Starting /dee2/code/volunteer_pipeline.sh ERR3317466 current disk space = 1524727386112 free memory = 1596437776 ERR3317466 SRAfilesize 290bb437f5f432b6d9dff812b6bfe972 ERR3317466.sra ERR3317466.sra file validated ERR3317466 is paired end ERR3317466 is conventional basespace ERR3317466 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3317466_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.47425 34.0 31.0 34.0 30.0 34.0 2 32.24925 34.0 31.0 34.0 30.0 34.0 3 32.773 34.0 31.0 34.0 31.0 34.0 4 36.3185 37.0 37.0 37.0 35.0 37.0 5 36.3315 37.0 37.0 37.0 35.0 37.0 6 36.19575 37.0 37.0 37.0 35.0 37.0 7 36.30375 37.0 37.0 37.0 35.0 37.0 8 36.34075 37.0 37.0 37.0 35.0 37.0 9 38.21125 39.0 39.0 39.0 37.0 39.0 10-11 38.108999999999995 39.0 39.0 39.0 36.0 39.0 12-13 38.109125 39.0 39.0 39.0 37.0 39.0 14-15 39.659875 41.0 40.0 41.0 37.0 41.0 16-17 39.669125 41.0 40.0 41.0 37.0 41.0 18-19 39.576499999999996 41.0 40.0 41.0 37.0 41.0 20-21 39.5505 41.0 40.0 41.0 37.0 41.0 22-23 39.423125 41.0 39.0 41.0 36.0 41.0 24-25 39.338499999999996 41.0 39.0 41.0 36.0 41.0 26-27 39.146375 41.0 39.0 41.0 35.5 41.0 28-29 38.9955 40.5 39.0 41.0 35.0 41.0 30-31 38.856 40.0 39.0 41.0 35.0 41.0 32-33 38.67675 40.0 38.0 41.0 34.5 41.0 34-35 38.399625 40.0 38.0 41.0 34.0 41.0 36-37 38.221000000000004 40.0 38.0 41.0 33.5 41.0 38-39 37.97475 40.0 38.0 41.0 33.0 41.0 40-41 37.71875 40.0 37.5 41.0 33.0 41.0 42-43 37.76225 40.0 37.0 41.0 33.0 41.0 44-45 37.629374999999996 40.0 37.0 41.0 33.0 41.0 46-47 37.326 40.0 36.5 41.0 32.5 41.0 48-49 37.056 40.0 36.0 41.0 31.5 41.0 50-51 37.37025 40.0 36.0 41.0 32.5 41.0 52-53 37.21175 40.0 35.5 41.0 32.5 41.0 54-55 36.91375 39.0 35.0 41.0 32.0 41.0 56-57 36.661249999999995 39.0 35.0 41.0 31.0 41.0 58-59 36.400375 38.5 35.0 41.0 31.5 41.0 60-61 35.9795 38.0 35.0 40.5 31.0 41.0 62-63 35.623374999999996 37.0 35.0 40.0 30.0 41.0 64-65 35.28325 36.5 35.0 40.0 29.5 41.0 66-67 34.8835 36.0 34.0 39.0 29.5 41.0 68-69 34.4525 35.5 34.0 39.0 29.0 41.0 70-71 34.11625 35.0 34.0 38.5 29.0 40.0 72-73 33.652249999999995 35.0 34.0 37.0 28.0 39.0 74-75 33.251375 35.0 34.0 37.0 27.5 39.0 76-77 31.90475 34.5 32.0 35.5 25.0 37.0 78-79 32.416125 35.0 33.0 36.0 26.0 37.0 80-81 32.310375 35.0 33.0 35.5 26.0 37.0 82-83 32.046125 35.0 33.0 35.0 25.5 36.5 84-85 31.715 35.0 33.0 35.0 24.5 36.0 86-87 31.431 35.0 33.0 35.0 24.0 36.0 88-89 31.192125 35.0 32.5 35.0 22.5 35.5 90-91 30.94325 35.0 32.0 35.0 21.5 35.0 92-93 30.657375000000002 35.0 32.0 35.0 18.5 35.0 94-95 30.361375000000002 35.0 32.0 35.0 17.0 35.0 96-97 30.036375 35.0 31.0 35.0 6.0 35.0 98-99 29.647 34.5 31.0 35.0 2.0 35.0 100-101 27.19875 32.5 25.5 34.5 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 3.0 3 0.0 4 0.0 5 2.0 6 0.0 7 4.0 8 2.0 9 6.0 10 2.0 11 4.0 12 9.0 13 9.0 14 11.0 15 7.0 16 10.0 17 8.0 18 9.0 19 11.0 20 15.0 21 20.0 22 26.0 23 13.0 24 19.0 25 17.0 26 26.0 27 33.0 28 42.0 29 63.0 30 79.0 31 77.0 32 114.0 33 140.0 34 195.0 35 310.0 36 552.0 37 1005.0 38 1035.0 39 122.