SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/merged_raw_data/RRBS20A040874_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 1 sequences will be trimmed by 3 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 3 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/tmp/8ca7969c-d1de-11eb-8a1c-f8f21e2f3ee9/trimmed/RRBS20A040874_val_2.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1350.07 s (36 us/read; 1.65 M reads/minute). === Summary === Total reads processed: 37,064,926 Reads with adapters: 24,872,469 (67.1%) Reads written (passing filters): 37,064,926 (100.0%) Total basepairs processed: 2,806,835,573 bp Total written (filtered): 2,735,629,988 bp (97.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24872469 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 4.2% C: 94.8% G: 0.2% T: 0.8% 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 24412578 9266231.5 0 24412578 2 9398 2316557.9 0 9398 3 13403 579139.5 0 13403 4 8088 144784.9 0 8088 5 2503 36196.2 0 2503 6 1324 9049.1 0 1324 7 1623 2262.3 0 1623 8 4162 565.6 0 4162 9 1478 141.4 0 1472 6 10 1333 35.3 1 395 938 11 527 8.8 1 95 432 12 499 2.2 1 121 378 13 1887 0.6 1 274 1613 14 1485 0.6 1 235 1250 15 928 0.6 1 130 798 16 1279 0.6 1 155 1124 17 1477 0.6 1 196 1281 18 776 0.6 1 121 655 19 1925 0.6 1 284 1641 20 2275 0.6 1 362 1913 21 119 0.6 1 20 99 22 137 0.6 1 16 121 23 1696 0.6 1 203 1493 24 3186 0.6 1 511 2675 25 2323 0.6 1 377 1946 26 4932 0.6 1 799 4133 27 1457 0.6 1 274 1183 28 421 0.6 1 69 352 29 222 0.6 1 21 201 30 250 0.6 1 37 213 31 2136 0.6 1 332 1804 32 1822 0.6 1 261 1561 33 6992 0.6 1 1060 5932 34 722 0.6 1 77 645 35 314 0.6 1 35 279 36 377 0.6 1 41 336 37 2858 0.6 1 372 2486 38 538 0.6 1 73 465 39 894 0.6 1 126 768 40 914 0.6 1 118 796 41 899 0.6 1 121 778 42 1769 0.6 1 285 1484 43 1296 0.6 1 171 1125 44 1728 0.6 1 252 1476 45 3295 0.6 1 446 2849 46 2127 0.6 1 287 1840 47 422 0.6 1 41 381 48 1096 0.6 1 159 937 49 1158 0.6 1 154 1004 50 2315 0.6 1 252 2063 51 1765 0.6 1 224 1541 52 1305 0.6 1 136 1169 53 276 0.6 1 42 234 54 1587 0.6 1 181 1406 55 869 0.6 1 98 771 56 216 0.6 1 22 194 57 873 0.6 1 111 762 58 1933 0.6 1 218 1715 59 1337 0.6 1 148 1189 60 1585 0.6 1 208 1377 61 1894 0.6 1 211 1683 62 2745 0.6 1 385 2360 63 3675 0.6 1 482 3193 64 1666 0.6 1 195 1471 65 494 0.6 1 61 433 66 784 0.6 1 91 693 67 949 0.6 1 113 836 68 1056 0.6 1 109 947 69 1562 0.6 1 229 1333 70 1909 0.6 1 327 1582 71 1813 0.6 1 328 1485 72 1625 0.6 1 244 1381 73 1798 0.6 1 234 1564 74 1905 0.6 1 290 1615 75 2428 0.6 1 376 2052 76 1740 0.6 1 218 1522 77 1512 0.6 1 133 1379 78 1398 0.6 1 153 1245 79 1730 0.6 1 214 1516 80 1450 0.6 1 167 1283 81 1805 0.6 1 267 1538 82 2474 0.6 1 509 1965 83 1881 0.6 1 262 1619 84 1646 0.6 1 190 1456 85 1793 0.6 1 212 1581 86 1174 0.6 1 152 1022 87 993 0.6 1 113 880 88 1282 0.6 1 179 1103 89 1042 0.6 1 68 974 90 638 0.6 1 30 608 91 746 0.6 1 78 668 92 544 0.6 1 43 501 93 576 0.6 1 46 530 94 555 0.6 1 51 504 95 301 0.6 1 17 284 96 360 0.6 1 25 335 97 361 0.6 1 26 335 98 236 0.6 1 17 219 99 239 0.6 1 17 222 100 229 0.6 1 13 216 101 217 0.6 1 20 197 102 241 0.6 1 15 226 103 210 0.6 1 20 190 104 183 0.6 1 17 166 105 158 0.6 1 15 143 106 88 0.6 1 11 77 107 122 0.6 1 15 107 108 116 0.6 1 23 93 109 217 0.6 1 24 193 110 168 0.6 1 21 147 111 44 0.6 1 10 34 112 16 0.6 1 3 13 113 2 0.6 1 0 2 114 8 0.6 1 2 6 115 3 0.6 1 2 1 116 3 0.6 1 1 2 117 2 0.6 1 1 1 118 1 0.6 1 1 119 3 0.6 1 3 120 1 0.6 1 0 1 121 2 0.6 1 1 1 124 2 0.6 1 2 125 1 0.6 1 1 126 1 0.6 1 1 127 2 0.6 1 2 128 5 0.6 1 5 129 2 0.6 1 1 1 130 1 0.6 1 1 131 6 0.6 1 6 132 7 0.6 1 7 133 6 0.6 1 6 134 8 0.6 1 7 1 135 29 0.6 1 28 1 136 39 0.6 1 37 2 137 7071 0.6 1 6954 117 138 281367 0.6 1 279376 1991 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/merged_raw_data/RRBS20A040874_val_2.fq.gz ============================================= 37064926 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 967530 (2.6%) 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: 37064926 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 471620 (1.27%)