Starting /dee2/code/volunteer_pipeline.sh SRR10225138 current disk space = 2818950254592 free memory = 1578579728 SRR10225138 SRAfilesize e82edcd664c14a09bcce27ebe6b3d4ad SRR10225138.sra SRR10225138.sra file validated SRR10225138 is paired end SRR10225138 is conventional basespace SRR10225138 read1 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR10225138_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.918 34.0 33.0 34.0 31.0 34.0 2 33.1055 34.0 33.0 34.0 31.0 34.0 3 33.18275 34.0 33.0 34.0 31.0 34.0 4 36.4935 37.0 37.0 37.0 35.0 37.0 5 36.42975 37.0 37.0 37.0 35.0 37.0 6 36.425 37.0 37.0 37.0 35.0 37.0 7 36.45775 37.0 37.0 37.0 35.0 37.0 8 36.39525 37.0 37.0 37.0 35.0 37.0 9 38.33275 39.0 39.0 39.0 37.0 39.0 10-11 38.248625000000004 39.0 39.0 39.0 37.0 39.0 12-13 38.269000000000005 39.0 39.0 39.0 37.0 39.0 14-15 39.889 41.0 40.0 41.0 38.0 41.0 16-17 39.760125 41.0 40.0 41.0 37.5 41.0 18-19 39.7705 41.0 40.0 41.0 37.5 41.0 20-21 39.769625 41.0 40.0 41.0 37.5 41.0 22-23 39.72925 41.0 40.0 41.0 37.0 41.0 24-25 39.710375 41.0 40.0 41.0 37.0 41.0 26-27 39.533375 41.0 40.0 41.0 36.5 41.0 28-29 39.402375000000006 41.0 39.5 41.0 36.5 41.0 30-31 39.239000000000004 41.0 39.0 41.0 36.0 41.0 32-33 39.08375 41.0 39.0 41.0 36.0 41.0 34-35 39.02075 40.0 39.0 41.0 35.0 41.0 36-37 38.897875 40.0 39.0 41.0 35.0 41.0 38-39 38.835375 40.0 38.0 41.0 35.0 41.0 40-41 38.687375 40.0 38.0 41.0 35.0 41.0 42-43 38.38125 40.0 38.0 41.0 34.0 41.0 44-45 38.741749999999996 40.0 38.5 41.0 35.0 41.0 46-47 38.761125 41.0 38.5 41.0 35.0 41.0 48-49 38.7 41.0 38.0 41.0 35.0 41.0 50-51 38.56425 40.5 38.0 41.0 34.0 41.0 52-53 38.467625 40.0 38.0 41.0 34.0 41.0 54-55 38.238 40.0 37.5 41.0 34.0 41.0 56-57 38.096000000000004 40.0 37.0 41.0 34.0 41.0 58-59 37.628249999999994 40.0 36.5 41.0 33.0 41.0 60-61 37.466625 39.0 36.0 41.0 33.0 41.0 62-63 37.170874999999995 39.0 35.0 41.0 33.0 41.0 64-65 36.825125 38.5 35.0 41.0 32.0 41.0 66-67 36.576625 37.5 35.0 40.0 32.0 41.0 68-69 36.148125 37.0 35.0 39.5 32.0 41.0 70-71 35.851375000000004 36.5 35.0 39.0 32.0 41.0 72-73 35.41375 36.0 35.0 39.0 32.0 40.5 74-75 34.4685 35.5 35.0 37.0 31.0 39.0 76-77 34.024375000000006 35.0 35.0 37.0 30.0 39.0 78-79 33.807 35.0 35.0 36.5 31.0 38.5 80-81 33.40375 35.0 34.0 36.0 29.5 37.0 82-83 33.167874999999995 35.0 34.0 36.0 30.0 37.0 84-85 33.015 35.0 34.0 35.0 30.0 36.5 86-87 32.843625 35.0 34.0 35.0 29.5 36.0 88-89 32.714625 35.0 34.0 35.0 29.5 36.0 90-91 32.5975 35.0 34.0 35.0 29.0 36.0 92-93 32.47225 35.0 34.0 35.0 29.0 35.5 94-95 32.344750000000005 35.0 34.0 35.0 29.0 35.0 96-97 32.1385 35.0 34.0 35.0 28.0 35.0 98-99 32.005125 35.0 34.0 35.0 27.5 35.0 100 31.96775 35.0 34.0 35.0 27.0 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 7 1.0 8 0.0 9 1.0 10 0.0 11 4.0 12 3.0 13 0.0 14 3.0 15 5.0 16 7.0 17 8.0 18 7.0 19 8.0 20 4.0 21 6.0 22 7.0 23 6.0 24 7.0 25 15.0 26 20.0 27 32.0 28 51.0 29 57.0 30 45.0 31 52.0 32 74.0 33 78.0 34 142.0 35 189.0 36 385.0 37 843.0 38 1595.0 39 345.