Starting /dee2/code/volunteer_pipeline.sh ERR10610836 current disk space = 1549367119872 free memory = 1600363960 ERR10610836 SRAfilesize 1ad0241e7d59202d644e05502c89b2ba ERR10610836.sra ERR10610836.sra file validated ERR10610836 is paired end ERR10610836 is conventional basespace ERR10610836 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR10610836_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 27.92 32.0 25.0 33.0 18.0 33.0 2 29.50025 31.0 28.0 33.0 18.0 33.0 3 29.9215 33.0 29.0 33.0 18.0 33.0 4 30.3325 33.0 31.0 33.0 25.0 34.0 5 30.262 33.0 31.0 33.0 15.0 34.0 6 32.33475 36.0 29.0 38.0 16.0 38.0 7 32.71125 37.0 29.0 38.0 16.0 38.0 8 33.6 38.0 33.0 38.0 16.0 38.0 9 33.5435 38.0 33.0 38.0 16.0 38.0 10-11 30.865375 35.0 23.0 38.0 16.0 38.0 12-13 33.36325 37.5 32.0 38.0 16.0 38.0 14-15 33.775625000000005 38.0 33.5 38.0 16.0 38.0 16-17 33.93000000000001 38.0 34.0 38.0 16.0 38.0 18-19 34.052125000000004 38.0 34.0 38.0 16.0 38.0 20-21 33.8035 38.0 34.0 38.0 16.0 38.0 22-23 33.88575 38.0 33.5 38.0 16.0 38.0 24-25 33.9315 38.0 34.0 38.0 16.0 38.0 26-27 33.80475 38.0 34.0 38.0 16.0 38.0 28-29 33.581125 38.0 33.5 38.0 16.0 38.0 30-31 33.137 38.0 31.0 38.0 16.0 38.0 32-33 33.67275 38.0 33.0 38.0 16.0 38.0 34-35 33.96875 38.0 34.0 38.0 16.0 38.0 36-37 33.8825 38.0 34.0 38.0 16.0 38.0 38-39 33.845875 38.0 34.0 38.0 16.0 38.0 40-41 33.589124999999996 38.0 33.0 38.0 16.0 38.0 42-43 34.093625 38.0 34.0 38.0 16.0 38.0 44-45 33.755250000000004 38.0 33.5 38.0 16.0 38.0 46-47 33.810125 38.0 34.0 38.0 16.0 38.0 48-49 33.907125 38.0 33.5 38.0 16.0 38.0 50-51 33.99875 38.0 34.0 38.0 16.0 38.0 52-53 33.960499999999996 38.0 34.0 38.0 16.0 38.0 54-55 34.005250000000004 38.0 34.0 38.0 16.0 38.0 56-57 33.84375 38.0 33.5 38.0 16.0 38.0 58-59 33.970375000000004 38.0 34.0 38.0 16.0 38.0 60-61 34.125125 38.0 34.0 38.0 20.5 38.0 62-63 34.139875 38.0 34.0 38.0 20.0 38.0 64-65 34.244375 38.0 34.0 38.0 24.0 38.0 66-67 34.276625 38.0 34.0 38.0 20.5 38.0 68-69 33.852000000000004 38.0 34.0 38.0 16.0 38.0 70-71 34.16275 38.0 34.0 38.0 20.0 38.0 72-73 34.15325 38.0 34.0 38.0 16.0 38.0 74-75 34.079499999999996 38.0 34.0 38.0 16.0 38.0 76-77 34.260999999999996 38.0 34.0 38.0 20.5 38.0 78-79 33.95399999999999 38.0 34.0 38.0 16.0 38.0 80-81 34.03575 38.0 34.0 38.0 19.0 38.0 82-83 33.902125 38.0 34.0 38.0 16.0 38.0 84-85 34.029125 38.0 34.0 38.0 18.5 38.0 86-87 33.93425 38.0 34.0 38.0 16.0 38.0 88-89 33.941 38.0 34.0 38.0 16.0 38.0 90-91 33.890875 38.0 34.0 38.0 16.0 38.0 92-93 33.678375 38.0 33.5 38.0 18.5 38.0 94-95 33.72425 38.0 34.0 38.0 15.5 38.0 96-97 33.944375 38.0 34.0 38.0 18.0 38.0 98-99 33.819125 38.0 34.0 38.0 18.5 38.0 100-101 32.870125 37.0 31.5 38.0 15.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 12.0 19 29.0 20 58.0 21 65.0 22 60.0 23 54.0 24 74.0 25 80.0 26 82.0 27 84.0 28 107.0 29 108.0 30 115.0 31 149.0 32 203.0 33 195.0 34 276.0 35 357.0 36 673.0 37 1218.