Starting /dee2/code/volunteer_pipeline.sh SRR28623307 current disk space = 3048578703360 free memory = 1467815824 SRR28623307 SRAfilesize 22aa3a20ea4718fa14aff4c54db5d3ab SRR28623307.sra SRR28623307.sra file validated SRR28623307 is paired end SRR28623307 is conventional basespace SRR28623307 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623307_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.32625 37.0 37.0 37.0 37.0 37.0 2 36.4615 37.0 37.0 37.0 37.0 37.0 3 36.598 37.0 37.0 37.0 37.0 37.0 4 36.592 37.0 37.0 37.0 37.0 37.0 5 36.6475 37.0 37.0 37.0 37.0 37.0 6 36.6165 37.0 37.0 37.0 37.0 37.0 7 36.5865 37.0 37.0 37.0 37.0 37.0 8 36.4665 37.0 37.0 37.0 37.0 37.0 9 36.5155 37.0 37.0 37.0 37.0 37.0 10-14 36.5577 37.0 37.0 37.0 37.0 37.0 15-19 36.5248 37.0 37.0 37.0 37.0 37.0 20-24 36.4844 37.0 37.0 37.0 37.0 37.0 25-29 36.4585 37.0 37.0 37.0 37.0 37.0 30-34 36.482299999999995 37.0 37.0 37.0 37.0 37.0 35-39 36.361599999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.4113 37.0 37.0 37.0 37.0 37.0 45-49 36.3912 37.0 37.0 37.0 37.0 37.0 50-54 36.295100000000005 37.0 37.0 37.0 37.0 37.0 55-59 36.2879 37.0 37.0 37.0 37.0 37.0 60-64 36.317099999999996 37.0 37.0 37.0 37.0 37.0 65-69 36.297399999999996 37.0 37.0 37.0 37.0 37.0 70-74 36.24390000000001 37.0 37.0 37.0 37.0 37.0 75-79 36.131800000000005 37.0 37.0 37.0 37.0 37.0 80-84 36.124399999999994 37.0 37.0 37.0 37.0 37.0 85-89 36.1023 37.0 37.0 37.0 37.0 37.0 90-94 36.0782 37.0 37.0 37.0 37.0 37.0 95-99 35.9442 37.0 37.0 37.0 37.0 37.0 100-104 36.0218 37.0 37.0 37.0 37.0 37.0 105-109 36.0153 37.0 37.0 37.0 37.0 37.0 110-114 35.875099999999996 37.0 37.0 37.0 37.0 37.0 115-119 35.919500000000006 37.0 37.0 37.0 37.0 37.0 120-124 35.7606 37.0 37.0 37.0 37.0 37.0 125-129 35.66330000000001 37.0 37.0 37.0 37.0 37.0 130-134 35.8571 37.0 37.0 37.0 37.0 37.0 135-139 35.708299999999994 37.0 37.0 37.0 37.0 37.0 140-144 35.42659999999999 37.0 37.0 37.0 37.0 37.0 145-149 35.4067 37.0 37.0 37.0 34.6 37.0 150-151 35.2605 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 2.0 24 3.0 25 4.0 26 2.0 27 13.0 28 14.0 29 28.0 30 16.0 31 43.0 32 49.0 33 86.0 34 157.0 35 396.0 36 2961.0 37 225.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.6131625219794 14.493845767395127 8.691283597086159 37.20170811353931 2 19.0 15.9 35.6 29.5 3 18.425 19.2 28.625 33.75 4 22.45 25.624999999999996 24.099999999999998 27.825 5 22.85 35.35 23.05 18.75 6 19.925 36.125 24.25 19.7 7 15.425 27.425 39.95 17.2 8 18.3 27.224999999999998 31.474999999999998 23.0 9 17.8 24.349999999999998 36.475 21.375 10-14 19.02 30.990000000000002 27.37 22.62 15-19 19.61 29.604999999999997 27.525 23.26 20-24 19.445 28.865000000000002 28.485 23.205000000000002 25-29 19.02 29.98 27.765 23.235 30-34 18.93 29.42 27.485 24.165 35-39 18.995 28.99 27.85 24.165 40-44 19.715 29.744999999999997 26.985 23.555 45-49 19.25 29.845 