0 9853 5 2519 43377.6 0 2519 6 1469 10844.4 0 1469 7 1933 2711.1 0 1933 8 1369 677.8 0 1369 9 819 169.4 0 769 50 10 5430 42.4 1 1483 3947 11 225 10.6 1 31 194 12 589 2.6 1 75 514 13 981 0.7 1 86 895 14 1108 0.7 1 84 1024 15 419 0.7 1 33 386 16 1013 0.7 1 89 924 17 1360 0.7 1 114 1246 18 476 0.7 1 35 441 19 1380 0.7 1 92 1288 20 1081 0.7 1 80 1001 21 135 0.7 1 25 110 22 282 0.7 1 16 266 23 1082 0.7 1 60 1022 24 3129 0.7 1 200 2929 25 985 0.7 1 75 910 26 1110 0.7 1 69 1041 27 510 0.7 1 50 460 28 876 0.7 1 83 793 29 199 0.7 1 13 186 30 676 0.7 1 39 637 31 407 0.7 1 29 378 32 1444 0.7 1 128 1316 33 1151 0.7 1 84 1067 34 425 0.7 1 36 389 35 935 0.7 1 63 872 36 738 0.7 1 36 702 37 662 0.7 1 35 627 38 502 0.7 1 30 472 39 563 0.7 1 44 519 40 459 0.7 1 30 429 41 689 0.7 1 28 661 42 854 0.7 1 52 802 43 616 0.7 1 48 568 44 619 0.7 1 38 581 45 900 0.7 1 60 840 46 614 0.7 1 36 578 47 549 0.7 1 36 513 48 1104 0.7 1 77 1027 49 813 0.7 1 45 768 50 408 0.7 1 20 388 51 807 0.7 1 50 757 52 1015 0.7 1 59 956 53 810 0.7 1 50 760 54 743 0.7 1 63 680 55 633 0.7 1 41 592 56 480 0.7 1 34 446 57 753 0.7 1 54 699 58 458 0.7 1 26 432 59 410 0.7 1 32 378 60 346 0.7 1 17 329 61 285 0.7 1 14 271 62 285 0.7 1 23 262 63 256 0.7 1 16 240 64 312 0.7 1 20 292 65 385 0.7 1 22 363 66 727 0.7 1 49 678 67 447 0.7 1 33 414 68 364 0.7 1 26 338 69 375 0.7 1 21 354 70 431 0.7 1 27 404 71 463 0.7 1 35 428 72 491 0.7 1 27 464 73 429 0.7 1 24 405 74 392 0.7 1 37 355 75 665 0.7 1 20 645 76 574 0.7 1 50 524 77 344 0.7 1 12 332 78 227 0.7 1 7 220 79 256 0.7 1 9 247 80 176 0.7 1 16 160 81 198 0.7 1 10 188 82 208 0.7 1 13 195 83 208 0.7 1 9 199 84 248 0.7 1 19 229 85 221 0.7 1 17 204 86 130 0.7 1 8 122 87 130 0.7 1 7 123 88 118 0.7 1 6 112 89 119 0.7 1 6 113 90 120 0.7 1 10 110 91 99 0.7 1 6 93 92 88 0.7 1 7 81 93 123 0.7 1 11 112 94 81 0.7 1 7 74 95 59 0.7 1 1 58 96 64 0.7 1 5 59 97 56 0.7 1 4 52 98 65 0.7 1 7 58 99 91 0.7 1 3 88 100 59 0.7 1 3 56 101 31 0.7 1 4 27 102 51 0.7 1 6 45 103 32 0.7 1 0 32 104 31 0.7 1 2 29 105 21 0.7 1 4 17 106 21 0.7 1 0 21 107 17 0.7 1 2 15 108 19 0.7 1 1 18 109 29 0.7 1 1 28 110 21 0.7 1 2 19 111 3 0.7 1 2 1 112 3 0.7 1 1 2 113 4 0.7 1 1 3 114 13 0.7 1 2 11 116 2 0.7 1 2 117 1 0.7 1 0 1 118 2 0.7 1 1 1 119 6 0.7 1 1 5 120 2 0.7 1 2 121 2 0.7 1 2 122 6 0.7 1 4 2 123 2 0.7 1 2 125 5 0.7 1 4 1 127 8 0.7 1 6 2 128 13 0.7 1 12 1 129 10 0.7 1 10 130 11 0.7 1 11 131 12 0.7 1 11 1 132 14 0.7 1 14 133 32 0.7 1 31 1 134 61 0.7 1 58 3 135 175 0.7 1 166 9 136 311 0.7 1 294 17 137 12456 0.7 1 12220 236 138 944612 0.7 1 932657 11955 WARNING: One or more of your adapter sequences may be incomplete. Please see the detailed output above. RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2//RRBS21T000231_val_2.fq.gz ============================================= 44418673 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 1606285 (3.6%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 0 (0.0%) Total number of sequences analysed for the sequence pair length validation: 44418673 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 1013833 (2.28%)