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 36.47147905098435 8.657243816254418 13.301362948006057 41.56991418475518 2 24.6 14.224999999999998 36.75 24.425 3 21.325 18.875 24.6 35.199999999999996 4 26.3 26.8 23.625 23.275000000000002 5 24.15 30.125 25.650000000000002 20.075000000000003 6 20.980245061265315 31.50787696924231 27.081770442610654 20.43010752688172 7 17.224999999999998 20.674999999999997 42.699999999999996 19.400000000000002 8 19.6 21.95 31.424999999999997 27.025 9 20.724999999999998 21.0 32.824999999999996 25.45 10-11 22.3 28.875 25.224999999999998 23.599999999999998 12-13 21.54288572143036 24.36859214803701 27.156789197299325 26.93173293323331 14-15 22.233337501563085 25.24696761285482 27.485306990121295 25.034387895460796 16-17 22.973986993496748 25.700350175087543 26.600800400200097 24.72486243121561 18-19 21.823411705852926 25.775387693846923 27.33866933466733 25.062531265632813 20-21 22.6 26.5375 26.224999999999998 24.637500000000003 22-23 22.818204551137786 26.494123530882717 26.344086021505376 24.343585896474117 24-25 22.2125 25.887500000000003 26.2125 25.687500000000004 26-27 22.9875 25.25 27.1 24.6625 28-29 23.0 25.8125 26.8375 24.349999999999998 30-31 22.2625 25.637500000000003 25.7125 26.387500000000003 32-33 22.237499999999997 25.2875 27.462500000000002 25.0125 34-35 23.1 25.637500000000003 26.5 24.762500000000003 36-37 23.200000000000003 25.4 26.5375 24.8625 38-39 22.15 24.9875 26.875 25.9875 40-41 22.7625 25.5 25.5375 26.200000000000003 42-43 22.55 24.9 27.1625 25.387500000000003 44-45 22.75 25.6125 26.687499999999996 24.95 46-47 23.625 25.4875 25.724999999999998 25.162499999999998 48-49 22.650000000000002 25.275 26.4625 25.6125 50-51 22.7125 26.1125 26.437500000000004 24.7375 52-53 22.8 26.025 25.8625 25.3125 54-55 22.6875 26.474999999999998 25.0625 25.775 56-57 22.075 26.087500000000002 26.75 25.087500000000002 58-59 22.575 25.937500000000004 25.3125 26.174999999999997 60-61 22.625 25.5 26.3125 25.5625 62-63 22.525000000000002 25.0 27.05 25.424999999999997 64-65 23.5375 25.8 26.325 24.337500000000002 66-67 22.25 25.525 25.85 26.375 68-69 22.5875 25.637500000000003 26.187500000000004 25.587500000000002 70-71 22.575 26.5 25.7625 25.162499999999998 72-73 23.425 24.4125 25.7375 26.424999999999997 74-75 23.3125 24.725 26.474999999999998 25.4875 76-77 21.875 26.05 26.575 25.5 78-79 23.3 25.0375 25.424999999999997 26.237500000000004 80-81 23.0 25.874999999999996 26.05 25.074999999999996 82-83 23.4625 25.587500000000002 25.7375 25.2125 84-85 23.6125 24.775 26.2875 25.324999999999996 86-87 22.912499999999998 25.75 25.85 25.4875 88-89 23.674999999999997 26.0375 25.275 25.0125 90-91 23.6375 25.8 25.7375 24.825 92-93 23.1375 25.2125 26.450000000000003 25.2 94-95 24.9375 25.4875 24.525 25.05 96-97 23.375 25.337500000000002 25.687500000000004 25.6 98-99 23.575 25.362499999999997 25.575 25.4875 100-101 23.2875 25.874999999999996 24.65 26.187500000000004 >>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 0.5 13 0.5 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 0.5 24 1.0 25 0.5 