Starting /dee2/code/volunteer_pipeline.sh SRR28623299 current disk space = 3049619570688 free memory = 1412613572 SRR28623299 SRAfilesize de1ce852c4b4083d6b708b08837e3110 SRR28623299.sra SRR28623299.sra file validated SRR28623299 is paired end SRR28623299 is conventional basespace SRR28623299 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623299_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 36.363 37.0 37.0 37.0 37.0 37.0 2 36.38 37.0 37.0 37.0 37.0 37.0 3 36.6105 37.0 37.0 37.0 37.0 37.0 4 36.5945 37.0 37.0 37.0 37.0 37.0 5 36.6285 37.0 37.0 37.0 37.0 37.0 6 36.53 37.0 37.0 37.0 37.0 37.0 7 36.61 37.0 37.0 37.0 37.0 37.0 8 36.4065 37.0 37.0 37.0 37.0 37.0 9 36.6015 37.0 37.0 37.0 37.0 37.0 10-14 36.5462 37.0 37.0 37.0 37.0 37.0 15-19 36.5236 37.0 37.0 37.0 37.0 37.0 20-24 36.527699999999996 37.0 37.0 37.0 37.0 37.0 25-29 36.4465 37.0 37.0 37.0 37.0 37.0 30-34 36.44950000000001 37.0 37.0 37.0 37.0 37.0 35-39 36.41170000000001 37.0 37.0 37.0 37.0 37.0 40-44 36.38549999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.3038 37.0 37.0 37.0 37.0 37.0 50-54 36.2557 37.0 37.0 37.0 37.0 37.0 55-59 36.2932 37.0 37.0 37.0 37.0 37.0 60-64 36.3038 37.0 37.0 37.0 37.0 37.0 65-69 36.1981 37.0 37.0 37.0 37.0 37.0 70-74 36.166399999999996 37.0 37.0 37.0 37.0 37.0 75-79 36.192099999999996 37.0 37.0 37.0 37.0 37.0 80-84 36.026599999999995 37.0 37.0 37.0 37.0 37.0 85-89 36.0599 37.0 37.0 37.0 37.0 37.0 90-94 35.9529 37.0 37.0 37.0 37.0 37.0 95-99 35.860200000000006 37.0 37.0 37.0 37.0 37.0 100-104 35.935599999999994 37.0 37.0 37.0 37.0 37.0 105-109 35.9082 37.0 37.0 37.0 37.0 37.0 110-114 35.90409999999999 37.0 37.0 37.0 37.0 37.0 115-119 35.8654 37.0 37.0 37.0 37.0 37.0 120-124 35.666 37.0 37.0 37.0 37.0 37.0 125-129 35.5942 37.0 37.0 37.0 37.0 37.0 130-134 35.7901 37.0 37.0 37.0 37.0 37.0 135-139 35.625 37.0 37.0 37.0 37.0 37.0 140-144 35.3397 37.0 37.0 37.0 34.6 37.0 145-149 35.2177 37.0 37.0 37.0 32.2 37.0 150-151 35.013999999999996 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 21 1.0 22 3.0 23 2.0 24 8.0 25 5.0 26 6.0 27 9.0 28 16.0 29 26.0 30 26.0 31 42.0 32 53.0 33 86.0 34 156.0 35 401.0 36 2927.0 37 233.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 33.450527373179305 13.033651431441488 10.597689603214464 42.91813159216474 2 18.075 15.825 35.825 30.275000000000002 3 17.0 21.325 27.1 34.575 4 22.0 28.775000000000002 23.05 26.174999999999997 5 24.2 33.625 23.05 19.125 6 20.275000000000002 38.125 22.650000000000002 18.95 7 14.75 28.175 41.325 15.75 8 17.025000000000002 27.500000000000004 30.0 25.474999999999998 9 17.849999999999998 24.95 34.675 22.525000000000002 10-14 19.685 30.795 27.279999999999998 22.24 15-19 19.175 29.235 28.194999999999997 23.395 20-24 19.62 29.48 28.13 22.770000000000003 25-29 19.675 29.54 27.04 23.745 30-34 19.545 29.75 27.139999999999997 23.565 35-39 