SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_4_S4_L002_R2_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: 426581). 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_4_S4_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 67.66 s (4 us/read; 13.83 M reads/minute). === Summary === Total reads processed: 15,591,852 Reads with adapters: 11,164,940 (71.6%) Reads written (passing filters): 15,591,852 (100.0%) Total basepairs processed: 2,338,777,800 bp Quality-trimmed: 8,987,489 bp (0.4%) Total written (filtered): 1,952,377,119 bp (83.5%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 11164940 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 30.1% C: 12.2% G: 21.8% T: 35.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2716063 3897963.0 0 2716063 2 365801 974490.8 0 365801 3 204110 243622.7 0 204110 4 111706 60905.7 0 111706 5 93686 15226.4 0 93686 6 82310 3806.6 0 82310 7 64821 951.7 0 64821 8 93347 237.9 0 93347 9 74551 59.5 0 74263 288 10 78346 14.9 1 72991 5355 11 85380 3.7 1 78328 7052 12 84150 0.9 1 77541 6609 13 96178 0.2 1 88615 7563 14 88433 0.2 1 80671 7762 15 72019 0.2 1 66503 5516 16 102952 0.2 1 94755 8197 17 86769 0.2 1 79687 7082 18 76619 0.2 1 70853 5766 19 98606 0.2 1 91042 7564 20 91841 0.2 1 84883 6958 21 80822 0.2 1 74556 6266 22 90084 0.2 1 83382 6702 23 95275 0.2 1 87967 7308 24 93761 0.2 1 86637 7124 25 105154 0.2 1 98108 7046 26 87685 0.2 1 80687 6998 27 96238 0.2 1 88248 7990 28 86982 0.2 1 81506 5476 29 96532 0.2 1 89458 7074 30 91145 0.2 1 85081 6064 31 100852 0.2 1 93803 7049 32 86615 0.2 1 80885 5730 33 99917 0.2 1 92622 7295 34 128321 0.2 1 119309 9012 35 68466 0.2 1 63767 4699 36 99171 0.2 1 91848 7323 37 104228 0.2 1 97074 7154 38 95840 0.2 1 89901 5939 39 91223 0.2 1 85899 5324 40 103901 0.2 1 97025 6876 41 100699 0.2 1 94360 6339 42 101648 0.2 1 95335 6313 43 91398 0.2 1 85693 5705 44 105931 0.2 1 98930 7001 45 111589 0.2 1 104455 7134 46 79183 0.2 1 74169 5014 47 99997 0.2 1 94251 5746 48 97219 0.2 1 91470 5749 49 102240 0.2 1 95693 6547 50 96699 0.2 1 90628 6071 51 118228 0.2 1 110940 7288 52 84607 0.2 1 79439 5168 53 104742 0.2 1 98960 5782 54 75371 0.2 1 71116 4255 55 98114 0.2 1 92755 5359 56 100972 0.2 1 94974 5998 57 94787 0.2 1 89866 4921 58 91176 0.2 1 86320 4856 59 91225 0.2 1 86196 5029 60 94303 0.2 1 88940 5363 61 95802 0.2 1 90516 5286 62 104062 0.2 1 98063 5999 63 134017 0.2 1 127276 6741 64 107807 0.2 1 103277 4530 65 71585 0.2 1 67908 3677 66 78177 0.2 1 74035 4142 67 77189 0.2 1 72913 4276 68 77503 0.2 1 73378 4125 69 76227 0.2 1 72009 4218 70 77805 0.2 1 73707 4098 71 80348 0.2 1 76129 4219 72 76686 0.2 1 72546 4140 73 78718 0.2 1 74553 4165 74 72998 0.2 1 69110 3888 75 69291 0.2 1 65521 3770 76 66128 0.2 1 62546 3582 77 65756 0.2 1 62222 3534 78 62918 0.2 1 59420 3498 79 59982 0.2 1 56797 3185 80 59872 0.2 1 56761 3111 81 57826 0.2 1 54814 3012 82 55215 0.2 1 52336 2879 83 53442 0.2 1 50600 2842 84 50951 0.2 1 48209 2742 85 49724 0.2 1 47191 2533 86 49032 0.2 1 46473 2559 87 49028 0.2 1 46704 2324 88 46498 0.2 1 44150 2348 89 42159 0.2 1 40004 2155 90 40296 0.2 1 38283 2013 91 37292 0.2 1 35403 1889 92 34841 0.2 1 33039 1802 93 33152 0.2 1 31479 1673 94 31763 0.2 1 30149 1614 95 30241 0.2 1 28665 1576 96 27836 0.2 1 26423 1413 97 25827 0.2 1 24589 1238 98 24001 0.2 1 22767 1234 99 23498 0.2 1 22301 1197 100 21732 0.2 1 20644 1088 101 19788 0.2 1 18836 952 102 17924 0.2 1 16990 934 103 15850 0.2 1 15000 850 104 14943 0.2 1 14170 773 105 13279 0.2 1 12646 633 106 11897 0.2 1 11297 600 107 10895 0.2 1 10336 559 108 9562 0.2 1 9057 505 109 8353 0.2 1 7873 480 110 7641 0.2 1 7229 412 111 7111 0.2 1 6763 348 112 6029 0.2 1 5694 335 113 5217 0.2 1 4974 243 114 4567 0.2 1 4342 225 115 3814 0.2 1 3593 221 116 3236 0.2 1 3069 167 117 2708 0.2 1 2550 158 118 2402 0.2 1 2269 133 119 1976 0.2 1 1850 126 120 1573 0.2 1 1480 93 121 1360 0.2 1 1290 70 122 1161 0.2 1 1085 76 123 1044 0.2 1 961 83 124 817 0.2 1 759 58 125 740 0.2 1 678 62 126 632 0.2 1 586 46 127 507 0.2 1 481 26 128 371 0.2 1 328 43 129 368 0.2 1 334 34 130 272 0.2 1 248 24 131 250 0.2 1 232 18 132 226 0.2 1 220 6 133 268 0.2 1 248 20 134 319 0.2 1 304 15 135 142 0.2 1 138 4 136 65 0.2 1 62 3 137 61 0.2 1 60 1 138 31 0.2 1 25 6 139 26 0.2 1 21 5 140 13 0.2 1 11 2 141 16 0.2 1 13 3 142 11 0.2 1 8 3 143 13 0.2 1 11 2 144 7 0.2 1 5 2 145 9 0.2 1 6 3 146 13 0.2 1 12 1 147 30 0.2 1 26 4 148 17 0.2 1 16 1 149 16 0.2 1 14 2 150 117 0.2 1 107 10 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_32psu_4_S4_L002_R2_001.fastq.gz ============================================= 15591852 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 15591852 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 73342 (0.47%)