26 0.0 27 1.0 28 2.5 29 4.5 30 7.0 31 7.0 32 8.0 33 10.0 34 18.5 35 28.5 36 50.5 37 73.0 38 84.0 39 106.5 40 135.0 41 159.5 42 175.0 43 187.5 44 200.0 45 213.5 46 235.5 47 234.5 48 207.5 49 180.5 50 177.0 51 155.5 52 131.0 53 139.5 54 124.0 55 112.0 56 113.5 57 105.5 58 92.5 59 82.5 60 77.5 61 66.5 62 59.0 63 55.0 64 44.5 65 36.5 66 26.5 67 21.0 68 19.5 69 10.0 70 7.0 71 8.0 72 2.5 73 0.0 74 0.0 75 0.5 76 0.5 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 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 pass #Base N-Count 1 0.95 2 0.0 3 0.0 4 0.0 5 0.0 6 0.025 7 0.0 8 0.0 9 0.0 10-11 0.0 12-13 0.025 14-15 0.0375 16-17 0.05 18-19 0.05 20-21 0.0 22-23 0.025 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 99.075 #Duplication Level Percentage of deduplicated Percentage of total 1 99.1672975018925 98.25 2 0.7317688619732526 1.4500000000000002 3 0.10093363613424174 0.3 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 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.037500000000000006 0.0 0.0 0.0 0.0 74-75 0.0625 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.1625 0.0 0.0 0.0 0.0 80-81 0.2375 0.0 0.0 0.0 0.0 82-83 0.2625 0.0 0.0 0.0 0.0 84-85 0.36250000000000004 0.0 0.0 0.0 0.0 86-87 0.44999999999999996 0.0 0.0 0.0 0.0 88-89 0.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCAGCA 15 0.009962372 47.493755 94-95 >>END_MODULE ERR10610836 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR10610836_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 29.7525 33.0 28.0 33.0 18.0 34.0 2 30.0505 33.0 30.0 33.0 18.0 34.0 3 30.1755 33.0 30.0 33.0 18.0 34.0 4 29.838 33.0 30.0 33.0 15.0 34.0 5 29.7675 33.0 30.0 33.0 15.0 34.0 6 33.14175 38.0 31.0 38.0 16.0 38.0 7 33.561 38.0 33.0 38.0 16.0 38.0 8 33.0635 38.0 31.0 38.0 16.0 38.0 9 33.36525 38.0 31.0 38.0 16.0 38.0 10-11 33.186625 38.0 31.0 38.0 16.0 38.0 12-13 33.395250000000004 38.0 33.0 38.0 16.0 38.0 14-15 33.23325 38.0 32.0 38.0 16.0 38.0 16-17 32.615375 37.5 29.5 38.0 16.0 38.0 18-19 33.14425 37.5 31.5 38.0 16.0 38.0 20-21 33.281625000000005 38.0 31.0 38.0 16.0 38.0 22-23 33.323625 38.0 32.0 38.0 16.0 38.0 24-25 33.244875 38.0 32.5 38.0 16.0 38.0 26-27 33.114374999999995 38.0 32.0 38.0 16.0 38.0 28-29 32.9785 38.0 31.0 38.0 16.0 38.0 30-31 33.025625 38.0 31.0 38.0 16.0 38.0 32-33 33.290625 38.0 32.5 38.0 16.0 38.0 34-35 33.327375 38.0 33.0 38.0 16.0 38.0 36-37 33.060874999999996 38.0 31.0 38.0 16.0 38.0 38-39 33.283249999999995 38.0 32.0 38.0 16.0 38.0 40-41 33.298875 38.0 32.5 38.0 16.0 38.0 42-43 33.03725 38.0 31.0 38.0 16.0 38.0 44-45 33.23925 38.0 32.0 38.0 16.0 38.0 46-47 33.183625 38.0 31.0 38.0 16.0 38.0 48-49 33.33525 38.0 32.0 38.0 16.0 38.0 50-51 33.175375 38.0 32.0 38.0 16.0 38.0 52-53 33.090625 38.0 31.0 38.0 16.0 38.0 54-55 33.111875 38.0 32.0 38.0 16.0 38.0 56-57 33.157875000000004 38.0 31.0 38.0 16.0 38.0 58-59 33.26575 38.0 32.0 38.0 16.0 38.0 60-61 33.252625 38.0 32.5 38.0 16.0 38.0 62-63 32.92425 37.5 30.0 38.0 16.0 38.0 64-65 33.29025 