Starting /dee2/code/volunteer_pipeline.sh SRR1797576 current disk space = 1525260763136 free memory = 1578314316 SRR1797576 SRAfilesize 1e23d8308fe05ea2eafedc5faf4d4ac7 SRR1797576.sra SRR1797576.sra file validated SRR1797576 is paired end SRR1797576 is conventional basespace SRR1797576 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797576_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 54 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.2175 34.0 34.0 34.0 31.0 34.0 2 32.91 34.0 34.0 34.0 31.0 34.0 3 33.39825 34.0 34.0 34.0 31.0 34.0 4 36.7255 37.0 37.0 37.0 35.0 37.0 5 36.74475 37.0 37.0 37.0 37.0 37.0 6 36.742 37.0 37.0 37.0 37.0 37.0 7 36.7615 37.0 37.0 37.0 37.0 37.0 8 36.76975 37.0 37.0 37.0 37.0 37.0 9 38.5895 39.0 39.0 39.0 38.0 39.0 10-14 38.933800000000005 39.4 39.2 39.4 38.2 39.4 15-19 40.211 41.0 40.2 41.0 38.8 41.0 20-24 40.0047 41.0 40.0 41.0 38.0 41.0 25-29 39.7709 41.0 40.0 41.0 37.6 41.0 30-34 39.580400000000004 41.0 40.0 41.0 36.4 41.0 35-39 39.297450000000005 41.0 39.2 41.0 35.0 41.0 40-44 38.7541 40.8 37.8 41.0 35.0 41.0 45-49 38.29415 40.0 36.2 41.0 34.6 41.0 50-54 37.72065 39.8 35.0 41.0 33.4 41.0 55-59 37.02275 38.6 35.0 41.0 33.0 41.0 60-64 36.3234 36.8 35.0 40.0 32.6 41.0 65-69 35.77385 35.6 35.0 39.2 32.8 41.0 70-74 34.93875 35.0 35.0 37.2 31.8 39.6 75-79 33.85799999999999 35.0 33.8 36.2 30.2 37.8 80-84 33.5552 35.0 34.0 35.0 30.8 36.6 85-89 32.682750000000006 35.0 33.0 35.0 28.4 35.6 90-94 32.413 35.0 33.0 35.0 27.6 35.0 95-99 31.959850000000007 35.0 32.8 35.0 25.8 35.0 100-104 31.6595 35.0 32.4 35.0 24.6 35.0 105-109 31.1413 34.2 31.4 35.0 23.8 35.0 110-114 30.652750000000005 34.0 31.2 35.0 20.8 35.0 115-119 29.903100000000002 34.0 29.8 35.0 17.8 35.0 120-124 28.687400000000004 33.6 28.2 35.0 6.8 35.0 125-129 27.791000000000004 33.0 26.2 35.0 2.0 35.0 130-134 26.83845 32.6 24.4 34.8 2.0 35.0 135-139 25.78695 32.0 22.0 34.6 2.0 35.0 140-144 24.4757 31.0 15.4 34.0 2.0 35.0 145-149 22.1149 30.6 2.0 34.0 2.0 35.0 150 14.41875 15.0 2.0 27.0 2.0 32.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 3.0 7 2.0 8 3.0 9 6.0 10 3.0 11 3.0 12 7.0 13 5.0 14 9.0 15 9.0 16 10.0 17 13.0 18 19.0 19 15.0 20 12.0 21 18.0 22 27.0 23 38.0 24 50.0 25 55.0 26 64.0 27 63.0 28 110.0 29 88.0 30 114.0 31 150.0 32 200.0 33 323.0 34 426.0 35 650.0 36 981.0 37 524.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 32.142857142857146 10.557872784150156 12.51303441084463 44.78623566214807 2 29.049999999999997 10.625 24.85 35.475 3 24.125 11.525 17.549999999999997 46.800000000000004 4 28.125 15.65 18.224999999999998 38.0 5 28.975 21.95 22.2 26.875 6 31.674999999999997 22.6 19.775000000000002 25.95 7 18.975 29.875 29.975 21.175 8 21.825 23.375 30.2 24.6 9 22.05 21.8 29.075 27.075 10-14 23.62 25.790000000000003 24.884999999999998 25.705 15-19 24.454454454454456 24.694694694694693 23.85885885885886 26.99199199199199 20-24 24.66 24.115000000000002 23.94 27.284999999999997 25-29 24.65 24.13 23.615 27.605 30-34 25.2 23.895 22.99 27.915 35-39 25.41 23.865 23.35 27.375 40-44 24.89 24.585 22.96 27.565 45-49 25.485000000000003 