Starting /dee2/code/volunteer_pipeline.sh ERR5052707 current disk space = 1526817607680 free memory = 1597311064 ERR5052707 SRAfilesize 1085bc54ca6f044127c7ef97537ad459 ERR5052707.sra ERR5052707.sra file validated ERR5052707 is paired end ERR5052707 is conventional basespace ERR5052707 read1 length is 70 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR5052707_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.37075 35.0 35.0 35.0 35.0 35.0 2 34.63375 35.0 35.0 35.0 35.0 35.0 3 34.743 35.0 35.0 35.0 35.0 35.0 4 34.74625 35.0 35.0 35.0 35.0 35.0 5 34.73875 35.0 35.0 35.0 35.0 35.0 6 39.58275 40.0 40.0 40.0 39.0 40.0 7 39.55875 40.0 40.0 40.0 39.0 40.0 8 39.4805 40.0 40.0 40.0 39.0 40.0 9 39.54475 40.0 40.0 40.0 39.0 40.0 10 39.5085 40.0 40.0 40.0 39.0 40.0 11 39.46925 40.0 40.0 40.0 39.0 40.0 12 39.45725 40.0 40.0 40.0 39.0 40.0 13 39.486 40.0 40.0 40.0 39.0 40.0 14 39.441 40.0 40.0 40.0 39.0 40.0 15 39.458 40.0 40.0 40.0 39.0 40.0 16 39.4645 40.0 40.0 40.0 39.0 40.0 17 39.44775 40.0 40.0 40.0 39.0 40.0 18 39.45125 40.0 40.0 40.0 39.0 40.0 19 39.46575 40.0 40.0 40.0 39.0 40.0 20 39.46375 40.0 40.0 40.0 39.0 40.0 21 39.4885 40.0 40.0 40.0 39.0 40.0 22 39.39425 40.0 40.0 40.0 39.0 40.0 23 39.428 40.0 40.0 40.0 39.0 40.0 24 39.4025 40.0 40.0 40.0 39.0 40.0 25 39.414 40.0 40.0 40.0 39.0 40.0 26 39.428 40.0 40.0 40.0 39.0 40.0 27 39.43125 40.0 40.0 40.0 39.0 40.0 28 39.41775 40.0 40.0 40.0 39.0 40.0 29 39.36375 40.0 40.0 40.0 39.0 40.0 30 39.38725 40.0 40.0 40.0 39.0 40.0 31 39.42075 40.0 40.0 40.0 39.0 40.0 32 39.425 40.0 40.0 40.0 39.0 40.0 33 39.397 40.0 40.0 40.0 39.0 40.0 34 39.456 40.0 40.0 40.0 39.0 40.0 35 39.465 40.0 40.0 40.0 39.0 40.0 36 39.426 40.0 40.0 40.0 39.0 40.0 37 39.41125 40.0 40.0 40.0 39.0 40.0 38 39.389 40.0 40.0 40.0 39.0 40.0 39 39.4275 40.0 40.0 40.0 39.0 40.0 40 39.44375 40.0 40.0 40.0 39.0 40.0 41 39.37525 40.0 40.0 40.0 39.0 40.0 42 39.401 40.0 40.0 40.0 39.0 40.0 43 39.462 40.0 40.0 40.0 39.0 40.0 44 39.37 40.0 40.0 40.0 39.0 40.0 45 39.36125 40.0 40.0 40.0 39.0 40.0 46 39.3845 40.0 40.0 40.0 39.0 40.0 47 39.37125 40.0 40.0 40.0 39.0 40.0 48 39.43075 40.0 40.0 40.0 39.0 40.0 49 39.40425 40.0 40.0 40.0 39.0 40.0 50 39.424 40.0 40.0 40.0 39.0 40.0 51 39.419 40.0 40.0 40.0 39.0 40.0 52 39.418 40.0 40.0 40.0 39.0 40.0 53 39.436 40.0 40.0 40.0 39.0 40.0 54 39.4615 40.0 40.0 40.0 39.0 40.0 55 39.44325 40.0 40.0 40.0 39.0 40.0 56 39.399 40.0 40.0 40.0 39.0 40.0 57 39.321 40.0 40.0 40.0 39.0 40.0 58 39.26375 40.0 40.0 40.0 39.0 40.0 59 39.37025 40.0 40.0 40.0 39.0 40.0 60 39.4035 40.0 40.0 40.0 39.0 40.0 61 39.3615 40.0 40.0 40.0 39.0 40.0 62 39.40925 40.0 40.0 40.0 39.0 40.0 63 39.43525 40.0 40.0 40.0 39.0 40.0 64 39.3835 40.0 40.0 40.0 39.0 40.0 65 39.3705 40.0 40.0 40.0 39.0 40.0 66 39.3835 40.0 40.0 40.0 39.0 40.0 67 39.37775 40.0 40.0 40.0 39.0 40.0 68 39.3695 40.0 40.0 40.0 39.0 40.0 69 39.375 40.0 40.0 40.0 39.0 40.0 70 39.378 40.0 40.0 40.0 39.0 40.