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 25.85212375458836 26.245411641321446 20.110120608285264 27.79234399580493 2 25.650000000000002 26.0 18.7 29.65 3 25.6 25.6 18.725 30.075000000000003 4 26.724999999999998 25.1 17.65 30.525000000000002 5 28.349999999999998 24.875 16.325 30.45 6 28.175 28.475 18.4 24.95 7 28.799999999999997 24.224999999999998 22.125 24.85 8 31.275 26.875 23.474999999999998 18.375 9 31.2 27.975 23.599999999999998 17.224999999999998 10-11 32.85 26.2625 22.0125 18.875 12-13 29.7 25.587500000000002 24.587500000000002 20.125 14-15 27.437499999999996 27.400000000000002 24.125 21.0375 16-17 27.0625 25.2375 25.124999999999996 22.575 18-19 25.074999999999996 27.2625 25.224999999999998 22.4375 20-21 24.5625 26.875 26.200000000000003 22.3625 22-23 25.662499999999998 27.187499999999996 24.575 22.575 24-25 24.637500000000003 25.8125 25.775 23.775 26-27 25.9625 26.0375 24.6625 23.3375 28-29 25.7375 25.575 25.7 22.9875 30-31 25.7375 25.224999999999998 26.3 22.7375 32-33 24.837500000000002 26.075 26.387500000000003 22.7 34-35 25.95 25.3 25.662499999999998 23.0875 36-37 25.35 26.637499999999996 25.4875 22.525000000000002 38-39 24.825 26.5125 25.95 22.7125 40-41 26.3625 24.575 25.674999999999997 23.3875 42-43 25.35 25.587500000000002 25.474999999999998 23.5875 44-45 25.412499999999998 26.1 26.0375 22.45 46-47 26.275 25.6 24.349999999999998 23.775 48-49 26.075 26.85 25.75 21.325 50-51 26.025 25.8 25.974999999999998 22.2 52-53 25.637500000000003 26.75 24.45 23.1625 54-55 25.224999999999998 26.9625 25.662499999999998 22.15 56-57 25.2 25.874999999999996 25.9875 22.9375 58-59 25.900000000000002 25.3125 24.5375 24.25 60-61 24.6875 27.200000000000003 25.7125 22.400000000000002 62-63 26.0 26.0125 24.5 23.4875 64-65 25.9875 26.224999999999998 25.0125 22.775000000000002 66-67 24.349999999999998 26.400000000000002 25.5 23.75 68-69 25.55 25.924999999999997 25.8125 22.7125 70-71 26.924999999999997 26.075 23.962500000000002 23.0375 72-73 24.762500000000003 26.5375 25.174999999999997 23.525 74-75 25.4875 25.624999999999996 25.074999999999996 23.8125 76-77 25.674999999999997 26.8 23.2375 24.2875 78-79 25.087500000000002 26.637499999999996 25.924999999999997 22.35 80-81 25.8625 27.0125 24.0125 23.1125 82-83 26.137500000000003 27.250000000000004 23.5375 23.075000000000003 84-85 26.187500000000004 25.9625 25.112499999999997 22.7375 86-87 25.912499999999998 27.55 24.2 22.3375 88-89 25.174999999999997 26.5 24.7 23.625 90-91 25.25 26.424999999999997 25.7125 22.6125 92-93 26.8 26.55 23.775 22.875 94-95 25.3 27.575 23.849999999999998 23.275000000000002 96-97 25.724999999999998 26.05 25.174999999999997 23.05 98-99 24.712500000000002 26.8625 24.05 24.375 100-101 24.875 27.0625 22.7375 25.324999999999996 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 2.0 1 1.5 2 1.0 3 0.5 4 0.5 5 0.5 6 0.5 7 1.0 8 0.5 9 0.0 10 0.0 11 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.5 19 1.0 20 1.0 21 1.0 22 1.0 23 1.5 24 3.0 25 3.5 26 4.0 27 4.5 28 5.5 29 6.0 30 8.0 31 15.0 32 18.5 33 19.0 34 27.0 35 34.5 36 45.5 37 54.5 38 62.0 39 86.0 40 