SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_2_S6_L001_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: 570994). Second best hit was smallRNA (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/8C_32psu_2_S6_L001_R2_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 49.06 s (4 us/read; 15.83 M reads/minute). === Summary === Total reads processed: 12,939,154 Reads with adapters: 10,288,624 (79.5%) Reads written (passing filters): 12,939,154 (100.0%) Total basepairs processed: 1,940,873,100 bp Quality-trimmed: 9,202,420 bp (0.5%) Total written (filtered): 1,495,378,762 bp (77.0%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 10288624 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.2% C: 13.0% G: 23.8% T: 34.9% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 1595771 3234788.5 0 1595771 2 240375 808697.1 0 240375 3 138443 202174.3 0 138443 4 81428 50543.6 0 81428 5 75038 12635.9 0 75038 6 64775 3159.0 0 64775 7 52085 789.7 0 52085 8 75127 197.4 0 75127 9 60527 49.4 0 60355 172 10 65326 12.3 1 62475 2851 11 69712 3.1 1 65682 4030 12 70487 0.8 1 66516 3971 13 78320 0.2 1 74147 4173 14 73989 0.2 1 69268 4721 15 60342 0.2 1 57080 3262 16 88180 0.2 1 83244 4936 17 69750 0.2 1 65392 4358 18 67540 0.2 1 63841 3699 19 85313 0.2 1 80354 4959 20 79769 0.2 1 75478 4291 21 70275 0.2 1 66324 3951 22 79177 0.2 1 74939 4238 23 82659 0.2 1 78081 4578 24 81915 0.2 1 77232 4683 25 93464 0.2 1 88557 4907 26 77147 0.2 1 72835 4312 27 85811 0.2 1 80374 5437 28 80396 0.2 1 76862 3534 29 85946 0.2 1 81104 4842 30 85726 0.2 1 81647 4079 31 92050 0.2 1 87288 4762 32 83804 0.2 1 79934 3870 33 92087 0.2 1 87200 4887 34 119466 0.2 1 113056 6410 35 67982 0.2 1 64809 3173 36 94466 0.2 1 89392 5074 37 100368 0.2 1 95090 5278 38 94027 0.2 1 89878 4149 39 91028 0.2 1 87016 4012 40 101155 0.2 1 95949 5206 41 98098 0.2 1 93343 4755 42 100747 0.2 1 96031 4716 43 92371 0.2 1 88129 4242 44 106061 0.2 1 101051 5010 45 109648 0.2 1 104507 5141 46 85668 0.2 1 81729 3939 47 104356 0.2 1 99808 4548 48 101281 0.2 1 96981 4300 49 106782 0.2 1 101997 4785 50 100514 0.2 1 95958 4556 51 125782 0.2 1 120079 5703 52 90772 0.2 1 86983 3789 53 109598 0.2 1 105306 4292 54 83322 0.2 1 79849 3473 55 107016 0.2 1 102862 4154 56 110967 0.2 1 106233 4734 57 104357 0.2 1 100229 4128 58 100691 0.2 1 96894 3797 59 102578 0.2 1 98489 4089 60 106303 0.2 1 102044 4259 61 108531 0.2 1 104028 4503 62 118161 0.2 1 113451 4710 63 158201 0.2 1 152213 5988 64 129612 0.2 1 125287 4325 65 83984 0.2 1 80809 3175 66 91901 0.2 1 88385 3516 67 89742 0.2 1 86128 3614 68 91530 0.2 1 88057 3473 69 90402 0.2 1 86917 3485 70 96053 0.2 1 92305 3748 71 99803 0.2 1 96104 3699 72 94159 0.2 1 90619 3540 73 98787 0.2 1 95125 3662 74 90680 0.2 1 87379 3301 75 86705 0.2 1 83434 3271 76 84928 0.2 1 81792 3136 77 84096 0.2 1 80874 3222 78 80178 0.2 1 77109 3069 79 77254 0.2 1 74397 2857 80 77028 0.2 1 74180 2848 81 75249 0.2 1 72550 2699 82 72339 0.2 1 69794 2545 83 70398 0.2 1 67790 2608 84 68189 0.2 1 65635 2554 85 66784 0.2 1 64244 2540 86 65482 0.2 1 63096 2386 87 67016 0.2 1 64553 2463 88 64151 0.2 1 61741 2410 89 57363 0.2 1 55205 2158 90 54985 0.2 1 52902 2083 91 52080 0.2 1 50216 1864 92 48422 0.2 1 46687 1735 93 47310 0.2 1 45600 1710 94 45459 0.2 1 43795 1664 95 43150 0.2 1 41608 1542 96 40380 0.2 1 38964 1416 97 36752 0.2 1 35440 1312 98 33446 0.2 1 32251 1195 99 33482 0.2 1 32255 1227 100 30657 0.2 1 29566 1091 101 28785 0.2 1 27832 953 102 27470 0.2 1 26566 904 103 25360 0.2 1 24494 866 104 23640 0.2 1 22887 753 105 21192 0.2 1 20482 710 106 19098 0.2 1 18446 652 107 16996 0.2 1 16368 628 108 15172 0.2 1 14616 556 109 14001 0.2 1 13446 555 110 12575 0.2 1 12154 421 111 11902 0.2 1 11531 371 112 10341 0.2 1 9986 355 113 8669 0.2 1 8372 297 114 7690 0.2 1 7405 285 115 6634 0.2 1 6377 257 116 5717 0.2 1 5480 237 117 4541 0.2 1 4344 197 118 4158 0.2 1 3977 181 119 3510 0.2 1 3351 159 120 2896 0.2 1 2771 125 121 2680 0.2 1 2560 120 122 2179 0.2 1 2075 104 123 1805 0.2 1 1731 74 124 1586 0.2 1 1495 91 125 1276 0.2 1 1206 70 126 1153 0.2 1 1112 41 127 891 0.2 1 852 39 128 721 0.2 1 684 37 129 559 0.2 1 529 30 130 484 0.2 1 453 31 131 369 0.2 1 355 14 132 299 0.2 1 280 19 133 268 0.2 1 245 23 134 297 0.2 1 280 17 135 162 0.2 1 155 7 136 110 0.2 1 102 8 137 81 0.2 1 76 5 138 67 0.2 1 59 8 139 34 0.2 1 30 4 140 26 0.2 1 23 3 141 15 0.2 1 15 142 15 0.2 1 15 143 8 0.2 1 8 144 6 0.2 1 4 2 145 17 0.2 1 15 2 146 13 0.2 1 12 1 147 33 0.2 1 27 6 148 14 0.2 1 14 149 8 0.2 1 6 2 150 114 0.2 1 107 7 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/8C_32psu_2_S6_L001_R2_001.fastq.gz ============================================= 12939154 sequences processed in total Total number of sequences analysed for the sequence pair length validation: 12939154 Number of sequence pairs removed because at least one read was shorter than the length cutoff (20 bp): 112994 (0.87%)