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 29.20953575909661 35.633626097867 21.279799247176914 13.877038895859473 2 35.075 31.125000000000004 18.025 15.775 3 30.875000000000004 34.175 20.0 14.95 4 29.375 29.099999999999998 23.400000000000002 18.125 5 26.174999999999997 29.75 23.0 21.075 6 30.025000000000002 27.325 23.875 18.775 7 28.625 27.450000000000003 24.224999999999998 19.7 8 23.875 32.425 25.825 17.875 9 24.65 30.775000000000002 25.374999999999996 19.2 10-11 25.0 30.375000000000004 25.7625 18.862499999999997 12-13 24.462500000000002 29.362500000000004 25.412499999999998 20.7625 14-15 23.825 29.325000000000003 25.575 21.275 16-17 22.650000000000002 29.6625 25.75 21.9375 18-19 23.6875 27.925 26.9125 21.475 20-21 23.25 28.999999999999996 26.450000000000003 21.3 22-23 24.4375 29.45 25.124999999999996 20.9875 24-25 23.3375 29.475 25.087500000000002 22.1 26-27 23.7375 28.225 27.1 20.9375 28-29 23.5375 29.1625 25.324999999999996 21.975 30-31 24.5 27.375 27.0125 21.1125 32-33 23.7375 28.787499999999998 25.887500000000003 21.587500000000002 34-35 22.6125 29.025000000000002 26.4625 21.9 36-37 23.6125 27.725 26.85 21.8125 38-39 25.025 28.512500000000003 26.5 19.9625 40-41 23.9 30.362499999999997 25.587500000000002 20.150000000000002 42-43 23.525 28.462500000000002 27.1 20.9125 44-45 22.7375 28.1875 26.1625 22.912499999999998 46-47 24.099999999999998 28.275 26.875 20.75 48-49 22.400000000000002 28.749999999999996 27.537499999999998 21.3125 50-51 23.775 27.9125 26.437500000000004 21.875 52-53 25.5 26.900000000000002 25.900000000000002 21.7 54-55 23.3125 27.3125 26.900000000000002 22.475 56-57 23.075000000000003 28.225 28.0875 20.6125 58-59 23.1 26.924999999999997 27.775 22.2 60-61 23.7875 27.5125 25.8125 22.8875 62-63 22.625 26.875 29.95 20.549999999999997 64-65 25.025 28.512500000000003 25.174999999999997 21.2875 66-67 23.7375 30.3 26.237500000000004 19.725 68-69 22.825 30.7375 25.974999999999998 20.4625 70-71 22.715339417427177 29.753719214901864 26.478309788723593 21.052631578947366 72-73 24.275 29.625 25.837500000000002 20.2625 74-75 23.2125 29.762499999999996 27.0625 19.9625 76-77 23.625 28.625 26.474999999999998 21.275 78-79 24.1625 27.8125 26.8 21.224999999999998 80-81 22.9375 28.675 27.1 21.2875 82-83 23.9375 26.924999999999997 26.937499999999996 22.2 84-85 23.75 29.212500000000002 26.275 20.7625 86-87 23.625 28.625 26.150000000000002 21.6 88-89 23.674999999999997 27.525 26.700000000000003 22.1 90-91 24.3625 28.212500000000002 26.7625 20.6625 92-93 24.325 27.900000000000002 27.3 20.474999999999998 94-95 24.025 27.150000000000002 27.375 21.45 96-97 24.4875 28.1875 26.174999999999997 21.15 98-99 23.7 27.875 27.250000000000004 21.175 100 23.075000000000003 28.525 26.85 21.55 >>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 0.0 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 0.5 19 0.5 20 1.0 21 1.5 22 2.5 23 2.0 24 0.5 25 4.5 26 5.0 27 5.5 28 8.5 29 9.5 30 10.5 31 13.5 32 17.5 33 22.5 34 33.0 35 51.5 36 69.5 37 90.0 38 114.5 39 152.0 40 195.5 41 220.5 42 249.0 43 285.0 44 279.5 45 274.5 46 268.0 47 232.5 48 209.0 49 183.0 50 155.0 51 154.0 52 137.0 53 106.0 54 89.0 55 69.0 56 56.0 57 38.0 