Starting /dee2/code/volunteer_pipeline.sh ERR1864430 current disk space = 3052644765696 free memory = 1582219776 ERR1864430 SRAfilesize 7813af98ef355a445e97d8235fc5001a ERR1864430.sra ERR1864430.sra file validated ERR1864430 is paired end ERR1864430 is conventional basespace ERR1864430 read1 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR1864430_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.30925 34.0 31.0 34.0 30.0 34.0 2 31.806 34.0 31.0 34.0 28.0 34.0 3 32.33875 34.0 31.0 34.0 30.0 34.0 4 35.81925 37.0 35.0 37.0 35.0 37.0 5 35.658 37.0 35.0 37.0 35.0 37.0 6 35.56325 37.0 35.0 37.0 33.0 37.0 7 35.58075 37.0 35.0 37.0 33.0 37.0 8 35.63525 37.0 36.0 37.0 35.0 37.0 9 37.32975 39.0 38.0 39.0 35.0 39.0 10-11 37.287875 39.0 38.0 39.0 34.5 39.0 12-13 37.06275 39.0 37.5 39.0 33.5 39.0 14-15 38.683375 41.0 39.0 41.0 34.5 41.0 16-17 38.573625 41.0 39.0 41.0 34.5 41.0 18-19 38.527625 41.0 39.0 41.0 34.0 41.0 20-21 38.41925 40.5 38.5 41.0 34.0 41.0 22-23 38.439 40.5 39.0 41.0 34.0 41.0 24-25 38.289125 40.5 38.0 41.0 34.0 41.0 26-27 38.169 40.0 38.0 41.0 34.0 41.0 28-29 38.071250000000006 40.0 38.0 41.0 33.0 41.0 30-31 38.046875 40.0 38.0 41.0 33.5 41.0 32-33 37.902375 40.0 38.0 41.0 33.0 41.0 34-35 37.678250000000006 40.0 38.0 41.0 32.5 41.0 36-37 37.575625 40.0 38.0 41.0 32.0 41.0 38-39 37.55775 40.0 38.0 41.0 32.5 41.0 40-41 37.37075 40.0 38.0 41.0 32.0 41.0 42-43 37.152875 40.0 37.0 41.0 31.5 41.0 44-45 37.117875 40.0 37.5 41.0 31.0 41.0 46-47 37.271874999999994 40.0 37.0 41.0 31.5 41.0 48-49 37.143874999999994 40.0 37.0 41.0 31.0 41.0 50-51 36.961124999999996 40.0 37.0 41.0 30.5 41.0 52-53 36.854625 40.0 36.5 41.0 31.0 41.0 54-55 36.593374999999995 40.0 36.0 41.0 30.0 41.0 56-57 36.443375 39.0 36.0 41.0 30.0 41.0 58-59 36.245999999999995 39.0 35.0 41.0 30.0 41.0 60-61 35.960375 39.0 35.0 41.0 29.5 41.0 62-63 35.624750000000006 38.5 35.0 40.0 29.0 41.0 64-65 35.0155 38.0 34.0 40.0 27.5 41.0 66-67 34.809124999999995 37.0 34.0 40.0 28.0 41.0 68-69 34.536249999999995 37.0 34.0 39.0 28.0 41.0 70-71 34.019000000000005 36.0 34.0 39.0 26.5 40.5 72-73 33.610749999999996 36.0 34.0 38.5 26.0 40.0 74-75 33.14125 35.0 33.0 37.5 26.0 39.5 76-77 31.94625 34.5 31.5 36.0 24.5 39.0 78-79 32.16375 35.0 32.0 36.0 25.0 38.5 80-81 31.978500000000004 35.0 32.0 36.0 25.0 37.0 82-83 31.728749999999998 35.0 32.0 35.5 25.0 37.0 84-85 31.436750000000004 35.0 32.0 35.0 24.0 36.5 86-87 31.257125000000002 35.0 32.0 35.0 24.0 36.0 88-89 30.897624999999998 34.0 32.0 35.0 20.0 36.0 90-91 30.573875 34.0 31.0 35.0 20.0 35.5 92-93 30.448749999999997 34.0 31.0 35.0 20.0 35.0 94-95 30.173125 34.0 31.0 35.0 17.5 35.0 96-97 29.861125 34.0 31.0 35.0 11.0 35.0 98-99 29.563125 34.0 31.0 35.0 2.0 35.0 100-101 28.662 33.5 30.0 34.5 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 22.0 3 18.0 4 7.0 5 4.0 6 6.0 7 6.0 8 6.0 9 6.0 10 14.0 11 6.0 12 8.0 13 7.0 14 7.0 15 8.0 16 13.0 17 16.0 18 12.0 19 14.0 20 15.0 21 18.0 22 16.0 23 22.0 24 16.0 25 12.0 26 31.0 27 30.0 28 43.0 29 49.0 30 47.0 31 80.0 32 108.0 33 124.0 34 162.0 35 291.0 36 506.0 37 924.0 38 1181.0 39 145.