Starting /dee2/code/volunteer_pipeline.sh SRR1797581 current disk space = 1515225886720 free memory = 1566958196 SRR1797581 SRAfilesize c12e9c63812935b0b8dc88d6353b8ceb SRR1797581.sra SRR1797581.sra file validated SRR1797581 is paired end SRR1797581 is conventional basespace SRR1797581 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797581_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 53 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.74075 34.0 34.0 34.0 31.0 34.0 2 32.6625 34.0 34.0 34.0 31.0 34.0 3 33.2485 34.0 34.0 34.0 31.0 34.0 4 36.6295 37.0 37.0 37.0 35.0 37.0 5 36.68225 37.0 37.0 37.0 35.0 37.0 6 36.68575 37.0 37.0 37.0 36.0 37.0 7 36.6495 37.0 37.0 37.0 36.0 37.0 8 36.69425 37.0 37.0 37.0 37.0 37.0 9 38.69175 39.0 39.0 39.0 39.0 39.0 10-14 38.9356 39.4 39.2 39.4 38.2 39.4 15-19 40.2313 41.0 40.0 41.0 38.8 41.0 20-24 40.137899999999995 41.0 40.0 41.0 38.2 41.0 25-29 39.74575 41.0 39.8 41.0 37.4 41.0 30-34 39.5287 41.0 39.8 41.0 36.4 41.0 35-39 39.17855 41.0 39.0 41.0 35.0 41.0 40-44 38.84625 41.0 38.2 41.0 35.0 41.0 45-49 38.25260000000001 40.0 36.2 41.0 34.4 41.0 50-54 37.7023 39.8 35.0 41.0 33.6 41.0 55-59 36.947599999999994 38.6 35.0 41.0 32.8 41.0 60-64 36.328250000000004 37.2 35.0 40.4 32.4 41.0 65-69 35.707550000000005 35.8 35.0 39.2 32.2 41.0 70-74 35.023450000000004 35.0 35.0 37.6 32.6 40.0 75-79 33.95935 35.0 34.0 36.2 30.8 38.2 80-84 33.6819 35.0 34.0 35.2 31.0 36.6 85-89 33.3134 35.0 34.0 35.0 30.4 36.0 90-94 32.90315 35.0 34.0 35.0 29.4 35.0 95-99 32.5601 35.0 33.4 35.0 28.2 35.0 100-104 31.97715 35.0 33.0 35.0 25.4 35.0 105-109 31.762549999999997 35.0 33.0 35.0 25.0 35.0 110-114 31.181100000000004 35.0 32.0 35.0 23.8 35.0 115-119 30.657399999999996 34.0 31.2 35.0 21.4 35.0 120-124 29.8755 34.0 30.4 35.0 15.8 35.0 125-129 29.28525 34.0 29.4 35.0 6.2 35.0 130-134 28.32945 33.6 28.2 35.0 2.0 35.0 135-139 27.300400000000003 33.0 25.8 35.0 2.0 35.0 140-144 26.4721 33.0 24.4 35.0 2.0 35.0 145-149 24.64195 32.0 12.0 34.8 2.0 35.0 150 17.6295 22.0 2.0 30.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 1.0 3 0.0 4 0.0 5 2.0 6 1.0 7 4.0 8 4.0 9 5.0 10 5.0 11 6.0 12 6.0 13 8.0 14 7.0 15 7.0 16 10.0 17 9.0 18 14.0 19 17.0 20 19.0 21 23.0 22 23.0 23 20.0 24 37.0 25 49.0 26 57.0 27 56.0 28 65.0 29 77.0 30 91.0 31 125.0 32 174.0 33 236.0 34 352.0 35 591.0 36 1087.0 37 808.0 38 4.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.036007413290974 11.675933280381255 13.290971670638072 42.9970876356897 2 30.225 11.325000000000001 22.875 35.575 3 23.599999999999998 12.950000000000001 17.7 45.75 4 28.475 17.275 17.2 37.05 5 30.875000000000004 21.224999999999998 21.075 26.825 6 32.675 22.3 18.925 26.1 7 19.900000000000002 28.425 31.7 19.975 8 21.85 23.05 28.875 26.224999999999998 9 22.35 20.025000000000002 28.825 28.799999999999997 