20.064999999999998 29.175 27.925 22.835 40-44 20.075000000000003 29.095 27.735 23.095 45-49 20.23 28.065 28.63 23.075000000000003 50-54 19.435 29.509999999999998 27.565 23.49 55-59 19.845 29.21 28.115000000000002 22.830000000000002 60-64 19.985 28.575 27.725 23.715 65-69 19.759999999999998 28.51 27.85 23.880000000000003 70-74 19.634999999999998 29.294999999999998 27.755000000000003 23.315 75-79 19.5 28.560000000000002 28.035 23.905 80-84 19.869999999999997 29.225 27.77 23.135 85-89 20.075000000000003 29.28 27.215 23.43 90-94 19.15 29.005 27.525 24.32 95-99 19.759999999999998 29.354999999999997 27.689999999999998 23.195 100-104 20.075000000000003 29.13 27.775 23.02 105-109 20.115 28.465 27.700000000000003 23.72 110-114 20.055 29.625 27.474999999999998 22.845 115-119 20.525 28.535 27.415 23.525 120-124 20.205000000000002 29.415000000000003 26.765 23.615 125-129 20.925 28.555000000000003 26.634999999999998 23.885 130-134 20.1 28.955 26.52 24.425 135-139 20.674999999999997 29.110000000000003 25.995 24.22 140-144 20.315 28.535 26.405 24.745 145-149 20.49 28.985 26.279999999999998 24.245 150-151 20.4125 28.675 26.2625 24.65 >>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 0.5 12 0.5 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 1.0 21 1.5 22 2.5 23 3.5 24 4.0 25 4.5 26 4.0 27 7.5 28 11.0 29 15.5 30 18.0 31 28.0 32 39.0 33 55.5 34 78.0 35 99.5 36 100.5 37 122.0 38 164.0 39 171.5 40 186.5 41 227.5 42 265.0 43 258.5 44 270.0 45 273.0 46 244.0 47 251.5 48 217.5 49 166.0 50 154.0 51 137.5 52 110.0 53 75.5 54 54.5 55 44.0 56 34.0 57 27.5 58 22.0 59 18.5 60 11.5 61 4.0 62 5.0 63 5.0 64 1.5 65 0.5 66 0.5 67 0.5 68 1.5 69 1.0 70 0.0 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 0.44999999999999996 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 85.45 #Duplication Level Percentage of deduplicated Percentage of total 1 85.83967232299591 73.35000000000001 2 11.966062024575775 20.45 3 1.6676418958455237 4.275 4 0.40959625511995323 1.4000000000000001 5 0.08777062609713282 0.375 6 0.029256875365710942 0.15 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 ATCAACTCTATTGGGATTTCCATAACCACCCTTGCACGGCGAAGTGGTTC 6 0.15 No Hit CGCAACTAAGAGAACAAGACGTTTAGCAGGAGGGTCCTTGAAGCGAGGCT 5 0.125 No Hit GGGCACTTGTAAAGCATGTGCTCAACATGGTCAGGGTTTAGTGCTGGGTC 5 0.125 No Hit GTCAACAAGTTTTCAAGGATCAGAACTGGAACAGCATCTCAGGTGCATAT 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 0.0125 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.0875 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1125 0.0 0.0 0.0 0.0 76-77 0.1875 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.2625 0.0 0.0 0.0 0.0 82-83 0.2875 0.0 0.0 0.0 0.0 84-85 0.32499999999999996 0.0 0.0 0.0 0.0 86-87 0.475 0.0 0.0 0.0 0.0 88-89 0.6125 0.0 0.0 0.0 0.0 90-91 0.7375 0.0 0.0 0.0 0.0 92-93 0.8875 0.0 0.0 0.0 0.0 94-95 1.0375 0.0 0.0 0.0 