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.859594383775345 6.2662506500260005 8.710348413936558 45.163806552262095 2 25.25 8.075000000000001 32.75 33.925 3 24.88122030507627 11.70292573143286 23.63090772693173 39.784946236559136 4 28.975 18.224999999999998 20.5 32.300000000000004 5 27.306826706676667 24.85621405351338 24.5311327831958 23.305826456614152 6 21.25 29.875 25.55 23.325000000000003 7 15.299999999999999 22.525000000000002 43.525000000000006 18.65 8 18.75 25.275 34.225 21.75 9 19.1 21.8 37.6 21.5 10-11 19.525000000000002 31.8125 27.9125 20.75 12-13 21.1375 25.637500000000003 30.275000000000002 22.95 14-15 20.3625 26.700000000000003 30.7625 22.175 16-17 21.825 27.6875 28.125 22.3625 18-19 20.6875 27.625 28.512500000000003 23.175 20-21 21.15 27.400000000000002 28.0875 23.3625 22-23 21.775 26.8625 27.3875 23.974999999999998 24-25 21.224999999999998 26.6625 28.537499999999998 23.575 26-27 20.8 27.875 28.050000000000004 23.275000000000002 28-29 21.4875 27.787499999999998 27.1625 23.5625 30-31 20.724999999999998 27.1125 28.6875 23.474999999999998 32-33 21.475 26.9125 28.462500000000002 23.150000000000002 34-35 21.6 26.9125 27.6 23.8875 36-37 21.5 26.387500000000003 28.6875 23.425 38-39 21.625 27.0625 27.187499999999996 24.125 40-41 20.6125 27.5625 28.1125 23.7125 42-43 21.6625 27.712500000000002 27.462500000000002 23.1625 44-45 21.912499999999998 26.8 27.6625 23.625 46-47 21.65 26.924999999999997 27.85 23.575 48-49 21.4875 27.212500000000002 27.5625 23.7375 50-51 20.65 27.85 27.3 24.2 52-53 20.967741935483872 27.881970492623154 27.68192048012003 23.468367091772944 54-55 20.4375 27.4125 27.825 24.325 56-57 20.95 27.8375 27.900000000000002 23.3125 58-59 21.5 27.725 26.987499999999997 23.7875 60-61 22.325 27.437499999999996 27.5125 22.725 62-63 21.375 27.325 26.937499999999996 24.3625 64-65 21.29016127015877 27.25340667583448 27.140892611576444 24.315539442430303 66-67 20.515064383047882 27.140892611576444 28.59107388423553 23.75296912114014 68-69 22.1055263815954 27.131782945736433 28.444611152788195 22.31807951987997 70-71 22.287499999999998 27.925 27.250000000000004 22.537499999999998 72-73 22.037499999999998 26.6125 27.5125 23.8375 74-75 21.90273784223028 27.815976997124643 27.203400425053132 23.07788473559195 76-77 22.025 26.924999999999997 27.5625 23.4875 78-79 21.875 27.55 27.925 22.650000000000002 80-81 22.0 28.375 26.75 22.875 82-83 22.112499999999997 28.212500000000002 26.674999999999997 23.0 84-85 21.675 27.125 27.375 23.825 86-87 21.975 26.9125 27.325 23.7875 88-89 21.95 28.037499999999998 27.1 22.912499999999998 90-91 21.175 28.375 27.025 23.425 92-93 21.224999999999998 27.3375 27.1125 24.325 94-95 21.1125 27.962500000000002 27.2625 23.6625 96-97 22.112499999999997 27.6875 26.937499999999996 23.2625 98-99 21.337500000000002 28.225 27.425 23.0125 100-101 21.5375 27.737499999999997 27.224999999999998 23.5 >>END_MODULE >>Per sequence GC content pass #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 0.5 16 0.5 17 0.0 18 0.0 19 0.0 20 1.0 21 1.0 22 2.5 23 2.5 24 0.5 25 2.0 26 3.5 27 6.0 28 7.5 29 