10-14 23.810000000000002 25.840000000000003 24.23 26.119999999999997 15-19 24.525 23.575 24.745 27.155 20-24 24.546227311365566 24.351217560878045 24.031201560078003 27.071353567678386 25-29 24.474999999999998 24.09 24.099999999999998 27.334999999999997 30-34 24.25 24.195 23.865 27.689999999999998 35-39 24.46 23.765 24.005000000000003 27.77 40-44 24.895 24.075 23.43 27.6 45-49 24.735 24.654999999999998 23.044999999999998 27.565 50-54 25.255 23.294999999999998 23.735 27.715 55-59 25.424999999999997 23.43 23.669999999999998 27.474999999999998 60-64 25.75 22.99 23.65 27.61 65-69 25.014999999999997 23.16 23.669999999999998 28.155 70-74 25.840000000000003 23.055 22.925 28.18 75-79 25.39 23.39 23.275000000000002 27.944999999999997 80-84 25.85 23.06 23.215 27.875 85-89 26.265 22.965 23.06 27.71 90-94 26.085 23.22 22.384999999999998 28.310000000000002 95-99 26.029999999999998 22.925 22.905 28.139999999999997 100-104 26.325 22.525000000000002 23.28 27.87 105-109 26.155 22.985 22.655 28.205000000000002 110-114 26.495 22.455 22.835 28.215 115-119 26.505000000000003 22.415 23.32 27.76 120-124 26.384999999999998 21.825 23.3 28.49 125-129 26.91 22.425 22.31 28.355000000000004 130-134 26.685 22.055 22.98 28.28 135-139 26.955000000000002 21.93 22.915 28.199999999999996 140-144 27.435 22.465 21.425 28.675 145-149 27.694999999999997 22.189999999999998 21.67 28.444999999999997 150 26.900000000000002 22.05 19.2 31.85 >>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 1.5 15 1.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.0 23 0.0 24 0.0 25 0.5 26 0.5 27 0.5 28 1.5 29 1.5 30 2.0 31 3.5 32 6.5 33 12.5 34 19.5 35 24.5 36 32.0 37 42.5 38 54.0 39 67.5 40 91.5 41 103.5 42 115.0 43 136.0 44 142.5 45 165.5 46 170.5 47 167.0 48 176.0 49 167.5 50 155.0 51 135.5 52 127.5 53 122.0 54 108.5 55 105.5 56 108.5 57 100.0 58 79.5 59 67.0 60 72.0 61 71.0 62 64.5 63 72.5 64 68.5 65 59.0 66 67.0 67 72.5 68 80.0 69 82.0 70 64.5 71 56.5 72 48.0 73 52.5 74 46.5 75 32.0 76 35.0 77 30.0 78 25.0 79 22.5 80 17.0 81 13.5 82 11.0 83 6.0 84 5.5 85 4.0 86 1.5 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content warn #Base N-Count 1 5.575 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 0.005 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.7 #Duplication Level Percentage of deduplicated Percentage of total 1 99.72417251755266 99.425 2 0.25075225677031093 0.5 3 0.025075225677031094 0.075 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0125 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 0.0125 0.0 0.0 54-55 0.025 0.0 0.025 0.0 0.0 56-57 0.025 0.0 0.025 0.0 0.0 58-59 0.025 0.0 0.025 0.0 0.0 60-61 0.025 0.0 0.025 0.0 0.0 62-63 0.025 0.0 0.025 0.0 0.0 64-65 0.025 0.0 0.025 0.0 0.0 66-67 0.025 0.0 0.025 0.0 0.0 68-69 0.025 0.0 0.025 0.0 0.0 70-71 0.025 0.0 