Starting /dee2/code/volunteer_pipeline.sh SRR12951289 current disk space = 1543444320256 free memory = 1601402908 SRR12951289 SRAfilesize c9e0be5eacedbfb8a0aca9a8ae919805 SRR12951289.sra SRR12951289.sra file validated SRR12951289 is paired end SRR12951289 is conventional basespace SRR12951289 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951289_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.599 37.0 37.0 37.0 37.0 37.0 2 36.181 37.0 37.0 37.0 37.0 37.0 3 36.5205 37.0 37.0 37.0 37.0 37.0 4 36.635 37.0 37.0 37.0 37.0 37.0 5 36.5855 37.0 37.0 37.0 37.0 37.0 6 36.6695 37.0 37.0 37.0 37.0 37.0 7 36.536 37.0 37.0 37.0 37.0 37.0 8 36.597 37.0 37.0 37.0 37.0 37.0 9 36.624 37.0 37.0 37.0 37.0 37.0 10-14 36.624399999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.58729999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.5435 37.0 37.0 37.0 37.0 37.0 25-29 36.5226 37.0 37.0 37.0 37.0 37.0 30-34 36.4645 37.0 37.0 37.0 37.0 37.0 35-39 36.4468 37.0 37.0 37.0 37.0 37.0 40-44 36.3814 37.0 37.0 37.0 37.0 37.0 45-49 36.119600000000005 37.0 37.0 37.0 37.0 37.0 50-54 36.311699999999995 37.0 37.0 37.0 37.0 37.0 55-59 35.9741 37.0 37.0 37.0 37.0 37.0 60-64 35.8975 37.0 37.0 37.0 37.0 37.0 65-69 35.7558 37.0 37.0 37.0 37.0 37.0 70-74 35.9477 37.0 37.0 37.0 37.0 37.0 75-79 36.2858 37.0 37.0 37.0 37.0 37.0 80-84 36.250299999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.284200000000006 37.0 37.0 37.0 37.0 37.0 90-94 36.2594 37.0 37.0 37.0 37.0 37.0 95-99 36.2287 37.0 37.0 37.0 37.0 37.0 100-104 36.209900000000005 37.0 37.0 37.0 37.0 37.0 105-109 36.2772 37.0 37.0 37.0 37.0 37.0 110-114 36.1315 37.0 37.0 37.0 37.0 37.0 115-119 36.173199999999994 37.0 37.0 37.0 37.0 37.0 120-124 36.09179999999999 37.0 37.0 37.0 37.0 37.0 125-129 36.068799999999996 37.0 37.0 37.0 37.0 37.0 130-134 36.0311 37.0 37.0 37.0 37.0 37.0 135-139 35.9437 37.0 37.0 37.0 37.0 37.0 140-144 35.792500000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.7453 37.0 37.0 37.0 37.0 37.0 150-151 35.569 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 3.0 24 3.0 25 6.0 26 9.0 27 10.0 28 9.0 29 14.0 30 33.0 31 30.0 32 40.0 33 92.0 34 210.0 35 279.0 36 2770.0 37 492.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.8 10.925 4.15 35.125 2 20.669687814702918 13.318227593152066 34.315206445115805 31.696878147029206 3 19.35 14.774999999999999 30.049999999999997 35.825 4 23.974999999999998 20.724999999999998 22.675 32.625 5 28.875 27.675 20.175 23.275000000000002 6 26.400000000000002 29.875 22.425 21.3 7 18.25 25.2 36.875 19.675 8 19.05 25.55 30.15 25.25 9 23.200000000000003 20.175 30.175 26.450000000000003 10-14 23.315 26.784999999999997 23.455000000000002 26.445 15-19 23.335 24.610000000000003 25.319999999999997 26.735 20-24 23.810000000000002 25.619999999999997 24.68 25.89 25-29 23.355 25.27 24.08 27.295 30-34 23.05 25.185000000000002 24.72 27.045 35-39 25.445 23.93 25.785000000000004 24.84 40-44 23.365 24.58 26.195 25.86 45-49 