27.139999999999997 23.765 50-54 19.59 29.085 27.875 23.45 55-59 20.13 29.080000000000002 27.72 23.07 60-64 19.650000000000002 29.145 27.439999999999998 23.765 65-69 19.885 29.14 27.415 23.56 70-74 19.7 29.360000000000003 27.465 23.474999999999998 75-79 19.575 28.84 27.575 24.01 80-84 20.175 28.98 27.595 23.25 85-89 19.744999999999997 28.535 27.785 23.935000000000002 90-94 19.950000000000003 29.12 27.67 23.26 95-99 19.765 28.965000000000003 28.275 22.994999999999997 100-104 20.27 29.005 27.445000000000004 23.28 105-109 20.565 28.585 27.48 23.369999999999997 110-114 19.86 29.12 28.18 22.84 115-119 20.41 29.13 26.715 23.745 120-124 20.445 28.549999999999997 26.96 24.044999999999998 125-129 20.365 29.18 26.76 23.695 130-134 20.945 28.845 26.450000000000003 23.76 135-139 20.794999999999998 29.07 26.795 23.34 140-144 20.79 28.689999999999998 26.55 23.97 145-149 21.025 28.595 26.490000000000002 23.89 150-151 21.837500000000002 28.8375 25.5125 23.8125 >>END_MODULE >>Per sequence GC content pass #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 1.0 19 3.0 20 2.5 21 1.0 22 1.5 23 4.5 24 6.5 25 5.5 26 6.5 27 9.5 28 14.0 29 16.5 30 29.0 31 42.5 32 52.5 33 53.5 34 58.0 35 90.5 36 107.0 37 109.5 38 145.0 39 197.0 40 200.0 41 205.0 42 233.0 43 247.5 44 265.0 45 258.0 46 254.5 47 237.0 48 217.5 49 192.0 50 153.0 51 134.5 52 108.5 53 85.5 54 61.0 55 43.5 56 39.0 57 31.0 58 19.5 59 13.5 60 12.0 61 9.0 62 4.0 63 3.5 64 5.5 65 4.5 66 3.5 67 2.0 68 0.0 69 0.5 70 0.5 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 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 0.475 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 86.15 #Duplication Level Percentage of deduplicated Percentage of total 1 86.76726639582124 74.75 2 10.766105629715613 18.55 3 2.1474172954149737 5.55 4 0.261172373766686 0.8999999999999999 5 0.05803830528148578 0.25 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 warn #Sequence Count Percentage Possible Source TAGCAGTAGCAGATAAGAATGCTCTTCCAGGCTGACGGTTGGCCAAGGGT 5 0.125 No Hit GGTTAATGGTGTATTCTCTAGTGACCACCTCCTCCTTTCTCCCCTTTGTT 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 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0125 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 0.0625 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.16249999999999998 0.0 0.0 0.0 0.0 74-75 0.2 0.0 0.0 0.0 0.0 76-77 0.275 0.0 0.0 0.0 0.0 78-79 0.3125 0.0 0.0 0.0 0.0 80-81 0.38749999999999996 0.0 0.0 0.0 0.0 82-83 0.4625 0.0 0.0 0.0 0.0 84-85 0.575 0.0 0.0 0.0 0.0 86-87 0.6 0.0 0.0 0.0 0.0 88-89 0.6375 0.0 0.0 0.0 0.0 90-91 0.875 0.0 0.0 0.0 0.0 92-93 1.1 0.0 0.0 0.0 0.0 94-95 1.2875 0.0 0.0 0.0 0.0 96-97 1.575 0.0 0.0 0.0 0.0 98-99 1.875 0.0 0.0 0.0 0.0 100-101 2.1625 0.0 0.0 0.0 0.0 102-103 2.425 0.0 0.0 0.0 0.0 104-105 2.625 0.0 0.0 0.0 0.0 106-107 2.9375 0.0 0.0 0.0 0.0 108-109 3.1875 0.0 0.0 0.0 