0.025 0.0 0.0 72-73 0.025 0.0 0.025 0.0 0.0 74-75 0.025 0.0 0.025 0.0 0.0 76-77 0.025 0.0 0.025 0.0 0.0 78-79 0.025 0.0 0.025 0.0 0.0 80-81 0.05 0.0 0.025 0.0 0.0 82-83 0.05 0.0 0.025 0.0 0.0 84-85 0.05 0.0 0.025 0.0 0.0 86-87 0.05 0.0 0.025 0.0 0.0 88-89 0.05 0.0 0.025 0.0 0.0 90-91 0.05 0.0 0.025 0.0 0.0 92-93 0.05 0.0 0.025 0.0 0.0 94-95 0.05 0.0 0.025 0.0 0.0 96-97 0.05 0.0 0.025 0.0 0.0 98-99 0.05 0.0 0.025 0.0 0.0 100-101 0.05 0.0 0.025 0.0 0.0 102-103 0.05 0.0 0.025 0.0 0.0 104-105 0.05 0.0 0.025 0.0 0.0 106-107 0.0625 0.0 0.025 0.0 0.0 108-109 0.075 0.0 0.025 0.0 0.0 110-111 0.1125 0.0 0.025 0.0 0.0 112-113 0.125 0.0 0.025 0.0 0.0 114-115 0.1375 0.0 0.025 0.0 0.0 116-117 0.16249999999999998 0.0 0.025 0.0 0.0 118-119 0.175 0.0 0.025 0.0 0.0 120-121 0.21250000000000002 0.0 0.025 0.0 0.0 122-123 0.2625 0.0 0.025 0.0 0.0 124-125 0.425 0.0 0.025 0.0 0.0 126-127 0.5375000000000001 0.0 0.025 0.0 0.0 128-129 0.625 0.0 0.025 0.0 0.0 130-131 0.95 0.0 0.025 0.0 0.0 132-133 1.25 0.0 0.025 0.0 0.0 134-135 1.525 0.0 0.025 0.0 0.0 136-137 1.8625 0.0 0.025 0.0 0.0 138 2.15 0.0 0.025 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATCAATG 10 0.0069790767 143.96251 7 >>END_MODULE SRR1797581 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797581_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 54 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.07325 34.0 33.0 34.0 31.0 34.0 2 33.24875 34.0 34.0 34.0 31.0 34.0 3 33.16025 34.0 34.0 34.0 31.0 34.0 4 36.5585 37.0 37.0 37.0 35.0 37.0 5 36.64825 37.0 37.0 37.0 35.0 37.0 6 36.575 37.0 37.0 37.0 35.0 37.0 7 36.489 37.0 37.0 37.0 35.0 37.0 8 36.584 37.0 37.0 37.0 35.0 37.0 9 38.524 39.0 39.0 39.0 38.0 39.0 10-14 38.8217 39.4 39.4 39.4 38.0 39.4 15-19 39.79350000000001 41.0 40.0 41.0 38.2 41.0 20-24 39.73695 41.0 40.0 41.0 37.8 41.0 25-29 39.410700000000006 41.0 39.8 41.0 36.2 41.0 30-34 38.838 40.4 38.6 41.0 35.0 41.0 35-39 38.78805 41.0 38.4 41.0 35.0 41.0 40-44 38.2133 40.0 36.8 41.0 34.6 41.0 45-49 37.595299999999995 39.8 35.0 41.0 33.4 41.0 50-54 36.5868 38.2 35.0 40.4 32.2 41.0 55-59 36.4168 37.4 35.0 41.0 32.6 41.0 60-64 36.0883 35.8 35.0 40.0 33.0 41.0 65-69 35.3285 35.0 35.0 38.8 32.4 41.0 70-74 34.63825 35.0 35.0 36.8 32.2 39.2 75-79 33.8301 35.0 34.4 35.6 30.8 37.6 80-84 33.24745 35.0 34.0 35.0 29.8 36.2 85-89 32.85145 35.0 34.0 35.0 29.0 35.6 90-94 32.42405 35.0 33.2 35.0 27.8 35.0 95-99 32.0955 35.0 33.0 35.0 26.6 35.0 100-104 31.786 35.0 33.0 35.0 25.6 35.0 105-109 31.30125 35.0 32.4 35.0 23.8 35.0 110-114 30.56805 34.4 31.2 35.0 20.2 35.0 115-119 30.0012 34.0 30.4 35.0 17.4 35.0 120-124 29.457 34.0 30.0 35.0 8.8 35.0 125-129 28.754 34.0 29.0 35.0 2.6 35.0 130-134 28.216700000000003 33.8 28.2 35.0 2.0 35.0 135-139 26.916050000000002 33.0 24.8 35.0 2.0 35.0 140-144 25.946099999999994 32.4 22.4 35.0 2.0 35.0 145-149 24.137700000000002 31.8 7.6 34.2 2.0 35.0 150 18.18975 23.0 2.0 31.0 2.0 34.