23.61 23.145 27.76 50-54 24.959999999999997 23.455000000000002 24.035 27.55 55-59 25.21 22.935 23.395 28.46 60-64 25.855 22.97 23.35 27.825 65-69 25.019999999999996 23.105 23.535 28.34 70-74 25.509999999999998 23.595 22.759999999999998 28.134999999999998 75-79 25.81 23.105 22.79 28.294999999999998 80-84 25.585 23.265 23.07 28.08 85-89 25.275 23.52 22.82 28.384999999999998 90-94 26.055 23.474999999999998 22.535 27.935 95-99 25.865 23.195 22.759999999999998 28.18 100-104 26.419999999999998 22.79 22.055 28.735 105-109 26.435 22.735 23.075000000000003 27.755000000000003 110-114 26.235000000000003 22.264999999999997 23.025000000000002 28.475 115-119 25.974999999999998 22.66 22.89 28.475 120-124 26.57 22.285 22.605 28.54 125-129 26.995 22.14 22.305 28.560000000000002 130-134 26.875 21.94 22.555 28.63 135-139 27.145000000000003 22.065 22.509999999999998 28.28 140-144 27.3 22.18 22.405 28.115000000000002 145-149 27.785 22.56 21.26 28.395 150 29.5 21.975 18.175 30.349999999999998 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 0.5 2 0.5 3 0.5 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 0.5 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 0.0 24 0.5 25 0.5 26 0.0 27 0.5 28 1.0 29 2.0 30 3.0 31 5.0 32 10.0 33 15.5 34 17.5 35 20.5 36 33.5 37 46.0 38 54.5 39 76.5 40 96.0 41 104.5 42 119.0 43 136.0 44 158.5 45 155.0 46 155.5 47 175.5 48 168.0 49 143.0 50 137.5 51 141.0 52 125.0 53 106.5 54 110.0 55 114.0 56 103.5 57 89.0 58 74.0 59 81.0 60 88.5 61 74.5 62 70.5 63 77.5 64 80.5 65 72.5 66 55.5 67 63.5 68 74.0 69 76.5 70 70.5 71 55.5 72 53.5 73 51.5 74 44.0 75 39.0 76 31.0 77 27.0 78 23.5 79 16.0 80 16.0 81 12.5 82 8.0 83 6.5 84 5.5 85 7.0 86 4.5 87 1.0 88 2.5 89 5.0 90 3.0 91 1.0 92 0.5 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 4.1000000000000005 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 0.1 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.775 #Duplication Level Percentage of deduplicated Percentage of total 1 99.77449260836883 99.55000000000001 2 0.22550739163117012 0.44999999999999996 3 0.0 0.0 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 0.0 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 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0125 0.0 0.0 0.0 0.0 106-107 0.025 0.0 0.0 0.0 0.0 108-109 0.025 0.0 0.0 0.0 0.0 110-111 0.037500000000000006 0.0 0.0 0.0 0.0 112-113 0.0625 0.0 0.0 0.0 0.0 114-115 0.075 0.0 0.0 0.0 0.0 116-117 0.125 0.0 0.0 0.0 0.0 118-119 0.1375 0.0 0.0 0.0 0.0 120-121 0.175 0.0 0.0 0.0 0.0 122-123 0.21250000000000002 0.0 0.0 0.0 0.0 124-125 0.2625 0.0 0.0 0.0 0.0 126-127 0.375 0.0 0.0 0.0 0.0 128-129 0.5125 0.0 0.0 0.0 0.0 130-131 0.8 0.0 0.0 0.0 0.0 132-133 0.975 0.0 0.0 0.0 0.0 134-135 1.225 0.0 0.0 0.0 0.0 136-137 1.5625 0.0 0.0 0.0 0.0 138 1.7 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAGGTG 10 0.0069808904 143.95 2 >>END_MODULE SRR1797576 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR1797576_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 55 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 32.78375 34.0 33.0 34.0 