38.0 32.0 38.0 16.0 38.0 66-67 33.26575 38.0 32.5 38.0 16.0 38.0 68-69 33.293 38.0 33.0 38.0 16.0 38.0 70-71 33.25875 38.0 33.0 38.0 16.0 38.0 72-73 33.23675 38.0 32.0 38.0 16.0 38.0 74-75 33.2775 38.0 32.5 38.0 16.0 38.0 76-77 33.26625 38.0 33.0 38.0 16.0 38.0 78-79 32.99875 38.0 31.0 38.0 16.0 38.0 80-81 33.027875 38.0 31.0 38.0 15.5 38.0 82-83 33.045375 38.0 31.0 38.0 15.5 38.0 84-85 32.883375 38.0 31.0 38.0 15.0 38.0 86-87 32.891 38.0 31.0 38.0 15.0 38.0 88-89 32.953875 38.0 31.0 38.0 15.0 38.0 90-91 32.825500000000005 38.0 31.0 38.0 15.0 38.0 92-93 32.7945 37.5 31.0 38.0 15.0 38.0 94-95 32.830875 38.0 31.0 38.0 15.0 38.0 96-97 32.715 37.5 31.0 38.0 15.0 38.0 98-99 32.740875 38.0 31.0 38.0 15.0 38.0 100-101 31.527625 36.0 27.5 38.0 15.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 16 1.0 17 5.0 18 34.0 19 57.0 20 66.0 21 72.0 22 74.0 23 82.0 24 75.0 25 98.0 26 99.0 27 121.0 28 111.0 29 116.0 30 157.0 31 142.0 32 185.0 33 198.0 34 249.0 35 339.0 36 505.0 37 1214.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 30.349999999999998 15.75 15.75 38.15 2 28.1 21.05 31.05 19.8 3 23.425 25.3 25.275 26.0 4 26.0 31.075000000000003 20.200000000000003 22.725 5 27.075 32.2 21.7 19.025 6 23.95 35.099999999999994 21.15 19.8 7 21.625 17.349999999999998 36.95 24.075 8 24.275 21.075 25.2 29.45 9 24.675 22.275 26.575 26.474999999999998 10-11 27.3375 27.975 20.5 24.1875 12-13 26.200000000000003 23.1625 24.637500000000003 26.0 14-15 25.45 25.587500000000002 24.7 24.2625 16-17 26.7625 24.224999999999998 24.55 24.462500000000002 18-19 25.662499999999998 25.124999999999996 25.275 23.9375 20-21 26.174999999999997 25.575 24.4 23.849999999999998 22-23 25.924999999999997 26.700000000000003 23.9875 23.3875 24-25 25.5 25.587500000000002 24.375 24.5375 26-27 25.837500000000002 26.0375 24.625 23.5 28-29 25.5375 25.05 25.224999999999998 24.1875 30-31 26.337500000000002 25.35 24.3625 23.95 32-33 25.324999999999996 26.3 23.7625 24.6125 34-35 25.95 25.8 23.9875 24.2625 36-37 25.387500000000003 26.25 24.125 24.2375 38-39 25.6125 25.6125 24.7875 23.9875 40-41 25.25 24.7875 25.650000000000002 24.3125 42-43 25.0 26.237500000000004 24.7875 23.974999999999998 44-45 26.1 25.7125 24.525 23.6625 46-47 26.0 25.412499999999998 24.837500000000002 23.75 48-49 25.85 24.9875 25.775 23.3875 50-51 24.8125 26.35 24.962500000000002 23.875 52-53 25.887500000000003 25.412499999999998 25.0625 23.6375 54-55 25.5625 26.25 24.474999999999998 23.7125 56-57 25.3 25.724999999999998 25.650000000000002 23.325000000000003 58-59 26.4125 25.162499999999998 24.45 23.974999999999998 60-61 25.4625 25.8 24.349999999999998 24.3875 62-63 24.90622655663916 26.319079769942487 25.481370342585645 23.293323330832706 64-65 26.144036009002253 26.36909227306827 23.893473368342086 23.593398349587396 66-67 25.0 26.700000000000003 25.025 23.275000000000002 68-69 25.453181647705964 26.040755094386796 25.115639454931866 23.39042380297537 70-71 25.074999999999996 25.837500000000002 25.662499999999998 