SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_1_S1_L002_R1_001.fastq.gz Trimming mode: paired-end Trim Galore version: 0.6.4_dev Cutadapt version: 2.4 Python version: could not detect Number of cores used for trimming: 8 Quality Phred score cutoff: 20 Quality encoding type selected: ASCII+33 Using Illumina adapter for trimming (count: 628232). Second best hit was Nextera (count: 0) 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 10 bp from their 5' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 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 10 bp from their 3' end to avoid poor qualities or biases All Read 2 sequences will be trimmed by 10 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 /gscratch/scrubbed/strigg/analyses/20200427/TG_PE_FASTQS/FastQC --threads 28 Output file will be GZIP compressed This is cutadapt 2.4 with Python 3.7.6 Command line parameters: -j 8 -e 0.1 -q 20 -O 1 -a AGATCGGAAGAGC /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_1_S1_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 69.90 s (4 us/read; 16.80 M reads/minute). === Summary === Total reads processed: 19,571,235 Reads with adapters: 16,407,295 (83.8%) Reads written (passing filters): 19,571,235 (100.0%) Total basepairs processed: 2,935,685,250 bp Quality-trimmed: 8,266,740 bp (0.3%) Total written (filtered): 2,130,672,037 bp (72.6%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 16407295 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.6% C: 14.6% G: 21.1% T: 34.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1871205 4892808.8 0 1871205 2 281413 1223202.2 0 281413 3 165620 305800.5 0 165620 4 102750 76450.1 0 102750 5 91621 19112.5 0 91621 6 89878 4778.1 0 89878 7 72653 1194.5 0 72653 8 92540 298.6 0 92540 9 93344 74.7 0 92169 1175 10 86372 18.7 1 80800 5572 11 99125 4.7 1 90406 8719 12 93690 1.2 1 86859 6831 13 96288 0.3 1 88938 7350 14 98016 0.3 1 89939 8077 15 102285 0.3 1 94257 8028 16 101242 0.3 1 92425 8817 17 123641 0.3 1 112025 11616 18 107224 0.3 1 99543 7681 19 90677 0.3 1 83921 6756 20 111453 0.3 1 102938 8515 21 124864 0.3 1 115203 9661 22 102217 0.3 1 95257 6960 23 124937 0.3 1 115301 9636 24 113499 0.3 1 102977 10522 25 124401 0.3 1 114862 9539 26 112120 0.3 1 104445 7675 27 128185 0.3 1 117570 10615 28 125849 0.3 1 115930 9919 29 134332 0.3 1 122337 11995 30 144690 0.3 1 135178 9512 31 111404 0.3 1 103047 8357 32 135894 0.3 1 125650 10244 33 131757 0.3 1 121043 10714 34 143190 0.3 1 131548 11642 35 157418 0.3 1 142743 14675 36 129247 0.3 1 119787 9460 37 149221 0.3 1 138285 10936 38 145468 0.3 1 133187 12281 39 172504 0.3 1 157173 15331 40 134071 0.3 1 124322 9749 41 180864 0.3 1 164818 16046 42 137219 0.3 1 124408 12811 43 239349 0.3 1 223461 15888 44 74486 0.3 1 66856 7630 45 161688 0.3 1 148747 12941 46 191505 0.3 1 176273 15232 47 179273 0.3 1 166898 12375 48 140851 0.3 1 128229 12622 49 208539 0.3 1 192459 16080 50 127958 0.3 1 118792 9166 51 162484 0.3 1 150649 11835 52 227313 0.3 1 208878 18435 53 230954 0.3 1 217665 13289 54 127985 0.3 1 117878 10107 55 190088 0.3 1 177776 12312 56 183666 0.3 1 171198 12468 57 212537 0.3 1 198874 13663 58 133097 0.3 1 125108 7989 59 104505 0.3 1 95591 8914 60 206694 0.3 1 193657 13037 61 190421 0.3 1 179352 11069 62 144000 0.3 1 134103 9897 63 180563 0.3 1 168547 12016 64 155217 0.3 1 145289 9928 65 158098 0.3 1 147007 11091 66 188945 0.3 1 175941 13004 67 211986 0.3 1 194786 17200 68 378408 0.3 1 357096 21312 69 162579 0.3 1 151778 10801 70 55965 0.3 1 49649 6316 71 63814 0.3 1 58189 5625 72 145461 0.3 1 136394 9067 73 166164 0.3 1 155484 10680 74 168411 0.3 1 157197 11214 75 167596 0.3 1 156098 11498 76 166388 0.3 1 154457 11931 77 167040 0.3 1 155459 11581 78 159704 0.3 1 148462 11242 79 158706 0.3 1 147370 11336 80 154542 0.3 1 143508 11034 81 154753 0.3 1 143966 10787 82 150886 0.3 1 140115 10771 83 145780 0.3 1 135596 10184 84 142086 0.3 1 132138 9948 85 137811 0.3 1 128196 9615 86 134898 0.3 1 125576 9322 87 129676 0.3 1 120849 8827 88 128629 0.3 1 119738 8891 89 123313 0.3 1 114615 8698 90 123132 0.3 1 114553 8579 91 117637 0.3 1 109407 8230 92 112493 0.3 1 104754 7739 93 106111 0.3 1 98757 7354 94 103337 0.3 1 96126 7211 95 95958 0.3 1 89095 6863 96 91266 0.3 1 84746 6520 97 86736 0.3 1 80632 6104 98 81864 0.3 1 75993 5871 99 80342 0.3 1 74325 6017 100 73408 0.3 1 68128 5280 101 68599 0.3 1 63783 4816 102 64339 0.3 1 59627 4712 103 59235 0.3 1 54992 4243 104 55526 0.3 1 51587 3939 105 49435 0.3 1 45975 3460 106 45302 0.3 1 42055 3247 107 41568 0.3 1 38569 2999 108 39344 0.3 1 36429 2915 109 35142 0.3 1 32532 2610 110 32440 0.3 1 30035 2405 111 29201 0.3 1 26917 2284 112 25771 0.3 1 23691 2080 113 22359 0.3 1 20490 1869 114 19994 0.3 1 18373 1621 115 17421 0.3 1 16000 1421 116 15295 0.3 1 14082 1213 117 13006 0.3 1 11960 1046 118 11522 0.3 1 10599 923 119 9598 0.3 1 8847 751 120 7795 0.3 1 7132 663 121 6634 0.3 1 6018 616 122 5895 0.3 1 5383 512 123 4806 0.3 1 4352 454 124 4169 0.3 1 3804 365 125 3459 0.3 1 3117 342 126 3006 0.3 1 2739 267 127 2458 0.3 1 2229 229 128 1849 0.3 1 1632 217 129 1614 0.3 1 1454 160 130 1309 0.3 1 1172 137 131 1113 0.3 1 990 123 132 1037 0.3 1 938 99 133 1203 0.3 1 1080 123 134 1440 0.3 1 1347 93 135 651 0.3 1 599 52 136 330 0.3 1 299 31 137 262 0.3 1 226 36 138 169 0.3 1 150 19 139 125 0.3 1 105 20 140 97 0.3 1 85 12 141 76 0.3 1 66 10 142 39 0.3 1 32 7 143 36 0.3 1 31 5 144 28 0.3 1 23 5 145 62 0.3 1 55 7 146 39 0.3 1 35 4 147 138 0.3 1 123 15 148 73 0.3 1 68 5 149 57 0.3 1 50 7 150 745 0.3 1 637 108 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_1_S1_L002_R1_001.fastq.gz ============================================= 19571235 sequences processed in total