58 30.0 59 29.5 60 23.5 61 19.0 62 16.5 63 12.5 64 9.5 65 5.0 66 3.5 67 5.0 68 6.0 69 5.0 70 2.5 71 2.5 72 2.0 73 1.0 74 0.5 75 1.5 76 3.0 77 2.0 78 0.5 79 0.0 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 0.375 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 0.0125 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 95.95 #Duplication Level Percentage of deduplicated Percentage of total 1 98.90568004168838 94.89999999999999 2 0.7816571130797291 1.5 3 0.13027618551328818 0.375 4 0.10422094841063052 0.4 5 0.0 0.0 6 0.02605523710265763 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.02605523710265763 0.44999999999999996 >50 0.02605523710265763 2.225 >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 AGATCGGAAGAGCACACGTCTGAACTCCAGTCACACTTGAATCTCGTATG 89 2.225 TruSeq Adapter, Index 8 (100% over 49bp) CAACACGGGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTG 18 0.44999999999999996 No Hit TACCTGGTTGATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCC 6 0.15 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 2.7 0.0 0.0 0.0 0.0 2 2.7 0.0 0.0 0.0 0.0 3 2.7 0.0 0.0 0.0 0.0 4 2.7 0.0 0.0 0.0 0.0 5 2.7 0.0 0.0 0.0 0.0 6 2.7 0.0 0.0 0.0 0.0 7 2.7 0.0 0.0 0.0 0.0 8 2.7 0.0 0.0 0.0 0.0 9 2.7 0.0 0.0 0.0 0.0 10-11 2.7 0.0 0.0 0.0 0.0 12-13 2.7125000000000004 0.0 0.0 0.0 0.0 14-15 2.725 0.0 0.0 0.0 0.0 16-17 2.725 0.0 0.0 0.0 0.0 18-19 2.725 0.0 0.0 0.0 0.0 20-21 2.75 0.0 0.0 0.0 0.0 22-23 2.7625 0.0 0.0 0.0 0.0 24-25 2.775 0.0 0.0 0.0 0.0 26-27 2.775 0.0 0.0 0.0 0.0 28-29 2.8 0.0 0.0 0.0 0.0 30-31 2.8 0.0 0.0 0.0 0.0 32-33 2.85 0.0 0.0 0.0 0.0 34-35 2.85 0.0 0.0 0.0 0.0 36-37 2.85 0.0 0.0 0.0 0.0 38-39 2.85 0.0 0.0 0.0 0.0 40-41 2.85 0.0 0.0 0.0 0.0 42-43 2.85 0.0 0.0 0.0 0.0 44-45 2.85 0.0 0.0 0.0 0.0 46-47 2.85 0.0 0.0 0.0 0.0 48-49 2.85 0.0 0.0 0.0 0.0 50-51 2.85 0.0 0.0 0.0 0.0 52-53 2.85 0.0 0.0 0.0 0.0 54-55 2.85 0.0 0.0 0.0 0.0 56-57 2.875 0.0 0.0 0.0 0.0 58-59 2.875 0.0 0.0 0.0 0.0 60-61 2.875 0.0 0.0 0.0 0.0 62-63 2.875 0.0 0.0 0.0 0.0 64-65 2.875 0.0 0.0 0.0 0.0 66-67 2.8875 0.0 0.0 0.0 0.0 68-69 2.9 0.0 0.0 0.0 0.0 70-71 2.925 0.0 0.0 0.0 0.0 72-73 2.9625000000000004 0.0 0.0 0.0 0.0 74-75 2.9875 0.0 0.0 0.0 0.0 76-77 3.0 0.0 0.0 0.0 0.0 78-79 3.025 0.0 0.0 0.0 0.0 80-81 3.025 0.0 0.0 0.0 0.0 82-83 3.025 0.0 0.0 0.0 0.0 84-85 3.025 0.0 0.0 0.0 0.0 86-87 3.0875000000000004 0.0 0.0 0.0 0.0 88 3.1 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATCGGA 25 4.9099104E-5 75.200005 2 TCGGAAG 25 4.9099104E-5 75.200005 4 CGGAAGA 25 4.9099104E-5 75.200005 5 AGAGCAC 25 4.9099104E-5 75.200005 9 ATCGGAA 25 4.9099104E-5 75.200005 3 GGAAGAG 25 4.9099104E-5 75.200005 6 AGATCGG 25 4.9099104E-5 75.200005 1 AAGAGCA 30 1.2116377E-4 62.666668 8 GAAGAGC 30 1.2116377E-4 62.666668 7 CTCCAGT 30 8.063304E-5 39.166668 24-25 ACACGTC 25 0.0016030063 37.600002 14-15 CACACGT 25 0.0016030063 37.600002 12-13 ACGTCTG 25 0.0016030063 37.600002 16-17 CCAGTCA 25 0.0016030063 37.600002 26-27 CACGTCT 25 0.0016030063 37.600002 14-15 ACTCCAG 25 0.0016030063 37.600002 24-25 GTCTGAA 25 0.0016030063 37.600002 18-19 AACTCCA 