129.5 41 158.5 42 177.5 43 202.0 44 199.0 45 202.0 46 201.0 47 206.5 48 204.5 49 180.5 50 169.5 51 148.0 52 133.5 53 133.5 54 119.5 55 99.5 56 87.0 57 82.0 58 80.5 59 67.0 60 62.5 61 62.0 62 53.0 63 43.5 64 40.5 65 38.0 66 33.0 67 39.5 68 33.0 69 19.5 70 18.5 71 26.0 72 28.5 73 21.0 74 11.0 75 9.0 76 11.0 77 10.0 78 9.0 79 7.0 80 6.5 81 4.5 82 4.5 83 4.0 84 2.5 85 2.5 86 2.5 87 1.5 88 1.5 89 1.0 90 0.5 91 1.0 92 0.5 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 pass #Base N-Count 1 4.65 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.0 14-15 0.0 16-17 0.0 18-19 0.0 20-21 0.0 22-23 0.0 24-25 0.0 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0 42-43 0.0 44-45 0.0 46-47 0.0 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0 66-67 0.0 68-69 0.0 70-71 0.0 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 98.02499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 98.75031879622546 96.8 2 0.9946442234123948 1.95 3 0.102014792144861 0.3 4 0.0510073960724305 0.2 5 0.0 0.0 6 0.02550369803621525 0.15 7 0.02550369803621525 0.17500000000000002 8 0.02550369803621525 0.2 9 0.02550369803621525 0.22499999999999998 >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 warn #Sequence Count Percentage Possible Source TGCAAATGGAGTCCTGAACTAGCCGCAGCTTGTGAAGTATGGAAGGCGAT 9 0.22499999999999998 No Hit AGCCGCAGCTTGTGAAGTATGGAAGGCGATCAAATTCGAGTTCGCGCCGG 8 0.2 No Hit TGCTCGTGAAGGTAATGAAATTATCCGAGCAGCTTGCAAATGGAGTCCTG 7 0.17500000000000002 No Hit ACTTAACTGGGGGATTCACCGCAAATACTACTTTGGCTCATTATTGCCGC 6 0.15 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.05 0.0 0.0 0.0 0.0 9 0.05 0.0 0.0 0.0 0.0 10-11 0.05 0.0 0.0 0.0 0.0 12-13 0.05 0.0 0.0 0.0 0.0 14-15 0.05 0.0 0.0 0.0 0.0 16-17 0.05 0.0 0.0 0.0 0.0 18-19 0.05 0.0 0.0 0.0 0.0 20-21 0.05 0.0 0.0 0.0 0.0 22-23 0.05 0.0 0.0 0.0 0.0 24-25 0.05 0.0 0.0 0.0 0.0 26-27 0.05 0.0 0.0 0.0 0.0 28-29 0.0625 0.0 0.0 0.0 0.0 30-31 0.125 0.0 0.0 0.0 0.0 32-33 0.175 0.0 0.0 0.0 0.0 34-35 0.2 0.0 0.0 0.0 0.0 36-37 0.2625 0.0 0.0 0.0 0.0 38-39 0.3125 0.0 0.0 0.0 0.0 40-41 0.325 0.0 0.0 0.0 0.0 42-43 0.375 0.0 0.0 0.0 0.0 44-45 0.4 0.0 0.0 0.0 0.0 46-47 0.475 0.0 0.0 0.0 0.0 48-49 0.5874999999999999 0.0 0.0 0.0 0.0 50-51 0.75 0.0 0.0 0.0 0.0 52-53 0.8625 0.0 0.0 0.0 0.0 54-55 1.0125 0.0 0.0 0.0 0.0 56-57 1.175 0.0 0.0 0.0 0.0 58-59 1.375 0.0 0.0 0.0 0.0 60-61 1.6125 0.0 0.0 0.0 0.0 62-63 1.8125 0.0 0.0 0.0 0.0 64-65 2.0125 0.0 0.0 0.0 0.0 66-67 2.2375 0.0 0.0 0.0 0.0 68-69 2.55 0.0 0.0 0.0 0.0 70-71 2.8375000000000004 0.0 0.0 0.0 0.0 72-73 3.2375 0.0 0.0 0.0 0.0 74-75 3.5999999999999996 0.0 0.0 0.0 0.0 76-77 4.0625 0.0 0.0 0.0 0.0 78-79 4.425 0.0 0.0 0.0 0.0 80-81 4.95 0.0 0.0 0.0 0.0 82-83 5.1875 0.0 0.0 0.0 0.0 84-85 5.775 0.0 0.0 0.0 0.0 86-87 6.45 0.0 0.0 0.0 0.0 88-89 7.