0.0 110-111 3.7 0.0 0.0 0.0 0.0 112-113 4.05 0.0 0.0 0.0 0.0 114-115 4.5625 0.0 0.0 0.0 0.0 116-117 5.125 0.0 0.0 0.0 0.0 118-119 5.4375 0.0 0.0 0.0 0.0 120-121 5.8 0.0 0.0 0.0 0.0 122-123 6.2 0.0 0.0 0.0 0.0 124-125 6.6375 0.0 0.0 0.0 0.0 126-127 7.15 0.0 0.0 0.0 0.0 128-129 7.8 0.0 0.0 0.0 0.0 130-131 8.3125 0.0 0.0 0.0 0.0 132-133 8.775 0.0 0.0 0.0 0.0 134-135 9.4125 0.0 0.0 0.0 0.0 136-137 9.8875 0.0 0.0 0.0 0.0 138-139 10.425 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAACCAA 10 0.006830828 145.0 5 CAGCCTT 10 0.006830828 145.0 1 AGCCTTC 10 0.006830828 145.0 2 >>END_MODULE SRR28623307 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623307_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.018 37.0 37.0 37.0 37.0 37.0 2 36.205 37.0 37.0 37.0 37.0 37.0 3 36.2485 37.0 37.0 37.0 37.0 37.0 4 36.0385 37.0 37.0 37.0 37.0 37.0 5 36.2275 37.0 37.0 37.0 37.0 37.0 6 36.2685 37.0 37.0 37.0 37.0 37.0 7 36.203 37.0 37.0 37.0 37.0 37.0 8 36.0865 37.0 37.0 37.0 37.0 37.0 9 36.1195 37.0 37.0 37.0 37.0 37.0 10-14 36.1346 37.0 37.0 37.0 37.0 37.0 15-19 36.017599999999995 37.0 37.0 37.0 37.0 37.0 20-24 35.9767 37.0 37.0 37.0 37.0 37.0 25-29 35.908100000000005 37.0 37.0 37.0 37.0 37.0 30-34 35.787600000000005 37.0 37.0 37.0 37.0 37.0 35-39 35.7944 37.0 37.0 37.0 37.0 37.0 40-44 35.7385 37.0 37.0 37.0 37.0 37.0 45-49 35.733799999999995 37.0 37.0 37.0 37.0 37.0 50-54 35.693200000000004 37.0 37.0 37.0 37.0 37.0 55-59 35.566 37.0 37.0 37.0 37.0 37.0 60-64 35.5361 37.0 37.0 37.0 37.0 37.0 65-69 35.5343 37.0 37.0 37.0 37.0 37.0 70-74 35.6154 37.0 37.0 37.0 37.0 37.0 75-79 35.5265 37.0 37.0 37.0 37.0 37.0 80-84 35.4609 37.0 37.0 37.0 37.0 37.0 85-89 35.392700000000005 37.0 37.0 37.0 37.0 37.0 90-94 35.342499999999994 37.0 37.0 37.0 37.0 37.0 95-99 35.41459999999999 37.0 37.0 37.0 37.0 37.0 100-104 35.29639999999999 37.0 37.0 37.0 34.6 37.0 105-109 35.2147 37.0 37.0 37.0 34.6 37.0 110-114 35.261700000000005 37.0 37.0 37.0 37.0 37.0 115-119 35.1807 37.0 37.0 37.0 34.6 37.0 120-124 35.2889 37.0 37.0 37.0 37.0 37.0 125-129 34.813100000000006 37.0 37.0 37.0 25.0 37.0 130-134 35.0489 37.0 37.0 37.0 29.8 37.0 135-139 34.910000000000004 37.0 37.0 37.0 25.0 37.0 140-144 34.9082 37.0 37.0 37.0 25.0 37.0 145-149 34.803 37.0 37.0 37.0 25.0 37.0 150-151 34.545249999999996 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per tile sequence quality pass #Tile Base Mean 1101 1 0.0 1101 2 0.0 1101 3 0.0 1101 4 0.0 1101 5 0.0 1101 6 0.0 1101 7 0.0 1101 8 0.0 1101 9 0.0 1101 10-14 0.0 1101 15-19 0.0 1101 20-24 0.0 1101 25-29 0.0 1101 30-34 0.0 1101 35-39 0.0 1101 40-44 0.0 1101 45-49 0.0 1101 50-54 0.0 1101 55-59 0.0 1101 60-64 0.0 1101 65-69 0.0 1101 70-74 0.0 1101 75-79 0.0 1101 80-84 0.0 1101 85-89 0.0 1101 90-94 0.0 1101 95-99 0.0 1101 100-104 0.0 1101 105-109 0.0 1101 110-114 0.0 1101 115-119 0.0 1101 120-124 0.0 1101 125-129 0.0 1101 130-134 0.0 1101 135-139 0.0 1101 140-144 0.0 1101 145-149 0.0 1101 150-151 0.