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 1.0 25 1.0 26 2.0 27 3.0 28 12.0 29 15.0 30 13.0 31 19.0 32 19.0 33 27.0 34 38.0 35 49.0 36 63.0 37 120.0 38 213.0 39 3405.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 27.601010101010097 9.8989898989899 7.222222222222221 55.27777777777778 2 19.379844961240313 12.353088272068018 39.034758689672415 29.232308077019255 3 19.375 13.950000000000001 24.525 42.15 4 25.674999999999997 21.25 20.625 32.45 5 27.224999999999998 27.275 24.2 21.3 6 22.925 30.049999999999997 24.925 22.1 7 18.925 23.799999999999997 38.35 18.925 8 19.375 23.425 32.550000000000004 24.65 9 19.05 20.5 36.225 24.224999999999998 10 21.025 33.925 24.85 20.200000000000003 11 23.75 25.75 23.875 26.625 12 22.15 23.225 27.425 27.200000000000003 13 23.1 24.4 27.474999999999998 25.025 14 22.15 25.974999999999998 27.275 24.6 15 22.35 23.825 27.625 26.200000000000003 16 22.325 25.324999999999996 25.85 26.5 17 23.075000000000003 25.775 25.575 25.575 18 22.225 24.875 26.325 26.575 19 23.150000000000002 26.0 25.775 25.074999999999996 20 22.7 26.1 25.224999999999998 25.974999999999998 21 21.825 25.45 25.474999999999998 27.250000000000004 22 22.55 26.35 24.9 26.200000000000003 23 21.25 26.924999999999997 26.55 25.275 24 22.900000000000002 25.85 26.3 24.95 25 23.175 25.7 24.975 26.150000000000002 26 23.575 25.424999999999997 24.9 26.1 27 21.8 25.85 26.224999999999998 26.125 28 21.9 26.6 25.0 26.5 29 23.075000000000003 24.5 25.624999999999996 26.8 30 22.975 24.55 25.900000000000002 26.575 31 23.125 25.775 25.25 25.85 32 23.549999999999997 25.775 26.325 24.349999999999998 33 21.85 25.374999999999996 25.3 27.474999999999998 34 22.55 26.575 25.724999999999998 25.15 35 22.675 26.125 25.324999999999996 25.874999999999996 36 22.8 25.575 25.874999999999996 25.75 37 23.200000000000003 25.25 26.025 25.525 38 22.225 25.974999999999998 26.700000000000003 25.1 39 22.6 24.75 26.1 26.55 40 24.474999999999998 24.575 25.974999999999998 24.975 41 22.55 25.900000000000002 25.775 25.775 42 23.200000000000003 26.75 25.85 24.2 43 22.45 25.724999999999998 25.55 26.275 44 23.150000000000002 25.4 25.474999999999998 25.974999999999998 45 22.0 24.375 26.450000000000003 27.175 46 23.150000000000002 24.625 24.8 27.425 47 22.625 25.624999999999996 26.450000000000003 25.3 48 21.7 25.374999999999996 26.75 26.174999999999997 49 22.625 25.974999999999998 24.85 26.55 50 23.825 24.125 26.400000000000002 25.650000000000002 51 22.05 25.45 26.25 26.25 52 22.075 26.6 24.9 26.424999999999997 53 23.375 25.174999999999997 25.124999999999996 26.325 54 22.8 