0.0 96-97 1.2625000000000002 0.0 0.0 0.0 0.0 98-99 1.5875 0.0 0.0 0.0 0.0 100-101 1.8625 0.0 0.0 0.0 0.0 102-103 2.1125 0.0 0.0 0.0 0.0 104-105 2.3625 0.0 0.0 0.0 0.0 106-107 2.675 0.0 0.0 0.0 0.0 108-109 3.1875 0.0 0.0 0.0 0.0 110-111 3.6 0.0 0.0 0.0 0.0 112-113 3.925 0.0 0.0 0.0 0.0 114-115 4.4 0.0 0.0 0.0 0.0 116-117 5.137499999999999 0.0 0.0 0.0 0.0 118-119 5.675 0.0 0.0 0.0 0.0 120-121 6.0875 0.0 0.0 0.0 0.0 122-123 6.612500000000001 0.0 0.0 0.0 0.0 124-125 6.987500000000001 0.0 0.0 0.0 0.0 126-127 7.65 0.0 0.0 0.0 0.0 128-129 8.4875 0.0 0.0 0.0 0.0 130-131 9.4 0.0 0.0 0.0 0.0 132-133 10.2 0.0 0.0 0.0 0.0 134-135 10.649999999999999 0.0 0.0 0.0 0.0 136-137 11.3375 0.0 0.0 0.0 0.0 138-139 11.9875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCCAAGC 10 0.006830828 145.0 1 >>END_MODULE SRR28623299 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR28623299_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 35.7985 37.0 37.0 37.0 37.0 37.0 2 36.063 37.0 37.0 37.0 37.0 37.0 3 36.032 37.0 37.0 37.0 37.0 37.0 4 36.1505 37.0 37.0 37.0 37.0 37.0 5 36.263 37.0 37.0 37.0 37.0 37.0 6 36.18 37.0 37.0 37.0 37.0 37.0 7 36.203 37.0 37.0 37.0 37.0 37.0 8 36.232 37.0 37.0 37.0 37.0 37.0 9 36.0845 37.0 37.0 37.0 37.0 37.0 10-14 36.1291 37.0 37.0 37.0 37.0 37.0 15-19 36.0377 37.0 37.0 37.0 37.0 37.0 20-24 36.055899999999994 37.0 37.0 37.0 37.0 37.0 25-29 36.0084 37.0 37.0 37.0 37.0 37.0 30-34 35.951699999999995 37.0 37.0 37.0 37.0 37.0 35-39 35.9605 37.0 37.0 37.0 37.0 37.0 40-44 35.8359 37.0 37.0 37.0 37.0 37.0 45-49 35.8786 37.0 37.0 37.0 37.0 37.0 50-54 35.8929 37.0 37.0 37.0 37.0 37.0 55-59 35.68730000000001 37.0 37.0 37.0 37.0 37.0 60-64 35.6803 37.0 37.0 37.0 37.0 37.0 65-69 35.72579999999999 37.0 37.0 37.0 37.0 37.0 70-74 35.7254 37.0 37.0 37.0 37.0 37.0 75-79 35.83910000000001 37.0 37.0 37.0 37.0 37.0 80-84 35.6375 37.0 37.0 37.0 37.0 37.0 85-89 35.568999999999996 37.0 37.0 37.0 37.0 37.0 90-94 35.4381 37.0 37.0 37.0 34.6 37.0 95-99 35.5255 37.0 37.0 37.0 37.0 37.0 100-104 35.4681 37.0 37.0 37.0 37.0 37.0 105-109 35.4501 37.0 37.0 37.0 34.6 37.0 110-114 35.4669 37.0 37.0 37.0 37.0 37.0 115-119 35.3313 37.0 37.0 37.0 32.2 37.0 120-124 35.2872 37.0 37.0 37.0 32.2 37.0 125-129 34.910900000000005 37.0 37.0 37.0 27.4 37.0 130-134 35.2589 37.0 37.0 37.0 32.2 37.0 135-139 35.0697 37.0 37.0 37.0 25.0 37.0 140-144 34.9776 37.0 37.0 37.0 25.0 37.0 145-149 34.9433 37.0 37.0 37.0 25.0 37.0 150-151 34.6055 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 1.0 13 3.0 14 3.0 15 2.0 16 2.0 17 1.0 18 1.0 19 1.0 20 1.0 21 6.0 22 9.0 23 8.0 24 8.0 25 7.0 26 13.0 27 15.0 28 18.0 29 28.0 30 36.0 31 37.0 32 84.0 33 138.0 34 264.0 35 737.0 36 2340.0 37 237.