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 16.0 14 9.0 15 11.0 16 8.0 17 9.0 18 3.0 19 3.0 20 6.0 21 4.0 22 18.0 23 16.0 24 8.0 25 7.0 26 13.0 27 17.0 28 13.0 29 18.0 30 28.0 31 29.0 32 67.0 33 96.0 34 178.0 35 602.0 36 2597.0 37 222.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 45.65 21.475 10.75 22.125 2 29.475 26.375 28.799999999999997 15.35 3 24.224999999999998 26.974999999999998 30.95 17.849999999999998 4 25.324999999999996 33.2 23.175 18.3 5 26.75 35.4 22.725 15.125 6 22.0 38.7 22.575 16.725 7 22.275 22.075 37.775 17.875 8 22.225 26.05 27.900000000000002 23.825 9 23.275000000000002 25.6 29.5 21.625 10-14 24.425 29.154999999999998 26.36 20.06 15-19 23.94 27.750000000000004 27.715 20.595 20-24 23.925 28.505000000000003 27.905 19.665 25-29 23.755000000000003 29.075 27.195000000000004 19.975 30-34 24.375 28.689999999999998 27.334999999999997 19.6 35-39 23.91 28.560000000000002 27.529999999999998 20.0 40-44 24.310000000000002 28.025 27.98 19.685 45-49 23.76 28.735 27.950000000000003 19.555 50-54 24.025 28.315 28.310000000000002 19.35 55-59 23.765 28.105000000000004 27.955000000000002 20.175 60-64 24.07 27.735 28.449999999999996 19.744999999999997 65-69 23.380000000000003 28.04 28.565 20.015 70-74 23.544999999999998 28.660000000000004 28.139999999999997 19.655 75-79 23.11 28.549999999999997 28.215 20.125 80-84 23.26 28.78 28.73 19.23 85-89 23.865 28.63 27.525 19.98 90-94 24.235 28.535 27.994999999999997 19.235 95-99 24.09 28.035 27.98 19.895 100-104 24.72 28.01 27.584999999999997 19.685 105-109 24.87 27.839999999999996 27.805000000000003 19.485 110-114 24.224999999999998 28.395 28.205000000000002 19.175 115-119 24.565 28.22 27.36 19.855 120-124 24.385 28.26 27.985 19.37 125-129 25.215 28.265 27.435 19.085 130-134 24.905 28.82 27.134999999999998 19.139999999999997 135-139 25.745 28.410000000000004 26.724999999999998 19.12 140-144 25.605 28.720000000000002 26.905 18.77 145-149 26.3 27.634999999999998 27.525 18.54 150-151 25.9625 29.675 26.325 18.0375 >>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 0.5 7 1.5 8 1.0 9 0.0 10 1.0 11 1.0 12 0.5 13 1.5 14 1.5 15 3.0 16 4.0 17 3.0 18 2.0 19 1.5 20 2.0 21 2.5 22 2.0 23 1.5 24 3.0 25 4.0 26 8.5 27 12.0 28 15.0 29 21.5 30 27.5 31 33.5 32 36.5 33 45.5 34 57.5 35 65.0 36 87.5 37 115.5 38 150.5 39 178.5 40 191.5 41 218.0 42 263.0 43 287.0 44 282.0 45 258.5 46 235.0 47 225.5 48 201.5 49 182.0 50 158.5 51 131.0 52 105.5 53 82.0 54 65.0 55 48.0 56 32.0 57 20.5 58 18.5 59 13.5 60 8.0 61 9.5 62 6.5 63 5.0 64 5.0 65 2.0 66 1.5 67 1.0 68 2.0 69 2.5 70 1.5 71 1.0 72 0.5 73 0.0 74 0.5 75 1.5 76 2.0 77 2.5 78 2.5 79 1.5 80 1.0 81 1.0 82 1.0 83 1.0 84 1.5 85 1.5 86 1.5 87 1.0 88 1.0 89 1.0 90 0.5 91 0.5 92 0.5 93 1.0 94 1.5 95 1.0 96 1.5 97 3.5 98 2.0 99 0.5 100 5.0 >>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 86.45 #Duplication Level Percentage of deduplicated Percentage of total 1 87.39155581260844 75.55 2 10.410641989589358 18.0 3 1.8796992481203008 4.875 4 0.20242914979757085 0.7000000000000001 5 0.08675534991324466 0.375 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.028918449971081547 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 20 0.5 No Hit CTGAGCTTGAGTGCATTCTTCTAAGTAAAAGAAATCCCTTAATTTCATCA 5 0.125 No Hit TGGACAGGTTCTTCTGTCTGTTCGCTGCAAGGACAGCAACAGTCACCATG 5 0.125 No Hit CCTCTCTTCCAAACATCTGTCTTCTTTCAAACACTAAGGCAACTCAGTCA 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 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0125 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 0.0625 0.0 0.0 0.0 0.0 64-65 0.1 0.0 0.0 0.0 0.0 66-67 0.125 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.15 0.0 0.0 0.0 0.0 72-73 0.175 0.0 0.0 0.0 0.0 74-75 0.225 0.0 0.0 0.0 0.0 76-77 0.3 0.0 0.0 0.0 0.0 78-79 0.3375 0.0 0.0 0.0 0.0 80-81 0.4125 0.0 0.0 0.0 0.0 82-83 0.5125 0.0 0.0 0.0 0.0 84-85 0.625 0.0 0.0 0.0 0.0 86-87 0.65 0.0 0.0 0.0 0.0 88-89 0.6875 0.0 0.0 0.0 0.0 90-91 0.9249999999999999 0.0 0.0 0.0 0.0 92-93 1.15 0.0 0.0 0.0 0.0 94-95 1.3375 0.0 0.0 0.0 0.0 96-97 1.625 0.0 0.0 0.0 0.0 98-99 1.925 0.0 0.0 0.0 0.0 100-101 2.2125 0.0 0.0 0.0 0.0 102-103 2.475 0.0 0.0 0.0 0.0 104-105 2.6875 0.0 0.0 0.0 0.0 106-107 3.025 0.0 0.0 0.0 0.0 108-109 3.2875 0.0 0.0 0.0 0.0 110-111 3.8 0.0 0.0 0.0 0.0 112-113 4.1625 0.0 0.0 0.0 0.0 114-115 4.6875 0.0 0.0 0.0 0.0 116-117 5.324999999999999 0.0 0.0 0.0 0.0 118-119 5.637499999999999 0.0 0.0 0.0 0.0 120-121 5.9875 0.0 0.0 0.0 0.0 122-123 6.375 0.0 0.0 0.0 0.0 124-125 6.7875 0.0 0.0 0.0 0.0 126-127 7.25 0.0 0.0 0.0 0.0 128-129 7.8875 0.0 0.0 0.0 0.0 130-131 8.412500000000001 0.0 0.0 0.0 0.0 132-133 8.8875 0.0 0.0 0.0 0.0 134-135 9.5375 0.0 0.0 0.0 0.0 136-137 9.9625 0.0 0.0 0.0 0.0 138-139 10.5 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra Read 1474731 spots for SRR28623307.sra Written 1474731 spots for SRR28623307.sra SRR ids: ['SRR28623307.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_djn_wuke SRR28623307.sra spots: 29494620 blocks: [[1, 1474731], [1474732, 2949462], [2949463, 4424193], [4424194, 5898924], [5898925, 7373655], [7373656, 8848386], [8848387, 10323117], [10323118, 11797848], [11797849, 13272579], [13272580, 14747310], [14747311, 16222041], [16222042, 17696772], [17696773, 19171503], [19171504, 20646234], [20646235, 22120965], [22120966, 23595696], [23595697, 25070427], [25070428, 26545158], [26545159, 28019889], [28019890, 29494620]] SRR28623307 file size 10890212 SRR28623307 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 SRR28623307 SRR28623307_1.fastq SRR28623307_2.fastq Input file: SRR28623307_1.fastq Paired file: SRR28623307_2.fastq trimmed: SRR28623307-trimmed-pair1.fastq, SRR28623307-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 