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3317466 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3317466_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 101 %GC 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.922 33.0 31.0 34.0 30.0 34.0 2 32.01175 34.0 31.0 34.0 30.0 34.0 3 32.04075 34.0 31.0 34.0 30.0 34.0 4 35.249 37.0 35.0 37.0 33.0 37.0 5 35.4175 37.0 35.0 37.0 33.0 37.0 6 35.571 37.0 35.0 37.0 35.0 37.0 7 35.576 37.0 37.0 37.0 35.0 37.0 8 35.561 37.0 37.0 37.0 35.0 37.0 9 37.2515 39.0 38.0 39.0 35.0 39.0 10-11 37.329625 39.0 38.0 39.0 35.0 39.0 12-13 37.306 39.0 38.0 39.0 35.0 39.0 14-15 38.838750000000005 41.0 40.0 41.0 36.0 41.0 16-17 38.860375 41.0 39.5 41.0 36.0 41.0 18-19 38.7215 41.0 39.0 41.0 35.0 41.0 20-21 38.673 41.0 39.0 41.0 35.0 41.0 22-23 38.62425 41.0 39.0 41.0 35.0 41.0 24-25 38.542 41.0 39.0 41.0 35.0 41.0 26-27 38.463499999999996 41.0 39.0 41.0 35.0 41.0 28-29 38.38975 41.0 39.0 41.0 35.0 41.0 30-31 38.210499999999996 41.0 39.0 41.0 34.0 41.0 32-33 38.07325 40.0 38.0 41.0 34.0 41.0 34-35 37.884 40.0 38.0 41.0 33.5 41.0 36-37 37.81225 40.0 38.0 41.0 33.5 41.0 38-39 37.58825 40.0 38.0 41.0 33.0 41.0 40-41 37.738 40.0 38.0 41.0 33.0 41.0 42-43 37.67275 40.0 38.0 41.0 33.0 41.0 44-45 37.548875 40.0 38.0 41.0 33.0 41.0 46-47 37.3845 40.0 38.0 41.0 33.0 41.0 48-49 37.254 40.0 37.5 41.0 32.5 41.0 50-51 36.3185 39.0 36.0 40.5 31.0 40.5 52-53 36.280625 39.0 35.5 40.5 30.5 41.0 54-55 36.493625 40.0 35.5 41.0 31.0 41.0 56-57 36.288624999999996 39.0 35.0 41.0 30.5 41.0 58-59 36.11175 39.0 35.0 41.0 30.0 41.0 60-61 35.789375 39.0 35.0 41.0 30.0 41.0 62-63 35.545375 38.0 35.0 40.5 30.0 41.0 64-65 35.20825000000001 37.0 35.0 40.0 29.0 41.0 66-67 35.24075 37.0 35.0 40.0 30.0 41.0 68-69 34.853750000000005 36.5 35.0 39.0 30.0 41.0 70-71 34.612125000000006 36.0 35.0 39.0 30.0 41.0 72-73 34.268 35.5 35.0 39.0 29.5 40.5 74-75 33.864999999999995 35.0 35.0 37.0 29.0 39.5 76-77 33.5205 35.0 34.0 37.0 29.0 39.0 78-79 33.2065 35.0 34.0 36.5 29.0 39.0 80-81 32.8165 35.0 34.0 36.0 28.5 37.0 82-83 32.566874999999996 35.0 34.0 36.0 27.0 37.0 84-85 32.37125 35.0 34.0 35.0 27.5 36.5 86-87 32.137249999999995 35.0 34.0 35.0 27.0 36.0 88-89 31.93175 35.0 33.0 35.0 26.0 36.0 90-91 31.738 35.0 33.0 35.0 25.0 36.0 92-93 31.485625 35.0 33.0 35.0 25.0 35.0 94-95 31.30725 35.0 33.0 35.0 24.0 35.0 96-97 31.0415 35.0 33.0 35.0 23.0 35.0 98-99 30.72 35.0 33.0 35.0 12.5 35.0 100-101 28.785874999999997 33.5 29.0 34.5 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 53.0 3 6.0 4 5.0 5 6.0 6 5.0 7 5.0 8 4.0 9 10.0 10 11.0 11 14.0 12 7.0 13 8.0 14 14.0 15 6.0 16 8.0 17 7.0 18 2.0 19 7.0 20 7.0 21 6.0 22 16.0 23 10.0 24 17.0 25 22.0 26 15.0 27 23.0 28 29.0 29 31.0 30 57.0 31 57.0 32 66.0 33 97.0 34 156.0 35 269.0 36 431.0 37 946.0 38 1297.0 39 270.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 28.4 12.6 28.299999999999997 30.7 2 25.974999999999998 11.1 25.25 37.675 3 23.525 12.975 28.4 35.099999999999994 4 24.175 11.625 27.075 37.125 5 25.7 14.75 23.175 36.375 6 26.1 19.3 27.975 26.625 7 19.425 23.775 39.75 17.05 8 17.65 25.674999999999997 35.8 20.875 9 18.0 28.825 34.55 18.625 10-11 19.94248562140535 27.344336084021002 32.13303325831458 20.580145036259065 12-13 19.46493311663958 28.328541067633456 31.741467683460435 20.465058132266535 