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 38.800000000000004 18.3 15.2 27.700000000000003 2 27.950000000000003 24.6 29.849999999999998 17.599999999999998 3 21.325 26.825 32.125 19.725 4 24.425 32.675 24.575 18.325 5 27.675 33.800000000000004 22.675 15.85 6 21.9 36.8 24.4 16.900000000000002 7 21.325 20.674999999999997 39.425 18.575 8 21.025 25.424999999999997 29.2 24.349999999999998 9 22.3 25.374999999999996 30.475 21.85 10-14 23.669999999999998 29.310000000000002 26.82 20.200000000000003 15-19 24.07 27.57 28.315 20.044999999999998 20-24 23.605 27.845 27.87 20.68 25-29 23.46 27.775 28.24 20.525 30-34 23.3 28.970000000000002 27.88 19.85 35-39 22.945 28.845 27.775 20.435 40-44 23.705000000000002 28.205000000000002 27.905 20.185 45-49 23.615 28.49 27.775 20.119999999999997 50-54 23.835 28.694999999999997 27.584999999999997 19.885 55-59 23.974999999999998 28.110000000000003 27.865000000000002 20.05 60-64 23.52 28.439999999999998 28.265 19.775000000000002 65-69 23.400000000000002 28.215 28.27 20.115 70-74 23.52 28.17 28.205000000000002 20.105 75-79 24.12 27.63 28.23 20.02 80-84 23.669999999999998 27.755000000000003 28.144999999999996 20.43 85-89 23.135 27.894999999999996 29.099999999999998 19.869999999999997 90-94 23.535 28.194999999999997 28.439999999999998 19.830000000000002 95-99 23.815 28.405 27.925 19.855 100-104 24.0 28.405 28.4 19.195 105-109 24.099999999999998 28.410000000000004 27.83 19.66 110-114 24.6 28.17 27.66 19.57 115-119 24.665 28.444999999999997 27.525 19.365 120-124 24.88 28.485 27.47 19.165 125-129 25.495 28.660000000000004 27.11 18.735 130-134 25.564999999999998 28.194999999999997 26.974999999999998 19.265 135-139 24.93 28.605000000000004 27.37 19.095000000000002 140-144 25.069999999999997 28.565 27.27 19.095000000000002 145-149 25.77 28.405 26.88 18.945 150-151 24.9375 29.575000000000003 25.874999999999996 19.6125 >>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 0.5 9 1.0 10 0.5 11 0.5 12 0.5 13 0.0 14 1.0 15 1.0 16 0.0 17 1.0 18 2.5 19 1.5 20 0.0 21 1.0 22 1.0 23 0.5 24 3.0 25 7.0 26 7.5 27 8.0 28 9.0 29 11.0 30 22.0 31 29.0 32 30.0 33 37.5 34 58.5 35 74.5 36 87.0 37 107.0 38 143.5 39 178.0 40 197.0 41 226.5 42 255.0 43 275.5 44 281.0 45 279.5 46 273.5 47 239.0 48 203.0 49 183.0 50 150.0 51 122.0 52 112.5 53 99.5 54 71.0 55 46.5 56 39.0 57 29.5 58 21.0 59 17.0 60 11.0 61 9.5 62 7.5 63 4.5 64 3.5 65 2.5 66 1.5 67 1.0 68 1.0 69 0.5 70 1.0 71 1.0 72 0.5 73 0.0 74 0.5 75 0.5 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.5 82 0.5 83 0.0 84 0.0 85 0.0 86 0.5 87 1.0 88 0.5 89 0.0 90 0.0 91 1.0 92 1.0 93 0.0 94 0.5 95 0.5 96 0.0 97 0.0 98 0.0 99 0.5 100 1.0 >>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 85.675 #Duplication Level Percentage of deduplicated Percentage of total 1 86.1686606361249 73.825 2 11.584476218266705 19.85 3 1.7508024511234317 4.5 4 0.3793405310767435 1.3 5 0.08754012255617158 0.375 6 0.02918004085205719 0.15 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 