SUMMARISING RUN PARAMETERS ========================== Input filename: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2/RRBS21T000219_val_1.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/4287720c-e7c4-11eb-b332-6c92bfc12f0e/trimmed/RRBS21T000219_val_1.fq.gz_qual_trimmed.fastq Processing reads on 1 core in single-end mode ... Finished in 1192.20 s (20 us/read; 3.01 M reads/minute). === Summary === Total reads processed: 59,821,506 Reads with adapters: 24,463,725 (40.9%) Reads written (passing filters): 59,821,506 (100.0%) Total basepairs processed: 5,751,757,172 bp Total written (filtered): 5,303,573,284 bp (92.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 24463725 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 26.2% C: 0.8% G: 22.0% T: 51.0% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 15247200 14955376.5 0 15247200 2 3891594 3738844.1 0 3891594 3 1496692 934711.0 0 1496692 4 379479 233677.8 0 379479 5 22086 58419.4 0 22086 6 12876 14604.9 0 12876 7 12604 3651.2 0 12604 8 10417 912.8 0 10417 9 15060 228.2 0 14182 878 10 17820 57.1 1 8022 9798 11 11421 14.3 1 1193 10228 12 4860 3.6 1 665 4195 13 4715 0.9 1 574 4141 14 10385 0.9 1 1363 9022 15 5897 0.9 1 771 5126 16 22080 0.9 1 2548 19532 17 21600 0.9 1 2890 18710 18 17067 0.9 1 6943 10124 19 387 0.9 1 48 339 20 4868 0.9 1 707 4161 21 187 0.9 1 17 170 22 837 0.9 1 119 718 23 4473 0.9 1 554 3919 24 19202 0.9 1 2508 16694 25 7596 0.9 1 1032 6564 26 1385 0.9 1 142 1243 27 5759 0.9 1 720 5039 28 12161 0.9 1 1613 10548 29 12961 0.9 1 1501 11460 30 3592 0.9 1 504 3088 31 447 0.9 1 28 419 32 4738 0.9 1 585 4153 33 8704 0.9 1 992 7712 34 10618 0.9 1 1272 9346 35 18071 0.9 1 2039 16032 36 4610 0.9 1 612 3998 37 2274 0.9 1 217 2057 38 11015 0.9 1 1189 9826 39 9063 0.9 1 1120 7943 40 1480 0.9 1 115 1365 41 22121 0.9 1 2637 19484 42 3433 0.9 1 404 3029 43 19613 0.9 1 2340 17273 44 3082 0.9 1 349 2733 45 5755 0.9 1 650 5105 46 1767 0.9 1 219 1548 47 3390 0.9 1 334 3056 48 13055 0.9 1 1637 11418 49 981 0.9 1 104 877 50 5619 0.9 1 645 4974 51 1781 0.9 1 226 1555 52 1262 0.9 1 138 1124 53 3634 0.9 1 424 3210 54 7877 0.9 1 936 6941 55 8211 0.9 1 1223 6988 56 3814 0.9 1 459 3355 57 4181 0.9 1 503 3678 58 2460 0.9 1 249 2211 59 1122 0.9 1 113 1009 60 2280 0.9 1 229 2051 61 2462 0.9 1 213 2249 62 12175 0.9 1 1679 10496 63 2707 0.9 1 349 2358 64 293 0.9 1 40 253 65 157 0.9 1 15 142 66 1429 0.9 1 228 1201 67 1163 0.9 1 104 1059 68 5899 0.9 1 661 5238 69 7490 0.9 1 708 6782 70 9182 0.9 1 1079 8103 71 1990 0.9 1 230 1760 72 817 0.9 1 88 729 73 1469 0.9 1 129 1340 74 2399 0.9 1 296 2103 75 2945 0.9 1 346 2599 76 2811 0.9 1 281 2530 77 3336 0.9 1 392 2944 78 3206 0.9 1 413 2793 79 3495 0.9 1 352 3143 80 2908 0.9 1 367 2541 81 2655 0.9 1 313 2342 82 2933 0.9 1 275 2658 83 3073 0.9 1 314 2759 84 2722 0.9 1 268 2454 85 3701 0.9 1 461 3240 86 2662 0.9 1 401 2261 87 2174 0.9 1 251 1923 88 1984 0.9 1 198 1786 89 1815 0.9 1 188 1627 90 1857 0.9 1 208 1649 91 2196 0.9 1 231 1965 92 1877 0.9 1 231 1646 93 1977 0.9 1 259 1718 94 2500 0.9 1 263 2237 95 1727 0.9 1 203 1524 96 1369 0.9 1 167 1202 97 1608 0.9 1 202 1406 98 1442 0.9 1 167 1275 99 1016 0.9 1 109 907 100 941 0.9 1 104 837 101 857 0.9 1 85 772 102 855 0.9 1 88 767 103 742 0.9 1 71 671 104 520 0.9 1 55 465 105 474 0.9 1 61 413 106 345 0.9 1 37 308 107 258 0.9 1 25 233 108 157 0.9 1 13 144 109 151 0.9 1 23 128 110 152 0.9 1 16 136 111 100 0.9 1 15 85 112 46 0.9 1 11 35 113 17 0.9 1 5 12 114 110 0.9 1 9 101 115 14 0.9 1 2 12 116 67 0.9 1 12 55 117 7 0.9 1 5 2 118 6 0.9 1 4 2 119 4 0.9 1 4 120 6 0.9 1 5 1 121 8 0.9 1 2 6 122 1 0.9 1 0 1 123 5 0.9 1 4 1 124 15 0.9 1 11 4 125 6 0.9 1 3 3 126 12 0.9 1 8 4 127 22 0.9 1 12 10 128 17 0.9 1 13 4 129 24 0.9 1 15 9 130 35 0.9 1 26 9 131 54 0.9 1 42 12 132 63 0.9 1 54 9 133 171 0.9 1 132 39 134 333 0.9 1 260 73 135 425 0.9 1 345 80 136 969 0.9 1 789 180 137 65893 0.9 1 61282 4611 138 2816463 0.9 1 2628267 188196 139 12 0.9 1 3 9 140 8 0.9 1 1 7 141 11 0.9 1 10 1 142 2 0.9 1 2 143 7 0.9 1 1 6 RUN STATISTICS FOR INPUT FILE: /sibcb2/bioinformatics2/heshutao/processing/test_BSworkflow/clean_data_2/RRBS21T000219_val_1.fq.gz ============================================= 59821506 sequences processed in total Sequences were truncated to a varying degree because of deteriorating qualities (Phred score quality cutoff: 20): 2072140 (3.5%) RRBS reads trimmed by additional 2 bp when adapter contamination was detected: 24463688 (40.9%)