14-15 19.607352757283984 26.02225834688008 31.98699512317119 22.38339377266475 16-17 20.24509190946605 26.147305239464803 29.035888458171815 24.571714392897338 18-19 19.984992496248125 27.56378189094547 29.477238619309652 22.973986993496748 20-21 21.48305614605477 26.960110041265473 28.735775915968485 22.821057896711267 22-23 21.48574287143572 25.65032516258129 28.62681340670335 24.23711855927964 24-25 19.829957489372344 26.981745436359088 29.544886221555387 23.643410852713178 26-27 21.462500000000002 26.775 27.075 24.6875 28-29 21.375 26.4125 26.900000000000002 25.3125 30-31 20.175 26.650000000000002 29.3375 23.8375 32-33 22.6875 26.337500000000002 26.8375 24.1375 34-35 20.45 25.7 27.474999999999998 26.375 36-37 21.1375 26.2875 28.012500000000003 24.5625 38-39 21.912499999999998 26.674999999999997 26.950000000000003 24.462500000000002 40-41 21.81522690336292 24.6530816352044 27.103387923490434 26.428303537942245 42-43 22.15 26.5125 27.5125 23.825 44-45 21.958234337876704 26.222333375015634 26.2348380642741 25.584594222833562 46-47 21.552694086760845 26.065758219777475 25.90323790473809 26.478309788723593 48-49 20.7375 27.737499999999997 26.6125 24.9125 50-51 21.6125 26.650000000000002 26.1 25.637500000000003 52-53 21.825 26.3625 26.087500000000002 25.724999999999998 54-55 21.3125 27.8875 27.6625 23.1375 56-57 21.15 26.1625 27.6125 25.074999999999996 58-59 21.712500000000002 26.3 26.6125 25.374999999999996 60-61 21.1625 25.912499999999998 27.6625 25.2625 62-63 21.775 26.7125 26.0625 25.45 64-65 21.990248781097637 24.415551943992998 27.65345668208526 25.9407425928241 66-67 22.0625 26.825 27.0875 24.025 68-69 22.4625 25.7875 26.6 25.15 70-71 21.677709713714215 26.365795724465556 26.040755094386796 25.91573946743343 72-73 22.112499999999997 26.487500000000004 25.874999999999996 25.525 74-75 22.48062015503876 26.244061015253813 25.568892223055762 25.70642660665166 76-77 22.112499999999997 26.35 25.775 25.7625 78-79 22.45 26.7125 26.525 24.3125 80-81 23.025000000000002 26.775 25.937500000000004 24.2625 82-83 23.400000000000002 25.174999999999997 25.025 26.400000000000002 84-85 24.4 26.05 26.05 23.5 86-87 24.65 26.5625 25.2 23.5875 88-89 23.3 25.624999999999996 25.4625 25.6125 90-91 24.1375 26.2125 25.937500000000004 23.7125 92-93 22.9875 26.3125 26.375 24.325 94-95 24.2375 26.5375 24.7875 24.4375 96-97 24.887500000000003 26.25 25.825 23.0375 98-99 24.075 26.687499999999996 24.762500000000003 24.474999999999998 100-101 24.065508188523566 25.703212901612705 25.015626953369168 25.21565195649456 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 14.0 1 8.0 2 2.5 3 2.5 4 3.0 5 2.5 6 1.0 7 2.0 8 2.0 9 1.5 10 1.0 11 1.5 12 2.5 13 2.0 14 1.0 15 1.5 16 2.0 17 0.5 18 1.0 19 1.5 20 0.5 21 2.0 22 2.5 23 2.5 24 3.0 25 1.5 26 1.5 27 3.5 28 8.5 29 12.5 30 15.5 31 21.0 32 25.0 33 34.0 34 49.5 35 55.5 36 60.0 37 81.0 38 100.0 39 120.0 40 150.0 41 192.5 42 214.5 43 208.0 44 201.0 45 194.0 46 193.0 47 181.5 48 176.0 49 166.0 50 160.5 51 154.0 52 132.5 53 113.5 54 87.5 55 80.5 56 89.0 57 84.0 