24.575 26.174999999999997 26.450000000000003 55 23.05 25.85 25.0 26.1 56 22.775000000000002 25.674999999999997 26.025 25.525 57 22.275 26.400000000000002 24.075 27.250000000000004 58 22.18054513628407 25.731432858214554 25.681420355088775 26.406601650412604 59 24.031007751937985 24.60615153788447 25.881470367591895 25.481370342585645 60 23.55588897224306 25.381345336334082 25.881470367591895 25.18129532383096 61 24.131032758189548 25.431357839459867 24.131032758189548 26.30657664416104 62 23.10577644411103 25.256314078519633 25.806451612903224 25.831457864466117 63 22.216662496872654 25.869402051538653 26.1195896922692 25.794345759319487 64 22.972972972972975 26.426426426426424 26.05105105105105 24.54954954954955 65 23.36589030803907 26.546456298522415 24.9686952166291 25.118958176809414 66 22.420286216419786 24.679889530504646 25.935224704996234 26.964599548079338 67 22.785768357305074 25.864244259399445 25.939944486500128 25.41004289679536 68 24.11311053984576 24.627249357326477 24.73007712082262 26.52956298200514 69 23.730224812656118 19.622536774909797 27.61587565917291 29.03136275326117 70 24.274406332453825 0.0 36.034677723332074 39.6909159442141 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.5 22 1.5 23 2.0 24 2.0 25 2.0 26 3.5 27 5.0 28 7.0 29 10.5 30 12.0 31 15.0 32 30.0 33 42.0 34 48.0 35 76.0 36 115.5 37 133.0 38 147.5 39 180.0 40 198.0 41 213.0 42 239.5 43 251.0 44 269.5 45 281.0 46 266.0 47 258.0 48 257.5 49 252.5 50 248.0 51 222.0 52 188.0 53 180.0 54 167.0 55 140.0 56 118.0 57 110.0 58 102.0 59 93.0 60 92.0 61 82.5 62 79.0 63 85.0 64 73.0 65 59.5 66 59.5 67 61.0 68 60.0 69 48.0 70 37.0 71 29.5 72 20.5 73 19.0 74 15.5 75 9.0 76 5.5 77 5.0 78 4.0 79 3.0 80 3.0 81 2.0 82 1.0 83 1.0 84 0.5 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content fail #Base N-Count 1 1.0 2 0.025 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 52 0.0 53 0.0 54 0.0 55 0.0 56 0.0 57 0.0 58 0.025 59 0.025 60 0.025 61 0.025 62 0.025 63 0.075 64 0.1 65 0.17500000000000002 66 0.42500000000000004 67 0.9249999999999999 68 2.75 69 9.925 70 33.675 >>END_MODULE >>Sequence Length Distribution pass #Length Count 70 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.55000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 99.57307885484681 99.125 2 0.4018081366147665 0.8 3 0.025113008538422906 0.075 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR5052707 read2 length is 70 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR5052707_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 70 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.4735 35.0 35.0 35.0 33.0 35.0 2 34.439 35.0 35.0 35.0 33.0 35.0 3 34.54025 35.0 35.0 35.0 34.0 35.0 4 34.43325 35.0 35.0 35.0 34.0 35.0 5 34.52925 35.0 