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 4.0 3 1.0 4 1.0 5 1.0 6 7.0 7 4.0 8 7.0 9 7.0 10 7.0 11 9.0 12 7.0 13 8.0 14 14.0 15 3.0 16 10.0 17 9.0 18 13.0 19 18.0 20 22.0 21 35.0 22 33.0 23 37.0 24 31.0 25 36.0 26 53.0 27 51.0 28 77.0 29 92.0 30 91.0 31 144.0 32 177.0 33 259.0 34 366.0 35 680.0 36 1060.0 37 619.0 38 7.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 29.475 17.424999999999997 11.675 41.425 2 35.21021021021021 23.523523523523522 18.16816816816817 23.0980980980981 3 24.0 27.0 21.075 27.925 4 28.299999999999997 23.825 21.099999999999998 26.775 5 30.825000000000003 25.650000000000002 19.650000000000002 23.875 6 26.0 30.8 18.425 24.775 7 25.05 16.825000000000003 30.625000000000004 27.500000000000004 8 26.974999999999998 21.325 21.825 29.875 9 27.650000000000002 20.45 25.025 26.875 10-14 27.91 24.060000000000002 20.89 27.139999999999997 15-19 27.955000000000002 23.745 22.195 26.105 20-24 28.255000000000003 23.615 21.68 26.450000000000003 25-29 28.575 22.735 21.65 27.04 30-34 28.189999999999998 23.47 21.834999999999997 26.505000000000003 35-39 28.465 23.22 21.654999999999998 26.66 40-44 28.32 22.895 21.495 27.29 45-49 27.889999999999997 22.759999999999998 22.255 27.095000000000002 50-54 27.83 23.294999999999998 21.82 27.055 55-59 28.71 23.015 21.82 26.455000000000002 60-64 28.04 23.044999999999998 22.165000000000003 26.75 65-69 28.610000000000003 22.86 22.305 26.224999999999998 70-74 29.13 22.545 22.255 26.07 75-79 28.305000000000003 22.66 22.515 26.52 80-84 28.255000000000003 23.26 21.85 26.634999999999998 85-89 28.410000000000004 22.74 22.29 26.56 90-94 28.27 22.935 22.41 26.384999999999998 95-99 27.83 22.855 22.585 26.729999999999997 100-104 28.749999999999996 22.89 22.59 25.77 105-109 28.804999999999996 23.275000000000002 22.115000000000002 25.805 110-114 28.720000000000002 23.225 22.220000000000002 25.835 115-119 28.84 22.98 23.0 25.180000000000003 120-124 28.810000000000002 22.994999999999997 22.525000000000002 25.669999999999998 125-129 28.9 23.47 21.72 25.91 130-134 28.8064403220161 22.991149557477875 22.421121056052804 25.781289064453222 135-139 28.63 23.155 22.435 25.779999999999998 140-144 29.244999999999997 23.125 21.95 25.679999999999996 145-149 29.59 23.25 21.325 25.835 150 29.375 23.375 20.125 27.125 >>END_MODULE >>Per sequence GC content fail #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 0.5 23 0.5 24 0.0 25 0.0 26 0.0 27 0.0 28 0.0 29 1.5 30 4.0 31 4.0 32 4.5 33 7.0 34 12.5 35 20.5 36 26.5 37 35.0 38 48.0 39 61.5 40 81.0 41 94.5 42 96.5 43 109.5 44 130.5 45 144.0 46 150.0 47 137.0 48 139.0 49 143.5 50 136.5 51 141.0 52 127.5 53 123.0 54 128.5 55 118.0 56 103.5 57 92.0 58 87.0 59 82.0 60 76.5 61 76.0 62 