31.0 34.0 2 33.1405 34.0 33.0 34.0 31.0 34.0 3 33.24725 34.0 33.0 34.0 31.0 34.0 4 36.4465 37.0 37.0 37.0 35.0 37.0 5 36.579 37.0 37.0 37.0 35.0 37.0 6 36.65125 37.0 37.0 37.0 37.0 37.0 7 36.6695 37.0 37.0 37.0 37.0 37.0 8 36.6015 37.0 37.0 37.0 37.0 37.0 9 38.49725 39.0 39.0 39.0 38.0 39.0 10-14 38.71775 39.4 39.2 39.4 37.8 39.4 15-19 39.9363 41.0 40.0 41.0 38.0 41.0 20-24 39.721849999999996 41.0 40.0 41.0 37.8 41.0 25-29 39.43405 41.0 39.6 41.0 37.0 41.0 30-34 38.752449999999996 40.0 38.4 41.0 35.0 41.0 35-39 38.58265 40.0 38.2 41.0 35.0 41.0 40-44 38.128750000000004 40.0 36.6 41.0 34.6 41.0 45-49 37.41745 39.8 35.0 41.0 33.0 41.0 50-54 36.459050000000005 38.2 35.0 40.4 32.2 40.8 55-59 35.9857 37.0 35.0 40.4 31.4 41.0 60-64 35.6925 35.6 35.0 39.8 32.2 41.0 65-69 35.14805 35.0 35.0 38.8 32.0 40.8 70-74 34.2078 35.0 34.6 36.8 30.4 39.2 75-79 33.46625 35.0 34.0 35.6 29.8 37.4 80-84 32.64955 35.0 33.2 35.0 27.8 36.2 85-89 32.16635 35.0 33.0 35.0 26.6 35.4 90-94 31.5293 35.0 32.6 35.0 24.6 35.0 95-99 31.33235 35.0 32.2 35.0 24.0 35.0 100-104 30.826900000000002 34.6 31.6 35.0 21.6 35.0 105-109 30.319100000000002 34.0 31.0 35.0 19.4 35.0 110-114 29.2933 34.0 29.2 35.0 12.6 35.0 115-119 28.944049999999997 34.0 28.6 35.0 7.6 35.0 120-124 28.43965 33.4 27.8 35.0 2.6 35.0 125-129 27.2055 33.0 25.2 35.0 2.0 35.0 130-134 26.1067 32.4 23.0 34.8 2.0 35.0 135-139 24.4829 31.0 16.8 34.0 2.0 35.0 140-144 23.116750000000003 30.4 3.6 34.0 2.0 35.0 145-149 21.2701 29.8 2.0 34.0 2.0 35.0 150 15.22375 17.0 2.0 29.0 2.0 33.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 6.0 3 3.0 4 3.0 5 3.0 6 7.0 7 6.0 8 3.0 9 16.0 10 7.0 11 10.0 12 6.0 13 9.0 14 7.0 15 15.0 16 17.0 17 9.0 18 25.0 19 17.0 20 25.0 21 29.0 22 27.0 23 45.0 24 44.0 25 52.0 26 65.0 27 92.0 28 97.0 29 121.0 30 138.0 31 175.0 32 228.0 33 302.0 34 403.0 35 661.0 36 893.0 37 427.0 38 7.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 27.083333333333332 18.04718875502008 11.370481927710843 43.49899598393574 2 36.3 24.25 17.05 22.400000000000002 3 24.224999999999998 24.85 22.3 28.625 4 28.275 24.4 20.724999999999998 26.6 5 31.900000000000002 25.674999999999997 19.075 23.35 6 26.375 31.025000000000002 17.9 24.7 7 24.8 17.974999999999998 30.049999999999997 27.175 8 28.325 20.549999999999997 22.8 28.325 9 26.424999999999997 21.425 24.375 27.775 10-14 28.46 23.93 20.73 26.88 15-19 27.955000000000002 23.43 21.755 26.86 20-24 28.02 23.919999999999998 21.709999999999997 26.35 25-29 28.54 23.150000000000002 21.415 26.895000000000003 30-34 28.044999999999998 22.939999999999998 22.235 26.779999999999998 35-39 28.32 23.59 21.445 26.645000000000003 40-44 28.955 22.62 22.15 26.275 45-49 28.005000000000003 23.635 21.584999999999997 26.775 50-54 29.299999999999997 22.985 21.2 26.515 55-59 28.76 22.765 21.625 26.85 60-64 27.900000000000002 22.99 22.375 26.735 65-69 28.1 23.04 22.470000000000002 26.39 70-74 28.64 22.695 22.79 25.874999999999996 75-79 27.99 22.835 22.720000000000002 26.455000000000002 80-84 29.065 23.05 22.075 25.81 85-89 29.020000000000003 22.515 22.29 26.174999999999997 90-94 