35.0 35.0 34.0 35.0 6 39.2725 40.0 40.0 40.0 39.0 40.0 7 39.27025 40.0 40.0 40.0 39.0 40.0 8 39.13525 40.0 40.0 40.0 39.0 40.0 9 39.25375 40.0 40.0 40.0 39.0 40.0 10 39.22325 40.0 40.0 40.0 39.0 40.0 11 39.323 40.0 40.0 40.0 39.0 40.0 12 39.2915 40.0 40.0 40.0 39.0 40.0 13 39.315 40.0 40.0 40.0 39.0 40.0 14 39.27925 40.0 40.0 40.0 39.0 40.0 15 39.2565 40.0 40.0 40.0 39.0 40.0 16 39.3005 40.0 40.0 40.0 39.0 40.0 17 39.24425 40.0 40.0 40.0 39.0 40.0 18 39.26725 40.0 40.0 40.0 39.0 40.0 19 39.3015 40.0 40.0 40.0 39.0 40.0 20 39.35 40.0 40.0 40.0 39.0 40.0 21 39.323 40.0 40.0 40.0 39.0 40.0 22 39.35475 40.0 40.0 40.0 39.0 40.0 23 39.32 40.0 40.0 40.0 39.0 40.0 24 39.29375 40.0 40.0 40.0 39.0 40.0 25 39.25425 40.0 40.0 40.0 39.0 40.0 26 39.24325 40.0 40.0 40.0 39.0 40.0 27 39.28225 40.0 40.0 40.0 39.0 40.0 28 39.25425 40.0 40.0 40.0 39.0 40.0 29 39.3715 40.0 40.0 40.0 39.0 40.0 30 39.31975 40.0 40.0 40.0 39.0 40.0 31 39.366 40.0 40.0 40.0 39.0 40.0 32 39.362 40.0 40.0 40.0 39.0 40.0 33 39.34325 40.0 40.0 40.0 39.0 40.0 34 39.3305 40.0 40.0 40.0 39.0 40.0 35 39.31175 40.0 40.0 40.0 39.0 40.0 36 39.27375 40.0 40.0 40.0 39.0 40.0 37 39.19675 40.0 40.0 40.0 39.0 40.0 38 39.337 40.0 40.0 40.0 39.0 40.0 39 39.285 40.0 40.0 40.0 39.0 40.0 40 39.277 40.0 40.0 40.0 39.0 40.0 41 39.25575 40.0 40.0 40.0 39.0 40.0 42 39.2545 40.0 40.0 40.0 39.0 40.0 43 39.222 40.0 40.0 40.0 39.0 40.0 44 39.1835 40.0 40.0 40.0 39.0 40.0 45 39.20425 40.0 40.0 40.0 39.0 40.0 46 39.23575 40.0 40.0 40.0 39.0 40.0 47 39.2425 40.0 40.0 40.0 39.0 40.0 48 39.17625 40.0 40.0 40.0 39.0 40.0 49 39.23325 40.0 40.0 40.0 39.0 40.0 50 39.27225 40.0 40.0 40.0 39.0 40.0 51 39.21475 40.0 40.0 40.0 39.0 40.0 52 39.24475 40.0 40.0 40.0 39.0 40.0 53 39.255 40.0 40.0 40.0 39.0 40.0 54 39.24475 40.0 40.0 40.0 39.0 40.0 55 39.23225 40.0 40.0 40.0 39.0 40.0 56 39.19025 40.0 40.0 40.0 39.0 40.0 57 39.235 40.0 40.0 40.0 39.0 40.0 58 39.19 40.0 40.0 40.0 39.0 40.0 59 39.212 40.0 40.0 40.0 39.0 40.0 60 39.215 40.0 40.0 40.0 39.0 40.0 61 39.18925 40.0 40.0 40.0 39.0 40.0 62 39.184 40.0 40.0 40.0 39.0 40.0 63 39.1375 40.0 40.0 40.0 39.0 40.0 64 39.17325 40.0 40.0 40.0 39.0 40.0 65 39.18525 40.0 40.0 40.0 39.0 40.0 66 39.16575 40.0 40.0 40.0 39.0 40.0 67 39.2005 40.0 40.0 40.0 39.0 40.0 68 39.2625 40.0 40.0 40.0 39.0 40.0 69 39.23075 40.0 40.0 40.0 39.0 40.0 70 39.191 40.0 40.0 40.0 39.0 40.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 3.0 19 2.0 20 5.0 21 5.0 22 5.0 23 5.0 24 5.0 25 1.0 26 11.0 27 13.0 28 11.0 29 13.0 30 10.0 31 15.0 32 19.0 33 23.0 34 36.0 35 49.0 36 70.0 37 100.0 38 224.0 39 3375.