8.0 30 11.0 31 17.5 32 24.0 33 32.5 34 43.5 35 60.5 36 78.5 37 84.5 38 107.5 39 144.5 40 175.5 41 188.0 42 201.0 43 234.0 44 251.5 45 265.0 46 258.5 47 239.5 48 226.0 49 194.5 50 176.0 51 165.0 52 133.0 53 114.0 54 96.5 55 70.5 56 77.5 57 68.0 58 46.5 59 39.0 60 33.0 61 27.5 62 14.0 63 11.5 64 12.5 65 10.0 66 8.5 67 5.0 68 3.0 69 2.5 70 3.0 71 3.0 72 1.5 73 1.5 74 1.0 75 1.5 76 1.5 77 0.5 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 3.85 2 0.0 3 0.025 4 0.0 5 0.025 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 0.025 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 0.0125 68-69 0.025 70-71 0.0 72-73 0.0 74-75 0.0125 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 97.725 #Duplication Level Percentage of deduplicated Percentage of total 1 98.33717063187515 96.1 2 1.2023535431056536 2.35 3 0.33256587362496803 0.975 4 0.07674597083653108 0.3 5 0.025581990278843697 0.125 6 0.025581990278843697 0.15 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 warn #Sequence Count Percentage Possible Source CCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGGA 6 0.15 No Hit GCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGC 5 0.125 No Hit >>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 0.0125 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.037500000000000006 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.0875 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.1375 0.0 0.0 0.0 0.0 74-75 0.2125 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.30000000000000004 0.0 0.0 0.0 0.0 80-81 0.4125 0.0 0.0 0.0 0.0 82-83 0.55 0.0 0.0 0.0 0.0 84-85 0.65 0.0 0.0 0.0 0.0 86-87 0.825 0.0 0.0 0.0 0.0 88-89 1.0375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATCATT 15 0.00997274 47.481247 12-13 >>END_MODULE ERR1864430 read2 length is 101 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR1864430_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.18425 34.0 31.0 34.0 30.0 34.0 2 32.3295 34.0 31.0 34.0 30.0 34.0 3 32.3005 34.0 31.0 34.0 30.0 34.0 4 35.65775 37.0 37.0 37.0 35.0 37.0 5 35.64525 37.0 37.0 37.0 33.0 37.0 6 35.65875 37.0 37.0 37.0 33.0 37.0 7 35.6725 37.0 36.0 37.0 35.0 37.0 8 35.6145 37.0 36.0 37.0 33.0 37.0 9 37.36375 39.0 38.0 39.0 35.0 39.0 10-11 37.20925 39.0 38.0 39.0 34.0 39.0 12-13 37.22775 39.0 38.0 39.0 34.0 39.0 14-15 38.45625 41.0 38.0 41.0 33.0 41.0 16-17 38.497125 41.0 38.0 41.0 34.0 41.0 18-19 38.47275 41.0 38.5 41.0 34.0 41.0 20-21 38.245374999999996 40.5 38.5 41.0 33.5 41.0 22-23 38.289625 40.0 38.0 41.0 34.0 41.0 24-25 37.996125000000006 40.0 38.0 41.0 33.0 41.0 26-27 37.930625 40.0 38.0 41.0 33.0 41.0 28-29 37.77925 40.0 38.0 41.0 32.0 41.0 30-31 37.771249999999995 40.0 38.0 41.0 32.5 41.0 32-33 37.6345 40.0 38.0 41.0 32.0 41.0 34-35 37.670375 40.0 38.0 41.0 33.0 41.0 36-37 37.662499999999994 40.0 38.0 41.0 32.5 41.0 38-39 37.475750000000005 40.0 38.0 41.0 31.5 41.0 40-41 37.356875 40.0 38.0 41.0 31.0 41.0 42-43 37.168875 40.0 37.5 41.0 31.0 41.0 44-45 36.793499999999995 40.0 36.5 41.0 30.0 41.0 46-47 36.589875 40.0 36.5 41.0 30.0 41.0 48-49 36.551375 