Starting /dee2/code/volunteer_pipeline.sh SRR10225142 current disk space = 3052054343680 free memory = 1575876080 SRR10225142 SRAfilesize c6f9b5e60f430759dd66b1d64154bc9b SRR10225142.sra SRR10225142.sra file validated SRR10225142 is paired end SRR10225142 is conventional basespace SRR10225142 read1 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR10225142_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.8 34.0 31.0 34.0 31.0 34.0 2 32.96225 34.0 33.0 34.0 31.0 34.0 3 33.05575 34.0 33.0 34.0 31.0 34.0 4 36.46325 37.0 37.0 37.0 35.0 37.0 5 36.4345 37.0 37.0 37.0 35.0 37.0 6 36.3495 37.0 37.0 37.0 35.0 37.0 7 36.38675 37.0 37.0 37.0 35.0 37.0 8 36.41875 37.0 37.0 37.0 35.0 37.0 9 38.2265 39.0 39.0 39.0 37.0 39.0 10-11 38.173 39.0 39.0 39.0 37.0 39.0 12-13 38.1935 39.0 39.0 39.0 37.0 39.0 14-15 39.852625 41.0 40.0 41.0 37.5 41.0 16-17 39.732875 41.0 40.0 41.0 37.0 41.0 18-19 39.664874999999995 41.0 40.0 41.0 37.0 41.0 20-21 39.632875 41.0 40.0 41.0 37.0 41.0 22-23 39.545874999999995 41.0 40.0 41.0 37.0 41.0 24-25 39.574125 41.0 40.0 41.0 37.0 41.0 26-27 39.4805 41.0 40.0 41.0 36.5 41.0 28-29 39.372125 41.0 39.0 41.0 36.0 41.0 30-31 39.23975 41.0 39.0 41.0 36.0 41.0 32-33 39.013374999999996 40.0 39.0 41.0 35.5 41.0 34-35 38.879625000000004 40.0 39.0 41.0 35.0 41.0 36-37 38.68025 40.0 38.0 41.0 35.0 41.0 38-39 38.632374999999996 40.0 38.0 41.0 35.0 41.0 40-41 38.53325 40.0 38.0 41.0 34.0 41.0 42-43 38.229625 40.0 38.0 41.0 34.0 41.0 44-45 38.514125 40.0 38.0 41.0 34.5 41.0 46-47 38.502250000000004 40.0 38.0 41.0 34.0 41.0 48-49 38.480125 40.0 38.0 41.0 34.0 41.0 50-51 38.4355 40.0 38.0 41.0 34.0 41.0 52-53 38.229 40.0 37.5 41.0 34.0 41.0 54-55 37.963 40.0 37.0 41.0 33.0 41.0 56-57 37.850625 40.0 37.0 41.0 33.5 41.0 58-59 37.434749999999994 39.5 36.0 41.0 33.0 41.0 60-61 37.24125 39.0 35.5 41.0 32.5 41.0 62-63 36.902874999999995 39.0 35.0 41.0 32.0 41.0 64-65 36.594125 38.5 35.0 40.5 32.0 41.0 66-67 36.307625 37.5 35.0 40.0 31.5 41.0 68-69 35.917625 37.0 35.0 39.0 31.5 41.0 70-71 35.615750000000006 36.0 35.0 39.0 32.0 41.0 72-73 35.216625 36.0 35.0 39.0 31.5 40.0 74-75 34.37425 35.0 35.0 37.0 30.5 39.0 76-77 34.0205 35.0 35.0 37.0 30.0 39.0 78-79 33.733000000000004 35.0 34.5 36.5 30.0 38.0 80-81 33.40025 35.0 34.0 36.0 30.0 37.0 82-83 33.195875 35.0 34.0 36.0 30.0 37.0 84-85 33.064125000000004 35.0 34.0 35.0 30.0 36.0 86-87 32.851375000000004 35.0 34.0 35.0 29.0 36.0 88-89 32.701125 35.0 34.0 35.0 29.0 36.0 90-91 32.49525 35.0 34.0 35.0 29.0 36.0 92-93 32.36925 35.0 34.0 35.0 29.0 35.5 94-95 32.1695 35.0 34.0 35.0 29.0 35.0 96-97 32.0195 35.0 34.0 35.0 27.0 35.0 98-99 31.956625 35.0 34.0 35.0 27.0 35.0 100 31.90875 35.0 34.0 35.0 28.0 35.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-11 0.0 1101 12-13 0.0 1101 14-15 0.0 1101 16-17 0.0 1101 18-19 0.0 1101 20-21 0.0 1101 22-23 0.0 1101 24-25 0.0 1101 26-27 0.0 1101 28-29 0.0 1101 30-31 0.0 1101 32-33 0.0 1101 34-35 0.0 1101 36-37 0.0 1101 38-39 0.0 1101 40-41 0.0 1101 42-43 0.0 1101 44-45 0.0 1101 46-47 0.0 1101 48-49 0.0 1101 50-51 0.0 1101 52-53 0.0 1101 54-55 0.0 1101 56-57 0.0 1101 58-59 0.0 1101 60-61 0.0 1101 62-63 0.0 1101 64-65 0.0 1101 66-67 0.0 1101 68-69 0.0 1101 70-71 0.0 