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 26.325 18.5 12.8 42.375 2 26.900000000000002 22.400000000000002 31.35 19.35 3 20.5 24.45 30.15 24.9 4 24.825 30.225 21.2 23.75 5 28.625 31.825 20.9 18.65 6 22.20555138784696 35.108777194298575 22.18054513628407 20.505126281570394 7 21.9 18.65 36.65 22.8 8 23.625 21.425 25.924999999999997 29.025000000000002 9 23.400000000000002 22.075 28.725 25.8 10 24.85 30.85 23.95 20.349999999999998 11 28.499999999999996 24.125 20.875 26.5 12 26.625 22.225 24.4 26.75 13 26.424999999999997 23.474999999999998 24.325 25.775 14 24.7 25.074999999999996 25.525 24.7 15 25.924999999999997 25.1 25.275 23.7 16 27.075 23.425 25.8 23.7 17 26.400000000000002 25.4 23.599999999999998 24.6 18 25.074999999999996 25.724999999999998 25.2 24.0 19 26.674999999999997 24.45 24.875 24.0 20 27.900000000000002 24.375 23.075000000000003 24.65 21 24.349999999999998 25.825 25.15 24.675 22 26.450000000000003 25.1 25.074999999999996 23.375 23 25.275 24.725 25.874999999999996 24.125 24 24.474999999999998 26.325 25.650000000000002 23.549999999999997 25 26.775 26.075 23.375 23.775 26 26.224999999999998 25.874999999999996 24.075 23.825 27 25.05 25.2 24.375 25.374999999999996 28 25.6 24.8 25.95 23.65 29 26.424999999999997 25.2 24.2 24.175 30 25.275 26.075 25.6 23.05 31 25.4 25.575 24.349999999999998 24.675 32 26.125 25.75 24.099999999999998 24.025 33 25.1 25.7 25.25 23.95 34 27.224999999999998 25.5 23.599999999999998 23.674999999999997 35 26.8 25.874999999999996 23.799999999999997 23.525 36 24.825 26.450000000000003 25.525 23.200000000000003 37 26.400000000000002 24.275 23.65 25.674999999999997 38 26.0 25.724999999999998 23.05 25.224999999999998 39 24.875 26.450000000000003 24.925 23.75 40 25.724999999999998 25.025 24.575 24.675 41 26.450000000000003 24.8 23.799999999999997 24.95 42 24.375 25.674999999999997 26.025 23.925 43 26.174999999999997 26.35 24.6 22.875 44 26.325 25.324999999999996 24.5 23.849999999999998 45 25.124999999999996 26.3 24.75 23.825 46 24.675 26.474999999999998 25.124999999999996 23.724999999999998 47 24.675 26.025 25.1 24.2 48 25.424999999999997 25.474999999999998 24.875 24.224999999999998 49 25.7 24.075 25.924999999999997 24.3 50 26.674999999999997 25.525 24.85 22.95 51 26.525 25.7 25.424999999999997 22.35 52 26.6 23.7 24.349999999999998 25.35 53 27.075 24.425 24.975 23.525 54 26.05 25.85 26.1 22.0 55 25.85 24.7 25.224999999999998 24.224999999999998 56 26.85 23.974999999999998 25.85 23.325000000000003 57 25.25 26.625 25.05 23.075000000000003 58 26.6816704176044 24.50612653163291 24.381095273818453 24.431107776944234 59 26.556639159789945 26.03150787696924 23.43085771442861 23.980995248812203 60 24.50612653163291 26.506626656664167 26.18154538634659 22.80570142535634 61 26.506626656664167 25.78144536134033 24.15603900975244 23.55588897224306 62 26.30657664416104 25.481370342585645 24.63115778944736 23.58089522380595 63 25.268951713785338 