23.425 72-73 25.525 25.1 25.650000000000002 23.724999999999998 74-75 25.35 26.2125 25.587500000000002 22.85 76-77 25.387500000000003 25.650000000000002 25.4 23.5625 78-79 25.7125 25.2625 25.650000000000002 23.375 80-81 25.85 26.650000000000002 24.925 22.575 82-83 26.55 25.825 24.275 23.35 84-85 25.624999999999996 25.887500000000003 25.05 23.4375 86-87 25.29066133266658 26.378297287160894 25.17814726840855 23.15289411176397 88-89 25.887500000000003 25.75 25.112499999999997 23.25 90-91 25.490686335791974 25.803225403175396 26.140767595949495 22.565320665083135 92-93 26.2125 25.2875 25.7375 22.7625 94-95 26.337500000000002 26.2625 24.775 22.625 96-97 25.887500000000003 26.174999999999997 24.6625 23.275000000000002 98-99 25.137500000000003 26.424999999999997 25.7375 22.7 100-101 26.2125 26.25 24.75 22.787499999999998 >>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 0.0 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 0.5 31 1.5 32 5.5 33 8.0 34 8.5 35 16.5 36 28.0 37 42.5 38 65.0 39 99.5 40 123.0 41 137.0 42 160.0 43 180.0 44 192.0 45 215.5 46 220.5 47 203.5 48 208.5 49 193.0 50 169.5 51 169.0 52 160.5 53 147.5 54 128.0 55 115.5 56 116.0 57 111.0 58 105.5 59 97.5 60 95.0 61 95.0 62 87.5 63 71.0 64 53.5 65 47.0 66 41.5 67 29.5 68 20.0 69 13.0 70 6.0 71 4.0 72 4.5 73 3.0 74 1.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 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 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 0.0 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 0.025 64-65 0.025 66-67 0.0 68-69 0.0125 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 0.0125 88-89 0.0 90-91 0.0125 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 99.3 #Duplication Level Percentage of deduplicated Percentage of total 1 99.34541792547836 98.65 2 0.6042296072507553 1.2 3 0.050352467270896276 0.15 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 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0125 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.0625 0.0 0.0 0.0 0.0 74-75 0.0875 0.0 0.0 0.0 0.0 76-77 0.1 0.0 0.0 0.0 0.0 78-79 0.1875 0.0 0.0 0.0 0.0 80-81 0.2625 0.0 0.0 0.0 0.0 82-83 0.2875 0.0 0.0 0.0 0.0 84-85 0.36250000000000004 0.0 0.0 0.0 0.0 86-87 0.44999999999999996 0.0 0.0 0.0 0.0 88-89 0.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627776 spots for ERR10610836.sra Written 627776 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra Read 627773 spots for ERR10610836.sra Written 627773 spots for ERR10610836.sra SRR ids: ['ERR10610836.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jf5sx1ic ERR10610836.sra spots: 12555463 blocks: [[1, 627773], [627774, 1255546], [1255547, 1883319], [1883320, 2511092], [2511093, 3138865], [3138866, 3766638], [3766639, 4394411], [4394412, 5022184], [5022185, 5649957], [5649958, 6277730], [6277731, 6905503], [6905504, 7533276], [7533277, 8161049], [8161050, 8788822], [8788823, 9416595], [9416596, 10044368], [10044369, 10672141], [10672142, 