1101 72-73 0.0 1101 74-75 0.0 1101 76-77 0.0 1101 78-79 0.0 1101 80-81 0.0 1101 82-83 0.0 1101 84-85 0.0 1101 86-87 0.0 1101 88-89 0.0 1101 90-91 0.0 1101 92-93 0.0 1101 94-95 0.0 1101 96-97 0.0 1101 98-99 0.0 1101 100 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 8 1.0 9 2.0 10 1.0 11 2.0 12 4.0 13 8.0 14 8.0 15 2.0 16 6.0 17 3.0 18 9.0 19 9.0 20 7.0 21 3.0 22 8.0 23 15.0 24 9.0 25 12.0 26 26.0 27 39.0 28 35.0 29 52.0 30 44.0 31 65.0 32 65.0 33 79.0 34 147.0 35 201.0 36 383.0 37 925.0 38 1486.0 39 344.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 30.97989949748744 35.82914572864321 20.57788944723618 12.613065326633166 2 35.15 30.875000000000004 18.075 15.9 3 31.4 32.725 22.075 13.8 4 29.075 31.05 23.9 15.975 5 27.400000000000002 28.825 24.15 19.625 6 30.3 27.275 25.05 17.375 7 29.599999999999998 27.900000000000002 24.975 17.525 8 24.15 30.725 27.150000000000002 17.974999999999998 9 24.2 32.1 25.974999999999998 17.724999999999998 10-11 25.887500000000003 29.15 26.1625 18.8 12-13 23.150000000000002 29.812499999999996 26.4625 20.575 14-15 23.474999999999998 29.675 25.7 21.15 16-17 23.65 28.812500000000004 26.625 20.9125 18-19 24.275 27.975 27.6375 20.1125 20-21 24.675 27.775 27.3625 20.1875 22-23 25.35 28.4125 25.8 20.4375 24-25 23.25 29.875 25.575 21.3 26-27 23.7 29.1625 27.4125 19.725 28-29 23.3375 29.5375 25.900000000000002 21.224999999999998 30-31 23.962500000000002 28.225 27.6875 20.125 32-33 23.8875 29.362500000000004 26.200000000000003 20.549999999999997 34-35 23.3125 28.1875 28.249999999999996 20.25 36-37 24.212500000000002 28.1375 27.85 19.8 38-39 24.7 28.3125 26.400000000000002 20.5875 40-41 24.25 28.6875 25.7125 21.349999999999998 42-43 24.425 28.375 26.650000000000002 20.549999999999997 44-45 24.075 28.1375 26.650000000000002 21.1375 46-47 23.7625 28.1 27.8125 20.325 48-49 23.974999999999998 28.4375 27.037499999999998 20.549999999999997 50-51 24.5375 28.549999999999997 25.324999999999996 21.587500000000002 52-53 25.162499999999998 28.050000000000004 25.9625 20.825 54-55 24.4375 26.7625 26.05 22.75 56-57 24.1875 26.974999999999998 28.212500000000002 20.625 58-59 23.2625 26.85 28.5625 21.325 60-61 24.925 26.85 26.224999999999998 22.0 62-63 24.1375 27.575 28.199999999999996 20.0875 64-65 24.8625 29.062500000000004 26.4625 19.6125 66-67 24.65 29.4375 26.700000000000003 19.2125 68-69 23.0 29.049999999999997 27.6625 20.2875 70-71 24.552845528455283 29.055659787367105 26.59161976235147 19.79987492182614 72-73 24.725 29.825000000000003 26.375 19.075 74-75 24.1625 28.8625 27.0125 19.9625 76-77 24.85 29.1625 26.387500000000003 19.6 78-79 25.35 27.775 27.025 19.85 80-81 24.49056132016502 28.141017627203404 27.078384798099762 20.290036254531817 82-83 25.2375 28.0625 26.625 20.075000000000003 84-85 24.3125 28.999999999999996 26.487500000000004 20.200000000000003 86-87 24.349999999999998 29.2875 26.437500000000004 19.925 88-89 24.212500000000002 27.575 26.950000000000003 21.2625 90-91 24.81870467616904 28.08202050512628 26.70667666916729 20.392598149537385 92-93 23.9375 28.262500000000003 27.35 20.45 94-95 24.2 27.962500000000002 28.3125 19.525000000000002 96-97 24.6 28.675 26.237500000000004 20.4875 98-99 24.8 27.8875 27.325 