23.895 24.2 25.430000000000003 26.474999999999998 50-54 24.610000000000003 24.135 24.69 26.565 55-59 22.765 23.68 25.47 28.084999999999997 60-64 23.715 23.905 25.82 26.56 65-69 23.945 25.790000000000003 24.279999999999998 25.985000000000003 70-74 26.745 24.21 24.21 24.834999999999997 75-79 26.72 23.54 23.915 25.825 80-84 26.395000000000003 23.765 24.099999999999998 25.740000000000002 85-89 26.784999999999997 24.060000000000002 23.415 25.740000000000002 90-94 26.905 24.525 23.285 25.285000000000004 95-99 27.1 24.145 23.79 24.965 100-104 26.875 24.625 22.95 25.55 105-109 27.49 24.195 22.855 25.46 110-114 27.305 24.565 23.02 25.11 115-119 27.55 24.62 23.085 24.745 120-124 27.694999999999997 23.94 22.675 25.69 125-129 27.245 23.66 23.085 26.009999999999998 130-134 27.595 24.349999999999998 23.095 24.959999999999997 135-139 27.37 23.865 22.900000000000002 25.865 140-144 26.82 23.555 23.865 25.759999999999998 145-149 27.310000000000002 22.634999999999998 23.605 26.450000000000003 150-151 27.900000000000002 22.8625 23.625 25.6125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 0.5 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 1.0 14 0.5 15 0.0 16 0.0 17 0.5 18 0.5 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 2.5 28 4.0 29 6.0 30 7.5 31 5.0 32 10.0 33 12.5 34 12.0 35 19.0 36 30.0 37 39.5 38 56.0 39 78.5 40 106.0 41 117.5 42 144.0 43 163.5 44 163.0 45 186.5 46 196.5 47 204.5 48 205.0 49 191.0 50 171.0 51 158.0 52 162.0 53 140.5 54 116.5 55 107.0 56 87.5 57 90.0 58 82.0 59 58.5 60 57.5 61 59.0 62 58.0 63 56.5 64 57.0 65 92.0 66 98.5 67 60.5 68 51.0 69 45.5 70 34.5 71 31.0 72 25.0 73 27.5 74 29.5 75 18.0 76 16.5 77 15.0 78 7.5 79 8.0 80 6.0 81 3.5 82 2.5 83 1.0 84 1.0 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 0.7000000000000001 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 76.44999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 80.1504251144539 61.275 2 15.075212557226948 23.05 3 3.4009156311314586 7.8 4 0.8829300196206671 2.7 5 0.1635055591890124 0.625 6 0.1635055591890124 0.75 7 0.032701111837802485 0.17500000000000002 8 0.032701111837802485 0.2 9 0.032701111837802485 0.22499999999999998 >10 0.032701111837802485 0.8 >50 0.032701111837802485 2.4 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGTTGTTATCTCGTAT 96 2.4 TruSeq Adapter, Index 2 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGTTGTTATCGCGTAT 32 0.8 TruSeq Adapter, Index 2 (97% over 37bp) GTCACTATCTCGGCAAAGTGTTGCCAGGGGATAATTTGCGCGCCTGCTGC 9 0.22499999999999998 No Hit CTCCACCACTGATTTCTCAAGGTTTGTCACAAATTGAGGGGAAATGTAGC 8 0.2 No Hit CGAAAACGAAGGAAAACCACAAAAGATAACAAAAGACCCGACTAGTATAA 7 0.17500000000000002 No Hit ACAAAACTCCGTACTTTATTTGAACAAGCAAATGGAGCTCGCGGCAGGCC 6 0.15 No Hit AGGTTGCAAGAACAATTAGCTGGATTGAGAATGCCTCCAAGTGCCTACCA 6 0.15 No Hit GTTCAGGGGAACTGTAGATCTCCATAGCAGCTCCATAGTAATCAGCGTAG 6 0.15 No Hit GAGACTGTTGTGTGATGTAATCTGGAGTACGGGGCTCAAGGATGCATAGG 6 0.15 No Hit CTTTGATCATCTTTCACGGGTTGACAGAGGATTGTCTAGAGCCCTAGACA 