Starting /dee2/code/volunteer_pipeline.sh SRR18694431 current disk space = 1526029680640 free memory = 1556768308 SRR18694431 SRAfilesize 36e388eb24a2f0bdf09897454203690c SRR18694431.sra SRR18694431.sra file validated SRR18694431 is paired end SRR18694431 is conventional basespace SRR18694431 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694431_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.101 37.0 37.0 37.0 37.0 37.0 2 35.958 37.0 37.0 37.0 37.0 37.0 3 36.263 37.0 37.0 37.0 37.0 37.0 4 36.5015 37.0 37.0 37.0 37.0 37.0 5 36.392 37.0 37.0 37.0 37.0 37.0 6 36.411 37.0 37.0 37.0 37.0 37.0 7 36.518 37.0 37.0 37.0 37.0 37.0 8 36.5095 37.0 37.0 37.0 37.0 37.0 9 36.5945 37.0 37.0 37.0 37.0 37.0 10-14 36.5655 37.0 37.0 37.0 37.0 37.0 15-19 36.588499999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.606100000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.475 37.0 37.0 37.0 37.0 37.0 30-34 36.5013 37.0 37.0 37.0 37.0 37.0 35-39 36.6509 37.0 37.0 37.0 37.0 37.0 40-44 36.5663 37.0 37.0 37.0 37.0 37.0 45-49 36.4073 37.0 37.0 37.0 37.0 37.0 50-54 36.4705 37.0 37.0 37.0 37.0 37.0 55-59 36.4538 37.0 37.0 37.0 37.0 37.0 60-64 36.5102 37.0 37.0 37.0 37.0 37.0 65-69 36.2265 37.0 37.0 37.0 37.0 37.0 70-74 36.407 37.0 37.0 37.0 37.0 37.0 75-79 36.4633 37.0 37.0 37.0 37.0 37.0 80-84 36.382999999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.182900000000004 37.0 37.0 37.0 37.0 37.0 90-94 35.3788 37.0 37.0 37.0 29.8 37.0 95-99 36.1454 37.0 37.0 37.0 37.0 37.0 100-104 36.152300000000004 37.0 37.0 37.0 37.0 37.0 105-109 36.1931 37.0 37.0 37.0 37.0 37.0 110-114 36.1862 37.0 37.0 37.0 37.0 37.0 115-119 36.466899999999995 37.0 37.0 37.0 37.0 37.0 120-124 36.5555 37.0 37.0 37.0 37.0 37.0 125-129 36.4625 37.0 37.0 37.0 37.0 37.0 130-134 36.491 37.0 37.0 37.0 37.0 37.0 135-139 36.3972 37.0 37.0 37.0 37.0 37.0 140-144 36.1886 37.0 37.0 37.0 37.0 37.0 145-149 36.1327 37.0 37.0 37.0 37.0 37.0 150-151 33.692 37.0 31.0 37.0 24.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 23 1.0 24 1.0 25 3.0 26 1.0 27 2.0 28 5.0 29 3.0 30 11.0 31 12.0 32 34.0 33 61.0 34 115.0 35 378.0 36 3198.0 37 175.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 52.725 9.525 5.175 32.574999999999996 2 22.615461847389557 9.889558232931726 34.7640562248996 32.730923694779115 3 20.65 16.425 24.474999999999998 38.45 4 25.525 21.625 23.875 28.975 5 26.55 28.9 22.95 21.6 6 24.375 30.7 22.375 22.55 7 17.424999999999997 24.349999999999998 39.050000000000004 19.175 8 19.15 23.875 30.275000000000002 26.700000000000003 9 20.8 21.625 32.875 24.7 10-14 22.705000000000002 26.525 26.6 24.169999999999998 15-19 23.235 25.25 25.650000000000002 25.865 20-24 23.36 25.0 26.229999999999997 25.41 25-29 22.689999999999998 25.765 26.075 25.47 30-34 23.35 24.77 26.650000000000002 25.230000000000004 35-39 22.24 26.275 26.040000000000003 25.445 40-44 23.11 26.015 26.1 24.775 45-49 23.419999999999998 25.5 25.905 25.174999999999997 50-54 23.369999999999997 25.840000000000003 25.77 25.019999999999996 55-59 23.79 25.555 25.629999999999995 25.025 60-64 23.645 25.495 25.61 25.25 65-69 23.355 25.165 26.32 25.16 70-74 23.635 25.695 25.185000000000002 25.485000000000003 75-79 23.005 25.955000000000002 25.28 25.759999999999998 80-84 24.15 25.445 25.319999999999997 25.085 85-89 23.18 25.995 25.025 25.8 90-94 