11299914], [11299915, 11927687], [11927688, 12555463]] ERR10610836 file size 3019075 ERR10610836 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 ERR10610836 ERR10610836_1.fastq ERR10610836_2.fastq Input file: ERR10610836_1.fastq Paired file: ERR10610836_2.fastq trimmed: ERR10610836-trimmed-pair1.fastq, ERR10610836-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 Fri Dec 6 20:44:10 2024 >> started Fri Dec 6 20:44:23 2024 >> done (12.578s) 12555463 read pairs processed; of these: 39 ( 0.00%) short read pairs filtered out after trimming by size control 1218 ( 0.01%) empty read pairs filtered out after trimming by size control 12554206 (99.99%) read pairs available; of these: 284761 ( 2.27%) trimmed read pairs available after processing 12269445 (97.73%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 2 0.00% 20 0 0.00% 21 0 0.00% 22 0 0.00% 23 1 0.00% 24 1 0.00% 25 4 0.00% 26 3 0.00% 27 1 0.00% 28 2 0.00% 29 4 0.00% 30 4 0.00% 31 6 0.00% 32 13 0.00% 33 5 0.00% 34 16 0.00% 35 6 0.00% 36 10 0.00% 37 21 0.00% 38 16 0.00% 39 22 0.00% 40 22 0.00% 41 30 0.00% 42 26 0.00% 43 37 0.00% 44 41 0.00% 45 37 0.00% 46 54 0.00% 47 66 0.00% 48 69 0.00% 49 65 0.00% 50 127 0.00% 51 115 0.00% 52 133 0.00% 53 129 0.00% 54 149 0.00% 55 142 0.00% 56 184 0.00% 57 221 0.00% 58 254 0.00% 59 250 0.00% 60 344 0.00% 61 378 0.00% 62 419 0.00% 63 426 0.00% 64 479 0.00% 65 522 0.00% 66 645 0.01% 67 749 0.01% 68 831 0.01% 69 922 0.01% 70 1009 0.01% 71 1209 0.01% 72 1377 0.01% 73 1499 0.01% 74 1737 0.01% 75 1978 0.02% 76 2166 0.02% 77 2383 0.02% 78 2782 0.02% 79 3114 0.02% 80 3428 0.03% 81 3910 0.03% 82 4485 0.04% 83 5011 0.04% 84 5779 0.05% 85 6267 0.05% 86 7072 0.06% 87 7580 0.06% 88 8711 0.07% 89 9743 0.08% 90 10753 0.09% 91 11963 0.10% 92 13041 0.10% 93 14279 0.11% 94 15632 0.12% 95 17134 0.14% 96 18466 0.15% 97 21125 0.17% 98 22601 0.18% 99 24215 0.19% 100 26308 0.21% 101 12269445 97.73% 12554206 reads passed initial QC criterion=sequence-density sequence-density=0.49 sequence-density-rank=1 fanout-score=2.75 fanout-score-rank=18 prefix-density=0.50 prefix-fanout=2.7 sequence=GGTGTTGTCGAAGCCGATGATGCGGACATAGGCGTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=28 fanout-score=48.21 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=2.2 sequence=TATATATATTACTGTTCACCAAATGAATATACTCAATATCTTTATATATGAACAAAAACTTTTCATGCCCAGCAATTGCTTGGATGCAATGCGGTACTTAGGTACAAAGAGTGAAACATCAGAATAATTAAAGTGGCATGCTTAAAAGGTGTAAAGGCAGCTGCCGTCGTCACTCCTTGCTGTTGGGTCGTAGTTCTCGGCATTCCGGTCAGTGCAACCTTCTGGGACGGGCAAATTACCTTGTTGTGCTCCTTTACCTCCTCCTATGCAGCTAGAGATGGTGTGTGTATGAAGAGTGTTCTAACCGTAGAAGGAACCAGTCTTCATGGCATCTGAGTTAGCATCTCCCAGAGCAGCCTCGCTCATGTACTTGTCAGCAAGCTGCACACGCTTGACATTGTCCTGCTCTTGGACGAGCATGTGGCCGTACTCCAGGAGCTTCTCGATTGTCATCTTTGGCTGCTCAAAGGACACCGGTCCATCCTTCGAGTTCACCAGCTTCTTGCCGATG criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=3.71 fanout-score-rank=12 prefix-density=0.40 prefix-fanout=3.4 sequence=GAGTTCAGCAAGGTCGGCTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=59.97 