Starting /dee2/code/volunteer_pipeline.sh SRR12951318 current disk space = 1543031066624 free memory = 1597132780 SRR12951318 SRAfilesize 35dd99114199307b47495eff5edda9b7 SRR12951318.sra SRR12951318.sra file validated SRR12951318 is paired end SRR12951318 is conventional basespace SRR12951318 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951318_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5915 37.0 37.0 37.0 37.0 37.0 2 36.258 37.0 37.0 37.0 37.0 37.0 3 36.486 37.0 37.0 37.0 37.0 37.0 4 36.6035 37.0 37.0 37.0 37.0 37.0 5 36.63 37.0 37.0 37.0 37.0 37.0 6 36.6355 37.0 37.0 37.0 37.0 37.0 7 36.5155 37.0 37.0 37.0 37.0 37.0 8 36.4955 37.0 37.0 37.0 37.0 37.0 9 36.6055 37.0 37.0 37.0 37.0 37.0 10-14 36.57340000000001 37.0 37.0 37.0 37.0 37.0 15-19 36.6074 37.0 37.0 37.0 37.0 37.0 20-24 36.5493 37.0 37.0 37.0 37.0 37.0 25-29 36.49979999999999 37.0 37.0 37.0 37.0 37.0 30-34 36.51049999999999 37.0 37.0 37.0 37.0 37.0 35-39 36.49250000000001 37.0 37.0 37.0 37.0 37.0 40-44 36.462300000000006 37.0 37.0 37.0 37.0 37.0 45-49 36.403099999999995 37.0 37.0 37.0 37.0 37.0 50-54 36.3849 37.0 37.0 37.0 37.0 37.0 55-59 36.3557 37.0 37.0 37.0 37.0 37.0 60-64 36.323800000000006 37.0 37.0 37.0 37.0 37.0 65-69 36.265699999999995 37.0 37.0 37.0 37.0 37.0 70-74 36.29960000000001 37.0 37.0 37.0 37.0 37.0 75-79 36.3103 37.0 37.0 37.0 37.0 37.0 80-84 36.3096 37.0 37.0 37.0 37.0 37.0 85-89 36.2734 37.0 37.0 37.0 37.0 37.0 90-94 36.2786 37.0 37.0 37.0 37.0 37.0 95-99 36.228899999999996 37.0 37.0 37.0 37.0 37.0 100-104 36.193599999999996 37.0 37.0 37.0 37.0 37.0 105-109 36.2197 37.0 37.0 37.0 37.0 37.0 110-114 36.1879 37.0 37.0 37.0 37.0 37.0 115-119 36.14540000000001 37.0 37.0 37.0 37.0 37.0 120-124 36.0873 37.0 37.0 37.0 37.0 37.0 125-129 35.976699999999994 37.0 37.0 37.0 37.0 37.0 130-134 36.00250000000001 37.0 37.0 37.0 37.0 37.0 135-139 35.8395 37.0 37.0 37.0 37.0 37.0 140-144 35.756 37.0 37.0 37.0 37.0 37.0 145-149 35.560199999999995 37.0 37.0 37.0 37.0 37.0 150-151 35.370000000000005 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 24 2.0 25 8.0 26 5.0 27 3.0 28 11.0 29 13.0 30 27.0 31 42.0 32 49.0 33 88.0 34 120.0 35 322.0 36 2844.0 37 466.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 53.325 10.65 4.75 31.275 2 22.22779729051681 11.51530356246864 31.184144505770195 35.07275464124435 3 20.599999999999998 15.1 27.750000000000004 36.55 4 24.275 23.375 23.425 28.925 5 26.950000000000003 27.474999999999998 22.3 23.275000000000002 6 24.725 31.05 21.4 22.825 7 17.7 24.75 38.425 19.125 8 20.549999999999997 25.45 28.050000000000004 25.95 9 21.875 19.925 31.825 26.375 10-14 23.25 25.729999999999997 25.629999999999995 25.39 15-19 23.54 25.119999999999997 25.4 25.94 20-24 23.305 25.374999999999996 25.03 26.290000000000003 25-29 23.665 24.925 25.290000000000003 26.119999999999997 30-34 23.365 25.019999999999996 25.290000000000003 26.325 35-39 23.849999999999998 25.195 24.67 26.284999999999997 40-44 23.830000000000002 24.83 24.94 26.400000000000002 45-49 23.65 25.369999999999997 24.474999999999998 26.505000000000003 50-54 23.78 25.44 24.98 25.8 