SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_1_S9_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: 511403). Second best hit was Nextera (count: 1) 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/8C_26psu_1_S9_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 69.90 s (4 us/read; 15.50 M reads/minute). === Summary === Total reads processed: 18,056,494 Reads with adapters: 13,833,491 (76.6%) Reads written (passing filters): 18,056,494 (100.0%) Total basepairs processed: 2,708,474,100 bp Quality-trimmed: 12,349,451 bp (0.5%) Total written (filtered): 2,141,212,582 bp (79.1%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13833491 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 29.0% C: 12.5% G: 24.0% T: 34.6% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2568781 4514123.5 0 2568781 2 366057 1128530.9 0 366057 3 212077 282132.7 0 212077 4 115719 70533.2 0 115719 5 101735 17633.3 0 101735 6 89696 4408.3 0 89696 7 71264 1102.1 0 71264 8 102329 275.5 0 102329 9 81047 68.9 0 80732 315 10 86697 17.2 1 80878 5819 11 94697 4.3 1 87025 7672 12 93974 1.1 1 86609 7365 13 107111 0.3 1 98790 8321 14 98830 0.3 1 90363 8467 15 81863 0.3 1 75568 6295 16 116617 0.3 1 107560 9057 17 98434 0.3 1 90554 7880 18 88102 0.3 1 81367 6735 19 112551 0.3 1 103902 8649 20 106499 0.3 1 98559 7940 21 94529 0.3 1 87451 7078 22 105525 0.3 1 97752 7773 23 111250 0.3 1 102948 8302 24 110289 0.3 1 101801 8488 25 123454 0.3 1 115174 8280 26 102700 0.3 1 94614 8086 27 115670 0.3 1 106461 9209 28 103454 0.3 1 96996 6458 29 116676 0.3 1 108241 8435 30 110369 0.3 1 103124 7245 31 123948 0.3 1 115651 8297 32 105488 0.3 1 98700 6788 33 122972 0.3 1 114148 8824 34 158602 0.3 1 147860 10742 35 85176 0.3 1 79388 5788 36 121188 0.3 1 112686 8502 37 129603 0.3 1 120852 8751 38 121650 0.3 1 114412 7238 39 117499 0.3 1 110622 6877 40 132022 0.3 1 123436 8586 41 127439 0.3 1 119665 7774 42 130897 0.3 1 122691 8206 43 118466 0.3 1 111262 7204 44 136805 0.3 1 128115 8690 45 143267 0.3 1 134250 9017 46 105232 0.3 1 98689 6543 47 132632 0.3 1 125125 7507 48 128580 0.3 1 121138 7442 49 134590 0.3 1 126196 8394 50 129680 0.3 1 121594 8086 51 156936 0.3 1 147378 9558 52 115575 0.3 1 108787 6788 53 141220 0.3 1 133568 7652 54 104058 0.3 1 98240 5818 55 134625 0.3 1 127372 7253 56 138566 0.3 1 130360 8206 57 132925 0.3 1 126016 6909 58 127424 0.3 1 120849 6575 59 127371 0.3 1 120396 6975 60 132296 0.3 1 124969 7327 61 135056 0.3 1 127808 7248 62 146657 0.3 1 138388 8269 63 193947 0.3 1 184650 9297 64 155657 0.3 1 148867 6790 65 105922 0.3 1 100517 5405 66 114816 0.3 1 108826 5990 67 114246 0.3 1 108023 6223 68 115039 0.3 1 108957 6082 69 113573 0.3 1 107431 6142 70 118689 0.3 1 112276 6413 71 124010 0.3 1 117553 6457 72 118164 0.3 1 111917 6247 73 122662 0.3 1 116340 6322 74 113578 0.3 1 107524 6054 75 108812 0.3 1 102905 5907 76 105084 0.3 1 99284 5800 77 105545 0.3 1 99708 5837 78 100872 0.3 1 95568 5304 79 97026 0.3 1 91844 5182 80 95305 0.3 1 90356 4949 81 93857 0.3 1 89014 4843 82 90295 0.3 1 85582 4713 83 87301 0.3 1 82821 4480 84 85471 0.3 1 81218 4253 85 82978 0.3 1 78704 4274 86 82245 0.3 1 78140 4105 87 82525 0.3 1 78515 4010 88 80619 0.3 1 76785 3834 89 73370 0.3 1 69724 3646 90 70068 0.3 1 66584 3484 91 65835 0.3 1 62601 3234 92 61556 0.3 1 58566 2990 93 59482 0.3 1 56574 2908 94 57109 0.3 1 54269 2840 95 53973 0.3 1 51267 2706 96 51596 0.3 1 49048 2548 97 47434 0.3 1 45017 2417 98 44668 0.3 1 42540 2128 99 43184 0.3 1 41061 2123 100 40483 0.3 1 38511 1972 101 37015 0.3 1 35171 1844 102 34179 0.3 1 32525 1654 103 31254 0.3 1 29799 1455 104 30003 0.3 1 28488 1515 105 26714 0.3 1 25377 1337 106 24481 0.3 1 23332 1149 107 22254 0.3 1 21123 1131 108 20003 0.3 1 19023 980 109 18094 0.3 1 17150 944 110 16326 0.3 1 15479 847 111 15507 0.3 1 14783 724 112 13504 0.3 1 12807 697 113 11779 0.3 1 11204 575 114 10207 0.3 1 9684 523 115 8697 0.3 1 8286 411 116 7460 0.3 1 7104 356 117 6031 0.3 1 5703 328 118 5441 0.3 1 5182 259 119 4540 0.3 1 4315 225 120 3964 0.3 1 3742 222 121 3581 0.3 1 3393 188 122 2805 0.3 1 2657 148 123 2429 0.3 1 2278 151 124 2051 0.3 1 1954 97 125 1777 0.3 1 1683 94 126 1416 0.3 1 1338 78 127 1308 0.3 1 1214 94 128 919 0.3 1 855 64 129 823 0.3 1 781 42 130 653 0.3 1 614 39 131 581 0.3 1 548 33 132 573 0.3 1 541 32 133 789 0.3 1 754 35 134 1231 0.3 1 1179 52 135 458 0.3 1 447 11 136 175 0.3 1 164 11 137 112 0.3 1 103 9 138 94 0.3 1 84 10 139 57 0.3 1 53 4 140 65 0.3 1 58 7 141 32 0.3 1 29 3 142 35 0.3 1 31 4 143 17 0.3 1 15 2 144 11 0.3 1 9 2 145 30 0.3 1 28 2 146 19 0.3 1 19 147 64 0.3 1 61 3 148 47 0.3 1 44 3 149 34 0.3 1 32 2 150 415 0.3 1 377 38 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_26psu_1_S9_L002_R2_001.fastq.gz ============================================= 18056494 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 18056494 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 151913 (0.84%)