SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_2_S14_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: 513491). 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_26psu_2_S14_L002_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 71.82 s (4 us/read; 14.35 M reads/minute). === Summary === Total reads processed: 17,174,050 Reads with adapters: 13,208,659 (76.9%) Reads written (passing filters): 17,174,050 (100.0%) Total basepairs processed: 2,576,107,500 bp Quality-trimmed: 11,281,504 bp (0.4%) Total written (filtered): 2,040,417,795 bp (79.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 13208659 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.5% C: 12.8% G: 23.5% T: 35.1% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 2393304 4293512.5 0 2393304 2 355208 1073378.1 0 355208 3 207534 268344.5 0 207534 4 112818 67086.1 0 112818 5 98722 16771.5 0 98722 6 88016 4192.9 0 88016 7 70973 1048.2 0 70973 8 100906 262.1 0 100906 9 80596 65.5 0 80310 286 10 85921 16.4 1 80103 5818 11 93456 4.1 1 85698 7758 12 91973 1.0 1 84465 7508 13 105255 0.3 1 96925 8330 14 97607 0.3 1 89028 8579 15 80440 0.3 1 74131 6309 16 114723 0.3 1 105648 9075 17 95977 0.3 1 87931 8046 18 85383 0.3 1 78648 6735 19 112212 0.3 1 103391 8821 20 104516 0.3 1 96596 7920 21 91790 0.3 1 84587 7203 22 103890 0.3 1 96083 7807 23 109193 0.3 1 100822 8371 24 108259 0.3 1 99753 8506 25 121670 0.3 1 113120 8550 26 100521 0.3 1 92626 7895 27 113578 0.3 1 104198 9380 28 101690 0.3 1 94983 6707 29 113641 0.3 1 105222 8419 30 108610 0.3 1 101210 7400 31 120920 0.3 1 112244 8676 32 104000 0.3 1 96851 7149 33 120229 0.3 1 111277 8952 34 153685 0.3 1 142847 10838 35 83436 0.3 1 77543 5893 36 120970 0.3 1 112035 8935 37 127408 0.3 1 118333 9075 38 119755 0.3 1 112084 7671 39 113420 0.3 1 106417 7003 40 129274 0.3 1 120419 8855 41 124811 0.3 1 116558 8253 42 127899 0.3 1 119534 8365 43 115450 0.3 1 107954 7496 44 133939 0.3 1 124786 9153 45 139673 0.3 1 130506 9167 46 102301 0.3 1 95697 6604 47 129785 0.3 1 121923 7862 48 125953 0.3 1 118248 7705 49 131617 0.3 1 122911 8706 50 126447 0.3 1 118299 8148 51 153054 0.3 1 143414 9640 52 111902 0.3 1 104877 7025 53 136845 0.3 1 129094 7751 54 100542 0.3 1 94550 5992 55 131225 0.3 1 123466 7759 56 134910 0.3 1 126386 8524 57 127245 0.3 1 120240 7005 58 123733 0.3 1 116761 6972 59 122876 0.3 1 115856 7020 60 129560 0.3 1 122153 7407 61 129535 0.3 1 122248 7287 62 141327 0.3 1 132778 8549 63 187124 0.3 1 177463 9661 64 148865 0.3 1 142160 6705 65 101493 0.3 1 96017 5476 66 109966 0.3 1 103977 5989 67 109147 0.3 1 102972 6175 68 110252 0.3 1 104088 6164 69 109266 0.3 1 102978 6288 70 115917 0.3 1 109437 6480 71 118081 0.3 1 111469 6612 72 111629 0.3 1 105360 6269 73 116346 0.3 1 109876 6470 74 106757 0.3 1 100604 6153 75 101733 0.3 1 95970 5763 76 99872 0.3 1 94223 5649 77 99194 0.3 1 93520 5674 78 93229 0.3 1 87953 5276 79 90739 0.3 1 85605 5134 80 89347 0.3 1 84416 4931 81 88970 0.3 1 84141 4829 82 84536 0.3 1 79929 4607 83 81530 0.3 1 77128 4402 84 78480 0.3 1 74228 4252 85 77346 0.3 1 73110 4236 86 75912 0.3 1 71909 4003 87 75393 0.3 1 71530 3863 88 73839 0.3 1 69922 3917 89 65607 0.3 1 62233 3374 90 63315 0.3 1 59995 3320 91 59514 0.3 1 56442 3072 92 55456 0.3 1 52465 2991 93 52632 0.3 1 49948 2684 94 51163 0.3 1 48481 2682 95 47871 0.3 1 45320 2551 96 45902 0.3 1 43474 2428 97 43468 0.3 1 41231 2237 98 40225 0.3 1 38177 2048 99 39861 0.3 1 37850 2011 100 35922 0.3 1 34182 1740 101 31906 0.3 1 30324 1582 102 28881 0.3 1 27260 1621 103 26612 0.3 1 25202 1410 104 25092 0.3 1 23747 1345 105 22553 0.3 1 21323 1230 106 20249 0.3 1 19195 1054 107 18698 0.3 1 17704 994 108 16333 0.3 1 15423 910 109 15105 0.3 1 14342 763 110 13538 0.3 1 12818 720 111 12635 0.3 1 11928 707 112 10864 0.3 1 10306 558 113 9370 0.3 1 8881 489 114 8127 0.3 1 7692 435 115 6826 0.3 1 6440 386 116 5914 0.3 1 5590 324 117 5167 0.3 1 4841 326 118 4505 0.3 1 4244 261 119 3657 0.3 1 3441 216 120 3157 0.3 1 2964 193 121 2768 0.3 1 2620 148 122 2319 0.3 1 2199 120 123 2119 0.3 1 1978 141 124 1696 0.3 1 1576 120 125 1359 0.3 1 1259 100 126 1191 0.3 1 1105 86 127 1007 0.3 1 955 52 128 721 0.3 1 673 48 129 632 0.3 1 599 33 130 537 0.3 1 494 43 131 454 0.3 1 423 31 132 387 0.3 1 367 20 133 461 0.3 1 442 19 134 637 0.3 1 611 26 135 279 0.3 1 264 15 136 164 0.3 1 153 11 137 121 0.3 1 110 11 138 99 0.3 1 89 10 139 86 0.3 1 79 7 140 59 0.3 1 52 7 141 49 0.3 1 44 5 142 39 0.3 1 36 3 143 48 0.3 1 45 3 144 41 0.3 1 36 5 145 47 0.3 1 41 6 146 121 0.3 1 118 3 147 643 0.3 1 616 27 148 431 0.3 1 416 15 149 244 0.3 1 225 19 150 2704 0.3 1 2570 134 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/16C_26psu_2_S14_L002_R2_001.fastq.gz ============================================= 17174050 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 17174050 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 127187 (0.74%)