TTTACATTACCACCTCACTCACTGCTTCTCCATCTCCCAGTGTAAAGATA 6 0.15 No Hit TCTAAACCCAAAGATCCAGTGAAGGGAAGAAAACCGATTAAAAAAAGAAA 5 0.125 No Hit TGAAAGCATATCTGTTGTTCTTGACAGGTTTGCTTCCATGGGTATTGACA 5 0.125 No Hit GCCATACTAGAGAACCCAAATGACAAGACAAAGGTGCACCTCATTTATGC 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 0.0125 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.0875 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.1125 0.0 0.0 0.0 0.0 76-77 0.1875 0.0 0.0 0.0 0.0 78-79 0.225 0.0 0.0 0.0 0.0 80-81 0.2625 0.0 0.0 0.0 0.0 82-83 0.2875 0.0 0.0 0.0 0.0 84-85 0.32499999999999996 0.0 0.0 0.0 0.0 86-87 0.475 0.0 0.0 0.0 0.0 88-89 0.6125 0.0 0.0 0.0 0.0 90-91 0.7375 0.0 0.0 0.0 0.0 92-93 0.8875 0.0 0.0 0.0 0.0 94-95 1.0375 0.0 0.0 0.0 0.0 96-97 1.2625000000000002 0.0 0.0 0.0 0.0 98-99 1.5875 0.0 0.0 0.0 0.0 100-101 1.8625 0.0 0.0 0.0 0.0 102-103 2.1125 0.0 0.0 0.0 0.0 104-105 2.35 0.0 0.0 0.0 0.0 106-107 2.6625 0.0 0.0 0.0 0.0 108-109 3.2125000000000004 0.0 0.0 0.0 0.0 110-111 3.625 0.0 0.0 0.0 0.0 112-113 4.0 0.0 0.0 0.0 0.0 114-115 4.487500000000001 0.0 0.0 0.0 0.0 116-117 5.275 0.0 0.0 0.0 0.0 118-119 5.825 0.0 0.0 0.0 0.0 120-121 6.2625 0.0 0.0 0.0 0.0 122-123 6.775 0.0 0.0 0.0 0.0 124-125 7.137499999999999 0.0 0.0 0.0 0.0 126-127 7.8 0.0 0.0 0.0 0.0 128-129 8.6125 0.0 0.0 0.0 0.0 130-131 9.524999999999999 0.0 0.0 0.0 0.0 132-133 10.35 0.0 0.0 0.0 0.0 134-135 10.8 0.0 0.0 0.0 0.0 136-137 11.5375 0.0 0.0 0.0 0.0 138-139 12.1875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra Read 1560883 spots for SRR28623299.sra Written 1560883 spots for SRR28623299.sra Read 1560882 spots for SRR28623299.sra Written 1560882 spots for SRR28623299.sra SRR ids: ['SRR28623299.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_d_mlxomz SRR28623299.sra spots: 31217641 blocks: [[1, 1560882], [1560883, 3121764], [3121765, 4682646], [4682647, 6243528], [6243529, 7804410], [7804411, 9365292], [9365293, 10926174], [10926175, 12487056], [12487057, 14047938], [14047939, 15608820], [15608821, 17169702], [17169703, 18730584], [18730585, 20291466], [20291467, 21852348], [21852349, 23413230], [23413231, 24974112], [24974113, 26534994], [26534995, 28095876], [28095877, 29656758], [29656759, 31217641]] SRR28623299 file size 11527032 SRR28623299 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 SRR28623299 SRR28623299_1.fastq SRR28623299_2.fastq Input file: SRR28623299_1.fastq Paired file: SRR28623299_2.fastq trimmed: SRR28623299-trimmed-pair1.fastq, SRR28623299-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 15:28:20 2025 >> started Tue Feb 11 15:28:56 2025 >> done (35.715s) 31217641 read pairs processed; of these: 29 ( 0.00%) short read pairs filtered out after trimming by size control 10140 ( 0.03%) empty read pairs filtered out after trimming by size control 31207472 (99.97%) read pairs available; of these: 5161416 (16.54%) trimmed