25 0.0016030063 37.600002 22-23 GAGCACA 25 0.0016030063 37.600002 10-11 GAACTCC 25 0.0016030063 37.600002 22-23 >>END_MODULE SRR10225138 read2 length is 100 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR10225138_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.3015 34.0 31.0 34.0 31.0 34.0 2 32.51725 34.0 31.0 34.0 31.0 34.0 3 32.4235 34.0 31.0 34.0 30.0 34.0 4 35.8625 37.0 37.0 37.0 35.0 37.0 5 35.80025 37.0 37.0 37.0 35.0 37.0 6 35.7165 37.0 36.0 37.0 35.0 37.0 7 35.691 37.0 37.0 37.0 35.0 37.0 8 35.69575 37.0 37.0 37.0 35.0 37.0 9 37.50725 39.0 39.0 39.0 35.0 39.0 10-11 37.531125 39.0 39.0 39.0 35.0 39.0 12-13 37.449 39.0 38.5 39.0 35.0 39.0 14-15 38.955375000000004 41.0 40.0 41.0 35.5 41.0 16-17 38.912375 41.0 40.0 41.0 36.0 41.0 18-19 38.683875 41.0 39.0 41.0 34.5 41.0 20-21 38.678375 41.0 39.0 41.0 35.0 41.0 22-23 38.490625 41.0 39.0 41.0 34.5 41.0 24-25 38.45975 41.0 39.0 41.0 34.0 41.0 26-27 38.38575 41.0 39.0 41.0 34.0 41.0 28-29 38.24575 40.5 38.5 41.0 34.0 41.0 30-31 38.059625 40.0 38.5 41.0 33.5 41.0 32-33 37.888374999999996 40.0 38.0 41.0 33.5 41.0 34-35 37.790625000000006 40.0 38.0 41.0 32.5 41.0 36-37 37.766999999999996 40.0 38.0 41.0 33.0 41.0 38-39 37.560249999999996 40.0 38.0 41.0 32.5 41.0 40-41 37.652 40.0 38.0 41.0 33.0 41.0 42-43 37.47075 40.0 38.0 41.0 32.5 41.0 44-45 37.43675 40.0 38.0 41.0 32.0 41.0 46-47 37.569375 40.0 38.0 41.0 32.0 41.0 48-49 37.565749999999994 40.0 38.0 41.0 32.5 41.0 50-51 37.532375 40.0 37.5 41.0 32.5 41.0 52-53 37.34 40.0 37.0 41.0 32.0 41.0 54-55 37.23625 40.0 37.0 41.0 32.0 41.0 56-57 37.002250000000004 40.0 36.0 41.0 32.0 41.0 58-59 36.74725 40.0 35.5 41.0 31.0 41.0 60-61 36.46325 39.0 35.0 41.0 31.0 41.0 62-63 36.245 39.0 35.0 41.0 31.0 41.0 64-65 35.670125 38.0 35.0 40.5 30.0 41.0 66-67 34.9895 37.0 35.0 40.0 28.5 41.0 68-69 34.386875 37.0 35.0 39.5 26.0 41.0 70-71 33.9945 36.5 34.5 39.0 26.0 41.0 72-73 33.541250000000005 36.0 34.0 39.0 26.0 40.5 74-75 33.108999999999995 35.0 34.0 37.5 24.5 39.5 76-77 32.856875 35.0 34.0 37.0 26.0 39.0 78-79 32.644 35.0 34.0 37.0 26.0 39.0 80-81 32.194625 35.0 34.0 36.0 24.5 37.0 82-83 31.98225 35.0 34.0 36.0 24.0 37.0 84-85 31.654 35.0 33.5 35.5 24.0 36.5 86-87 31.400875 35.0 33.0 35.0 21.5 36.0 88-89 31.21375 35.0 33.0 35.0 20.5 36.0 90-91 31.0165 35.0 33.0 35.0 19.5 36.0 92-93 30.8045 35.0 33.0 35.0 18.0 35.5 94-95 30.61325 35.0 33.0 35.0 9.5 35.0 96-97 30.442375 35.0 32.5 35.0 2.0 35.0 98-99 30.30775 35.0 32.5 35.0 2.0 35.0 100 30.2435 35.0 33.0 35.0 2.0 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 35.0 3 12.0 4 3.0 5 5.0 6 5.0 7 9.0 8 9.0 9 7.0 10 1.0 11 7.0 12 10.0 13 6.0 14 8.0 15 11.0 16 6.0 17 8.0 18 8.0 19 12.0 20 12.0 21 9.0 22 19.0 23 18.0 24 32.0 25 56.0 26 41.0 27 27.0 28 27.0 29 26.0 30 53.0 31 68.0 32 91.0 33 87.0 34 138.0 35 188.0 36 327.0 37 757.0 38 1482.0 39 380.