19.9875 100 25.3 27.975 25.825 20.9 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 1.0 9 0.5 10 0.0 11 0.0 12 1.0 13 1.0 14 0.0 15 0.5 16 0.5 17 1.0 18 1.0 19 2.5 20 4.5 21 2.5 22 3.0 23 5.0 24 3.5 25 3.5 26 5.5 27 6.5 28 9.5 29 12.0 30 16.5 31 19.5 32 24.0 33 34.5 34 50.5 35 67.0 36 78.5 37 87.5 38 109.0 39 152.0 40 200.0 41 227.5 42 240.0 43 250.5 44 254.0 45 260.0 46 256.5 47 226.5 48 210.5 49 210.0 50 175.5 51 129.5 52 103.0 53 95.5 54 88.0 55 74.0 56 56.5 57 39.5 58 25.5 59 20.5 60 23.5 61 22.0 62 17.0 63 16.5 64 14.0 65 9.0 66 7.5 67 3.0 68 6.5 69 8.0 70 5.0 71 6.0 72 3.5 73 2.5 74 3.0 75 1.5 76 1.0 77 0.5 78 0.5 79 0.5 80 0.5 81 0.5 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 0.5 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 0.0625 72-73 0.0 74-75 0.0 76-77 0.0 78-79 0.0 80-81 0.0125 82-83 0.0 84-85 0.0 86-87 0.0 88-89 0.0 90-91 0.025 92-93 0.0 94-95 0.0 96-97 0.0 98-99 0.0 100 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 100 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.72500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 98.64194306607469 94.425 2 1.149125097936798 2.1999999999999997 3 0.05223295899712719 0.15 4 0.05223295899712719 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 0.07834943849569079 1.35 >50 0.026116479498563595 1.675 >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 fail #Sequence Count Percentage Possible Source AGATCGGAAGAGCACACGTCTGAACTCCAGTCACTTAGGCATCTCGTATG 67 1.675 TruSeq Adapter, Index 3 (100% over 49bp) CAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTG 30 0.75 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 14 0.35000000000000003 No Hit AACACGGACCAAGGAGTCTGACATGTGTGCGAGTCAACGGGCGAGTAAAC 10 0.25 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 2.05 0.0 0.0 0.0 0.0 2 2.05 0.0 0.0 0.0 0.0 3 2.05 0.0 0.0 0.0 0.0 4 2.05 0.0 0.0 0.0 0.0 5 2.05 0.0 0.0 0.0 0.0 6 2.05 0.0 0.0 0.0 0.0 7 2.05 0.0 0.0 0.0 0.0 8 2.05 0.0 0.0 0.0 0.0 9 2.075 0.0 0.0 0.0 0.0 10-11 2.075 0.0 0.0 0.0 0.0 12-13 2.1 0.0 0.0 0.0 0.0 14-15 2.1 0.0 0.0 0.0 0.0 16-17 2.1 0.0 0.0 0.0 0.0 18-19 2.1 0.0 0.0 0.0 0.0 20-21 2.1 0.0 0.0 0.0 0.0 22-23 2.1 0.0 0.0 0.0 0.0 24-25 2.1 0.0 0.0 0.0 0.0 26-27 2.1 0.0 0.0 0.0 0.0 28-29 2.1 0.0 0.0 0.0 0.0 30-31 2.1 0.0 0.0 0.0 0.0 32-33 2.1 0.0 0.0 0.0 0.0 34-35 2.1 0.0 0.0 0.0 0.0 36-37 2.1 0.0 0.0 0.0 0.0 38-39 2.1 0.0 0.0 0.0 0.0 40-41 2.1 0.0 0.0 0.0 0.0 42-43 2.1 0.0 0.0 0.0 0.0 44-45 2.1 0.0 0.0 0.0 0.0 46-47 2.1 0.0 0.0 0.0 0.0 48-49 2.1 0.0 0.0 0.0 0.0 50-51 2.1 0.0 0.0 0.0 0.0 52-53 2.1 0.0 0.0 0.0 0.0 54-55 2.1 0.0 0.0 0.0 0.0 56-57 2.1 0.0 0.0 0.0 0.0 58-59 2.1 0.0 0.0 0.0 0.0 60-61 2.1 0.0 0.0 0.0 0.0 62-63 2.1 0.0 0.0 0.0 0.0 64-65 2.125 0.0 0.0 0.0 0.0 66-67 2.125 0.0 0.0 0.0 0.0 68-69 2.125 0.0 0.0 0.0 0.0 70-71 2.125 0.0 0.0 0.0 0.0 72-73 2.1375 0.0 0.0 0.0 0.0 74-75 2.1624999999999996 0.0 0.0 0.0 0.0 76-77 2.175 0.0 0.0 0.0 0.0 78-79 2.175 0.0 0.0 0.0 0.0 80-81 2.2 0.0 0.0 0.0 0.0 82-83 2.225 0.0 0.0 0.0 0.0 84-85 2.2625 0.0 0.0 0.0 0.0 86-87 2.325 0.0 0.0 0.0 0.0 88 2.375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR10225142 read2 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR10225142_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 