29.744999999999997 22.375 21.985 25.895000000000003 95-99 28.610000000000003 23.155 22.03 26.205000000000002 100-104 28.785 23.305 22.009999999999998 25.900000000000002 105-109 28.565 22.71 22.869999999999997 25.855 110-114 28.935 22.57 22.720000000000002 25.775 115-119 28.585 22.775000000000002 22.05 26.590000000000003 120-124 28.335 22.695 22.830000000000002 26.14 125-129 29.39 23.015 22.055 25.540000000000003 130-134 29.385 22.235 22.665 25.715 135-139 29.12 23.105 22.439999999999998 25.335 140-144 28.96 22.56 21.67 26.810000000000002 145-149 29.64 22.71 21.645 26.005 150 28.549999999999997 23.3 19.75 28.4 >>END_MODULE >>Per sequence GC content fail #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 0.5 15 0.5 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.5 26 0.5 27 2.0 28 4.5 29 4.0 30 3.5 31 3.0 32 5.0 33 11.0 34 12.0 35 14.5 36 24.0 37 37.5 38 49.5 39 61.5 40 75.0 41 99.5 42 108.0 43 108.5 44 129.5 45 136.5 46 136.5 47 157.5 48 165.0 49 142.0 50 130.0 51 119.0 52 113.5 53 117.0 54 112.5 55 112.0 56 102.5 57 84.5 58 78.0 59 86.5 60 85.5 61 81.5 62 89.0 63 86.0 64 75.5 65 78.0 66 79.0 67 79.5 68 83.5 69 89.0 70 81.5 71 70.5 72 68.5 73 62.5 74 63.5 75 50.5 76 45.5 77 43.5 78 31.5 79 22.0 80 19.5 81 19.5 82 10.5 83 7.0 84 6.0 85 5.0 86 4.0 87 2.5 88 2.5 89 2.5 90 3.0 91 1.5 92 0.0 93 1.0 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 0.4 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.625 #Duplication Level Percentage of deduplicated Percentage of total 1 99.62358845671268 99.25 2 0.37641154328732745 0.75 3 0.0 0.0 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 0.0 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 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0125 0.0 0.0 0.0 0.0 106-107 0.025 0.0 0.0 0.0 0.0 108-109 0.025 0.0 0.0 0.0 0.0 110-111 0.037500000000000006 0.0 0.0 0.0 0.0 112-113 0.0625 0.0 0.0 0.0 0.0 114-115 0.075 0.0 0.0 0.0 0.0 116-117 0.125 0.0 0.0 0.0 0.0 118-119 0.1375 0.0 0.0 0.0 0.0 120-121 0.175 0.0 0.0 0.0 0.0 122-123 0.21250000000000002 0.0 0.0 0.0 0.0 124-125 0.2875 0.0 0.0 0.0 0.0 126-127 0.38749999999999996 0.0 0.0 0.0 0.0 128-129 0.5125 0.0 0.0 0.0 0.0 130-131 0.825 0.0 0.0 0.0 0.0 132-133 1.0125 0.0 0.0 0.0 0.0 134-135 1.2375 0.0 0.0 0.0 0.0 136-137 1.5499999999999998 0.0 0.0 0.0 0.0 138 1.675 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGTACCA 10 0.006973645 144.0 4 TCATCAC 10 0.006973645 144.0 7 AGGAGAA 10 0.006973645 144.0 4 GGGGGGG 90 0.0051234453 11.2 135-139 >>END_MODULE Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107852 spots for SRR1797576.sra Written 1107852 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra Read 1107850 spots for SRR1797576.sra Written 1107850 spots for SRR1797576.sra SRR ids: ['SRR1797576.