79.0 63 79.5 64 84.5 65 84.0 66 75.0 67 76.0 68 83.5 69 87.0 70 78.5 71 73.0 72 72.5 73 67.0 74 58.0 75 54.0 76 47.5 77 31.5 78 27.0 79 29.0 80 18.5 81 11.5 82 10.0 83 8.0 84 6.0 85 2.5 86 1.5 87 0.5 88 1.0 89 2.0 90 2.0 91 2.5 92 2.0 93 1.5 94 1.0 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 0.1 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 0.005 135-139 0.0 140-144 0.0 145-149 0.0 150 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.7 #Duplication Level Percentage of deduplicated Percentage of total 1 99.74924774322969 99.45 2 0.20060180541624875 0.4 3 0.05015045135406219 0.15 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0125 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 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.05 0.0 0.0 0.0 0.0 84-85 0.05 0.0 0.0 0.0 0.0 86-87 0.05 0.0 0.0 0.0 0.0 88-89 0.05 0.0 0.0 0.0 0.0 90-91 0.075 0.0 0.0 0.0 0.0 92-93 0.075 0.0 0.0 0.0 0.0 94-95 0.075 0.0 0.0 0.0 0.0 96-97 0.075 0.0 0.0 0.0 0.0 98-99 0.075 0.0 0.0 0.0 0.0 100-101 0.075 0.0 0.0 0.0 0.0 102-103 0.075 0.0 0.0 0.0 0.0 104-105 0.075 0.0 0.0 0.0 0.0 106-107 0.0875 0.0 0.0 0.0 0.0 108-109 0.1 0.0 0.0 0.0 0.0 110-111 0.1375 0.0 0.0 0.0 0.0 112-113 0.15 0.0 0.0 0.0 0.0 114-115 0.16249999999999998 0.0 0.0 0.0 0.0 116-117 0.1875 0.0 0.0 0.0 0.0 118-119 0.2 0.0 0.0 0.0 0.0 120-121 0.2375 0.0 0.0 0.0 0.0 122-123 0.2875 0.0 0.0 0.0 0.0 124-125 0.4375 0.0 0.0 0.0 0.0 126-127 0.5375000000000001 0.0 0.0 0.0 0.0 128-129 0.6125 0.0 0.0 0.0 0.0 130-131 0.925 0.0 0.0 0.0 0.0 132-133 1.275 0.0 0.0 0.0 0.0 134-135 1.575 0.0 0.0 0.0 0.0 136-137 1.9875 0.0 0.0 0.0 0.0 138 2.275 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTAGACG 10 0.006973645 144.0 2 >>END_MODULE Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361633 spots for SRR1797581.sra Written 1361633 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra Read 1361618 spots for SRR1797581.sra Written 1361618 spots for SRR1797581.sra SRR ids: ['SRR1797581.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__9omo7dk SRR1797581.sra spots: 27232375 blocks: [[1, 1361618], [1361619, 2723236], [2723237, 4084854], [4084855, 5446472], [5446473, 6808090], [6808091, 8169708], [8169709, 9531326], [9531327, 10892944], [10892945, 12254562], [12254563, 13616180], [13616181, 14977798], [14977799, 16339416], [16339417, 17701034], [17701035, 19062652], [19062653, 20424270], [20424271, 21785888], [21785889, 23147506], [23147507, 24509124], [24509125, 25870742], [25870743, 27232375]] SRR1797581 file size 9153269 SRR1797581 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 SRR1797581 SRR1797581_1.fastq SRR1797581_2.fastq Input file: SRR1797581_1.fastq Paired file: SRR1797581_2.fastq trimmed: SRR1797581-trimmed-pair1.fastq, SRR1797581-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 