23.755000000000003 26.06 25.295 24.89 95-99 23.135 25.705 25.615 25.545 100-104 24.315 25.55 24.490000000000002 25.645 105-109 23.57 25.82 25.255 25.355 110-114 23.595 25.785000000000004 25.345000000000002 25.275 115-119 24.04 25.624999999999996 24.995 25.34 120-124 23.365 25.314999999999998 25.27 26.05 125-129 23.665 26.090000000000003 24.415 25.83 130-134 23.68 25.4 25.074999999999996 25.845000000000002 135-139 23.97 25.28 25.255 25.495 140-144 24.060000000000002 25.69 24.72 25.53 145-149 23.53 26.245 24.37 25.855 150-151 24.0125 25.362499999999997 23.9875 26.637499999999996 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 1.0 6 1.5 7 0.5 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.5 20 0.5 21 0.0 22 0.5 23 0.5 24 1.0 25 1.0 26 1.5 27 3.0 28 5.5 29 10.0 30 11.0 31 13.5 32 18.0 33 18.5 34 26.0 35 34.5 36 50.5 37 74.5 38 88.0 39 97.0 40 115.5 41 136.0 42 167.0 43 185.0 44 183.5 45 194.0 46 196.5 47 211.0 48 216.5 49 181.5 50 151.0 51 136.0 52 131.0 53 134.5 54 130.0 55 99.5 56 86.5 57 94.0 58 92.5 59 94.0 60 85.0 61 66.0 62 56.5 63 60.5 64 58.0 65 56.5 66 44.5 67 33.5 68 34.5 69 31.0 70 25.0 71 19.5 72 15.5 73 7.5 74 2.5 75 4.0 76 4.5 77 1.5 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 0.0 2 0.4 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 85.925 #Duplication Level Percentage of deduplicated Percentage of total 1 86.67442537096305 74.47500000000001 2 11.405295315682281 19.6 3 1.3383764911259821 3.45 4 0.46552225778295026 1.6 5 0.08728542333430317 0.375 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.02909514111143439 0.5 >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 GTGCACACCAGGAACATCGAGTCGGAAGACTGCTTATTCAGGAATGCTTT 20 0.5 No Hit CTGTAGTAGATATTCGGTTGACTACAATGAGTTCATAGAACCATACCACA 5 0.125 No Hit CTGAAGAATCCTTCGGTTGTTGATTACCAATCATCTGAGTTTGAGGCATG 5 0.125 No Hit CTCTTCTCGGTGTCAACCATGACGATGCCGTAGCCGTTTCCCTTCTTCAC 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 0.0125 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 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 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.0875 0.0 0.0 0.0 0.0 76-77 0.16249999999999998 0.0 0.0 0.0 0.0 78-79 0.25 0.0 0.0 0.0 0.0 80-81 0.32499999999999996 0.0 0.0 0.0 0.0 82-83 0.4125 0.0 0.0 0.0 0.0 84-85 0.4625 0.0 0.0 0.0 0.0 86-87 0.5875 0.0 0.0 0.0 0.0 88-89 0.65 0.0 0.0 0.0 0.0 90-91 0.7125 0.0 0.0 0.0 0.0 92-93 0.85 0.0 0.0 0.0 0.0 94-95 1.0 0.0 0.0 0.0 0.0 96-97 1.25 0.0 0.0 0.0 0.0 98-99 1.4375 0.0 0.0 0.0 0.0 100-101 1.625 0.0 0.0 0.0 0.0 102-103 1.8875 0.0 0.0 0.0 0.0 104-105 2.1875 0.0 0.0 0.0 0.0 106-107 2.5625 0.0 0.0 0.0 0.0 108-109 2.9625 0.0 0.0 0.0 0.0 110-111 3.35 0.0 0.0 0.0 0.0 112-113 3.6500000000000004 0.0 0.0 0.0 0.0 114-115 4.075 0.0 0.0 0.0 0.0 116-117 4.475 0.0 0.0 0.0 0.0 118-119 4.8 0.0 0.0 0.0 0.0 120-121 5.199999999999999 0.0 0.0 0.0 0.0 122-123 5.612500000000001 0.0 0.0 0.0 0.0 124-125 6.175000000000001 0.0 0.0 0.0 0.0 126-127 6.6625 0.0 0.0 0.0 0.0 128-129 7.1125 0.0 0.0 0.0 0.0 130-131 7.7375 0.0 0.0 0.0 0.0 132-133 8.5625 0.0 0.0 0.0 0.0 134-135 9.1875 0.0 0.0 0.0 0.0 136-137 9.875 0.0 0.0 0.0 0.0 138-139 10.8 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GTAGAGC 10 0.006830828 145.0 145 TTTCACC 10 0.006830828 145.0 6 TCAGTCA 10 0.006830828 145.0 2 GGAAGGT 10 0.006830828 