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_t6uhixer SRR1797576.sra spots: 22157002 blocks: [[1, 1107850], [1107851, 2215700], [2215701, 3323550], [3323551, 4431400], [4431401, 5539250], [5539251, 6647100], [6647101, 7754950], [7754951, 8862800], [8862801, 9970650], [9970651, 11078500], [11078501, 12186350], [12186351, 13294200], [13294201, 14402050], [14402051, 15509900], [15509901, 16617750], [16617751, 17725600], [17725601, 18833450], [18833451, 19941300], [19941301, 21049150], [21049151, 22157002]] SRR1797576 file size 7443305 SRR1797576 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 SRR1797576 SRR1797576_1.fastq SRR1797576_2.fastq Input file: SRR1797576_1.fastq Paired file: SRR1797576_2.fastq trimmed: SRR1797576-trimmed-pair1.fastq, SRR1797576-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 Mon Dec 9 13:13:01 2024 >> started Mon Dec 9 13:14:43 2024 >> done (102.235s) 22157002 read pairs processed; of these: 42557 ( 0.19%) short read pairs filtered out after trimming by size control 28529 ( 0.13%) empty read pairs filtered out after trimming by size control 22085916 (99.68%) read pairs available; of these: 17034483 (77.13%) trimmed read pairs available after processing 5051433 (22.87%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 21 0.00% 19 27 0.00% 20 51 0.00% 21 78 0.00% 22 125 0.00% 23 161 0.00% 24 177 0.00% 25 234 0.00% 26 315 0.00% 27 345 0.00% 28 525 0.00% 29 556 0.00% 30 627 0.00% 31 737 0.00% 32 809 0.00% 33 943 0.00% 34 1007 0.00% 35 1086 0.00% 36 1270 0.01% 37 1371 0.01% 38 1454 0.01% 39 1557 0.01% 40 1621 0.01% 41 1730 0.01% 42 1796 0.01% 43 2036 0.01% 44 2144 0.01% 45 2249 0.01% 46 2339 0.01% 47 2430 0.01% 48 2678 0.01% 49 2792 0.01% 50 2917 0.01% 51 3146 0.01% 52 3309 0.01% 53 3439 0.02% 54 3666 0.02% 55 3782 0.02% 56 4051 0.02% 57 4198 0.02% 58 4449 0.02% 59 4491 0.02% 60 4940 0.02% 61 5012 0.02% 62 5287 0.02% 63 5631 0.03% 64 5899 0.03% 65 6315 0.03% 66 6510 0.03% 67 6803 0.03% 68 7257 0.03% 69 7646 0.03% 70 8072 0.04% 71 8412 0.04% 72 8677 0.04% 73 9394 0.04% 74 10050 0.05% 75 10517 0.05% 76 11222 0.05% 77 11833 0.05% 78 12680 0.06% 79 13408 0.06% 80 14127 0.06% 81 15241 0.07% 82 16183 0.07% 83 17649 0.08% 84 21192 0.10% 85 22288 0.10% 86 23358 0.11% 87 24435 0.11% 88 25459 0.12% 89 27025 0.12% 90 28024 0.13% 91 29091 0.13% 92 30320 0.14% 93 31507 0.14% 94 32919 0.15% 95 34059 0.15% 96 35897 0.16% 97 37020 0.17% 98 38528 0.17% 99 40428 0.18% 100 40539 0.18% 101 42357 0.19% 102 44261 0.20% 103 46657 0.21% 104 48797 0.22% 105 52206 0.24% 106 55282 0.25% 107 58278 0.26% 108 61373 0.28% 109 65755 0.30% 110 68915 0.31% 111 73110 0.33% 112 76876 0.35% 113 80392 0.36% 114 86690 0.39% 115 93460 0.42% 116 99204 0.45% 117 104546 0.47% 118 111232 0.50% 119 116855 0.53% 120 125679 0.57% 121 134216 0.61% 122 145187 0.66% 123 152045 0.69% 124 159287 0.72% 125 172798 0.78% 126 180328 0.82% 127 195132 0.88% 128 208024 0.94% 129 222401 1.01% 130 237767 1.08% 131 259664 1.18% 132 277996 1.26% 133 297395 1.35% 134 310320 1.41% 135 325927 1.48% 136 345377 1.56% 137 366661 1.66% 138 391633 1.77% 139 419235 1.90% 140 451175 2.04% 141 483219 2.19% 142 521096 2.36% 143 568778 2.58% 144 637844 2.89% 145 733608 3.32% 146 873271 3.95% 147 1101035 4.99% 148 1496826 6.78% 149 3030720 13.72% 150 5051433 22.87% 22085916 reads passed initial QC criterion=sequence-density sequence-density=0.27 sequence-density-rank=1 fanout-score=15.72 fanout-score-rank=10 prefix-density=0.56 prefix-fanout=7.8 sequence=CTCCAGCTCCTT criterion=fanout-score sequence-density=0.04 sequence-density-rank=29 fanout-score=558.26 fanout-score-rank=1 prefix-density=0.85 prefix-fanout=23.