55-59 23.805 25.345000000000002 24.7 26.150000000000002 60-64 24.39 24.735 24.990000000000002 25.885 65-69 23.49 25.230000000000004 24.915000000000003 26.365 70-74 24.404999999999998 24.89 24.425 26.279999999999998 75-79 24.395 24.45 24.610000000000003 26.545 80-84 24.545 24.29 24.64 26.525 85-89 24.279999999999998 25.540000000000003 24.535 25.645 90-94 24.575 24.965 23.93 26.529999999999998 95-99 24.7 25.314999999999998 24.055 25.929999999999996 100-104 24.165 25.380000000000003 23.799999999999997 26.655 105-109 25.47 24.87 23.075000000000003 26.584999999999997 110-114 24.740000000000002 25.31 24.115000000000002 25.835 115-119 24.529999999999998 24.985 24.065 26.419999999999998 120-124 24.305 25.285000000000004 23.724999999999998 26.685 125-129 25.355 24.945 23.48 26.22 130-134 24.895 24.46 24.165 26.479999999999997 135-139 24.305 24.895 23.805 26.995 140-144 24.224999999999998 25.335 23.415 27.025 145-149 24.425 24.935 23.555 27.084999999999997 150-151 24.3 25.662499999999998 24.075 25.9625 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 1.0 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 0.0 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 0.5 27 2.5 28 2.5 29 2.5 30 5.5 31 5.0 32 9.0 33 22.5 34 31.0 35 39.5 36 49.0 37 47.0 38 64.5 39 89.5 40 109.5 41 136.0 42 159.0 43 177.0 44 183.0 45 181.5 46 198.0 47 197.5 48 183.0 49 171.5 50 156.5 51 163.0 52 151.0 53 127.5 54 113.0 55 105.0 56 99.5 57 82.0 58 72.5 59 70.0 60 54.5 61 54.5 62 61.5 63 59.5 64 55.5 65 54.5 66 55.5 67 58.5 68 62.5 69 53.0 70 40.5 71 34.0 72 31.5 73 27.0 74 23.5 75 20.5 76 14.0 77 10.5 78 9.0 79 4.0 80 0.5 81 1.0 82 2.5 83 2.0 84 0.5 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.35000000000000003 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 83.45 #Duplication Level Percentage of deduplicated Percentage of total 1 84.36189334931098 70.39999999999999 2 12.462552426602755 20.8 3 2.396644697423607 6.0 4 0.5991611743559018 2.0 5 0.11983223487118035 0.5 6 0.05991611743559017 0.3 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 AGGCATTTGATTGAATGATTGAGTTATAGATCTACTGATATGAATATGTA 6 0.15 No Hit GTACCACCAACTGAACCAGCCACCATTGTTTGGCAGTATGAGGCAACACA 6 0.15 No Hit GACGCTCCTCACAGCTTCCTCGAGCTTGGCCATGTCGGTCTCATCATCCC 5 0.125 No Hit GGGATGGTGGCCAAGTGGACCATGAAGACGGCGAAGCCGATTGGGAGGGG 5 0.125 No Hit ACTAGAAGAGCCTTTAGAGATATCATCAATCTGCATAGCTTCGGTTTCGG 5 0.125 No Hit GCTTCGTTGACGGTGATGTTGCGGCCATCCAGGTCCTTGCCGTTCATGCC 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.037500000000000006 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.16249999999999998 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.3125 0.0 0.0 0.0 0.0 80-81 0.4625 0.0 0.0 0.0 0.0 82-83 0.525 0.0 0.0 0.0 0.0 84-85 0.575 0.0 0.0 0.0 0.0 86-87 0.675 0.0 0.0 0.0 0.0 88-89 0.8125 0.0 0.0 0.0 0.0 90-91 1.0875 0.0 0.0 0.0 0.0 92-93 1.275 0.0 0.0 0.0 0.0 94-95 1.45 0.0 0.0 0.0 0.0 96-97 1.6 0.0 0.0 0.0 0.0 98-99 2.025 0.0 0.0 0.0 0.0 100-101 2.4749999999999996 0.0 0.0 0.0 0.0 102-103 2.9875 0.0 0.0 0.0 0.0 104-105 3.4625000000000004 0.0 0.0 0.0 0.0 106-107 4.0 0.0 0.0 0.0 0.0 