SUMMARISING RUN PARAMETERS ========================== Input filename: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_2_S18_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: 743143). 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/CTRL_8C_26psu_2_S18_L002_R1_001.fastq.gz Processing reads on 8 cores in single-end mode ... Finished in 54.06 s (3 us/read; 18.84 M reads/minute). === Summary === Total reads processed: 16,972,486 Reads with adapters: 15,279,419 (90.0%) Reads written (passing filters): 16,972,486 (100.0%) Total basepairs processed: 2,545,872,900 bp Quality-trimmed: 5,170,443 bp (0.2%) Total written (filtered): 1,660,911,595 bp (65.2%) === Adapter 1 === Sequence: AGATCGGAAGAGC; Type: regular 3'; Length: 13; Trimmed: 15279419 times. No. of allowed errors: 0-9 bp: 0; 10-13 bp: 1 Bases preceding removed adapters: A: 28.1% C: 17.9% G: 21.2% T: 32.7% none/other: 0.0% Overview of removed sequences length count expect max.err error counts 1 937714 4243121.5 0 937714 2 159877 1060780.4 0 159877 3 104645 265195.1 0 104645 4 64394 66298.8 0 64394 5 60206 16574.7 0 60206 6 60143 4143.7 0 60143 7 49779 1035.9 0 49779 8 63607 259.0 0 63607 9 63633 64.7 0 62858 775 10 59492 16.2 1 55609 3883 11 70292 4.0 1 63860 6432 12 65718 1.0 1 60580 5138 13 68404 0.3 1 63070 5334 14 69496 0.3 1 63637 5859 15 74672 0.3 1 68604 6068 16 72665 0.3 1 66207 6458 17 90074 0.3 1 81360 8714 18 80053 0.3 1 74306 5747 19 65594 0.3 1 60638 4956 20 83351 0.3 1 76880 6471 21 92562 0.3 1 85115 7447 22 78449 0.3 1 72991 5458 23 93136 0.3 1 85970 7166 24 87973 0.3 1 80003 7970 25 95468 0.3 1 87873 7595 26 87079 0.3 1 80742 6337 27 100093 0.3 1 91614 8479 28 99879 0.3 1 92166 7713 29 105478 0.3 1 95962 9516 30 116678 0.3 1 108856 7822 31 86678 0.3 1 80098 6580 32 107759 0.3 1 99613 8146 33 109432 0.3 1 99874 9558 34 138284 0.3 1 125790 12494 35 117450 0.3 1 109376 8074 36 91614 0.3 1 84735 6879 37 124777 0.3 1 114386 10391 38 138573 0.3 1 126348 12225 39 118413 0.3 1 109918 8495 40 138324 0.3 1 126104 12220 41 158476 0.3 1 144761 13715 42 109596 0.3 1 99995 9601 43 214148 0.3 1 200447 13701 44 58836 0.3 1 52468 6368 45 143215 0.3 1 132338 10877 46 142842 0.3 1 132071 10771 47 146328 0.3 1 136022 10306 48 147735 0.3 1 136182 11553 49 164993 0.3 1 151819 13174 50 138531 0.3 1 129039 9492 51 154359 0.3 1 142921 11438 52 163104 0.3 1 149477 13627 53 181208 0.3 1 168727 12481 54 135823 0.3 1 125879 9944 55 172933 0.3 1 159987 12946 56 212770 0.3 1 198564 14206 57 137905 0.3 1 126707 11198 58 179533 0.3 1 168232 11301 59 154787 0.3 1 143238 11549 60 178048 0.3 1 165291 12757 61 178798 0.3 1 166319 12479 62 194586 0.3 1 181612 12974 63 159546 0.3 1 147478 12068 64 175838 0.3 1 164219 11619 65 199150 0.3 1 185246 13904 66 207681 0.3 1 193071 14610 67 227820 0.3 1 208839 18981 68 430170 0.3 1 406697 23473 69 101761 0.3 1 93311 8450 70 37741 0.3 1 31764 5977 71 116561 0.3 1 108649 7912 72 170878 0.3 1 160245 10633 73 185808 0.3 1 173840 11968 74 185713 0.3 1 173236 12477 75 186685 0.3 1 173898 12787 76 187774 0.3 1 174524 13250 77 190253 0.3 1 177207 13046 78 180228 0.3 1 167656 12572 79 181970 0.3 1 169235 12735 80 180269 0.3 1 167504 12765 81 180129 0.3 1 167834 12295 82 176778 0.3 1 164262 12516 83 174648 0.3 1 162652 11996 84 170683 0.3 1 158618 12065 85 167207 0.3 1 155648 11559 86 165775 0.3 1 154402 11373 87 159710 0.3 1 148769 10941 88 161141 0.3 1 150001 11140 89 154725 0.3 1 143979 10746 90 156314 0.3 1 145746 10568 91 151370 0.3 1 140729 10641 92 145834 0.3 1 135746 10088 93 137534 0.3 1 127986 9548 94 136265 0.3 1 126825 9440 95 127646 0.3 1 118675 8971 96 123166 0.3 1 114494 8672 97 117318 0.3 1 109181 8137 98 111017 0.3 1 103130 7887 99 109081 0.3 1 101041 8040 100 101164 0.3 1 94080 7084 101 96193 0.3 1 89369 6824 102 90471 0.3 1 84087 6384 103 85738 0.3 1 79491 6247 104 80436 0.3 1 74816 5620 105 72717 0.3 1 67687 5030 106 67684 0.3 1 62759 4925 107 62704 0.3 1 58171 4533 108 59951 0.3 1 55617 4334 109 54357 0.3 1 50236 4121 110 50115 0.3 1 46382 3733 111 45371 0.3 1 41955 3416 112 40800 0.3 1 37574 3226 113 35447 0.3 1 32646 2801 114 32325 0.3 1 29802 2523 115 28709 0.3 1 26438 2271 116 25389 0.3 1 23337 2052 117 21950 0.3 1 20122 1828 118 19200 0.3 1 17593 1607 119 16278 0.3 1 14896 1382 120 14121 0.3 1 12882 1239 121 12963 0.3 1 11779 1184 122 10628 0.3 1 9652 976 123 9232 0.3 1 8435 797 124 7617 0.3 1 6893 724 125 6474 0.3 1 5870 604 126 5569 0.3 1 5024 545 127 4721 0.3 1 4238 483 128 3597 0.3 1 3214 383 129 3083 0.3 1 2780 303 130 2334 0.3 1 2063 271 131 2035 0.3 1 1816 219 132 1850 0.3 1 1686 164 133 2327 0.3 1 2083 244 134 4554 0.3 1 4279 275 135 1805 0.3 1 1652 153 136 606 0.3 1 541 65 137 448 0.3 1 385 63 138 325 0.3 1 262 63 139 199 0.3 1 170 29 140 136 0.3 1 115 21 141 92 0.3 1 70 22 142 61 0.3 1 44 17 143 68 0.3 1 60 8 144 63 0.3 1 59 4 145 123 0.3 1 108 15 146 160 0.3 1 140 20 147 706 0.3 1 621 85 148 490 0.3 1 450 40 149 296 0.3 1 261 35 150 3088 0.3 1 2616 472 RUN STATISTICS FOR INPUT FILE: /gscratch/srlab/strigg/data/Ssalar/FASTQS/RAW/CTRL_8C_26psu_2_S18_L002_R1_001.fastq.gz ============================================= 16972486 sequences processed in total