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.025 16.150000000000002 15.5 28.325 2 30.2 7.074999999999999 20.225 42.5 3 20.0 9.125 19.6 51.275000000000006 4 22.475 8.200000000000001 21.375 47.949999999999996 5 24.224999999999998 10.45 22.125 43.2 6 31.10777694423606 11.927981995498875 27.131782945736433 29.83245811452863 7 20.75 26.174999999999997 32.425 20.65 8 16.025 30.975 33.375 19.625 9 16.825000000000003 32.525 31.45 19.2 10-11 19.225 30.337500000000002 31.45 18.987499999999997 12-13 18.4125 28.6375 30.4875 22.4625 14-15 18.787499999999998 27.35 32.300000000000004 21.5625 16-17 19.1875 28.212500000000002 29.4875 23.1125 18-19 19.2375 28.499999999999996 30.337500000000002 21.925 20-21 18.675 29.462500000000002 29.9875 21.875 22-23 21.6 28.762500000000003 27.9125 21.725 24-25 20.325 29.675 27.537499999999998 22.4625 26-27 18.7625 31.112499999999997 28.1375 21.987499999999997 28-29 20.6375 30.312499999999996 26.5875 22.4625 30-31 20.075000000000003 28.8375 27.987499999999997 23.1 32-33 20.1125 28.000000000000004 28.725 23.1625 34-35 20.7875 30.099999999999998 26.625 22.4875 36-37 19.275000000000002 30.1875 27.712500000000002 22.825 38-39 19.325 28.6875 28.8375 23.150000000000002 40-41 20.5875 28.1 27.575 23.7375 42-43 20.9875 28.175 28.962500000000002 21.875 44-45 21.45 27.962500000000002 27.6875 22.900000000000002 46-47 19.175 28.125 28.249999999999996 24.45 48-49 21.1375 27.925 27.500000000000004 23.4375 50-51 20.125 28.487499999999997 26.687499999999996 24.7 52-53 18.7 30.25 28.675 22.375 54-55 19.7125 29.312500000000004 28.237499999999997 22.7375 56-57 19.625 30.025000000000002 28.449999999999996 21.9 58-59 19.8625 29.9 27.725 22.5125 60-61 19.225 31.337500000000002 26.5 22.9375 62-63 19.375 29.9875 27.8625 22.775000000000002 64-65 20.4625 30.337500000000002 26.924999999999997 22.275 66-67 19.7625 30.562499999999996 27.025 22.650000000000002 68-69 20.025000000000002 30.2125 26.4125 23.35 70-71 20.375 29.9625 27.325 22.3375 72-73 20.474999999999998 29.375 27.125 23.025000000000002 74-75 21.3625 29.175 25.937500000000004 23.525 76-77 21.224999999999998 29.3375 26.4625 22.975 78-79 21.0 29.5375 26.787499999999998 22.675 80-81 20.575 28.8375 27.275 23.3125 82-83 20.4375 28.775000000000002 26.9125 23.875 84-85 21.099999999999998 28.012500000000003 27.85 23.0375 86-87 21.15 28.9875 27.525 22.3375 88-89 21.0375 29.062500000000004 26.275 23.625 90-91 20.1125 29.5375 26.900000000000002 23.45 92-93 21.8 28.925 26.9125 22.3625 94-95 21.1125 28.1 27.150000000000002 23.6375 96-97 21.587500000000002 29.275000000000002 26.2875 22.85 98-99 21.637500000000003 28.6875 26.787499999999998 22.8875 100 21.5 28.375 26.075 24.05 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 1.0 12 1.0 13 0.0 14 0.5 15 1.5 16 3.0 17 4.0 18 2.0 19 0.0 20 1.5 21 4.0 22 3.5 23 3.5 24 7.0 25 6.0 26 11.0 27 16.5 28 15.0 29 18.0 30 28.0 31 43.0 32 48.5 33 60.5 34 70.0 35 80.5 36 108.5 37 123.0 38 132.0 39 147.5 40 177.0 41 205.5 42 214.0 43 219.0 44 223.5 45 229.5 46 226.5 47 203.0 48 186.0 49 166.0 50 139.0 51 127.5 52 111.5 53 95.0 54 74.0 55 63.0 56 63.5 57 58.5 58 55.5 59 53.0 60 43.0 61 31.0 62 22.0 63 10.0 64 6.5 65 8.0 66 8.0 67 4.5 68 2.0 69 5.0 70 6.5 71 4.0 72 4.0 73 6.0 74 4.0 75 0.5 76 0.0 77 0.5 78 0.5 79 0.0 80 0.0 81 0.0 82 0.5 83 0.5 