100 %GC 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.263 34.0 31.0 34.0 30.0 34.0 2 32.39125 34.0 31.0 34.0 31.0 34.0 3 32.31775 34.0 31.0 34.0 30.0 34.0 4 35.737 37.0 37.0 37.0 35.0 37.0 5 35.6855 37.0 35.0 37.0 35.0 37.0 6 35.65425 37.0 35.0 37.0 35.0 37.0 7 35.62575 37.0 36.0 37.0 35.0 37.0 8 35.65075 37.0 37.0 37.0 35.0 37.0 9 37.44625 39.0 39.0 39.0 35.0 39.0 10-11 37.446125 39.0 39.0 39.0 35.0 39.0 12-13 37.3675 39.0 38.5 39.0 35.0 39.0 14-15 38.847125 41.0 40.0 41.0 36.0 41.0 16-17 38.832750000000004 41.0 40.0 41.0 35.5 41.0 18-19 38.670625 41.0 39.0 41.0 34.5 41.0 20-21 38.613375000000005 41.0 39.0 41.0 34.5 41.0 22-23 38.45675 41.0 39.0 41.0 34.5 41.0 24-25 38.346125 41.0 39.0 41.0 34.0 41.0 26-27 38.255625 41.0 39.0 41.0 34.0 41.0 28-29 38.158375 40.0 39.0 41.0 34.0 41.0 30-31 37.940124999999995 40.0 38.0 41.0 33.0 41.0 32-33 37.8455 40.0 38.0 41.0 32.5 41.0 34-35 37.694375 40.0 38.0 41.0 33.0 41.0 36-37 37.610375 40.0 38.0 41.0 33.0 41.0 38-39 37.508624999999995 40.0 38.0 41.0 32.5 41.0 40-41 37.4325 40.0 38.0 41.0 32.5 41.0 42-43 37.171375 40.0 37.5 41.0 32.0 41.0 44-45 37.297124999999994 40.0 37.5 41.0 32.5 41.0 46-47 37.571749999999994 40.0 38.0 41.0 33.0 41.0 48-49 37.433499999999995 40.0 38.0 41.0 32.5 41.0 50-51 37.299875 40.0 38.0 41.0 32.0 41.0 52-53 37.13375 40.0 37.0 41.0 32.0 41.0 54-55 36.981625 40.0 37.0 41.0 31.5 41.0 56-57 36.752375 40.0 36.0 41.0 31.5 41.0 58-59 36.592375000000004 40.0 36.0 41.0 31.0 41.0 60-61 36.37425 39.0 35.0 41.0 31.0 41.0 62-63 36.196749999999994 39.0 35.0 41.0 31.0 41.0 64-65 35.69225 38.0 35.0 40.5 30.0 41.0 66-67 35.155 37.5 35.0 40.0 29.0 41.0 68-69 34.620374999999996 37.0 35.0 39.5 28.5 41.0 70-71 34.21075 36.5 35.0 39.0 28.0 41.0 72-73 33.7915 36.0 34.5 39.0 27.0 40.5 74-75 33.34075 35.5 34.0 37.5 26.0 39.5 76-77 33.041 35.0 34.0 37.0 26.5 39.0 78-79 32.808625 35.0 34.0 37.0 26.5 39.0 80-81 32.412625 35.0 34.0 36.0 26.0 37.5 82-83 32.177 35.0 34.0 36.0 25.5 37.0 84-85 31.874125 35.0 34.0 35.5 24.5 37.0 86-87 31.672 35.0 34.0 35.0 25.0 36.0 88-89 31.489375000000003 35.0 33.0 35.0 24.5 36.0 90-91 31.308625 35.0 33.0 35.0 24.0 36.0 92-93 31.110625 35.0 33.0 35.0 21.5 35.0 94-95 30.925625 35.0 33.0 35.0 20.0 35.0 96-97 30.831625 35.0 33.0 35.0 20.0 35.0 98-99 30.796125 35.0 33.0 35.0 19.0 35.0 100 30.712 35.0 33.0 35.0 19.0 35.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-11 0.0 1101 12-13 0.0 1101 14-15 0.0 1101 16-17 0.0 1101 18-19 0.0 1101 20-21 0.0 1101 22-23 0.0 1101 24-25 0.0 1101 26-27 0.0 1101 28-29 0.0 1101 30-31 0.0 1101 32-33 0.0 1101 34-35 0.0 1101 36-37 0.0 1101 38-39 0.0 1101 40-41 0.0 1101 42-43 0.0 1101 44-45 0.0 1101 46-47 0.0 1101 48-49 0.0 1101 50-51 0.0 1101 52-53 0.0 1101 54-55 0.0 1101 56-57 0.0 1101 58-59 0.0 1101 60-61 0.0 1101 62-63 0.0 1101 64-65 0.0 1101 66-67 0.0 1101 68-69 0.0 1101 70-71 0.0 1101 72-73 0.0 1101 74-75 0.0 1101 76-77 0.0 1101 78-79 0.0 1101 80-81 0.0 1101 82-83 0.0 1101 84-85 0.0 1101 86-87 0.0 1101 88-89 0.0 1101 90-91 0.0 1101 92-93 0.0 1101 94-95 0.0 1101 96-97 0.0 1101 98-99 0.0 1101 100 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 43.0 3 8.0 4 5.0 5 3.0 6 6.0 7 13.0 8 10.0 9 4.0 10 11.0 11 5.0 12 8.0 13 13.0 14 5.0 15 2.0 16 7.0 17 15.0 18 17.0 19 11.0 20 7.0 21 8.0 22 17.0 23 15.0 24 18.0 25 51.0 26 22.0 27 20.0 28 24.0 29 46.0 30 44.0 31 56.0 32 79.0 33 95.0 34 114.0 35 197.0 36 367.0 37 784.0 38 1496.0 39 354.