58 68.0 59 60.5 60 51.5 61 46.5 62 42.5 63 37.5 64 37.0 65 30.5 66 24.5 67 22.0 68 22.5 69 18.5 70 19.5 71 17.5 72 13.0 73 10.5 74 8.0 75 7.5 76 5.0 77 7.0 78 7.0 79 4.5 80 4.5 81 5.0 82 3.0 83 0.5 84 0.0 85 0.5 86 0.5 87 0.0 88 0.5 89 0.5 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 pass #Base N-Count 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 10-11 0.025 12-13 0.0125 14-15 0.0375 16-17 0.0375 18-19 0.05 20-21 0.0375 22-23 0.05 24-25 0.025 26-27 0.0 28-29 0.0 30-31 0.0 32-33 0.0 34-35 0.0 36-37 0.0 38-39 0.0 40-41 0.0125 42-43 0.0 44-45 0.0375 46-47 0.0125 48-49 0.0 50-51 0.0 52-53 0.0 54-55 0.0 56-57 0.0 58-59 0.0 60-61 0.0 62-63 0.0 64-65 0.0125 66-67 0.0 68-69 0.0 70-71 0.0125 72-73 0.0 74-75 0.025 76-77 0.0 78-79 0.0 80-81 0.0 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.0 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100-101 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 101 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 97.425 #Duplication Level Percentage of deduplicated Percentage of total 1 98.92224788298691 96.375 2 0.7441621760328458 1.4500000000000002 3 0.12830382345393893 0.375 4 0.07698229407236336 0.3 5 0.0 0.0 6 0.051321529381575574 0.3 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.07698229407236336 1.2 >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 warn #Sequence Count Percentage Possible Source TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 25 0.625 No Hit TGGGGATGAAAAATAGAAAACTCAAAGCAATGTCAGAGTTGACAAAACTG 13 0.325 No Hit TCTTCATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 10 0.25 No Hit TCTTTATATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 6 0.15 No Hit TCTTCGTATTTAGTTTTATCTATTAATCGATAGTATCTACCGGCGCGAAC 6 0.15 No Hit >>END_MODULE >>Adapter Content warn #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 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.037500000000000006 0.0 0.0 0.0 0.0 30-31 0.1 0.0 0.0 0.0 0.0 32-33 0.15 0.0 0.0 0.0 0.0 34-35 0.175 0.0 0.0 0.0 0.0 36-37 0.2375 0.0 0.0 0.0 0.0 38-39 0.2875 0.0 0.0 0.0 0.0 40-41 0.3 0.0 0.0 0.0 0.0 42-43 0.325 0.0 0.0 0.0 0.0 44-45 0.35 0.0 0.0 0.0 0.0 46-47 0.4125 0.0 0.0 0.0 0.0 48-49 0.5125 0.0 0.0 0.0 0.0 50-51 0.675 0.0 0.0 0.0 0.0 52-53 0.7625 0.0 0.0 0.0 0.0 54-55 0.9125 0.0 0.0 0.0 0.0 56-57 1.075 0.0 0.0 0.0 0.0 58-59 1.2625 0.0 0.0 0.0 0.0 60-61 1.4875 0.0 0.0 0.0 0.0 62-63 1.7 0.0 0.0 0.0 0.0 64-65 1.9 0.0 0.0 0.0 0.0 66-67 2.1125 0.0 0.0 0.0 0.0 68-69 2.45 0.0 0.0 0.0 0.0 70-71 2.775 0.0 0.0 0.0 0.0 72-73 3.1875 0.0 0.0 0.0 0.0 74-75 3.6375 0.0 0.0 0.0 0.0 76-77 4.0875 0.0 0.0 0.0 0.0 78-79 4.4625 0.0 0.0 0.0 0.0 80-81 4.9875 0.0 0.0 0.0 0.0 82-83 5.2625 0.0 0.0 0.0 0.0 84-85 5.8125 0.0 0.0 0.0 0.0 86-87 6.525 0.0 0.0 0.0 0.0 88-89 7.0375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGCACCA 15 0.009957196 47.5 90-91 >>END_MODULE Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra Read 1913963 spots for ERR3317466.sra Written 1913963 spots for ERR3317466.sra Read 1913947 spots for ERR3317466.sra Written 1913947 spots for ERR3317466.sra SRR ids: ['ERR3317466.