39.5 36.0 41.0 30.0 41.0 50-51 36.334125 39.5 36.5 40.5 29.5 41.0 52-53 36.549875 39.5 36.5 40.5 30.5 41.0 54-55 36.61775 40.0 36.0 41.0 30.0 41.0 56-57 36.60375 40.0 36.0 41.0 30.0 41.0 58-59 36.371875 39.5 36.0 41.0 29.0 41.0 60-61 35.836749999999995 39.0 35.0 41.0 28.0 41.0 62-63 35.708124999999995 38.5 35.0 41.0 29.0 41.0 64-65 35.35625 38.0 35.0 40.0 28.0 41.0 66-67 34.97775 37.0 35.0 40.0 28.0 41.0 68-69 34.506375000000006 37.0 34.5 39.0 27.0 41.0 70-71 34.082625 36.0 34.0 39.0 26.5 41.0 72-73 33.619625 36.0 34.0 39.0 26.0 40.0 74-75 32.999125 35.0 33.0 37.0 25.0 39.0 76-77 32.7 35.0 33.0 37.0 25.5 39.0 78-79 32.22325 35.0 33.0 36.5 24.5 38.5 80-81 31.939 35.0 32.5 36.0 24.0 37.0 82-83 31.302875 35.0 31.5 35.5 21.5 37.0 84-85 31.1245 35.0 31.5 35.0 21.0 36.5 86-87 30.836624999999998 35.0 31.0 35.0 20.0 36.0 88-89 30.567999999999998 34.0 31.0 35.0 19.5 36.0 90-91 30.39225 34.0 31.0 35.0 18.0 35.5 92-93 30.1885 34.0 31.0 35.0 17.5 35.0 94-95 29.9715 34.0 31.0 35.0 14.5 35.0 96-97 29.6495 34.0 30.5 35.0 4.5 35.0 98-99 29.183125 34.0 30.0 35.0 2.0 35.0 100-101 28.136875 33.5 28.5 34.5 2.0 35.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 17.0 3 2.0 4 6.0 5 7.0 6 5.0 7 7.0 8 10.0 9 10.0 10 15.0 11 9.0 12 11.0 13 10.0 14 11.0 15 15.0 16 15.0 17 12.0 18 9.0 19 10.0 20 22.0 21 11.0 22 19.0 23 15.0 24 20.0 25 32.0 26 34.0 27 39.0 28 48.0 29 58.0 30 67.0 31 82.0 32 91.0 33 135.0 34 203.0 35 247.0 36 433.0 37 982.0 38 1095.0 39 186.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 28.025 18.65 15.325 38.0 2 26.474999999999998 24.45 32.15 16.925 3 20.45 26.825 30.2 22.525000000000002 4 22.55 33.650000000000006 23.125 20.674999999999997 5 26.375 34.599999999999994 21.95 17.075000000000003 6 19.8 38.125 22.7 19.375 7 20.549999999999997 21.425 37.65 20.375 8 22.025 24.675 28.999999999999996 24.3 9 21.125 24.224999999999998 31.15 23.5 10-11 23.1 31.7375 24.0375 21.125 12-13 23.9125 25.3 27.200000000000003 23.5875 14-15 23.6125 28.7 27.075 20.6125 16-17 23.0875 28.4375 26.8125 21.6625 18-19 22.900000000000002 28.249999999999996 27.275 21.575 20-21 23.3875 27.6625 27.575 21.375 22-23 24.7 27.825 26.887499999999996 20.5875 24-25 22.8125 27.750000000000004 26.787499999999998 22.650000000000002 26-27 22.1875 29.3375 26.8 21.675 28-29 21.9625 28.0875 27.5625 22.3875 30-31 22.287499999999998 27.975 27.737499999999997 22.0 32-33 23.3 28.3875 27.787499999999998 20.525 34-35 23.474999999999998 27.8875 27.0625 21.575 36-37 22.9375 28.8625 26.724999999999998 21.475 38-39 22.7375 28.050000000000004 27.1375 22.075 40-41 23.5875 28.287499999999998 26.737499999999997 21.3875 42-43 23.35 28.4125 26.900000000000002 21.337500000000002 44-45 23.125 27.9375 27.400000000000002 21.5375 46-47 23.5625 28.000000000000004 26.787499999999998 21.65 48-49 23.3125 27.700000000000003 27.0125 21.975 50-51 23.825 27.625 27.1625 21.3875 52-53 23.025000000000002 26.8125 28.075 22.0875 54-55 23.549999999999997 27.5125 26.887499999999996 22.05 56-57 22.650000000000002 28.1875 26.787499999999998 22.375 58-59 22.8375 27.462500000000002 28.199999999999996 21.5 