read pairs available after processing 26046056 (83.46%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 4 0.00% 20 2 0.00% 21 5 0.00% 22 12 0.00% 23 5 0.00% 24 7 0.00% 25 7 0.00% 26 6 0.00% 27 11 0.00% 28 12 0.00% 29 12 0.00% 30 10 0.00% 31 16 0.00% 32 31 0.00% 33 26 0.00% 34 26 0.00% 35 31 0.00% 36 44 0.00% 37 27 0.00% 38 32 0.00% 39 61 0.00% 40 63 0.00% 41 96 0.00% 42 81 0.00% 43 87 0.00% 44 102 0.00% 45 115 0.00% 46 130 0.00% 47 158 0.00% 48 158 0.00% 49 222 0.00% 50 242 0.00% 51 243 0.00% 52 293 0.00% 53 368 0.00% 54 368 0.00% 55 429 0.00% 56 511 0.00% 57 608 0.00% 58 725 0.00% 59 800 0.00% 60 968 0.00% 61 1091 0.00% 62 1304 0.00% 63 1430 0.00% 64 1636 0.01% 65 1885 0.01% 66 2043 0.01% 67 2371 0.01% 68 2597 0.01% 69 3096 0.01% 70 3590 0.01% 71 4040 0.01% 72 4741 0.02% 73 5562 0.02% 74 6048 0.02% 75 6870 0.02% 76 7578 0.02% 77 8467 0.03% 78 9258 0.03% 79 10173 0.03% 80 11602 0.04% 81 12722 0.04% 82 14282 0.05% 83 15996 0.05% 84 17533 0.06% 85 19312 0.06% 86 20522 0.07% 87 22217 0.07% 88 23393 0.07% 89 25010 0.08% 90 26551 0.09% 91 28995 0.09% 92 30800 0.10% 93 33206 0.11% 94 35733 0.11% 95 38102 0.12% 96 39481 0.13% 97 41402 0.13% 98 43270 0.14% 99 44374 0.14% 100 46699 0.15% 101 48338 0.15% 102 50822 0.16% 103 53217 0.17% 104 55705 0.18% 105 58461 0.19% 106 60546 0.19% 107 61667 0.20% 108 63135 0.20% 109 65000 0.21% 110 65617 0.21% 111 67987 0.22% 112 69979 0.22% 113 70862 0.23% 114 73735 0.24% 115 76660 0.25% 116 78523 0.25% 117 79510 0.25% 118 81708 0.26% 119 82371 0.26% 120 83449 0.27% 121 85094 0.27% 122 86441 0.28% 123 87632 0.28% 124 90470 0.29% 125 91701 0.29% 126 94330 0.30% 127 95737 0.31% 128 96873 0.31% 129 97721 0.31% 130 99373 0.32% 131 99643 0.32% 132 100391 0.32% 133 102789 0.33% 134 103444 0.33% 135 105042 0.34% 136 105793 0.34% 137 107928 0.35% 138 108467 0.35% 139 110077 0.35% 140 110682 0.35% 141 111991 0.36% 142 112067 0.36% 143 112079 0.36% 144 114294 0.37% 145 115103 0.37% 146 115167 0.37% 147 116581 0.37% 148 117866 0.38% 149 117852 0.38% 150 119357 0.38% 151 26046056 83.46% 31207472 reads passed initial QC criterion=sequence-density sequence-density=0.13 sequence-density-rank=1 fanout-score=2.93 fanout-score-rank=36 prefix-density=0.13 prefix-fanout=2.8 sequence=GTGGACTCCTTCTGGAT criterion=fanout-score sequence-density=0.03 sequence-density-rank=40 fanout-score=121.11 fanout-score-rank=1 prefix-density=0.19 prefix-fanout=16.1 sequence=TCTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAA criterion=sequence-density sequence-density=0.14 sequence-density-rank=1 fanout-score=14.34 fanout-score-rank=16 prefix-density=0.14 prefix-fanout=14.3 sequence=GAGAGAGAGAGTTAAGACAATGGCCTCGAAGAAATCTGCAATCGTATTACCTGGTTCAAAGGTGTTGAAGCACATAGTTTTTGTACGGTTTAATGATGGGATCACTGATGAACAAATTGAGAA criterion=fanout-score sequence-density=0.02 sequence-density-rank=35 fanout-score=383.01 