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_yt1jrytt ERR3317466.sra spots: 38278956 blocks: [[1, 1913947], [1913948, 3827894], [3827895, 5741841], [5741842, 7655788], [7655789, 9569735], [9569736, 11483682], [11483683, 13397629], [13397630, 15311576], [15311577, 17225523], [17225524, 19139470], [19139471, 21053417], [21053418, 22967364], [22967365, 24881311], [24881312, 26795258], [26795259, 28709205], [28709206, 30623152], [30623153, 32537099], [32537100, 34451046], [34451047, 36364993], [36364994, 38278956]] ERR3317466 file size 9211602 ERR3317466 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 ERR3317466 ERR3317466_1.fastq ERR3317466_2.fastq Input file: ERR3317466_1.fastq Paired file: ERR3317466_2.fastq trimmed: ERR3317466-trimmed-pair1.fastq, ERR3317466-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 10:13:41 2024 >> started Tue Dec 10 10:14:18 2024 >> done (36.623s) 38278956 read pairs processed; of these: 260281 ( 0.68%) short read pairs filtered out after trimming by size control 676711 ( 1.77%) empty read pairs filtered out after trimming by size control 37341964 (97.55%) read pairs available; of these: 11394685 (30.51%) trimmed read pairs available after processing 25947279 (69.49%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 762 0.00% 19 795 0.00% 20 1141 0.00% 21 1364 0.00% 22 1726 0.00% 23 2397 0.01% 24 3029 0.01% 25 3611 0.01% 26 4295 0.01% 27 4940 0.01% 28 5493 0.01% 29 6476 0.02% 30 7314 0.02% 31 10914 0.03% 32 9896 0.03% 33 10262 0.03% 34 12864 0.03% 35 13064 0.03% 36 14422 0.04% 37 15193 0.04% 38 17755 0.05% 39 19136 0.05% 40 18936 0.05% 41 20940 0.06% 42 21938 0.06% 43 23661 0.06% 44 25349 0.07% 45 25959 0.07% 46 27561 0.07% 47 32458 0.09% 48 32734 0.09% 49 33725 0.09% 50 37686 0.10% 51 38262 0.10% 52 39404 0.11% 53 43240 0.12% 54 48442 0.13% 55 49831 0.13% 56 51482 0.14% 57 55112 0.15% 58 58931 0.16% 59 74930 0.20% 60 85598 0.23% 61 92047 0.25% 62 97933 0.26% 63 102883 0.28% 64 110640 0.30% 65 122452 0.33% 66 129874 0.35% 67 127617 0.34% 68 127971 0.34% 69 130253 0.35% 70 134630 0.36% 71 140678 0.38% 72 149720 0.40% 73 157097 0.42% 74 156079 0.42% 75 155087 0.42% 76 156219 0.42% 77 163253 0.44% 78 179194 0.48% 79 175930 0.47% 80 180371 0.48% 81 184100 0.49% 82 184375 0.49% 83 193165 0.52% 84 199564 0.53% 85 217469 0.58% 86 223435 0.60% 87 230814 0.62% 88 232670 0.62% 89 263650 0.71% 90 245673 0.66% 91 252602 0.68% 92 267073 0.72% 93 279923 0.75% 94 308117 0.83% 95 352390 0.94% 96 376118 1.01% 97 432884 1.16% 98 534750 1.43% 99 731673 1.96% 100 1881284 5.04% 101 25947279 69.49% 37341964 reads passed initial QC criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=24 prefix-density=0.41 prefix-fanout=2.0 sequence=AGGTACTGGACAATGTGGAAGCTGCCCATGTTCGGGTGCACCGACGCCACGCAGGTGCT criterion=fanout-score sequence-density=0.10 sequence-density-rank=13 fanout-score=79.96 fanout-score-rank=1 prefix-density=0.65 prefix-fanout=12.7 sequence=GCCGCCGCCGCCA criterion=sequence-density