Feb 11 16:55:27 2025 >> started Tue Feb 11 16:56:05 2025 >> done (37.967s) 29494620 read pairs processed; of these: 24 ( 0.00%) short read pairs filtered out after trimming by size control 35094 ( 0.12%) empty read pairs filtered out after trimming by size control 29459502 (99.88%) read pairs available; of these: 4642749 (15.76%) trimmed read pairs available after processing 24816753 (84.24%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 2 0.00% 20 4 0.00% 21 1 0.00% 22 6 0.00% 23 3 0.00% 24 4 0.00% 25 5 0.00% 26 7 0.00% 27 8 0.00% 28 12 0.00% 29 9 0.00% 30 14 0.00% 31 8 0.00% 32 9 0.00% 33 18 0.00% 34 22 0.00% 35 22 0.00% 36 31 0.00% 37 23 0.00% 38 43 0.00% 39 31 0.00% 40 40 0.00% 41 61 0.00% 42 62 0.00% 43 74 0.00% 44 68 0.00% 45 73 0.00% 46 84 0.00% 47 100 0.00% 48 135 0.00% 49 156 0.00% 50 176 0.00% 51 204 0.00% 52 270 0.00% 53 249 0.00% 54 281 0.00% 55 310 0.00% 56 357 0.00% 57 432 0.00% 58 433 0.00% 59 612 0.00% 60 645 0.00% 61 782 0.00% 62 909 0.00% 63 1017 0.00% 64 1122 0.00% 65 1311 0.00% 66 1489 0.01% 67 1679 0.01% 68 1863 0.01% 69 2107 0.01% 70 2533 0.01% 71 2939 0.01% 72 3440 0.01% 73 3896 0.01% 74 4519 0.02% 75 4869 0.02% 76 5665 0.02% 77 6119 0.02% 78 6922 0.02% 79 7738 0.03% 80 8339 0.03% 81 9640 0.03% 82 10894 0.04% 83 11794 0.04% 84 13374 0.05% 85 14993 0.05% 86 15863 0.05% 87 17320 0.06% 88 18318 0.06% 89 19791 0.07% 90 21260 0.07% 91 23280 0.08% 92 24984 0.08% 93 27346 0.09% 94 29136 0.10% 95 30886 0.10% 96 33007 0.11% 97 35075 0.12% 98 35993 0.12% 99 37778 0.13% 100 39385 0.13% 101 41086 0.14% 102 43633 0.15% 103 46039 0.16% 104 47911 0.16% 105 50616 0.17% 106 52184 0.18% 107 53946 0.18% 108 55979 0.19% 109 57179 0.19% 110 58277 0.20% 111 60179 0.20% 112 61711 0.21% 113 63497 0.22% 114 66390 0.23% 115 68867 0.23% 116 70164 0.24% 117 71987 0.24% 118 74005 0.25% 119 74711 0.25% 120 76422 0.26% 121 77755 0.26% 122 78843 0.27% 123 81074 0.28% 124 83107 0.28% 125 83619 0.28% 126 85909 0.29% 127 87828 0.30% 128 89130 0.30% 129 89911 0.31% 130 91256 0.31% 131 92405 0.31% 132 93441 0.32% 133 95077 0.32% 134 95477 0.32% 135 97112 0.33% 136 98404 0.33% 137 99571 0.34% 138 101247 0.34% 139 101914 0.35% 140 102895 0.35% 141 103986 0.35% 142 104912 0.36% 143 104843 0.36% 144 107489 0.36% 145 108565 0.37% 146 107735 0.37% 147 108381 0.37% 148 109401 0.37% 149 110147 0.37% 150 112052 0.38% 151 24816753 84.24% 29459502 reads passed initial QC criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=14.76 fanout-score-rank=9 prefix-density=0.15 prefix-fanout=14.8 sequence=GGATCGGAAGAGCACACGTCTGAACTCCAGTCACGTAACGACATCTCGTATGCCGTCTTCTGCTTGAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=40 fanout-score=143.79 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=13.6 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAA criterion=sequence-density