6 0.15 No Hit CTCCAGCTCCTTGAGCACCTGCGTGGCGTCGGTGCACCCGAACATGGGCA 5 0.125 No Hit CTCCAACTCTTTCGTCAACTCCTCCATTGTTTTCTTTAAGTTGGCTTTGC 5 0.125 No Hit GGCAGCATTGATGAAGCCAGAGGCGCTAGGGATGCAGCAGAGGACGATGG 5 0.125 No Hit CCTTAATTTACATCCATGCTTTGATGGTAATTTCGCACTCCATCATACGG 5 0.125 No Hit GCTGCTCTGGCTGCACTCCGCCTCCGTCGACTCTTCCGGTGTCGCGCGCT 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.0375 0.0 0.0 0.0 0.0 46-47 0.075 0.0 0.0 0.0 0.0 48-49 0.075 0.0 0.0 0.0 0.0 50-51 0.075 0.0 0.0 0.0 0.0 52-53 0.075 0.0 0.0 0.0 0.0 54-55 0.0875 0.0 0.0 0.0 0.0 56-57 0.1 0.0 0.0 0.0 0.0 58-59 0.125 0.0 0.0 0.0 0.0 60-61 0.125 0.0 0.0 0.0 0.0 62-63 0.175 0.0 0.0 0.0 0.0 64-65 0.225 0.0 0.0125 0.0 0.0 66-67 0.25 0.0 0.025 0.0 0.0 68-69 0.3 0.0 0.025 0.0 0.0 70-71 0.3875 0.0 0.025 0.0 0.0 72-73 0.4 0.0 0.025 0.0 0.0 74-75 0.4 0.0 0.025 0.0 0.0 76-77 0.5249999999999999 0.0 0.025 0.0 0.0 78-79 0.625 0.0 0.025 0.0 0.0 80-81 0.6875 0.0 0.025 0.0 0.0 82-83 0.8500000000000001 0.0 0.025 0.0 0.0 84-85 1.1 0.0 0.025 0.0 0.0 86-87 1.325 0.0 0.025 0.0 0.0 88-89 1.5499999999999998 0.0 0.025 0.0 0.0 90-91 1.775 0.0 0.025 0.0 0.0 92-93 2.1125 0.0 0.025 0.0 0.0 94-95 2.85 0.0 0.025 0.0 0.0 96-97 3.2 0.0 0.025 0.0 0.0 98-99 3.6375 0.0 0.025 0.0 0.0 100-101 4.05 0.0 0.025 0.0 0.0 102-103 4.5375 0.0 0.025 0.0 0.0 104-105 5.074999999999999 0.0 0.025 0.0 0.0 106-107 5.9 0.0 0.025 0.0 0.0 108-109 6.825 0.0 0.025 0.0 0.0 110-111 7.4625 0.0 0.025 0.0 0.0 112-113 8.225000000000001 0.0 0.025 0.0 0.0 114-115 9.025 0.0 0.025 0.0 0.0 116-117 10.0625 0.0 0.025 0.0 0.0 118-119 10.75 0.0 0.025 0.0 0.0 120-121 11.3875 0.0 0.025 0.0 0.0 122-123 12.275 0.0 0.025 0.0 0.0 124-125 13.35 0.0 0.025 0.0 0.0 126-127 14.225000000000001 0.0 0.025 0.0 0.0 128-129 15.175 0.0 0.025 0.0 0.0 130-131 16.3375 0.0 0.025 0.0 0.0 132-133 17.35 0.0 0.025 0.0 0.0 134-135 18.2 0.0 0.025 0.0 0.0 136-137 18.9 0.0 0.025 0.0 0.0 138-139 19.4375 0.0 0.025 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CATCAAT 10 0.006830828 145.0 145 AGAGCAC 75 2.1205773E-5 48.333336 8 GAAGAGC 80 3.1063704E-5 45.3125 6 GAGCACA 80 3.1063704E-5 45.3125 9 CGGAAGA 80 3.1063704E-5 45.3125 4 ATCGGAA 80 3.1063704E-5 45.3125 2 AAGAGCA 85 4.444814E-5 42.64706 7 TCGGAAG 85 4.444814E-5 42.64706 3 GATCGGA 90 6.229055E-5 40.27778 1 GGAAGAG 90 6.229055E-5 40.27778 5 AGGGGGG 20 0.00593511 29.0 65-69 GTATGCC 30 0.0014437955 24.166668 45-49 TATGCCG 30 0.0014437955 24.166668 45-49 CGTATGC 30 0.0014437955 24.166668 45-49 TCTTCTG 30 0.0014437955 24.166668 55-59 CTTCTGC 30 0.0014437955 24.166668 55-59 TGCCGTC 35 0.0035366106 20.714287 50-54 CCGTCTT 35 0.0035366106 20.714287 50-54 ATGCCGT 35 0.0035366106 20.714287 45-49 GCCGTCT 35 0.0035366106 20.714287 50-54 >>END_MODULE SRR12951289 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951289_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.327 37.0 37.0 37.0 37.0 37.0 2 36.0725 37.0 37.0 37.0 37.0 37.0 3 35.935 37.0 37.0 37.0 37.0 37.0 4 36.068 37.0 37.0 37.0 