108-109 4.574999999999999 0.0 0.0 0.0 0.0 110-111 5.025 0.0 0.0 0.0 0.0 112-113 5.4625 0.0 0.0 0.0 0.0 114-115 6.05 0.0 0.0 0.0 0.0 116-117 6.699999999999999 0.0 0.0 0.0 0.0 118-119 7.2375 0.0 0.0 0.0 0.0 120-121 7.7875 0.0 0.0 0.0 0.0 122-123 8.375 0.0 0.0 0.0 0.0 124-125 8.925 0.0 0.0 0.0 0.0 126-127 9.575 0.0 0.0 0.0 0.0 128-129 10.25 0.0 0.0 0.0 0.0 130-131 10.912500000000001 0.0 0.0 0.0 0.0 132-133 11.662500000000001 0.0 0.0 0.0 0.0 134-135 12.5 0.0 0.0 0.0 0.0 136-137 13.325 0.0 0.0 0.0 0.0 138-139 14.2 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGGATTT 10 0.006830828 145.0 5 GATTTGT 10 0.006830828 145.0 7 GGTGGAT 10 0.006830828 145.0 3 GTGGATT 10 0.006830828 145.0 4 TTTGTAC 10 0.006830828 145.0 9 >>END_MODULE SRR12951318 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12951318_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 51 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.3135 37.0 37.0 37.0 37.0 37.0 2 36.077 37.0 37.0 37.0 37.0 37.0 3 36.105 37.0 37.0 37.0 37.0 37.0 4 36.1735 37.0 37.0 37.0 37.0 37.0 5 36.224 37.0 37.0 37.0 37.0 37.0 6 36.2025 37.0 37.0 37.0 37.0 37.0 7 36.17 37.0 37.0 37.0 37.0 37.0 8 36.3 37.0 37.0 37.0 37.0 37.0 9 36.1935 37.0 37.0 37.0 37.0 37.0 10-14 36.272999999999996 37.0 37.0 37.0 37.0 37.0 15-19 36.258300000000006 37.0 37.0 37.0 37.0 37.0 20-24 36.152100000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.1509 37.0 37.0 37.0 37.0 37.0 30-34 36.0789 37.0 37.0 37.0 37.0 37.0 35-39 36.096999999999994 37.0 37.0 37.0 37.0 37.0 40-44 36.052499999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.0438 37.0 37.0 37.0 37.0 37.0 50-54 35.9921 37.0 37.0 37.0 37.0 37.0 55-59 35.9813 37.0 37.0 37.0 37.0 37.0 60-64 35.95100000000001 37.0 37.0 37.0 37.0 37.0 65-69 35.9161 37.0 37.0 37.0 37.0 37.0 70-74 35.90409999999999 37.0 37.0 37.0 37.0 37.0 75-79 35.9261 37.0 37.0 37.0 37.0 37.0 80-84 35.90500000000001 37.0 37.0 37.0 37.0 37.0 85-89 35.8709 37.0 37.0 37.0 37.0 37.0 90-94 35.8931 37.0 37.0 37.0 37.0 37.0 95-99 35.9152 37.0 37.0 37.0 37.0 37.0 100-104 35.761100000000006 37.0 37.0 37.0 37.0 37.0 105-109 35.7793 37.0 37.0 37.0 37.0 37.0 110-114 35.78959999999999 37.0 37.0 37.0 37.0 37.0 115-119 35.81 37.0 37.0 37.0 37.0 37.0 120-124 35.720600000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.64 37.0 37.0 37.0 37.0 37.0 130-134 35.5336 37.0 37.0 37.0 37.0 37.0 135-139 35.6119 37.0 37.0 37.0 37.0 37.0 140-144 35.4891 37.0 37.0 37.0 37.0 37.0 145-149 35.2592 37.0 37.0 37.0 32.2 37.0 150-151 34.9435 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 9.0 14 5.0 15 2.0 16 4.0 17 3.0 18 0.0 19 3.0 20 3.0 21 6.0 22 8.0 23 7.0 24 7.0 25 15.0 26 11.0 27 9.0 28 9.0 29 7.0 30 14.0 31 27.0 32 47.0 33 87.0 34 148.0 35 513.0 36 2728.0 37 327.