60-61 23.674999999999997 27.5625 27.224999999999998 21.5375 62-63 23.0 26.700000000000003 27.925 22.375 64-65 23.0875 27.625 27.3 21.987499999999997 66-67 23.9375 27.400000000000002 27.037499999999998 21.625 68-69 23.05 28.4 27.55 21.0 70-71 24.125 28.1 26.200000000000003 21.575 72-73 23.474999999999998 27.675 27.5625 21.2875 74-75 24.5125 28.175 26.2125 21.099999999999998 76-77 22.875 29.049999999999997 26.9125 21.1625 78-79 22.650000000000002 27.8875 27.1625 22.3 80-81 23.0375 28.762500000000003 26.375 21.825 82-83 24.0125 28.7375 25.9625 21.2875 84-85 23.724999999999998 28.3625 26.237500000000004 21.675 86-87 23.3625 27.500000000000004 27.125 22.0125 88-89 24.8 26.8125 26.9125 21.475 90-91 23.575 28.375 27.0 21.05 92-93 24.3625 28.3625 25.775 21.5 94-95 23.674999999999997 27.462500000000002 27.675 21.1875 96-97 24.4125 26.487500000000004 27.900000000000002 21.2 98-99 23.25 28.287499999999998 26.087500000000002 22.375 100-101 25.412499999999998 27.437499999999996 26.0125 21.1375 >>END_MODULE >>Per sequence GC content pass #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 0.5 21 0.5 22 1.5 23 2.0 24 1.5 25 4.5 26 6.0 27 6.5 28 7.0 29 9.5 30 14.5 31 17.5 32 25.0 33 30.5 34 40.0 35 58.0 36 80.0 37 95.0 38 117.5 39 157.0 40 180.0 41 210.0 42 238.5 43 240.0 44 249.0 45 274.5 46 262.0 47 236.5 48 231.5 49 199.5 50 164.0 51 151.0 52 123.0 53 91.0 54 95.0 55 83.5 56 60.0 57 49.0 58 42.0 59 34.0 60 21.5 61 14.5 62 13.5 63 14.0 64 9.5 65 6.0 66 2.5 67 4.5 68 6.0 69 3.5 70 1.5 71 2.0 72 2.5 73 2.0 74 1.5 75 1.0 76 0.5 77 0.0 78 0.0 79 1.0 80 1.0 81 0.0 82 0.0 83 0.5 84 0.5 85 0.5 86 0.5 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 0.0 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 99.14206409285894 98.225 2 0.7822356800403736 1.55 3 0.0757002271006813 0.22499999999999998 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 0.0125 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.037500000000000006 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.0875 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.125 0.0 0.0 0.0 0.0 72-73 0.1375 0.0 0.0 0.0 0.0 74-75 0.2125 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.30000000000000004 0.0 0.0 0.0 0.0 80-81 0.4125 0.0 0.0 0.0 0.0 82-83 0.55 0.0 0.0 0.0 0.0 84-85 0.65 0.0 0.0 0.0 0.0 86-87 0.825 0.0 0.0 0.0 0.0 88-89 1.0375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877720 spots for ERR1864430.sra Written 877720 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra Read 877708 spots for ERR1864430.sra Written 877708 spots for ERR1864430.sra SRR ids: ['ERR1864430.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_tuwkmtzz ERR1864430.sra spots: 17554172 blocks: [[1, 877708], [877709, 1755416], [1755417, 2633124], [2633125, 3510832], [3510833, 4388540], [4388541, 5266248], [5266249, 6143956], [6143957, 7021664], [7021665, 7899372], [7899373, 8777080], [8777081, 9654788], [9654789, 10532496], [10532497, 11410204], [11410205, 12287912], [12287913, 13165620], [13165621, 14043328], [14043329, 14921036], [14921037, 15798744], [15798745, 16676452], [16676453, 