Dec 12 03:25:29 2024 >> started Thu Dec 12 03:26:23 2024 >> done (54.437s) 27232375 read pairs processed; of these: 60102 ( 0.22%) short read pairs filtered out after trimming by size control 42314 ( 0.16%) empty read pairs filtered out after trimming by size control 27129959 (99.62%) read pairs available; of these: 19625390 (72.34%) trimmed read pairs available after processing 7504569 (27.66%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 31 0.00% 19 30 0.00% 20 63 0.00% 21 112 0.00% 22 196 0.00% 23 244 0.00% 24 313 0.00% 25 399 0.00% 26 474 0.00% 27 599 0.00% 28 706 0.00% 29 845 0.00% 30 960 0.00% 31 1166 0.00% 32 1295 0.00% 33 1396 0.01% 34 1528 0.01% 35 1738 0.01% 36 1866 0.01% 37 2117 0.01% 38 2207 0.01% 39 2366 0.01% 40 2411 0.01% 41 2672 0.01% 42 2835 0.01% 43 2962 0.01% 44 3172 0.01% 45 3236 0.01% 46 3583 0.01% 47 3697 0.01% 48 3920 0.01% 49 4151 0.02% 50 4289 0.02% 51 4545 0.02% 52 4811 0.02% 53 5096 0.02% 54 5269 0.02% 55 5542 0.02% 56 5856 0.02% 57 6177 0.02% 58 6473 0.02% 59 6786 0.03% 60 7058 0.03% 61 7565 0.03% 62 7594 0.03% 63 8051 0.03% 64 8726 0.03% 65 8935 0.03% 66 9490 0.03% 67 9916 0.04% 68 10418 0.04% 69 10944 0.04% 70 11609 0.04% 71 12143 0.04% 72 12911 0.05% 73 13509 0.05% 74 14249 0.05% 75 14978 0.06% 76 16056 0.06% 77 16920 0.06% 78 17896 0.07% 79 19040 0.07% 80 20205 0.07% 81 21740 0.08% 82 23256 0.09% 83 24850 0.09% 84 29470 0.11% 85 31746 0.12% 86 33010 0.12% 87 34949 0.13% 88 36500 0.13% 89 38229 0.14% 90 39947 0.15% 91 41784 0.15% 92 42517 0.16% 93 44652 0.16% 94 46541 0.17% 95 48331 0.18% 96 50521 0.19% 97 52058 0.19% 98 54420 0.20% 99 56724 0.21% 100 58116 0.21% 101 59954 0.22% 102 62175 0.23% 103 65258 0.24% 104 68553 0.25% 105 72940 0.27% 106 77115 0.28% 107 81884 0.30% 108 86109 0.32% 109 91732 0.34% 110 95233 0.35% 111 101408 0.37% 112 105940 0.39% 113 109526 0.40% 114 117413 0.43% 115 127294 0.47% 116 131959 0.49% 117 135305 0.50% 118 143595 0.53% 119 150736 0.56% 120 161743 0.60% 121 173812 0.64% 122 184152 0.68% 123 193755 0.71% 124 209606 0.77% 125 218556 0.81% 126 223878 0.83% 127 236120 0.87% 128 249201 0.92% 129 267311 0.99% 130 286922 1.06% 131 302013 1.11% 132 313232 1.15% 133 337579 1.24% 134 350460 1.29% 135 367462 1.35% 136 385753 1.42% 137 406355 1.50% 138 427126 1.57% 139 457866 1.69% 140 485725 1.79% 141 519365 1.91% 142 559615 2.06% 143 603968 2.23% 144 669427 2.47% 145 765458 2.82% 146 906326 3.34% 147 1146839 4.23% 148 1603125 5.91% 149 3552803 13.10% 150 7504569 27.66% 27129959 reads passed initial QC criterion=sequence-density sequence-density=0.15 sequence-density-rank=1 fanout-score=2.70 fanout-score-rank=37 prefix-density=0.17 prefix-fanout=2.3 sequence=GCCCAGGCGAGGCCGCCCACGAAGCA criterion=fanout-score sequence-density=0.03 sequence-density-rank=37 fanout-score=706.62 fanout-score-rank=1 