37.0 37.0 5 36.1555 37.0 37.0 37.0 37.0 37.0 6 36.0045 37.0 37.0 37.0 37.0 37.0 7 36.045 37.0 37.0 37.0 37.0 37.0 8 35.9975 37.0 37.0 37.0 37.0 37.0 9 35.9335 37.0 37.0 37.0 37.0 37.0 10-14 35.79729999999999 37.0 37.0 37.0 37.0 37.0 15-19 35.816700000000004 37.0 37.0 37.0 37.0 37.0 20-24 35.6664 37.0 37.0 37.0 37.0 37.0 25-29 35.422399999999996 37.0 37.0 37.0 37.0 37.0 30-34 35.3394 37.0 37.0 37.0 37.0 37.0 35-39 35.363099999999996 37.0 37.0 37.0 37.0 37.0 40-44 35.3937 37.0 37.0 37.0 37.0 37.0 45-49 35.2877 37.0 37.0 37.0 37.0 37.0 50-54 35.1952 37.0 37.0 37.0 37.0 37.0 55-59 35.206 37.0 37.0 37.0 37.0 37.0 60-64 35.370999999999995 37.0 37.0 37.0 37.0 37.0 65-69 35.26049999999999 37.0 37.0 37.0 37.0 37.0 70-74 35.076800000000006 37.0 37.0 37.0 32.2 37.0 75-79 35.0039 37.0 37.0 37.0 32.2 37.0 80-84 35.104200000000006 37.0 37.0 37.0 29.8 37.0 85-89 35.260000000000005 37.0 37.0 37.0 37.0 37.0 90-94 35.437599999999996 37.0 37.0 37.0 37.0 37.0 95-99 35.4836 37.0 37.0 37.0 37.0 37.0 100-104 35.4163 37.0 37.0 37.0 37.0 37.0 105-109 35.3985 37.0 37.0 37.0 37.0 37.0 110-114 35.3644 37.0 37.0 37.0 37.0 37.0 115-119 35.4487 37.0 37.0 37.0 37.0 37.0 120-124 35.2278 37.0 37.0 37.0 37.0 37.0 125-129 35.145799999999994 37.0 37.0 37.0 34.6 37.0 130-134 34.8038 37.0 37.0 37.0 25.0 37.0 135-139 34.68939999999999 37.0 37.0 37.0 25.0 37.0 140-144 34.4208 37.0 37.0 37.0 25.0 37.0 145-149 34.0628 37.0 37.0 37.0 25.0 37.0 150-151 33.7375 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 6.0 13 7.0 14 10.0 15 11.0 16 8.0 17 8.0 18 1.0 19 4.0 20 10.0 21 8.0 22 14.0 23 21.0 24 19.0 25 16.0 26 20.0 27 18.0 28 29.0 29 44.0 30 34.0 31 56.0 32 66.0 33 145.0 34 219.0 35 547.0 36 2391.0 37 288.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.025 21.0 6.45 23.525 2 34.150000000000006 21.325 24.725 19.8 3 26.55 23.7 28.325 21.425 4 29.4 30.8 19.225 20.575 5 29.7 32.225 19.2 18.875 6 27.075 33.875 18.05 21.0 7 27.775 19.525000000000002 30.925000000000004 21.775 8 26.325 21.575 22.650000000000002 29.45 9 27.0 22.725 24.05 26.224999999999998 10-14 29.42 24.755 21.709999999999997 24.115000000000002 15-19 29.604999999999997 24.13 22.205 24.060000000000002 20-24 29.2 23.830000000000002 23.015 23.955000000000002 25-29 28.999999999999996 23.919999999999998 22.715 24.365000000000002 30-34 29.244999999999997 24.224999999999998 22.935 23.595 35-39 29.609999999999996 24.16 22.79 23.44 40-44 29.255 23.885 23.1 23.76 45-49 28.33 24.59 23.849999999999998 23.23 50-54 28.74 24.195 23.494999999999997 23.57 55-59 29.425 24.305 22.73 23.54 60-64 29.470000000000002 24.205 23.0 23.325000000000003 65-69 29.4 23.46 23.630000000000003 23.51 70-74 29.599999999999998 24.04 22.915 23.445 75-79 29.205 24.615000000000002 23.0 23.18 80-84 29.17 23.544999999999998 23.72 23.565 85-89 29.665000000000003 23.990000000000002 23.064999999999998 23.28 90-94 29.535 24.845 22.365 23.255 95-99 30.375000000000004 23.14 23.215 23.27 100-104 30.769999999999996 24.495 22.23 