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.475 15.375 16.85 28.299999999999997 2 28.799999999999997 6.4750000000000005 20.0 44.725 3 16.650000000000002 8.025 19.225 56.10000000000001 4 19.5 7.124999999999999 20.4 52.97500000000001 5 22.325 11.425 22.5 43.75 6 30.55763940985246 12.42810702675669 26.93173293323331 30.08252063015754 7 19.225 27.05 32.425 21.3 8 15.25 31.225 33.300000000000004 20.225 9 14.7 32.125 32.95 20.225 10-11 17.3375 29.5375 31.7875 21.337500000000002 12-13 17.599999999999998 27.9375 31.7875 22.675 14-15 18.2625 28.125 32.375 21.2375 16-17 18.425 28.525 30.112499999999997 22.9375 18-19 18.4875 28.299999999999997 31.5125 21.7 20-21 18.0625 30.075000000000003 29.8375 22.025 22-23 20.075000000000003 30.612499999999997 28.525 20.7875 24-25 18.8125 30.887500000000003 28.125 22.175 26-27 18.512500000000003 31.0 28.237499999999997 22.25 28-29 20.3375 29.9 27.3125 22.45 30-31 18.45 29.5375 28.4125 23.599999999999998 32-33 18.925 27.925 29.7875 23.3625 34-35 19.2625 30.2625 27.762500000000003 22.7125 36-37 18.0625 29.95 28.65 23.3375 38-39 18.4875 29.375 28.849999999999998 23.2875 40-41 19.7625 28.9125 27.3375 23.9875 42-43 19.825 29.875 28.050000000000004 22.25 44-45 20.349999999999998 28.675 28.175 22.8 46-47 19.4625 29.175 27.737499999999997 23.625 48-49 19.55 28.9125 27.2625 24.275 50-51 19.2375 28.6875 27.6125 24.462500000000002 52-53 18.8375 30.475 27.750000000000004 22.9375 54-55 18.8875 29.8375 28.1625 23.1125 56-57 18.7 29.312500000000004 29.299999999999997 22.6875 58-59 18.95 29.062500000000004 28.825 23.1625 60-61 18.275 30.4875 27.35 23.8875 62-63 19.2625 29.8375 27.875 23.025000000000002 64-65 20.1375 29.675 26.724999999999998 23.4625 66-67 17.7625 30.925000000000004 27.8625 23.45 68-69 18.5 30.2375 27.650000000000002 23.6125 70-71 19.1875 30.5 27.575 22.7375 72-73 19.8375 30.0 26.8375 23.325000000000003 74-75 19.4375 29.4125 27.725 23.425 76-77 19.8375 29.575000000000003 27.0125 23.575 78-79 20.125 30.15 25.8625 23.8625 80-81 20.1875 29.475 27.0625 23.275000000000002 82-83 19.0875 29.862499999999997 26.924999999999997 24.125 84-85 20.7875 28.1125 26.75 24.349999999999998 86-87 19.8 30.0375 25.924999999999997 24.2375 88-89 20.3625 29.2375 26.437500000000004 23.962500000000002 90-91 19.7 29.925 25.8 24.575 92-93 21.275 28.625 26.450000000000003 23.65 94-95 20.4625 29.612500000000004 27.6375 22.287499999999998 96-97 19.287499999999998 29.1375 27.725 23.849999999999998 98-99 19.9625 28.675 27.987499999999997 23.375 100 19.3 29.599999999999998 27.400000000000002 23.7 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.0 5 0.0 6 0.0 7 0.5 8 0.5 9 0.0 10 0.0 11 0.0 12 0.5 13 1.5 14 1.0 15 1.5 16 1.5 17 0.5 18 0.5 19 2.0 20 2.0 21 4.0 22 5.0 23 3.5 24 7.0 25 11.5 26 13.5 27 14.5 28 22.5 29 28.0 30 31.0 31 40.5 32 53.0 33 66.5 34 84.5 35 109.0 36 125.0 37 138.5 38 152.5 39 169.0 40 194.0 41 218.5 42 225.0 43 205.0 44 198.0 45 211.5 46 222.5 47 198.0 48 160.0 49 149.0 50 124.5 51 