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 0.5 >>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 95.39999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 98.13941299790356 93.625 2 1.519916142557652 2.9000000000000004 3 0.052410901467505246 0.15 4 0.10482180293501049 0.4 5 0.07861635220125787 0.375 6 0.052410901467505246 0.3 7 0.026205450733752623 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.026205450733752623 2.075 >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 83 2.075 Illumina Single End PCR Primer 1 (100% over 50bp) GCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCC 7 0.17500000000000002 No Hit CCCTCGCGGTACTTGTTTGCTATCGGTCTCTCGCCCGTATTTAGCCTTGG 6 0.15 No Hit GCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCC 6 0.15 No Hit ATCCCATCATCCCACCATGACCATCACCAACATTAATCTCACAAACCACA 5 0.125 No Hit CCCCTCTTCGGCCTTCAAAGTTCTCATTTGAATATTTGCTACTACCACCA 5 0.125 No Hit GCCACCATCTACCATCTATACATACATCCCATCATCCCACCATGACCATC 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 2.5 0.0 0.0 0.0 0.0 2 2.5 0.0 0.0 0.0 0.0 3 2.5 0.0 0.0 0.0 0.0 4 2.5 0.0 0.0 0.0 0.0 5 2.5 0.0 0.0 0.0 0.0 6 2.5 0.0 0.0 0.0 0.0 7 2.5 0.0 0.0 0.0 0.0 8 2.5 0.0 0.0 0.0 0.0 9 2.5 0.0 0.0 0.0 0.0 10-11 2.5 0.0 0.0 0.0 0.0 12-13 2.5125 0.0 0.0 0.0 0.0 14-15 2.525 0.0 0.0 0.0 0.0 16-17 2.525 0.0 0.0 0.0 0.0 18-19 2.55 0.0 0.0 0.0 0.0 20-21 2.575 0.0 0.0 0.0 0.0 22-23 2.5875000000000004 0.0 0.0 0.0 0.0 24-25 2.6 0.0 0.0 0.0 0.0 26-27 2.6 0.0 0.0 0.0 0.0 28-29 2.6375 0.0 0.0 0.0 0.0 30-31 2.65 0.0 0.0 0.0 0.0 32-33 2.7 0.0 0.0 0.0 0.0 34-35 2.7 0.0 0.0 0.0 0.0 36-37 2.7 0.0 0.0 0.0 0.0 38-39 2.7125000000000004 0.0 0.0 0.0 0.0 40-41 2.725 0.0 0.0 0.0 0.0 42-43 2.725 0.0 0.0 0.0 0.0 44-45 2.725 0.0 0.0 0.0 0.0 46-47 2.725 0.0 0.0 0.0 0.0 48-49 2.725 0.0 0.0 0.0 0.0 50-51 2.725 0.0 0.0 0.0 0.0 52-53 2.725 0.0 0.0 0.0 0.0 54-55 2.725 0.0 0.0 0.0 0.0 56-57 2.75 0.0 0.0 0.0 0.0 58-59 2.75 0.0 0.0 0.0 0.0 60-61 2.75 0.0 0.0 0.0 0.0 62-63 2.75 0.0 0.0 0.0 0.0 64-65 2.75 0.0 0.0 0.0 0.0 66-67 2.75 0.0 0.0 0.0 0.0 68-69 2.75 0.0 0.0 0.0 0.0 70-71 2.775 0.0 0.0 0.0 0.0 72-73 2.8125 0.0 0.0 0.0 0.0 74-75 2.8375000000000004 0.0 0.0 0.0 0.0 76-77 2.85 0.0 0.0 0.0 0.0 78-79 2.875 0.0 0.0 0.0 0.0 80-81 2.875 0.0 0.0 0.0 0.0 82-83 2.875 0.0 0.0 0.0 0.0 84-85 2.875 0.0 0.0 0.0 0.0 86-87 2.9375 0.0 0.0 0.0 0.0 88 2.95 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAGAGCG 15 6.4061093E-4 94.0 8 GATCGGA 15 6.4061093E-4 94.0 2 GAAGAGC 15 6.4061093E-4 94.0 7 TCGGAAG 15 6.4061093E-4 94.0 4 CGGAAGA 15 6.4061093E-4 94.0 5 AGAGCGT 15 6.4061093E-4 94.0 9 ATCGGAA 15 6.4061093E-4 94.0 3 GGAAGAG 15 6.4061093E-4 94.0 6 AGATCGG 20 0.0020083564 70.5 1 GTAGATC 20 5.3435756E-4 47.0 32-33 TGTAGAT 20 5.3435756E-4 47.0 30-31 GTGTAGA 25 0.0016030063 37.600002 30-31 GCCGTAT 25 0.0016030063 37.600002 48-49 CGCCGTA 25 0.0016030063 37.600002 46-47 ATTAAAA 35 0.008330873 26.857141 56-57 >>END_MODULE Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712573 spots for SRR10225138.sra Written 5712573 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra Read 5712570 spots for SRR10225138.sra Written 5712570 spots for SRR10225138.sra SRR ids: ['SRR10225138.