26.319739804853644 25.04378283712785 23.367525644233176 64 26.576576576576578 25.05005005005005 25.275275275275277 23.0980980980981 65 26.885492357805063 25.783011776497116 24.429967426710096 22.90152843898772 66 25.783797341359417 25.859041886129923 25.63330825181841 22.72385252069225 67 26.520312894272013 23.64370426444613 25.46050971486248 24.37547312641938 68 27.333504757006942 23.8364618153767 24.787863203908458 24.042170223707892 69 26.896360100027785 19.588774659627674 27.090858571825503 26.424006668519034 70 27.165062916358252 0.0 35.86232420429312 36.97261287934863 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.5 20 1.0 21 1.0 22 2.0 23 3.0 24 2.5 25 1.5 26 3.5 27 6.0 28 7.5 29 12.0 30 15.0 31 20.0 32 29.5 33 34.0 34 45.0 35 75.0 36 107.0 37 120.0 38 139.0 39 171.5 40 185.0 41 198.5 42 238.5 43 265.0 44 256.5 45 264.0 46 261.0 47 242.0 48 232.0 49 221.0 50 220.0 51 205.5 52 180.0 53 169.0 54 164.0 55 148.0 56 131.5 57 126.0 58 108.5 59 95.5 60 100.0 61 90.5 62 87.0 63 93.0 64 87.5 65 78.0 66 68.0 67 62.0 68 70.5 69 58.0 70 37.0 71 33.5 72 27.5 73 25.0 74 24.5 75 22.0 76 14.0 77 8.0 78 6.0 79 3.5 80 3.0 81 2.5 82 1.5 83 1.0 84 0.5 85 0.0 86 0.0 87 0.0 88 0.0 89 0.5 90 1.0 91 0.5 92 0.5 93 1.0 94 0.5 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content fail #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.025 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 0.0 30 0.0 31 0.0 32 0.0 33 0.0 34 0.0 35 0.0 36 0.0 37 0.0 38 0.0 39 0.0 40 0.0 41 0.0 42 0.0 43 0.0 44 0.0 45 0.0 46 0.0 47 0.0 48 0.0 49 0.0 50 0.0 51 0.0 52 0.0 53 0.0 54 0.0 55 0.0 56 0.0 57 0.0 58 0.025 59 0.025 60 0.025 61 0.025 62 0.025 63 0.075 64 0.1 65 0.22499999999999998 66 0.325 67 0.9249999999999999 68 2.775 69 10.025 70 32.45 >>END_MODULE >>Sequence Length Distribution pass #Length Count 70 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.35000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 99.47156517362859 98.825 2 0.45294413688978363 0.8999999999999999 3 0.025163563160543533 0.075 4 0.050327126321087066 0.2 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10 0.0 0.0 0.0 0.0 0.0 11 0.0 0.0 0.0 0.0 0.0 12 0.0 0.0 0.0 0.0 0.0 13 0.0 0.0 0.0 0.0 0.0 14 0.0 0.0 0.0 0.0 0.0 15 0.0 0.0 0.0 0.0 0.0 16 0.0 0.0 0.0 0.0 0.0 17 0.0 0.0 0.0 0.0 0.0 18 0.0 0.0 0.0 0.0 0.0 19 0.0 0.0 0.0 0.0 0.0 20 0.0 0.0 0.0 0.0 0.0 21 0.0 0.0 0.0 0.0 0.0 22 0.0 0.0 0.0 0.0 0.0 23 0.0 0.0 0.0 0.0 0.0 24 0.0 0.0 0.0 0.0 0.0 25 0.0 0.0 0.0 0.0 0.0 26 0.0 0.0 0.0 0.0 0.0 27 0.0 0.0 0.0 0.0 0.0 28 0.0 0.0 0.0 0.0 0.0 29 0.0 0.0 0.0 0.0 0.0 30 0.0 0.0 0.0 0.0 0.0 31 0.0 0.0 0.0 0.0 0.0 32 0.0 0.0 0.0 0.0 0.0 33 0.0 0.0 0.0 0.0 0.0 34 0.0 0.0 0.0 0.0 0.0 35 0.0 0.0 0.0 0.0 0.0 36 0.0 0.0 0.0 0.0 0.0 37 0.0 0.0 0.0 