17554172]] ERR1864430 file size 4212557 ERR1864430 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 ERR1864430 ERR1864430_1.fastq ERR1864430_2.fastq Input file: ERR1864430_1.fastq Paired file: ERR1864430_2.fastq trimmed: ERR1864430-trimmed-pair1.fastq, ERR1864430-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 Thu Feb 13 09:40:36 2025 >> started Thu Feb 13 09:48:32 2025 >> done (475.258s) 17554172 read pairs processed; of these: 277919 ( 1.58%) short read pairs filtered out after trimming by size control 311588 ( 1.78%) empty read pairs filtered out after trimming by size control 16964665 (96.64%) read pairs available; of these: 4078175 (24.04%) trimmed read pairs available after processing 12886490 (75.96%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 144 0.00% 19 301 0.00% 20 549 0.00% 21 660 0.00% 22 873 0.01% 23 1059 0.01% 24 1246 0.01% 25 1509 0.01% 26 1858 0.01% 27 2099 0.01% 28 2327 0.01% 29 2716 0.02% 30 3102 0.02% 31 3533 0.02% 32 4003 0.02% 33 4326 0.03% 34 4810 0.03% 35 4910 0.03% 36 5584 0.03% 37 6015 0.04% 38 6333 0.04% 39 7014 0.04% 40 7282 0.04% 41 7828 0.05% 42 8128 0.05% 43 8531 0.05% 44 8924 0.05% 45 9417 0.06% 46 9682 0.06% 47 10004 0.06% 48 10784 0.06% 49 11187 0.07% 50 11681 0.07% 51 12335 0.07% 52 12821 0.08% 53 13214 0.08% 54 13532 0.08% 55 14385 0.08% 56 15268 0.09% 57 16076 0.09% 58 16821 0.10% 59 21355 0.13% 60 25344 0.15% 61 25829 0.15% 62 26986 0.16% 63 27155 0.16% 64 28092 0.17% 65 29492 0.17% 66 31181 0.18% 67 31844 0.19% 68 32507 0.19% 69 34165 0.20% 70 34854 0.21% 71 36596 0.22% 72 38271 0.23% 73 39693 0.23% 74 40601 0.24% 75 41522 0.24% 76 42479 0.25% 77 44087 0.26% 78 46887 0.28% 79 49387 0.29% 80 52934 0.31% 81 54670 0.32% 82 57367 0.34% 83 59561 0.35% 84 63314 0.37% 85 66799 0.39% 86 71192 0.42% 87 74702 0.44% 88 76180 0.45% 89 81407 0.48% 90 88828 0.52% 91 97965 0.58% 92 108157 0.64% 93 121180 0.71% 94 136737 0.81% 95 158597 0.93% 96 188678 1.11% 97 233957 1.38% 98 302859 1.79% 99 406696 2.40% 100 565197 3.33% 101 12886490 75.96% 16964665 reads passed initial QC criterion=sequence-density sequence-density=0.14 sequence-density-rank=1 fanout-score=2.87 fanout-score-rank=32 prefix-density=0.28 prefix-fanout=1.5 sequence=TCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAAAGCAACATCCGCCAATCCCTGGTCGGCATCGTTTATGGTTGAGACTAGGACGGTATCTGATCGTCTTCGAGCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTTCGCAGTTGTTCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATGCCCCCGACTGTCCCTGTTAATCATTACTCCGATCCCGAAGGCCAACACAATAGGATCGAAATCCTATGATGTTATCCCATGCTAATGTATCCAGAGCGTAGGCTTGCTTTGAGCACTCTAATTTCTTCAAAGTAACAGCACCGGAGGCACGACCCGGCCAGTTAAGGCCAGGAGCGCATCGCCGGTAGAAGGGACGAGGCGACCGGTGCACACCTGAGGCGGACCGGCCGACCCAACCCAAAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=47.40 fanout-score-rank=1 prefix-density=0.18 prefix-fanout=3.0 sequence=AGCCTTGACAAATGGACCTACGAGGAGGAAGCCATGGGCCAGCCCCACCTCGATTCCGCGGAGAAGTGGACTGACTGCTGTCCTGTAGGCGGGGAGGTTGGACAGGTACCATGCAATCAGCGGGCTTGATGTAACGGGAGTCTCAAGACTTCCAATGAAGGGATCGCCATTGATTGGTTGAACCACTTGGTAAGTTGGCTTGTCTGCTTGAACGGCTTTGACAGTGAAGCTTCTCTTGTT