145.0 6 GGGAAGG 10 0.006830828 145.0 5 >>END_MODULE SRR18694431 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR18694431_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 34.2015 37.0 37.0 37.0 25.0 37.0 2 34.9595 37.0 37.0 37.0 25.0 37.0 3 35.062 37.0 37.0 37.0 25.0 37.0 4 35.0295 37.0 37.0 37.0 25.0 37.0 5 35.108 37.0 37.0 37.0 25.0 37.0 6 35.121 37.0 37.0 37.0 25.0 37.0 7 35.174 37.0 37.0 37.0 25.0 37.0 8 35.2905 37.0 37.0 37.0 25.0 37.0 9 35.4525 37.0 37.0 37.0 37.0 37.0 10-14 35.494 37.0 37.0 37.0 37.0 37.0 15-19 35.59060000000001 37.0 37.0 37.0 37.0 37.0 20-24 35.3533 37.0 37.0 37.0 34.6 37.0 25-29 35.5057 37.0 37.0 37.0 32.2 37.0 30-34 35.8129 37.0 37.0 37.0 37.0 37.0 35-39 35.5338 37.0 37.0 37.0 37.0 37.0 40-44 35.356500000000004 37.0 37.0 37.0 29.8 37.0 45-49 35.496500000000005 37.0 37.0 37.0 34.6 37.0 50-54 34.997400000000006 37.0 37.0 37.0 32.2 37.0 55-59 34.423199999999994 37.0 37.0 37.0 25.0 37.0 60-64 35.0616 37.0 37.0 37.0 27.4 37.0 65-69 34.1491 37.0 34.6 37.0 27.4 37.0 70-74 33.0848 37.0 29.8 37.0 22.2 37.0 75-79 33.5802 37.0 34.6 37.0 22.2 37.0 80-84 34.5789 37.0 37.0 37.0 25.0 37.0 85-89 32.753499999999995 37.0 32.2 37.0 19.4 37.0 90-94 34.1103 37.0 37.0 37.0 25.0 37.0 95-99 33.97019999999999 37.0 37.0 37.0 25.0 37.0 100-104 33.438399999999994 37.0 37.0 37.0 25.0 37.0 105-109 34.2859 37.0 37.0 37.0 25.0 37.0 110-114 34.6096 37.0 37.0 37.0 25.0 37.0 115-119 34.5784 37.0 37.0 37.0 25.0 37.0 120-124 34.1456 37.0 37.0 37.0 25.0 37.0 125-129 34.049499999999995 37.0 37.0 37.0 25.0 37.0 130-134 33.6951 37.0 34.6 37.0 25.0 37.0 135-139 32.155699999999996 37.0 27.4 37.0 13.8 37.0 140-144 31.6214 37.0 25.0 37.0 11.0 37.0 145-149 31.097799999999996 37.0 25.0 37.0 11.0 37.0 150-151 30.933500000000002 37.0 25.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 2.0 18 2.0 19 1.0 20 2.0 21 1.0 22 1.0 23 6.0 24 8.0 25 8.0 26 6.0 27 22.0 28 26.0 29 41.0 30 88.0 31 171.0 32 291.0 33 527.0 34 1159.0 35 1408.0 36 230.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.949999999999996 20.474999999999998 7.725 24.85 2 31.775 21.224999999999998 27.525 19.475 3 24.025 24.474999999999998 29.5 22.0 4 26.174999999999997 29.299999999999997 21.0 23.525 5 27.975 33.875 18.575 19.575 6 23.549999999999997 35.925000000000004 19.175 21.349999999999998 7 22.3 21.2 32.9 23.599999999999998 8 22.85 22.575 25.2 29.375 9 23.625 23.325000000000003 28.225 24.825 10-14 26.105 25.53 23.845 24.52 15-19 25.330000000000002 25.045 24.97 24.654999999999998 20-24 25.645 25.715 24.575 24.065 25-29 25.595000000000002 25.185000000000002 24.785 24.435000000000002 30-34 25.169999999999998 25.679999999999996 24.575 24.575 35-39 25.27 25.740000000000002 24.585 24.404999999999998 40-44 26.105 25.430000000000003 24.865000000000002 23.599999999999998 45-49 25.5 26.16 24.560000000000002 23.78 50-54 24.27 25.235000000000003 26.44 24.055 55-59 25.365 25.775 24.635 24.224999999999998 60-64 25.61 25.31 25.619999999999997 23.46 65-69 26.490000000000002 25.0 24.54 23.97 70-74 25.97 25.465 25.130000000000003 23.435 75-79 26.650000000000002 24.240000000000002 25.21 23.9 80-84 25.185000000000002 26.029999999999998 24.81 23.974999999999998 85-89 23.04 27.97 24.89 24.099999999999998 90-94 25.64 25.619999999999997 24.935 23.805 95-99 25.345000000000002 26.169999999999998 24.47 24.015 100-104 