22.505 105-109 30.2 23.695 23.244999999999997 22.86 110-114 31.369999999999997 24.185000000000002 22.395 22.05 115-119 31.25 24.435000000000002 21.94 22.375 120-124 32.24 24.099999999999998 22.355 21.305 125-129 32.684999999999995 23.75 22.305 21.26 130-134 32.73 24.18 22.325 20.765 135-139 33.425 23.405 23.09 20.080000000000002 140-144 33.900000000000006 23.064999999999998 23.105 19.93 145-149 35.38 23.080000000000002 22.205 19.335 150-151 36.025 23.549999999999997 21.6625 18.7625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 4 0.5 5 0.5 6 0.5 7 0.5 8 0.0 9 0.0 10 0.0 11 1.0 12 1.5 13 1.5 14 2.0 15 1.0 16 0.0 17 0.5 18 1.0 19 1.0 20 0.5 21 1.5 22 2.5 23 2.0 24 1.5 25 1.5 26 3.5 27 3.5 28 2.0 29 3.0 30 5.0 31 6.5 32 7.0 33 6.5 34 8.5 35 23.0 36 35.0 37 42.5 38 59.5 39 70.0 40 93.0 41 127.0 42 130.0 43 138.0 44 159.0 45 169.5 46 181.0 47 191.0 48 176.5 49 168.0 50 165.0 51 152.5 52 144.5 53 131.5 54 118.0 55 103.5 56 92.5 57 82.5 58 78.5 59 85.0 60 85.0 61 69.5 62 63.5 63 65.0 64 55.5 65 52.0 66 59.5 67 62.0 68 61.5 69 52.5 70 39.0 71 35.0 72 33.5 73 27.5 74 20.5 75 18.0 76 18.0 77 12.5 78 7.5 79 7.0 80 5.5 81 4.0 82 2.5 83 2.0 84 3.5 85 4.0 86 3.0 87 1.5 88 2.0 89 4.0 90 7.0 91 6.0 92 5.0 93 5.0 94 3.5 95 4.5 96 6.0 97 11.5 98 15.0 99 23.0 100 34.5 >>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 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 78.3 #Duplication Level Percentage of deduplicated Percentage of total 1 81.4176245210728 63.74999999999999 2 13.537675606641125 21.2 3 3.6079182630906765 8.475000000000001 4 0.9578544061302682 3.0 5 0.2234993614303959 0.8750000000000001 6 0.15964240102171137 0.75 7 0.031928480204342274 0.17500000000000002 8 0.031928480204342274 0.2 9 0.0 0.0 >10 0.0 0.0 >50 0.031928480204342274 1.575 >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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 63 1.575 No Hit GTCTAATTGCAGAGCTTGAAAACAAAGCTAGGCCAGTCAAGGGCAGTGGT 8 0.2 No Hit GTTTGATATCGCCGCGGACACGCTGCATTGGCGTCTAGTGAGTGGTATTT 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGG 6 0.15 No Hit AATGATTACAACCTACCTCTTCTCAGTAGGGTGCCCTATAAGACGATTCG 6 0.15 No Hit ACCATGTCAGAGCTGCAGACATGTGAAGTTATCTTGAGCTCTAACTGTAA 6 0.15 No Hit CACATCAAAACCACCTGCGACGGTGGAATGGGAATAGGATATGTTTATTG 6 0.15 No Hit CCACCAGACTTAGCTGCTCTGAGTGCACCAATGCCAATAAATGGCACGGC 6 0.15 No Hit AGAAAAGCTACTGGAATACAACCACGTTTTCCTTATGTTGTTGACTCATT 5 0.125 No Hit ACAATCTCAAGACTCTAAAGCTCAATAATGCAATCCCTCTTGATAAGGTT 5 0.125 No Hit TCTACCTGCTGCTTGCAACCATGGCACCCACCGTGATGGCTTCCTCCGCC 5 0.125 No Hit GGTTGGAAGAGGGTACCCACCCTCCGATAGCGTTGGATCTTCCCATGTGC 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGT 5 0.125 No Hit CATGCTTAGATGGTAGCGCTAGTGCTTGCTGCCCTGATTCTAATCTTGTG 5 0.125 No Hit CCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAA 5 0.125 No Hit >>END_MODULE >>Adapter Content fail #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 0.025 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.0625 