0.0 0.0 38 0.0 0.0 0.0 0.0 0.0 39 0.0 0.0 0.0 0.0 0.0 40 0.0 0.0 0.0 0.0 0.0 41 0.0 0.0 0.0 0.0 0.0 42 0.0 0.0 0.0 0.0 0.0 43 0.0 0.0 0.0 0.0 0.0 44 0.0 0.0 0.0 0.0 0.0 45 0.0 0.0 0.0 0.0 0.0 46 0.0 0.0 0.0 0.0 0.0 47 0.0 0.0 0.0 0.0 0.0 48 0.0 0.0 0.0 0.0 0.0 49 0.0 0.0 0.0 0.0 0.0 50 0.0 0.0 0.0 0.0 0.0 51 0.0 0.0 0.0 0.0 0.0 52 0.0 0.0 0.0 0.0 0.0 53 0.0 0.0 0.0 0.0 0.0 54 0.0 0.0 0.0 0.0 0.0 55 0.0 0.0 0.0 0.0 0.0 56 0.0 0.0 0.0 0.0 0.0 57 0.0 0.0 0.0 0.0 0.0 58 0.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306578 spots for ERR5052707.sra Written 306578 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra Read 306568 spots for ERR5052707.sra Written 306568 spots for ERR5052707.sra SRR ids: ['ERR5052707.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5jdvw2d4 ERR5052707.sra spots: 6131370 blocks: [[1, 306568], [306569, 613136], [613137, 919704], [919705, 1226272], [1226273, 1532840], [1532841, 1839408], [1839409, 2145976], [2145977, 2452544], [2452545, 2759112], [2759113, 3065680], [3065681, 3372248], [3372249, 3678816], [3678817, 3985384], [3985385, 4291952], [4291953, 4598520], [4598521, 4905088], [4905089, 5211656], [5211657, 5518224], [5518225, 5824792], [5824793, 6131370]] ERR5052707 file size 1087586 ERR5052707 completed basic pipeline successfully skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -q 10 -k inf -t 20 -o ERR5052707 ERR5052707_1.fastq ERR5052707_2.fastq Input file: ERR5052707_1.fastq Paired file: ERR5052707_2.fastq trimmed: ERR5052707-trimmed-pair1.fastq, ERR5052707-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Dec 10 08:15:53 2024 >> started Tue Dec 10 08:15:59 2024 >> done (5.475s) 6131370 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 15 ( 0.00%) empty read pairs filtered out after trimming by size control 6131355 (100.00%) read pairs available; of these: 31 ( 0.00%) trimmed read pairs available after processing 6131324 (100.00%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 35 1 0.00% 36 1 0.00% 37 0 0.00% 38 0 0.00% 39 0 0.00% 40 0 0.00% 41 0 0.00% 42 0 0.00% 43 0 0.00% 44 0 0.00% 45 1 0.00% 46 0 0.00% 47 0 0.00% 48 0 0.00% 49 1 0.00% 50 0 0.00% 51 1 0.00% 52 0 0.00% 53 1 0.00% 54 2 0.00% 55 0 0.00% 56 0 0.00% 57 0 0.00% 58 0 0.00% 59 0 0.00% 60 0 0.00% 61 0 0.00% 62 0 0.00% 63 0 0.00% 64 0 0.00% 65 0 0.00% 66 0 0.00% 67 0 0.00% 68 0 0.00% 69 23 0.00% 70 6131324 100.00% 6131355 reads passed initial QC criterion=sequence-density sequence-density=0.15 sequence-density-rank=1 fanout-score=2.19 fanout-score-rank=31 prefix-density=0.16 prefix-fanout=2.1 sequence=GATCTCGCCGAAG criterion=fanout-score sequence-density=0.05 sequence-density-rank=6 fanout-score=259.68 fanout-score-rank=1 prefix-density=0.49 prefix-fanout=26.2 sequence=CTTCTTCTTGTC criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=2.07 fanout-score-rank=28 prefix-density=0.29 prefix-fanout=2.1 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.05 sequence-density-rank=25 fanout-score=252.88 fanout-score-rank=1 prefix-density=0.60 prefix-fanout=19.3 sequence=CGCCGCCGCCGA ERR5052707 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 08:16:33 Started mapping on | Dec 10 08:16:33 Finished on | Dec 10 08:16:49 Mapping speed, Million of reads per hour | 1379.55 Number of input reads | 6131355 Average input read length | 139 UNIQUE READS: Uniquely mapped reads number | 5901216 Uniquely mapped reads % | 96.25% Average mapped length | 138.72 Number of splices: Total | 2985459 Number of splices: Annotated (sjdb) | 2844074 Number of splices: GT/AG | 2947044 Number of splices: GC/AG | 33902 Number of splices: AT/AC | 1511 Number of splices: Non-canonical | 3002 Mismatch rate per base, % | 0.20% Deletion rate per base | 0.01% Deletion average length | 1.89 Insertion rate per base | 0.01% Insertion average length | 1.70 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 88836 % of reads mapped to multiple loci | 1.45% Number of reads mapped to too many loci | 12594 % of reads mapped to too many loci | 0.21% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.50% % of reads unmapped: other | 0.60% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 141303 141303 141303 N_multimapping 88836 88836 88836 N_noFeature 190013 5757880 226747 N_ambiguous 126330 555 19889 UnstrandedReadsAssigned:5584873 PositiveStrandReadsAssigned:142781 NegativeStrandReadsAssigned:5654580 Dataset is classified negative stranded MeadianReadLen=70 20thPercentileLength=70 echo kmer=65 ERR5052707 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: ERR5052707-trimmed-pair1.fastq ERR5052707-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 6,131,355 reads, 5,721,529 reads pseudoaligned [quant] estimated average fragment length: 187.603 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,041 rounds 52973 ERR5052707.ke.tsv 35125 ERR5052707.se.tsv 88098 total ==> ERR5052707.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 749.539 2.24534 0.787083 PNS24247 1044 857.397 15.705 4.81269 PNS24249 1928 1741.4 46.2063 6.97165 PNS24246 1044 857.397 15.705 4.81269 PNS24248 1044 857.397 15.705 4.81269 PNS24244 1471 1284.4 47.4334 9.70324 PNS24243 293 125.169 0 0 KQK14069 1603 1416.4 7251.3 1345.13 KQK14071 474 291.123 160.611 144.954 ==> ERR5052707.se.tsv <== BRADI_1g14170v3 8106 BRADI_1g53295v3 40 BRADI_1g59795v3 240 BRADI_1g07683v3 0 BRADI_1g00485v3 8 BRADI_1g20270v3 384 BRADI_1g74790v3 122 BRADI_1g09890v3 0 BRADI_1g77505v3 210 BRADI_1g48960v3 0 ERR5052707 completed mapping pipeline successfully