25.735000000000003 25.974999999999998 24.9 23.39 105-109 25.580000000000002 25.69 25.525 23.205000000000002 110-114 26.400000000000002 25.465 24.595 23.54 115-119 26.200000000000003 26.05 24.610000000000003 23.14 120-124 26.005 26.02 24.91 23.064999999999998 125-129 26.815 25.905 25.080000000000002 22.2 130-134 26.735 26.009999999999998 24.97 22.285 135-139 27.339999999999996 25.91 24.685000000000002 22.065 140-144 27.145000000000003 26.355 24.12 22.38 145-149 27.735 26.19 24.05 22.025 150-151 25.5375 26.0 26.6 21.8625 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.5 24 1.0 25 3.0 26 3.0 27 0.5 28 1.0 29 4.5 30 9.0 31 11.5 32 15.5 33 22.5 34 30.5 35 42.0 36 53.0 37 63.5 38 85.0 39 104.0 40 113.5 41 127.0 42 138.0 43 146.0 44 160.5 45 181.5 46 193.5 47 195.0 48 192.0 49 182.0 50 160.5 51 156.0 52 160.5 53 132.5 54 108.0 55 105.0 56 103.5 57 108.0 58 105.5 59 92.5 60 82.5 61 81.5 62 80.0 63 80.0 64 69.0 65 54.0 66 56.5 67 47.0 68 35.5 69 27.0 70 17.0 71 16.0 72 14.5 73 10.0 74 6.0 75 3.0 76 2.5 77 1.5 78 1.0 79 0.5 80 0.0 81 0.0 82 0.0 83 0.0 84 0.5 85 0.5 86 0.0 87 0.5 88 0.5 89 0.0 90 0.5 91 0.5 92 0.0 93 0.5 94 0.5 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 10-14 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 87.275 #Duplication Level Percentage of deduplicated Percentage of total 1 88.22686909195073 77.0 2 10.0830707533658 17.599999999999998 3 1.1458034947006588 3.0 4 0.429676310512747 1.5 5 0.057290174735032943 0.25 6 0.028645087367516472 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.028645087367516472 0.5 >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 GTGCTGACACGGCTGGACAGGAAAGCTTCCCAGATCAAGGTTCTACCATT 20 0.5 No Hit CACACAGGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCAAGTT 6 0.15 No Hit GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 5 0.125 No Hit ACACAGGCAAAACACAGCTGATTCGTGTACTCGATCTCCCCAGCAAGTTA 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 0.0125 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 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 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.1375 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.2875 0.0 0.0 0.0 0.0 82-83 0.3625 0.0 0.0 0.0 0.0 84-85 0.4 0.0 0.0 0.0 0.0 86-87 0.5125 0.0 0.0 0.0 0.0 88-89 0.575 0.0 0.0 0.0 0.0 90-91 0.6375 0.0 0.0 0.0 0.0 92-93 0.775 0.0 0.0 0.0 0.0 94-95 0.925 0.0 0.0 0.0 0.0 96-97 1.1749999999999998 0.0 0.0 0.0 0.0 98-99 1.3625 0.0 0.0 0.0 0.0 100-101 1.55 0.0 0.0 0.0 0.0 102-103 1.8125 0.0 0.0 0.0 0.0 104-105 2.1125 0.0 0.0 0.0 0.0 106-107 2.4875 0.0 0.0 0.0 0.0 108-109 2.8625 0.0 0.0 0.0 0.0 110-111 3.25 0.0 0.0 0.0 0.0 112-113 3.55 0.0 0.0 0.0 0.0 114-115 3.95 0.0 0.0 0.0 0.0 116-117 4.35 0.0 0.0 0.0 0.0 118-119 4.675 0.0 0.0 0.0 0.0 120-121 5.074999999999999 0.0 0.0 0.0 0.0 122-123 5.487500000000001 0.0 0.0 0.0 0.0 124-125 6.050000000000001 0.0 0.0 0.0 0.0 126-127 6.5375 0.0 0.0 0.0 0.0 128-129 6.9875 0.0 0.0 0.0 0.0 130-131 7.6 0.0 0.0 0.0 0.0 132-133 8.4125 0.0 0.0 0.0 0.0 134-135 9.0125 0.0 0.0 0.0 0.0 136-137 9.7 0.0 0.0 0.0 0.0 138-139 10.