0.0 0.0 0.0 0.0 56-57 0.075 0.0 0.0 0.0 0.0 58-59 0.1 0.0 0.0 0.0 0.0 60-61 0.1 0.0 0.0 0.0 0.0 62-63 0.15 0.0 0.0 0.0 0.0 64-65 0.2 0.0 0.0 0.0 0.0 66-67 0.225 0.0 0.0 0.0 0.0 68-69 0.275 0.0 0.0 0.0 0.0 70-71 0.3625 0.0 0.0 0.0 0.0 72-73 0.375 0.0 0.0 0.0 0.0 74-75 0.375 0.0 0.0 0.0 0.0 76-77 0.5 0.0 0.0 0.0 0.0 78-79 0.6 0.0 0.0 0.0 0.0 80-81 0.6625 0.0 0.0 0.0 0.0 82-83 0.825 0.0 0.0 0.0 0.0 84-85 1.075 0.0 0.0 0.0 0.0 86-87 1.3 0.0 0.0 0.0 0.0 88-89 1.525 0.0 0.0 0.0 0.0 90-91 1.75 0.0 0.0 0.0 0.0 92-93 2.0875 0.0 0.0 0.0 0.0 94-95 2.7874999999999996 0.0 0.0 0.0 0.0 96-97 3.1 0.0 0.0 0.0 0.0 98-99 3.5375 0.0 0.0 0.0 0.0 100-101 3.95 0.0 0.0 0.0 0.0 102-103 4.4625 0.0 0.0 0.0 0.0 104-105 5.025 0.0 0.0 0.0 0.0 106-107 5.8625 0.0 0.0 0.0 0.0 108-109 6.8 0.0 0.0 0.0 0.0 110-111 7.4375 0.0 0.0 0.0 0.0 112-113 8.2 0.0 0.0 0.0 0.0 114-115 8.975 0.0 0.0 0.0 0.0 116-117 10.0125 0.0 0.0 0.0 0.0 118-119 10.725 0.0 0.0 0.0 0.0 120-121 11.3875 0.0 0.0 0.0 0.0 122-123 12.2875 0.0 0.0 0.0 0.0 124-125 13.375 0.0 0.0 0.0 0.0 126-127 14.274999999999999 0.0 0.0 0.0 0.0 128-129 15.2125 0.0 0.0 0.0 0.0 130-131 16.3625 0.0 0.0 0.0 0.0 132-133 17.375 0.0 0.0 0.0 0.0 134-135 18.2375 0.0 0.0 0.0 0.0 136-137 18.975 0.0 0.0 0.0 0.0 138-139 19.5625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGAAAGT 10 0.006830828 145.0 1 AGGAGGG 10 0.006830828 145.0 6 GAGGAGG 45 0.008957279 48.333332 5 >>END_MODULE Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445817 spots for SRR12951289.sra Written 1445817 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra Read 1445806 spots for SRR12951289.sra Written 1445806 spots for SRR12951289.sra SRR ids: ['SRR12951289.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_i0x352_3 SRR12951289.sra spots: 28916131 blocks: [[1, 1445806], [1445807, 2891612], [2891613, 4337418], [4337419, 5783224], [5783225, 7229030], [7229031, 8674836], [8674837, 10120642], [10120643, 11566448], [11566449, 13012254], [13012255, 14458060], [14458061, 15903866], [15903867, 17349672], [17349673, 18795478], [18795479, 20241284], [20241285, 21687090], [21687091, 23132896], [23132897, 24578702], [24578703, 26024508], [26024509, 27470314], [27470315, 28916131]] SRR12951289 file size 9805266 SRR12951289 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 SRR12951289 SRR12951289_1.fastq SRR12951289_2.fastq Input file: SRR12951289_1.fastq Paired file: SRR12951289_2.fastq trimmed: SRR12951289-trimmed-pair1.fastq, SRR12951289-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 Sat Dec 7 10:36:49 2024 >> started Sat Dec 7 10:37:20 2024 >> done (31.481s) 28916131 read pairs processed; of these: 401 ( 0.00%) short read pairs filtered out after trimming by size control 735729 ( 2.54%) empty read pairs filtered out after trimming by size control 28180001 (97.45%) read pairs available; of these: 7073946 (25.10%) trimmed read pairs available after processing 21106055 (74.90%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 