fanout-score-rank=1 prefix-density=0.11 prefix-fanout=6.6 sequence=AGGCTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTGCCTTTGGAGCCAGAAACAATGGCCTCGGCTACTATCCTCAAATCGTCTTTCCTTCCCAAGAAGTCCGAATGGGGCACCACCCGCCAGGCTGCCACTCCCAAGCAGATGACCGTCTCCATGGTTGTCCGTGCCAGCGCATACGCTGATGAACTTGTCAAGACCGCGAAAACCATCGCATCACCAGGAAGGGGCATCCTAGCCATGGATGAGTCCAATGCTACCTGTGGAAAGAGACTTGACTCGATTGGCCTTGAGAACACTGAGGCTAACCGCCAGGCTTACCGTACCCTCCTTGTCACTCCACCAGGCCTGGGAAATTACATCTCTGGTGCTATCCTCTTCGAGGAGACCCTCTACCAATCGACTGTTGATGGCAAGAAGATTGTTGACATCCTTGTCGAGCAGGGAATCGTTCCCGGCATCAAGGTTGACAAGGGTCTTGTGCCACTCGTTGGTTC ERR10610836 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 20:45:13 Started mapping on | Dec 06 20:45:13 Finished on | Dec 06 20:47:59 Mapping speed, Million of reads per hour | 272.26 Number of input reads | 12554206 Average input read length | 201 UNIQUE READS: Uniquely mapped reads number | 11399279 Uniquely mapped reads % | 90.80% Average mapped length | 200.22 Number of splices: Total | 7878457 Number of splices: Annotated (sjdb) | 7405307 Number of splices: GT/AG | 7773741 Number of splices: GC/AG | 93979 Number of splices: AT/AC | 2372 Number of splices: Non-canonical | 8365 Mismatch rate per base, % | 0.86% Deletion rate per base | 0.01% Deletion average length | 2.04 Insertion rate per base | 0.01% Insertion average length | 1.80 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 179550 % of reads mapped to multiple loci | 1.43% Number of reads mapped to too many loci | 8085 % of reads mapped to too many loci | 0.06% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 7.15% % of reads unmapped: other | 0.55% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 975377 975377 975377 N_multimapping 179550 179550 179550 N_noFeature 331079 11103016 392040 N_ambiguous 275410 1038 40716 UnstrandedReadsAssigned:10792790 PositiveStrandReadsAssigned:295225 NegativeStrandReadsAssigned:10966523 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR10610836 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: ERR10610836-trimmed-pair1.fastq ERR10610836-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,554,206 reads, 11,257,896 reads pseudoaligned [quant] estimated average fragment length: 178.075 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,133 rounds 52973 ERR10610836.ke.tsv 35125 ERR10610836.se.tsv 88098 total ==> ERR10610836.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 759.07 0 0 PNS24247 1044 866.925 35.6338 5.46339 PNS24249 1928 1750.93 17.932 1.36126 PNS24246 1044 866.925 35.6338 5.46339 PNS24248 1044 866.925 35.6338 5.46339 PNS24244 1471 1293.93 40.1665 4.12607 PNS24243 293 123.63 0 0 KQK14069 1603 1425.93 256.923 23.949 KQK14071 474 298.504 11.7237 5.22028 ==> ERR10610836.se.tsv <== BRADI_1g14170v3 302 BRADI_1g53295v3 51 BRADI_1g59795v3 191 BRADI_1g07683v3 0 BRADI_1g00485v3 1 BRADI_1g20270v3 131 BRADI_1g74790v3 78 BRADI_1g09890v3 0 BRADI_1g77505v3 227 BRADI_1g48960v3 0 ERR10610836 completed mapping pipeline successfully