104.0 52 89.5 53 77.5 54 70.0 55 61.0 56 57.5 57 54.0 58 61.0 59 53.0 60 35.5 61 30.0 62 21.5 63 13.5 64 10.5 65 9.0 66 9.0 67 8.0 68 6.5 69 4.0 70 2.0 71 0.5 72 3.5 73 7.0 74 6.5 75 2.5 76 0.5 77 1.5 78 1.5 79 0.5 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 0.5 90 0.5 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 0.025 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 100 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.05 #Duplication Level Percentage of deduplicated Percentage of total 1 97.15576820839978 91.375 2 1.8872939925571504 3.55 3 0.4784688995215311 1.35 4 0.23923444976076555 0.8999999999999999 5 0.13290802764486975 0.625 6 0.0 0.0 7 0.0 0.0 8 0.026581605528973953 0.2 9 0.026581605528973953 0.22499999999999998 >10 0.026581605528973953 0.25 >50 0.026581605528973953 1.525 >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 fail #Sequence Count Percentage Possible Source AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTAGATCTCGGTGGTCGCC 61 1.525 Illumina Single End PCR Primer 1 (100% over 50bp) GCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCC 10 0.25 No Hit GCCCCCAACTTTCGTTCTTGATTAATGAAAACATCCTTGGCAAATGCTTT 9 0.22499999999999998 No Hit CCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGG 8 0.2 No Hit GGGTCCAAAAAGAGGGGCAGCGCCCCGCCTCCGATTCACGGAATAAGTAA 5 0.125 No Hit GACGCGTACACAAGACAAAGGATTTATAGGAACCCTTTGCTGTTTATTAT 5 0.125 No Hit GCGCCTGCTGCCTTCCTTGGATGTGGTAGCCGTTTCTCAGGCTCCCTCTC 5 0.125 No Hit TCTCCGTCACCCGTCACCACCATGGTAGGCCTCTATCCTACCATCGAAAG 5 0.125 No Hit CGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCT 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 1.825 0.0 0.0 0.0 0.0 2 1.825 0.0 0.0 0.0 0.0 3 1.825 0.0 0.0 0.0 0.0 4 1.825 0.0 0.0 0.0 0.0 5 1.825 0.0 0.0 0.0 0.0 6 1.825 0.0 0.0 0.0 0.0 7 1.825 0.0 0.0 0.0 0.0 8 1.825 0.0 0.0 0.0 0.0 9 1.85 0.0 0.0 0.0 0.0 10-11 1.85 0.0 0.0 0.0 0.0 12-13 1.875 0.0 0.0 0.0 0.0 14-15 1.875 0.0 0.0 0.0 0.0 16-17 1.875 0.0 0.0 0.0 0.0 18-19 1.8875 0.0 0.0 0.0 0.0 20-21 1.9 0.0 0.0 0.0 0.0 22-23 1.9 0.0 0.0 0.0 0.0 24-25 1.9 0.0 0.0 0.0 0.0 26-27 1.95 0.0 0.0 0.0 0.0 28-29 1.975 0.0 0.0 0.0 0.0 30-31 1.975 0.0 0.0 0.0 0.0 32-33 1.975 0.0 0.0 0.0 0.0 34-35 1.975 0.0 0.0 0.0 0.0 36-37 1.975 0.0 0.0 0.0 0.0 38-39 1.975 0.0 0.0 0.0 0.0 40-41 1.975 0.0 0.0 0.0 0.0 42-43 1.975 0.0 0.0 0.0 0.0 44-45 1.975 0.0 0.0 0.0 0.0 46-47 1.975 0.0 0.0 0.0 0.0 48-49 1.975 0.0 0.0 0.0 0.0 50-51 1.975 0.0 0.0 0.0 0.0 52-53 1.975 0.0 0.0 0.0 0.0 54-55 1.975 0.0 0.0 0.0 0.0 56-57 1.975 0.0 0.0 0.0 0.0 58-59 1.975 0.0 0.0 0.0 0.0 60-61 1.975 0.0 0.0 0.0 0.0 62-63 1.975 0.0 0.0 0.0 0.0 64-65 2.0 0.0 0.0 0.0 0.0 66-67 2.0 0.0 0.0 0.0 0.0 68-69 2.0 0.0 0.0 0.0 0.0 70-71 2.0 0.0 0.0 0.0 0.0 72-73 2.0125 0.0 0.0 0.0 0.0 74-75 2.0374999999999996 0.0 0.0 0.0 0.0 76-77 2.05 0.0 0.0 0.0 0.0 78-79 2.05 0.0 0.0 0.0 0.0 80-81 2.075 0.0 0.0 0.0 0.0 82-83 2.1 0.0 0.0 0.0 0.0 84-85 2.1375 0.0 0.0 0.0 0.0 86-87 2.2 0.0 0.0 0.0 0.0 88 2.25 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCCCTCC 15 6.4061093E-4 94.0 1 >>END_MODULE Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951791 spots for SRR10225142.sra Written 3951791 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra Read 3951779 spots for SRR10225142.sra Written 3951779 spots for SRR10225142.sra SRR ids: ['SRR10225142.