48 0.00% 19 34 0.00% 20 55 0.00% 21 100 0.00% 22 88 0.00% 23 161 0.00% 24 140 0.00% 25 140 0.00% 26 208 0.00% 27 137 0.00% 28 177 0.00% 29 170 0.00% 30 222 0.00% 31 202 0.00% 32 203 0.00% 33 233 0.00% 34 218 0.00% 35 260 0.00% 36 242 0.00% 37 244 0.00% 38 430 0.00% 39 327 0.00% 40 454 0.00% 41 375 0.00% 42 381 0.00% 43 406 0.00% 44 434 0.00% 45 533 0.00% 46 507 0.00% 47 587 0.00% 48 656 0.00% 49 749 0.00% 50 867 0.00% 51 899 0.00% 52 1087 0.00% 53 1065 0.00% 54 1249 0.00% 55 1416 0.01% 56 1590 0.01% 57 1797 0.01% 58 1939 0.01% 59 2407 0.01% 60 2529 0.01% 61 2929 0.01% 62 3143 0.01% 63 3737 0.01% 64 3948 0.01% 65 4181 0.01% 66 4933 0.02% 67 5406 0.02% 68 6351 0.02% 69 7045 0.02% 70 8082 0.03% 71 9710 0.03% 72 10310 0.04% 73 11618 0.04% 74 13386 0.05% 75 14120 0.05% 76 15534 0.06% 77 16382 0.06% 78 18176 0.06% 79 19949 0.07% 80 21883 0.08% 81 24932 0.09% 82 28631 0.10% 83 30854 0.11% 84 33218 0.12% 85 35806 0.13% 86 39382 0.14% 87 40041 0.14% 88 43693 0.16% 89 45609 0.16% 90 50283 0.18% 91 52737 0.19% 92 55907 0.20% 93 61109 0.22% 94 63726 0.23% 95 67512 0.24% 96 70466 0.25% 97 71347 0.25% 98 70623 0.25% 99 73765 0.26% 100 76337 0.27% 101 78629 0.28% 102 81129 0.29% 103 85596 0.30% 104 87012 0.31% 105 89633 0.32% 106 91697 0.33% 107 92152 0.33% 108 94937 0.34% 109 96620 0.34% 110 100358 0.36% 111 99264 0.35% 112 103936 0.37% 113 107359 0.38% 114 109328 0.39% 115 111931 0.40% 116 114955 0.41% 117 115459 0.41% 118 112942 0.40% 119 113625 0.40% 120 112976 0.40% 121 114090 0.40% 122 116938 0.41% 123 121030 0.43% 124 123965 0.44% 125 122962 0.44% 126 125512 0.45% 127 126824 0.45% 128 126756 0.45% 129 127414 0.45% 130 129206 0.46% 131 126179 0.45% 132 126866 0.45% 133 127932 0.45% 134 127523 0.45% 135 129504 0.46% 136 130473 0.46% 137 130390 0.46% 138 130914 0.46% 139 128283 0.46% 140 127391 0.45% 141 130882 0.46% 142 128944 0.46% 143 127685 0.45% 144 127918 0.45% 145 128730 0.46% 146 128537 0.46% 147 130624 0.46% 148 129490 0.46% 149 129078 0.46% 150 129601 0.46% 151 21106055 74.90% 28180001 reads passed initial QC criterion=sequence-density sequence-density=0.44 sequence-density-rank=1 fanout-score=1.97 fanout-score-rank=40 prefix-density=0.44 prefix-fanout=2.0 sequence=TCATTGAATAAGTAAAGAAACGATAAAGGTAGTGGTATTTCACCGGCGCCGAAGCTCCCACTTATTCTACACCCTCTATGTCTCTTCACAATGTCAAACTAGAGTCAAGCTCAACAGGGTCTTCTTTCCCCGCTTATTTTGCCAAGCCCGTTCCCTTGGCTGTGGTTTCGCTAGATAGTAGATAGGGACAGTGGGAATCTCGTTAATCCATTCATGCGCGTCACTAATTAGATGACGAGGCATTTGGCTACCTTAAGAGAGTCATAGTTACTCCCGCCGTTTACCCGCGCTTGGTTGAATTTCTTCACTTTGACATTCAGAGCACTGGGCAGAAATCACATTGCGTCAACACCACTTTCTGGCCATCGCAATGCTATGTTTTAATTAGACAGTCAGATTCCCCTTGTCCGTACCAGTTCATAGTTGGTAGTTAA criterion=fanout-score sequence-density=0.34 sequence-density-rank=21 fanout-score=25.62 fanout-score-rank=1 prefix-density=0.29 prefix-fanout=25.6 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACCGGTTGTTATCTCGTATGCCGTCTTCTGCTTGAAAA criterion=sequence-density sequence-density=0.54 sequence-density-rank=1 