sequence-density=0.14 sequence-density-rank=1 fanout-score=2.50 fanout-score-rank=35 prefix-density=0.15 prefix-fanout=2.3 sequence=TGACATCGTTGA criterion=fanout-score sequence-density=0.08 sequence-density-rank=14 fanout-score=338.28 fanout-score-rank=1 prefix-density=0.98 prefix-fanout=26.1 sequence=AAGAAGAAGAAA SRR28623307 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 16:56:53 Started mapping on | Feb 11 16:56:53 Finished on | Feb 11 17:00:59 Mapping speed, Million of reads per hour | 431.11 Number of input reads | 29459502 Average input read length | 293 UNIQUE READS: Uniquely mapped reads number | 27101082 Uniquely mapped reads % | 91.99% Average mapped length | 291.94 Number of splices: Total | 24649127 Number of splices: Annotated (sjdb) | 24065321 Number of splices: GT/AG | 24223837 Number of splices: GC/AG | 329456 Number of splices: AT/AC | 24078 Number of splices: Non-canonical | 71756 Mismatch rate per base, % | 0.42% Deletion rate per base | 0.03% Deletion average length | 2.99 Insertion rate per base | 0.03% Insertion average length | 2.40 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 737938 % of reads mapped to multiple loci | 2.50% Number of reads mapped to too many loci | 154450 % of reads mapped to too many loci | 0.52% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.67% % of reads unmapped: other | 0.31% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1620482 1620482 1620482 N_multimapping 737938 737938 737938 N_noFeature 1146988 26747255 1312886 N_ambiguous 354619 2131 165333 UnstrandedReadsAssigned:25599475 PositiveStrandReadsAssigned:351696 NegativeStrandReadsAssigned:25622863 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR28623307 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR28623307-trimmed-pair1.fastq SRR28623307-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 29,459,502 reads, 26,081,603 reads pseudoaligned [quant] estimated average fragment length: 230.244 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,101 rounds 52401 SRR28623307.ke.tsv 34699 SRR28623307.se.tsv 87100 total ==> SRR28623307.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1788.76 1039 21.1492 Potri.005G024800.1.v4.1 1035 805.756 633 28.6042 Potri.004G059700.1.v4.1 961 731.787 89 4.42828 Potri.007G009000.2.v4.1 1416 1186.76 0 0 Potri.003G141000.2.v4.1 2943 2713.76 845.44 11.3433 Potri.016G087400.1.v4.1 270 93.9358 2108.4 817.244 Potri.015G069301.1.v4.1 564 340.975 0 0 Potri.010G195200.1.v4.1 1773 1543.76 105.905 2.49785 Potri.012G127500.1.v4.1 977 747.777 4767 232.115 ==> SRR28623307.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 636 Potri.001G233950.v4.1 1 Potri.001G122700.v4.1 614 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 6 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 7 Potri.001G452600.v4.1 14 SRR28623307 completed mapping pipeline successfully