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGGAAA 10 0.006830828 145.0 2 CCAAACT 10 0.006830828 145.0 145 GAAAACC 10 0.006830828 145.0 5 AACCCCC 10 0.006830828 145.0 8 GATTGCT 10 0.006830828 145.0 4 TCAGAAG 10 0.006830828 145.0 3 ACCCCCG 10 0.006830828 145.0 9 AAAACCC 10 0.006830828 145.0 6 GGAAAAC 10 0.006830828 145.0 4 >>END_MODULE Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748515 spots for SRR18694431.sra Written 748515 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra Read 748506 spots for SRR18694431.sra Written 748506 spots for SRR18694431.sra SRR ids: ['SRR18694431.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_4ibiwxkp SRR18694431.sra spots: 14970129 blocks: [[1, 748506], [748507, 1497012], [1497013, 2245518], [2245519, 2994024], [2994025, 3742530], [3742531, 4491036], [4491037, 5239542], [5239543, 5988048], [5988049, 6736554], [6736555, 7485060], [7485061, 8233566], [8233567, 8982072], [8982073, 9730578], [9730579, 10479084], [10479085, 11227590], [11227591, 11976096], [11976097, 12724602], [12724603, 13473108], [13473109, 14221614], [14221615, 14970129]] SRR18694431 file size 5065804 SRR18694431 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 SRR18694431 SRR18694431_1.fastq SRR18694431_2.fastq Input file: SRR18694431_1.fastq Paired file: SRR18694431_2.fastq trimmed: SRR18694431-trimmed-pair1.fastq, SRR18694431-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 Tue Dec 10 06:44:18 2024 >> started Tue Dec 10 06:44:36 2024 >> done (18.387s) 14970129 read pairs processed; of these: 180 ( 0.00%) short read pairs filtered out after trimming by size control 3117 ( 0.02%) empty read pairs filtered out after trimming by size control 14966832 (99.98%) read pairs available; of these: 2260063 (15.10%) trimmed read pairs available after processing 12706769 (84.90%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 8 0.00% 20 17 0.00% 21 19 0.00% 22 20 0.00% 23 28 0.00% 24 27 0.00% 25 23 0.00% 26 30 0.00% 27 18 0.00% 28 37 0.00% 29 29 0.00% 30 42 0.00% 31 39 0.00% 32 41 0.00% 33 42 0.00% 34 37 0.00% 35 50 0.00% 36 44 0.00% 37 51 0.00% 38 74 0.00% 39 44 0.00% 40 45 0.00% 41 55 0.00% 42 75 0.00% 43 71 0.00% 44 83 0.00% 45 66 0.00% 46 83 0.00% 47 51 0.00% 48 70 0.00% 49 91 0.00% 50 106 0.00% 51 106 0.00% 52 153 0.00% 53 134 0.00% 54 134 0.00% 55 176 0.00% 56 153 0.00% 57 211 0.00% 58 273 0.00% 59 269 0.00% 60 313 0.00% 61 405 0.00% 62 485 0.00% 63 449 0.00% 64 514 0.00% 65 541 0.00% 66 630 0.00% 67 683 0.00% 68 797 0.01% 69 875 0.01% 70 1058 0.01% 71 1255 0.01% 72 1389 0.01% 73 1686 0.01% 74 1847 0.01% 75 1876 0.01% 76 2105 0.01% 77 2361 0.02% 78 2524 0.02% 79 2971 0.02% 80 3459 0.02% 81 3951 0.03% 82 4452 0.03% 83 4871 0.03% 84 5307 0.04% 85 5818 0.04% 86 6218 0.04% 87 6434 0.04% 88 7138 0.05% 89 7650 0.05% 90 8590 0.06% 91 9560 0.06% 92 10365 0.07% 93 11139 0.07% 94 12285 0.08% 95 12551 0.08% 96 13150 0.09% 97 13707 0.09% 98 14209 0.09% 99 15316 0.10% 100 16546 0.11% 101 17075 0.11% 102 18560 0.12% 103 19806 0.13% 104 20706 0.14% 105 21465 0.14% 106 22401 0.15% 107 22498 0.15% 108 23491 0.16% 109 24453 0.16% 110 25530 0.17% 111 26584 0.18% 112 28008 0.19% 113 29096 0.19% 114 30823 0.21% 115 31919 0.21% 116 32716 0.22% 117 33002 0.22% 118 33474 0.22% 119 33751 0.23% 120 35671 0.24% 121 36503 0.24% 122 37236 0.25% 123 39480 0.26% 124 41021 0.27% 125 42334 0.28% 126 42571 0.28% 127 43198 0.29% 128 43610 0.29% 129 44920 0.30% 130 44612 0.30% 131 45522 0.30% 132 47124 0.31% 133 49162 0.33% 134 50271 0.34% 135 51090 0.34% 136 51753 0.35% 137 52496 