fanout-score=3.55 fanout-score-rank=6 prefix-density=0.56 prefix-fanout=3.4 sequence=TATGTTGGGACCCGAAAGATGGTGAACTATGCCTGAATAGGGCGAAGCCAGAGGAAACTCTGGTGGAGGCTCGTAGCGGTTCTGACGTGCAAATCGATCGTCAAATTTGGGTATAGGGGCGAAAGACTAATCGAACCATCTAGTAGCTGGTTCCTGCCGAAGTTTCCCTCAGGATAGCAGAAACTCACATCAGTTCTATGAGGTAAAGCGAATGATTAGAGGCCTTGGGGTTGAAACAACCTTAACCTATTCTCAAACTTTAAATATGTAGGAAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=43 fanout-score=16.73 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=3.0 sequence=GATCCTGCCAGTAGTCATATGCTTGTCTCAAAGATTAAGCCATGCATGTCTAAGTTTAAGCA SRR12951289 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 10:39:00 Started mapping on | Dec 07 10:39:01 Finished on | Dec 07 10:45:12 Mapping speed, Million of reads per hour | 273.44 Number of input reads | 28180001 Average input read length | 286 UNIQUE READS: Uniquely mapped reads number | 22565023 Uniquely mapped reads % | 80.07% Average mapped length | 287.45 Number of splices: Total | 22645647 Number of splices: Annotated (sjdb) | 21222334 Number of splices: GT/AG | 22346930 Number of splices: GC/AG | 248487 Number of splices: AT/AC | 15547 Number of splices: Non-canonical | 34683 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.69 Insertion rate per base | 0.01% Insertion average length | 2.37 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 250496 % of reads mapped to multiple loci | 0.89% Number of reads mapped to too many loci | 58567 % of reads mapped to too many loci | 0.21% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 8.10% % of reads unmapped: other | 10.73% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 5364482 5364482 5364482 N_multimapping 250496 250496 250496 N_noFeature 689956 22024715 855375 N_ambiguous 442107 3151 68014 UnstrandedReadsAssigned:21432960 PositiveStrandReadsAssigned:537157 NegativeStrandReadsAssigned:21641634 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=138 echo kmer=133 SRR12951289 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: SRR12951289-trimmed-pair1.fastq SRR12951289-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,180,001 reads, 22,091,272 reads pseudoaligned [quant] estimated average fragment length: 236.88 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,204 rounds 52973 SRR12951289.ke.tsv 35125 SRR12951289.se.tsv 88098 total ==> SRR12951289.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 700.681 0 0 PNS24247 1044 808.12 65.6767 5.62591 PNS24249 1928 1692.12 236.538 9.6767 PNS24246 1044 808.12 65.6767 5.62591 PNS24248 1044 808.12 65.6767 5.62591 PNS24244 1471 1235.12 64.4318 3.61117 PNS24243 293 116.346 0 0 KQK14069 1603 1367.12 673.316 34.0934 KQK14071 474 260.779 19.231 5.10491 ==> SRR12951289.se.tsv <== BRADI_1g14170v3 720 BRADI_1g53295v3 24 BRADI_1g59795v3 320 BRADI_1g07683v3 0 BRADI_1g00485v3 97 BRADI_1g20270v3 4001 BRADI_1g74790v3 151 BRADI_1g09890v3 26 BRADI_1g77505v3 405 BRADI_1g48960v3 8 SRR12951289 completed mapping pipeline successfully