prefix-density=0.84 prefix-fanout=23.8 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=3.49 fanout-score-rank=32 prefix-density=0.32 prefix-fanout=3.2 sequence=CTGCAAGTGCGGCA criterion=fanout-score sequence-density=0.10 sequence-density-rank=15 fanout-score=291.79 fanout-score-rank=1 prefix-density=1.18 prefix-fanout=24.1 sequence=CGCCGCCGCCGG SRR1797581 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 12 03:27:07 Started mapping on | Dec 12 03:27:08 Finished on | Dec 12 03:29:32 Mapping speed, Million of reads per hour | 678.25 Number of input reads | 27129959 Average input read length | 278 UNIQUE READS: Uniquely mapped reads number | 25985083 Uniquely mapped reads % | 95.78% Average mapped length | 277.72 Number of splices: Total | 21585222 Number of splices: Annotated (sjdb) | 20265915 Number of splices: GT/AG | 21277034 Number of splices: GC/AG | 253659 Number of splices: AT/AC | 18741 Number of splices: Non-canonical | 35788 Mismatch rate per base, % | 0.27% Deletion rate per base | 0.02% Deletion average length | 2.37 Insertion rate per base | 0.01% Insertion average length | 2.30 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 364585 % of reads mapped to multiple loci | 1.34% Number of reads mapped to too many loci | 67888 % of reads mapped to too many loci | 0.25% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.01% % of reads unmapped: other | 1.62% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 808988 808988 808988 N_multimapping 364585 364585 364585 N_noFeature 758997 25203782 1160637 N_ambiguous 450768 3893 74325 UnstrandedReadsAssigned:24775318 PositiveStrandReadsAssigned:777408 NegativeStrandReadsAssigned:24750121 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=142 echo kmer=137 SRR1797581 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: SRR1797581-trimmed-pair1.fastq SRR1797581-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,129,959 reads, 24,932,815 reads pseudoaligned [quant] estimated average fragment length: 207.566 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,131 rounds 52973 SRR1797581.ke.tsv 35125 SRR1797581.se.tsv 88098 total ==> SRR1797581.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 729.623 31.5703 2.40755 PNS24247 1044 837.434 35.2413 2.34152 PNS24249 1928 1721.43 758.181 24.5063 PNS24246 1044 837.434 35.2413 2.34152 PNS24248 1044 837.434 35.2413 2.34152 PNS24244 1471 1264.43 67.5249 2.97141 PNS24243 293 95.6624 0 0 KQK14069 1603 1396.43 1242.24 49.4973 KQK14071 474 269.173 105.966 21.9043 ==> SRR1797581.se.tsv <== BRADI_1g14170v3 1389 BRADI_1g53295v3 90 BRADI_1g59795v3 533 BRADI_1g07683v3 0 BRADI_1g00485v3 104 BRADI_1g20270v3 1737 BRADI_1g74790v3 19 BRADI_1g09890v3 0 BRADI_1g77505v3 440 BRADI_1g48960v3 0 SRR1797581 completed mapping pipeline successfully