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 48.025 20.7 6.625 24.65 2 30.8 23.150000000000002 24.825 21.224999999999998 3 23.825 23.25 30.425 22.5 4 26.200000000000003 30.2 19.55 24.05 5 28.199999999999996 32.875 17.849999999999998 21.075 6 25.124999999999996 34.225 19.375 21.275 7 22.775000000000002 21.95 32.7 22.575 8 24.05 22.900000000000002 23.825 29.225 9 23.95 21.2 27.875 26.974999999999998 10-14 27.155 24.63 22.805 25.41 15-19 26.545 25.105 23.115 25.235000000000003 20-24 26.955000000000002 25.014999999999997 23.425 24.605 25-29 27.11 24.26 24.044999999999998 24.585 30-34 26.86 24.94 23.525 24.675 35-39 27.04 24.425 23.73 24.805 40-44 26.69 24.85 23.755000000000003 24.705 45-49 26.090000000000003 24.169999999999998 24.63 25.11 50-54 26.83 24.709999999999997 23.625 24.834999999999997 55-59 26.93 24.505 24.21 24.355 60-64 27.245 24.37 24.34 24.044999999999998 65-69 27.450000000000003 24.865000000000002 23.625 24.060000000000002 70-74 26.83 24.77 23.82 24.58 75-79 27.255000000000003 24.240000000000002 24.709999999999997 23.794999999999998 80-84 26.405 24.6 24.26 24.735 85-89 26.955000000000002 24.395 24.88 23.77 90-94 27.525 24.279999999999998 24.13 24.065 95-99 27.565 24.48 23.705000000000002 24.25 100-104 27.01 24.54 24.23 24.22 105-109 27.875 25.374999999999996 23.16 23.59 110-114 27.465 25.09 23.56 23.885 115-119 28.09 25.16 23.415 23.335 120-124 28.27 25.009999999999998 23.65 23.07 125-129 28.01 25.4 23.51 23.080000000000002 130-134 28.38 25.28 23.294999999999998 23.044999999999998 135-139 28.999999999999996 25.165 23.265 22.57 140-144 28.544999999999998 25.85 23.29 22.314999999999998 145-149 28.83 25.669999999999998 23.055 22.445 150-151 28.762500000000003 24.212500000000002 24.075 22.95 >>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 1.0 10 1.0 11 0.5 12 0.5 13 0.5 14 1.0 15 1.0 16 0.5 17 0.0 18 0.5 19 0.5 20 0.5 21 0.5 22 1.0 23 1.5 24 1.0 25 1.0 26 1.0 27 1.0 28 2.5 29 5.0 30 6.0 31 8.0 32 12.5 33 16.5 34 22.0 35 28.0 36 43.5 37 50.5 38 57.0 39 81.5 40 100.0 41 100.0 42 116.0 43 149.0 44 182.0 45 196.5 46 203.5 47 197.5 48 181.0 49 165.5 50 134.5 51 139.0 52 149.0 53 123.0 54 108.0 55 97.0 56 85.0 57 98.5 58 100.0 59 96.5 60 91.0 61 80.0 62 71.0 63 68.0 64 69.0 65 60.5 66 53.5 67 52.5 68 48.0 69 38.0 70 44.0 71 43.0 72 30.5 73 29.5 74 32.0 75 29.0 76 18.0 77 14.5 78 12.0 79 7.0 80 3.5 81 1.0 82 2.5 83 2.5 84 1.0 85 2.5 86 2.5 87 0.5 88 0.0 89 0.5 90 0.5 91 0.5 92 1.0 93 2.5 94 2.0 95 0.5 96 1.0 97 0.5 98 1.5 99 4.5 100 6.0 >>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 83.275 #Duplication Level Percentage of deduplicated Percentage of total 1 84.71930351245872 70.55 2 11.918342839987991 19.85 3 2.461723206244371 6.15 4 0.6004202942059442 2.0 5 0.18012608826178325 0.75 6 0.09006304413089163 0.44999999999999996 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.03002101471029721 0.25 >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 10 0.25 No Hit GGTGGGTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGT 6 0.15 No Hit AAAAGAACCACAATTGTGGAATGACATATTCAAGTTTTTGAAAAAAGGTA 6 0.15 No Hit GGTAAAATTACAATTCTATTGGACAAACTAATTAGCTAGTCGTCTAAAAA 6 0.15 No Hit GCAAGCACTGGTCAAGGATTCACGCAGTTTACAGAGCACAGGAAACGAGC 5 0.125 No Hit AAGGAACGTGCCACAACTGAAGATGATATGGAAGGCGCTAACCAAGACTC 5 0.125 No Hit CAGCAACCCACGTTGGAGCAGCAGCAGAGAGCCGGAGCGCCACCAGCCAT 5 0.125 No Hit GAGGAGAAGAAGGCAGCTGAGGAACGTGCTGCCAAAGTTAAGGCTTCTGG 5 0.125 No Hit