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_frb_rl4d SRR10225142.sra spots: 79035592 blocks: [[1, 3951779], [3951780, 7903558], [7903559, 11855337], [11855338, 15807116], [15807117, 19758895], [19758896, 23710674], [23710675, 27662453], [27662454, 31614232], [31614233, 35566011], [35566012, 39517790], [39517791, 43469569], [43469570, 47421348], [47421349, 51373127], [51373128, 55324906], [55324907, 59276685], [59276686, 63228464], [63228465, 67180243], [67180244, 71132022], [71132023, 75083801], [75083802, 79035592]] SRR10225142 file size 21611856 SRR10225142 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 SRR10225142 SRR10225142_1.fastq SRR10225142_2.fastq Input file: SRR10225142_1.fastq Paired file: SRR10225142_2.fastq trimmed: SRR10225142-trimmed-pair1.fastq, SRR10225142-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 Wed Feb 12 00:04:13 2025 >> started Wed Feb 12 00:05:30 2025 >> done (77.322s) 79035592 read pairs processed; of these: 499238 ( 0.63%) short read pairs filtered out after trimming by size control 2440077 ( 3.09%) empty read pairs filtered out after trimming by size control 76096277 (96.28%) read pairs available; of these: 10505414 (13.81%) trimmed read pairs available after processing 65590863 (86.19%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 18644 0.02% 19 11935 0.02% 20 16141 0.02% 21 7037 0.01% 22 4441 0.01% 23 5275 0.01% 24 11842 0.02% 25 13012 0.02% 26 10154 0.01% 27 7618 0.01% 28 5259 0.01% 29 6655 0.01% 30 6756 0.01% 31 5101 0.01% 32 5452 0.01% 33 4306 0.01% 34 3612 0.00% 35 3964 0.01% 36 4155 0.01% 37 4559 0.01% 38 4971 0.01% 39 5409 0.01% 40 6211 0.01% 41 6444 0.01% 42 6725 0.01% 43 7681 0.01% 44 8021 0.01% 45 8683 0.01% 46 8955 0.01% 47 9614 0.01% 48 10185 0.01% 49 11176 0.01% 50 11978 0.02% 51 12912 0.02% 52 13859 0.02% 53 14839 0.02% 54 16604 0.02% 55 18507 0.02% 56 18686 0.02% 57 20314 0.03% 58 21806 0.03% 59 116982 0.15% 60 124010 0.16% 61 79315 0.10% 62 86871 0.11% 63 93677 0.12% 64 93486 0.12% 65 98658 0.13% 66 104657 0.14% 67 107436 0.14% 68 106647 0.14% 69 110033 0.14% 70 114482 0.15% 71 112128 0.15% 72 114859 0.15% 73 123121 0.16% 74 122286 0.16% 75 127739 0.17% 76 138719 0.18% 77 130554 0.17% 78 130622 0.17% 79 134852 0.18% 80 141737 0.19% 81 148015 0.19% 82 151762 0.20% 83 165590 0.22% 84 170903 0.22% 85 172026 0.23% 86 165179 0.22% 87 184174 0.24% 88 198197 0.26% 89 221497 0.29% 90 257505 0.34% 91 385331 0.51% 92 272387 0.36% 93 324395 0.43% 94 337166 0.44% 95 1338834 1.76% 96 457069 0.60% 97 568973 0.75% 98 800272 1.05% 99 1273770 1.67% 100 65590863 86.19% 76096277 reads passed initial QC criterion=sequence-density sequence-density=0.39 sequence-density-rank=1 fanout-score=3.34 fanout-score-rank=18 prefix-density=1.30 prefix-fanout=1.0 sequence=CCCCTAGTAACTGCGAGTGAAGAGGGACAAGCTCAAATTTTAAATCTATCGGGTTTTA criterion=fanout-score sequence-density=0.01 sequence-density-rank=31 fanout-score=131.05 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=11.5 sequence=GAGAAGATGATCCAGGAGAAAAAGGCTAAGCAACAGCAGCTCAAGAAACAGGTGTGGGATGGAAAGCCATGTGAAGAAAAGAAAGA