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=25.6 sequence=ACAAGAAGATCAACTGTCTCTCTGCCTGGTTTGTATTCCAAGAAATGGAGAAAGTCCAAAAGCTCTTTTGTGTGGCTCTATTGCTTGCAGTACTAGCCATAGCAAGCAATATTGCGAATGCCCAGAGTACCATATGCAAAATGCCTGTTGCTGGCCTAATGTCATGCAAGCCTTCTGTAACTCCTCCTAACCCTACCGCACCCTCGGCAGACTGCTGCTCGGCACTTTCGCATGCTGACATAAACTGCCTTTGCTCCTACAAAAATTCCAACCTGCTCCCTTCCCTTGGAATCGACCCAAAACTTGCCATGCAGCTCCCTGGCAAGTGCA SRR28623299 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 15:29:40 Started mapping on | Feb 11 15:29:40 Finished on | Feb 11 15:33:11 Mapping speed, Million of reads per hour | 532.45 Number of input reads | 31207472 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 29098592 Uniquely mapped reads % | 93.24% Average mapped length | 291.26 Number of splices: Total | 26206271 Number of splices: Annotated (sjdb) | 25538653 Number of splices: GT/AG | 25725294 Number of splices: GC/AG | 373349 Number of splices: AT/AC | 28049 Number of splices: Non-canonical | 79579 Mismatch rate per base, % | 0.44% Deletion rate per base | 0.03% Deletion average length | 2.96 Insertion rate per base | 0.03% Insertion average length | 2.39 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 726680 % of reads mapped to multiple loci | 2.33% Number of reads mapped to too many loci | 219573 % of reads mapped to too many loci | 0.70% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.48% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1382200 1382200 1382200 N_multimapping 726680 726680 726680 N_noFeature 1351799 28726498 1546473 N_ambiguous 347951 2867 168462 UnstrandedReadsAssigned:27398842 PositiveStrandReadsAssigned:369227 NegativeStrandReadsAssigned:27383657 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR28623299 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: SRR28623299-trimmed-pair1.fastq SRR28623299-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 31,207,472 reads, 27,750,809 reads pseudoaligned [quant] estimated average fragment length: 229.266 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,101 rounds 52401 SRR28623299.ke.tsv 34699 SRR28623299.se.tsv 87100 total ==> SRR28623299.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1789.73 2041 39.0206 Potri.005G024800.1.v4.1 1035 806.734 1371 58.1496 Potri.004G059700.1.v4.1 961 732.763 519 24.235 Potri.007G009000.2.v4.1 1416 1187.73 0 0 Potri.003G141000.2.v4.1 2943 2714.73 829.752 10.4583 Potri.016G087400.1.v4.1 270 95.031 2337.92 841.79 Potri.015G069301.1.v4.1 564 341.901 0 0 Potri.010G195200.1.v4.1 1773 1544.73 32 0.70882 Potri.012G127500.1.v4.1 977 748.746 14315 654.179 ==> SRR28623299.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 2139 Potri.001G233950.v4.1 8 Potri.001G122700.v4.1 577 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 47 Potri.001G452600.v4.1 14 SRR28623299 completed mapping pipeline successfully