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.28 sequence-density-rank=1 fanout-score=11.65 fanout-score-rank=21 prefix-density=0.43 prefix-fanout=7.5 sequence=AAGGAGCTGGAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=36 fanout-score=1799.83 fanout-score-rank=1 prefix-density=1.07 prefix-fanout=21.2 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGA SRR1797576 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 09 13:17:02 Started mapping on | Dec 09 13:17:05 Finished on | Dec 09 13:19:20 Mapping speed, Million of reads per hour | 588.96 Number of input reads | 22085916 Average input read length | 279 UNIQUE READS: Uniquely mapped reads number | 21037723 Uniquely mapped reads % | 95.25% Average mapped length | 278.40 Number of splices: Total | 17465616 Number of splices: Annotated (sjdb) | 16558959 Number of splices: GT/AG | 17230866 Number of splices: GC/AG | 192857 Number of splices: AT/AC | 14612 Number of splices: Non-canonical | 27281 Mismatch rate per base, % | 0.26% Deletion rate per base | 0.02% Deletion average length | 2.33 Insertion rate per base | 0.01% Insertion average length | 2.17 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 332474 % of reads mapped to multiple loci | 1.51% Number of reads mapped to too many loci | 67771 % of reads mapped to too many loci | 0.31% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.01% % of reads unmapped: other | 1.93% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 737468 737468 737468 N_multimapping 332474 332474 332474 N_noFeature 477824 20374211 834272 N_ambiguous 371646 3521 69387 UnstrandedReadsAssigned:20188253 PositiveStrandReadsAssigned:659991 NegativeStrandReadsAssigned:20134064 Dataset is classified negative stranded MeadianReadLen=149 20thPercentileLength=137 echo kmer=133 SRR1797576 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: SRR1797576-trimmed-pair1.fastq SRR1797576-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 22,085,916 reads, 20,313,127 reads pseudoaligned [quant] estimated average fragment length: 213.13 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,232 rounds 52973 SRR1797576.ke.tsv 35125 SRR1797576.se.tsv 88098 total ==> SRR1797576.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 724.029 61.8718 5.71625 PNS24247 1044 831.87 7.92085 0.636928 PNS24249 1928 1715.87 278.149 10.8434 PNS24246 1044 831.87 7.92085 0.636928 PNS24248 1044 831.87 7.92085 0.636928 PNS24244 1471 1258.87 26.2171 1.39309 PNS24243 293 91.5909 1 0.730334 KQK14069 1603 1390.87 42.1666 2.02795 KQK14071 474 263.378 2.83337 0.719611 ==> SRR1797576.se.tsv <== BRADI_1g14170v3 45 BRADI_1g53295v3 16 BRADI_1g59795v3 293 BRADI_1g07683v3 0 BRADI_1g00485v3 172 BRADI_1g20270v3 2997 BRADI_1g74790v3 10 BRADI_1g09890v3 0 BRADI_1g77505v3 254 BRADI_1g48960v3 0 SRR1797576 completed mapping pipeline successfully