sequence-density=0.31 sequence-density-rank=1 fanout-score=1.85 fanout-score-rank=29 prefix-density=0.57 prefix-fanout=1.0 sequence=ATGCACTGCACTTGCCTGGTGTTGTCGA criterion=fanout-score sequence-density=0.01 sequence-density-rank=39 fanout-score=111.14 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=2.3 sequence=TATAAGAAAGAAAGTGATTTTCTCAACTCTTTCAAACTTTTAGGAATTCACATATGCAAGCTAGCTCCTCGATCGAGAGCCAGGTTGCTACACACAACAACAATCTTGGGGATGAAAAATAGAAAACTCAAAGCAATGTCAGAGTTGACAAAACTGAGCTGACACTTTATATATGGTCCATCTTAATACGGAGCTGTCCTTGGTTGTTTATGCCTTGCCGGATTCCTCGCAGCCCGGTGGCTT ERR3317466 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 10:14:54 Started mapping on | Dec 10 10:14:54 Finished on | Dec 10 10:16:45 Mapping speed, Million of reads per hour | 1211.09 Number of input reads | 37341964 Average input read length | 192 UNIQUE READS: Uniquely mapped reads number | 33022362 Uniquely mapped reads % | 88.43% Average mapped length | 190.74 Number of splices: Total | 20409234 Number of splices: Annotated (sjdb) | 19368476 Number of splices: GT/AG | 20107906 Number of splices: GC/AG | 266733 Number of splices: AT/AC | 16356 Number of splices: Non-canonical | 18239 Mismatch rate per base, % | 0.41% Deletion rate per base | 0.00% Deletion average length | 1.21 Insertion rate per base | 0.00% Insertion average length | 1.25 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2943363 % of reads mapped to multiple loci | 7.88% Number of reads mapped to too many loci | 104412 % of reads mapped to too many loci | 0.28% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.83% % of reads unmapped: other | 1.58% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1555177 1555177 1555177 N_multimapping 2943363 2943363 2943363 N_noFeature 1318655 2933399 30708457 N_ambiguous 980884 310708 18641 UnstrandedReadsAssigned:30722823 PositiveStrandReadsAssigned:29778255 NegativeStrandReadsAssigned:2295264 Dataset is classified positive stranded MeadianReadLen=101 20thPercentileLength=99 echo kmer=95 ERR3317466 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: ERR3317466-trimmed-pair1.fastq ERR3317466-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 37,341,964 reads, 32,100,910 reads pseudoaligned [quant] estimated average fragment length: 192.474 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,177 rounds 52973 ERR3317466.ke.tsv 35125 ERR3317466.se.tsv 88098 total ==> ERR3317466.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 744.857 0 0 PNS24247 1044 852.526 39.2259 2.14313 PNS24249 1928 1736.53 133.057 3.56894 PNS24246 1044 852.526 39.2259 2.14313 PNS24248 1044 852.526 39.2259 2.14313 PNS24244 1471 1279.53 218.265 7.94547 PNS24243 293 133.99 3 1.04288 KQK14069 1603 1411.53 2953.99 97.4775 KQK14071 474 292.301 11.728 1.86887 ==> ERR3317466.se.tsv <== BRADI_1g14170v3 3329 BRADI_1g53295v3 143 BRADI_1g59795v3 703 BRADI_1g07683v3 0 BRADI_1g00485v3 86 BRADI_1g20270v3 1929 BRADI_1g74790v3 444 BRADI_1g09890v3 7 BRADI_1g77505v3 447 BRADI_1g48960v3 1 ERR3317466 completed mapping pipeline successfully