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_of3ooxid SRR10225138.sra spots: 114251403 blocks: [[1, 5712570], [5712571, 11425140], [11425141, 17137710], [17137711, 22850280], [22850281, 28562850], [28562851, 34275420], [34275421, 39987990], [39987991, 45700560], [45700561, 51413130], [51413131, 57125700], [57125701, 62838270], [62838271, 68550840], [68550841, 74263410], [74263411, 79975980], [79975981, 85688550], [85688551, 91401120], [91401121, 97113690], [97113691, 102826260], [102826261, 108538830], [108538831, 114251403]] SRR10225138 file size 31260375 SRR10225138 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 SRR10225138 SRR10225138_1.fastq SRR10225138_2.fastq Input file: SRR10225138_1.fastq Paired file: SRR10225138_2.fastq trimmed: SRR10225138-trimmed-pair1.fastq, SRR10225138-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 Apr 10 16:11:28 2025 >> started Thu Apr 10 16:14:03 2025 >> done (154.618s) 114251403 read pairs processed; of these: 788385 ( 0.69%) short read pairs filtered out after trimming by size control 5055736 ( 4.43%) empty read pairs filtered out after trimming by size control 108407282 (94.88%) read pairs available; of these: 15321552 (14.13%) trimmed read pairs available after processing 93085730 (85.87%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 34663 0.03% 19 22408 0.02% 20 30686 0.03% 21 13273 0.01% 22 8268 0.01% 23 9732 0.01% 24 20830 0.02% 25 24466 0.02% 26 19061 0.02% 27 14352 0.01% 28 10161 0.01% 29 12192 0.01% 30 12469 0.01% 31 8745 0.01% 32 9124 0.01% 33 6795 0.01% 34 5068 0.00% 35 5563 0.01% 36 6046 0.01% 37 6719 0.01% 38 7309 0.01% 39 7924 0.01% 40 9168 0.01% 41 9511 0.01% 42 10361 0.01% 43 11410 0.01% 44 11845 0.01% 45 13143 0.01% 46 13492 0.01% 47 14019 0.01% 48 15457 0.01% 49 16782 0.02% 50 17934 0.02% 51 19548 0.02% 52 20574 0.02% 53 22402 0.02% 54 24656 0.02% 55 27678 0.03% 56 27950 0.03% 57 30686 0.03% 58 32283 0.03% 59 186287 0.17% 60 191538 0.18% 61 113886 0.11% 62 121460 0.11% 63 130541 0.12% 64 130877 0.12% 65 136185 0.13% 66 144445 0.13% 67 152987 0.14% 68 151992 0.14% 69 158052 0.15% 70 162707 0.15% 71 158573 0.15% 72 163799 0.15% 73 174183 0.16% 74 174367 0.16% 75 186741 0.17% 76 200932 0.19% 77 186985 0.17% 78 188756 0.17% 79 196786 0.18% 80 200024 0.18% 81 220312 0.20% 82 228408 0.21% 83 242714 0.22% 84 258777 0.24% 85 261212 0.24% 86 246117 0.23% 87 279461 0.26% 88 292652 0.27% 89 320910 0.30% 90 379405 0.35% 91 560855 0.52% 92 394804 0.36% 93 464864 0.43% 94 476762 0.44% 95 1961839 1.81% 96 643584 0.59% 97 817330 0.75% 98 1140724 1.05% 99 1873966 1.73% 100 93085730 85.87% 108407282 reads passed initial QC criterion=sequence-density sequence-density=0.23 sequence-density-rank=1 fanout-score=5.03 fanout-score-rank=16 prefix-density=0.33 prefix-fanout=3.5 sequence=AGAAAATGTCTGG criterion=fanout-score sequence-density=0.11 sequence-density-rank=12 fanout-score=199.09 fanout-score-rank=1 prefix-density=0.86 prefix-fanout=25.2 sequence=AAGAAGAAGAAA criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=3.76 fanout-score-rank=21 prefix-density=0.25 prefix-fanout=2.9 sequence=GGAGACTTGTACTTGTAAGGGTGCGTTGGTGGTGG criterion=fanout-score sequence-density=0.01 sequence-density-rank=30 fanout-score=958.50 fanout-score-rank=1 prefix-density=0.41 prefix-fanout=28.2 sequence=AAAACAAAAATCAGAGTCAATTGTTTATTTTAAATTCCAAACTTCGCACATCATCTAAAGCCTTGTACTCGTAAACCACAAAATCGAAAAAAAAGCGCCTCAATTCATCATCTCCATGCTTCAGCTTCAAGCTT SRR10225138 testing PE reads STAR mapping to Ensembl genome Started job on | Apr 10 16:14:35 Started mapping on | Apr 10 16:14:35 Finished on | Apr 10 16:26:51 Mapping speed, Million of reads per hour | 530.25 Number of input reads | 108407282 Average input read length | 196 UNIQUE READS: Uniquely mapped reads number | 92926978 Uniquely mapped reads % | 85.72% Average mapped length | 194.94 Number of splices: Total | 40519895 Number of splices: Annotated (sjdb) | 39391357 Number of splices: GT/AG | 39647552 Number of splices: GC/AG | 559509 Number of splices: AT/AC | 57430 Number of splices: Non-canonical | 255404 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.04% Deletion average length | 2.56 Insertion rate per base | 0.03% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 4407502 % of reads mapped to multiple loci | 4.07% Number of reads mapped to too many loci | 6143110 % of reads mapped to too many loci | 5.67% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.12% % of reads unmapped: other | 0.43% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 11588688 11588688 11588688 N_multimapping 4407502 4407502 4407502 N_noFeature 3339677 4143345 91306955 N_ambiguous 1529312 700489 17363 UnstrandedReadsAssigned:88057989 PositiveStrandReadsAssigned:88083144 NegativeStrandReadsAssigned:1602660 Dataset is classified positive stranded MeadianReadLen=100 20thPercentileLength=100 echo kmer=95 SRR10225138 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: SRR10225138-trimmed-pair1.fastq SRR10225138-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 108,407,282 reads, 93,437,754 reads pseudoaligned [quant] estimated average fragment length: 261.366 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,247 rounds 52401 SRR10225138.ke.tsv 34699 SRR10225138.se.tsv 87100 total ==> SRR10225138.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1757.63 11536.4 48.8884 Potri.005G024800.1.v4.1 1035 774.634 2560 24.6155 Potri.004G059700.1.v4.1 961 700.634 1109 11.7898 Potri.007G009000.2.v4.1 1416 1155.63 2 0.0128907 Potri.003G141000.2.v4.1 2943 2682.63 2777 7.71045 Potri.016G087400.1.v4.1 270 61.2477 8546 1039.29 Potri.015G069301.1.v4.1 564 304.178 0 0 Potri.010G195200.1.v4.1 1773 1512.63 901 4.43666 Potri.012G127500.1.v4.1 977 716.634 38260 397.661 ==> SRR10225138.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 258 Potri.001G233950.v4.1 5 Potri.001G122700.v4.1 2563 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 5 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 4 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 930 SRR10225138 completed mapping pipeline successfully