0.35% 138 51838 0.35% 139 52650 0.35% 140 52569 0.35% 141 53760 0.36% 142 55102 0.37% 143 56805 0.38% 144 57628 0.39% 145 59578 0.40% 146 60455 0.40% 147 62288 0.42% 148 60908 0.41% 149 60945 0.41% 150 60989 0.41% 151 12706769 84.90% 14966832 reads passed initial QC criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=2.32 fanout-score-rank=26 prefix-density=0.38 prefix-fanout=2.2 sequence=AACATGGAGAACATGGCGAGGCGGCCGTTCTTGATCTCCTTCACCTTGAGCTCAGCGAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=29 fanout-score=200.05 fanout-score-rank=1 prefix-density=0.35 prefix-fanout=11.2 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.55 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=37 prefix-density=0.56 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.14 sequence-density-rank=24 fanout-score=44.78 fanout-score-rank=1 prefix-density=0.42 prefix-fanout=14.8 sequence=TTCTTCTTCCTC SRR18694431 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 10 06:45:30 Started mapping on | Dec 10 06:45:30 Finished on | Dec 10 06:47:18 Mapping speed, Million of reads per hour | 498.89 Number of input reads | 14966832 Average input read length | 294 UNIQUE READS: Uniquely mapped reads number | 14070416 Uniquely mapped reads % | 94.01% Average mapped length | 292.92 Number of splices: Total | 14561301 Number of splices: Annotated (sjdb) | 13604762 Number of splices: GT/AG | 14352139 Number of splices: GC/AG | 176205 Number of splices: AT/AC | 6036 Number of splices: Non-canonical | 26921 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.01% Deletion average length | 2.44 Insertion rate per base | 0.01% Insertion average length | 2.40 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 201488 % of reads mapped to multiple loci | 1.35% Number of reads mapped to too many loci | 20884 % of reads mapped to too many loci | 0.14% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.39% % of reads unmapped: other | 1.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 694928 694928 694928 N_multimapping 201488 201488 201488 N_noFeature 788714 13687657 911869 N_ambiguous 313903 1956 55255 UnstrandedReadsAssigned:12967799 PositiveStrandReadsAssigned:380803 NegativeStrandReadsAssigned:13103292 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR18694431 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: SRR18694431-trimmed-pair1.fastq SRR18694431-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 14,966,832 reads, 13,311,427 reads pseudoaligned [quant] estimated average fragment length: 247.506 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,179 rounds 52973 SRR18694431.ke.tsv 35125 SRR18694431.se.tsv 88098 total ==> SRR18694431.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 689.914 0 0 PNS24247 1044 797.494 64.5623 9.16844 PNS24249 1928 1681.49 21.8567 1.47209 PNS24246 1044 797.494 64.5623 9.16844 PNS24248 1044 797.494 64.5623 9.16844 PNS24244 1471 1224.49 100.456 9.29106 PNS24243 293 103.278 0 0 KQK14069 1603 1356.49 402.981 33.6442 KQK14071 474 249.374 2.49953 1.13514 ==> SRR18694431.se.tsv <== BRADI_1g14170v3 466 BRADI_1g53295v3 33 BRADI_1g59795v3 939 BRADI_1g07683v3 0 BRADI_1g00485v3 0 BRADI_1g20270v3 361 BRADI_1g74790v3 195 BRADI_1g09890v3 0 BRADI_1g77505v3 133 BRADI_1g48960v3 0 SRR18694431 completed mapping pipeline successfully