criterion=sequence-density sequence-density=0.47 sequence-density-rank=1 fanout-score=2.03 fanout-score-rank=35 prefix-density=0.43 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=35 fanout-score=159.77 fanout-score-rank=1 prefix-density=0.21 prefix-fanout=10.5 sequence=TCTTCTCTCTGTCTTCTTGATTCCTTGTTTTTCGTTCTGTTTATTACAGCAGCAATACCATAATCATGTCTCAGACTGTTGTCCTCAAGGTTGGTATGTCATGCGAAGGCTGTGTTGGGGCTGTGAAAAGGGTTTTGGGAAAAATGGAAGGTGTGGAATCATATGACATTGATTTGAAGGAGCAAAAAGTCACAGTGAAAGGAAATGTGCAGCCAGATGCTGTTCTTCAGACCGTCTCTAAGACCGGGAAGAAGACTGCCTTCTGGGAAGCAGAGGCACCAGCTGAACCCGCAA ERR1864430 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 10:34:38 Started mapping on | Feb 13 10:35:19 Finished on | Feb 13 11:05:40 Mapping speed, Million of reads per hour | 33.54 Number of input reads | 16964665 Average input read length | 195 UNIQUE READS: Uniquely mapped reads number | 15789625 Uniquely mapped reads % | 93.07% Average mapped length | 195.34 Number of splices: Total | 9441725 Number of splices: Annotated (sjdb) | 9274375 Number of splices: GT/AG | 9273500 Number of splices: GC/AG | 144584 Number of splices: AT/AC | 7279 Number of splices: Non-canonical | 16362 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.01% Deletion average length | 2.54 Insertion rate per base | 0.01% Insertion average length | 2.57 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 432996 % of reads mapped to multiple loci | 2.55% Number of reads mapped to too many loci | 624373 % of reads mapped to too many loci | 3.68% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 0.45% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 764204 764204 764204 N_multimapping 432996 432996 432996 N_noFeature 753390 15567395 835414 N_ambiguous 202207 797 61567 UnstrandedReadsAssigned:14834028 PositiveStrandReadsAssigned:221433 NegativeStrandReadsAssigned:14892644 Dataset is classified negative stranded MeadianReadLen=101 20thPercentileLength=101 echo kmer=97 ERR1864430 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: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: ERR1864430-trimmed-pair1.fastq ERR1864430-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,964,665 reads, 15,403,360 reads pseudoaligned [quant] estimated average fragment length: 160.503 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,076 rounds 52401 ERR1864430.ke.tsv 34699 ERR1864430.se.tsv 87100 total ==> ERR1864430.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1858.5 781 24.0958 Potri.005G024800.1.v4.1 1035 875.497 235.043 15.3938 Potri.004G059700.1.v4.1 961 801.503 31 2.21773 Potri.007G009000.2.v4.1 1416 1256.5 0 0 Potri.003G141000.2.v4.1 2943 2783.5 845.078 17.4084 Potri.016G087400.1.v4.1 270 116.696 731 359.181 Potri.015G069301.1.v4.1 564 404.58 0 0 Potri.010G195200.1.v4.1 1773 1613.5 29 1.03058 Potri.012G127500.1.v4.1 977 817.503 133 9.32857 ==> ERR1864430.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 97 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 296 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 6 ERR1864430 completed mapping pipeline successfully