criterion=sequence-density sequence-density=0.60 sequence-density-rank=1 fanout-score=2.88 fanout-score-rank=18 prefix-density=1.74 prefix-fanout=1.0 sequence=GGTCTCTCGCCGTTATTTAGCCTTAGGAGAAATTTACCTCCCATTTTAAGCTGCAATCCCAAACAACTTGACTCTTAGAAAGCGTATCGTAAAACGCAAATGATCAACCGGACGGGATTATCACCCTCCAT criterion=fanout-score sequence-density=0.08 sequence-density-rank=17 fanout-score=140.32 fanout-score-rank=1 prefix-density=0.55 prefix-fanout=19.1 sequence=TCATCATCATCACCATCACCATCCCTGATTGATCTTTGATTCACAACAAGACCAACCAACCGTACAATGTTTACATAACTTGGGATAATCTCACAAGAAAGAAAGA SRR10225142 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 12 00:06:06 Started mapping on | Feb 12 00:06:06 Finished on | Feb 12 00:16:39 Mapping speed, Million of reads per hour | 432.78 Number of input reads | 76096277 Average input read length | 196 UNIQUE READS: Uniquely mapped reads number | 59850410 Uniquely mapped reads % | 78.65% Average mapped length | 194.97 Number of splices: Total | 23603009 Number of splices: Annotated (sjdb) | 22911332 Number of splices: GT/AG | 23069914 Number of splices: GC/AG | 346933 Number of splices: AT/AC | 36687 Number of splices: Non-canonical | 149475 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.04% Deletion average length | 2.44 Insertion rate per base | 0.03% Insertion average length | 2.30 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 2722359 % of reads mapped to multiple loci | 3.58% Number of reads mapped to too many loci | 6514054 % of reads mapped to too many loci | 8.56% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 8.15% % of reads unmapped: other | 1.06% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 13855402 13855402 13855402 N_multimapping 2722359 2722359 2722359 N_noFeature 2851994 3556574 58591999 N_ambiguous 1000365 436742 13073 UnstrandedReadsAssigned:55998051 PositiveStrandReadsAssigned:55857094 NegativeStrandReadsAssigned:1245338 Dataset is classified positive stranded MeadianReadLen=100 20thPercentileLength=100 echo kmer=95 SRR10225142 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: SRR10225142-trimmed-pair1.fastq SRR10225142-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 76,096,277 reads, 60,631,733 reads pseudoaligned [quant] estimated average fragment length: 262.595 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,244 rounds 52401 SRR10225142.ke.tsv 34699 SRR10225142.se.tsv 87100 total ==> SRR10225142.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1756.4 13837.8 87.8104 Potri.005G024800.1.v4.1 1035 773.405 1033 14.8867 Potri.004G059700.1.v4.1 961 699.412 2558 40.7635 Potri.007G009000.2.v4.1 1416 1154.4 0 0 Potri.003G141000.2.v4.1 2943 2681.4 2036 8.46291 Potri.016G087400.1.v4.1 270 59.2081 5172.91 973.773 Potri.015G069301.1.v4.1 564 302.834 0 0 Potri.010G195200.1.v4.1 1773 1511.4 138 1.01766 Potri.012G127500.1.v4.1 977 715.405 7008 109.181 ==> SRR10225142.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 93 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 980 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 3 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 2 Potri.001G416900.v4.1 31 Potri.001G452600.v4.1 982 SRR10225142 completed mapping pipeline successfully