GAGCGAACACGCTCGCTGCGGGGTACTCCAAGGGGACTGGACTTGCCGCG 5 0.125 No Hit GCTAGACTCCAATTCTTTACGCCAGCACAACAAAGGCTCAATTCATTCCT 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.037500000000000006 0.0 0.0 0.0 0.0 68-69 0.05 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.16249999999999998 0.0 0.0 0.0 0.0 76-77 0.25 0.0 0.0 0.0 0.0 78-79 0.3125 0.0 0.0 0.0 0.0 80-81 0.4625 0.0 0.0 0.0 0.0 82-83 0.525 0.0 0.0 0.0 0.0 84-85 0.575 0.0 0.0 0.0 0.0 86-87 0.675 0.0 0.0 0.0 0.0 88-89 0.8125 0.0 0.0 0.0 0.0 90-91 1.0875 0.0 0.0 0.0 0.0 92-93 1.275 0.0 0.0 0.0 0.0 94-95 1.45 0.0 0.0 0.0 0.0 96-97 1.575 0.0 0.0 0.0 0.0 98-99 2.025 0.0 0.0 0.0 0.0 100-101 2.4875 0.0 0.0 0.0 0.0 102-103 3.0125 0.0 0.0 0.0 0.0 104-105 3.4875 0.0 0.0 0.0 0.0 106-107 3.9875 0.0 0.0 0.0 0.0 108-109 4.550000000000001 0.0 0.0 0.0 0.0 110-111 5.0 0.0 0.0 0.0 0.0 112-113 5.4125 0.0 0.0 0.0 0.0 114-115 6.025 0.0 0.0 0.0 0.0 116-117 6.6875 0.0 0.0 0.0 0.0 118-119 7.2375 0.0 0.0 0.0 0.0 120-121 7.7875 0.0 0.0 0.0 0.0 122-123 8.375 0.0 0.0 0.0 0.0 124-125 8.9375 0.0 0.0 0.0 0.0 126-127 9.625 0.0 0.0 0.0 0.0 128-129 10.337499999999999 0.0 0.0 0.0 0.0 130-131 11.0125 0.0 0.0 0.0 0.0 132-133 11.7625 0.0 0.0 0.0 0.0 134-135 12.55 0.0 0.0 0.0 0.0 136-137 13.350000000000001 0.0 0.0 0.0 0.0 138-139 14.25 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AATCCAC 10 0.006830828 145.0 145 GAGTGGC 10 0.006830828 145.0 6 AGTGGCG 10 0.006830828 145.0 7 TGGCGGG 10 0.006830828 145.0 9 CCCTCCA 10 0.006830828 145.0 145 AGGAGTG 10 0.006830828 145.0 4 GGAGTGG 10 0.006830828 145.0 5 TGGCCTC 10 0.006830828 145.0 8 >>END_MODULE Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363447 spots for SRR12951318.sra Written 1363447 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra Read 1363435 spots for SRR12951318.sra Written 1363435 spots for SRR12951318.sra SRR ids: ['SRR12951318.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1fm6f2zi SRR12951318.sra spots: 27268712 blocks: [[1, 1363435], [1363436, 2726870], [2726871, 4090305], [4090306, 5453740], [5453741, 6817175], [6817176, 8180610], [8180611, 9544045], [9544046, 10907480], [10907481, 12270915], [12270916, 13634350], [13634351, 14997785], [14997786, 16361220], [16361221, 17724655], [17724656, 19088090], [19088091, 20451525], [20451526, 21814960], [21814961, 23178395], [23178396, 24541830], [24541831, 25905265], [25905266, 27268712]] SRR12951318 file size 9245400 SRR12951318 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 SRR12951318 SRR12951318_1.fastq SRR12951318_2.fastq Input file: SRR12951318_1.fastq Paired file: SRR12951318_2.fastq trimmed: SRR12951318-trimmed-pair1.fastq, SRR12951318-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 Sat Dec 7 11:40:22 2024 >> started Sat Dec 7 11:40:54 2024 >> done (31.920s) 27268712 read pairs processed; of these: 206 ( 0.00%) short read pairs filtered out after trimming by size control 86834 ( 0.32%) empty read pairs filtered out after trimming by size control 27181672 (99.68%) read pairs available; of these: 4771600 (17.55%) trimmed read pairs available after processing 22410072 (82.45%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 18 0.00% 19 25 0.00% 20 28 0.00% 21 37 0.00% 22 50 0.00% 23 57 0.00% 24 62 0.00% 25 70 0.00% 26 91 0.00% 27 85 0.00% 28 101 0.00% 29 107 0.00% 30 122 0.00% 31 99 0.00% 32 98 0.00% 33 90 0.00% 34 103 0.00% 35 128 0.00% 36 117 0.00% 37 117 0.00% 38 126 0.00% 39 135 0.00% 40 125 0.00% 41 115 0.00% 42 166 0.00% 43 146 0.00% 44 181 0.00% 45 186 0.00% 46 218 0.00% 47 224 0.00% 48 194 0.00% 49 301 0.00% 50 308 0.00% 51 372 0.00% 52 381 0.00% 53 370 0.00% 54 440 0.00% 55 440 0.00% 56 512 0.00% 57 650 0.00% 58 722 0.00% 59 833 0.00% 60 956 0.00% 61 1065 0.00% 62 1159 0.00% 63 1224 0.00% 64 1432 0.01% 65 1623 0.01% 66 1747 0.01% 67 2003 0.01% 68 2233 0.01% 69 2632 0.01% 70 2919 0.01% 71 3487 0.01% 72 3894 0.01% 73 4600 0.02% 74 4812 0.02% 75 5268 0.02% 76 5921 0.02% 77 6529 0.02% 78 7318 0.03% 79 8146 0.03% 80 9194 0.03% 81 10278 0.04% 82 11513 0.04% 83 13005 0.05% 84 14276 0.05% 85 15917 0.06% 86 16391 0.06% 87 18267 0.07% 88 19597 0.07% 89 20152 0.07% 90 22398 0.08% 91 24556 0.09% 92 25896 0.10% 93 28594 0.11% 94 30817 0.11% 95 32300 0.12% 96 34131 0.13% 97 35545 0.13% 98 36878 0.14% 99 38446 0.14% 100 41128 0.15% 101 42526 0.16% 102 45110 0.17% 103 47888 0.18% 104 49336 0.18% 105 52257 0.19% 106 54194 0.20% 107 54757 0.20% 108 56810 0.21% 109 58250 0.21% 110 59697 0.22% 111 61556 0.23% 112 65179 0.24% 113 66390 0.24% 114 69580 0.26% 115 71663 0.26% 116 72431 0.27% 117 74892 0.28% 118 76142 0.28% 119 76923 0.28% 120 76954 0.28% 121 79873 0.29% 122 80926 0.30% 123 83821 0.31% 124 87432 0.32% 125 87581 0.32% 126 89582 0.33% 127 90355 0.33% 128 90608 0.33% 129 93071 0.34% 130 93647 0.34% 131 93814 0.35% 132 95687 0.35% 133 98714 0.36% 134 98899 0.36% 135 100738 0.37% 136 102574 0.38% 137 101809 0.37% 138 103131 0.38% 139 103369 0.38% 140 103508 0.38% 141 104792 0.39% 142 105777 0.39% 143 106383 0.39% 144 108546 0.40% 145 109893 0.40% 146 109146 0.40% 147 108953 0.40% 148 109553 0.40% 149 109706 0.40% 150 110180 0.41% 151 22410072 82.45% 27181672 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=4.23 fanout-score-rank=25 prefix-density=0.34 prefix-fanout=3.0 sequence=GAACCGGAACCG criterion=fanout-score sequence-density=0.04 sequence-density-rank=35 fanout-score=328.00 fanout-score-rank=1 prefix-density=0.73 prefix-fanout=16.4 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.92 sequence-density-rank=1 fanout-score=2.04 fanout-score-rank=34 prefix-density=0.93 prefix-fanout=2.0 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.12 sequence-density-rank=14 fanout-score=177.71 fanout-score-rank=1 prefix-density=1.00 prefix-fanout=21.8 sequence=CGCCGCCGCCGC SRR12951318 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 11:41:36 Started mapping on | Dec 07 11:41:41 Finished on | Dec 07 11:44:46 Mapping speed, Million of reads per hour | 528.94 Number of input reads | 27181672 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 25591637 Uniquely mapped reads % | 94.15% Average mapped length | 291.38 Number of splices: Total | 24489701 Number of splices: Annotated (sjdb) | 22757323 Number of splices: GT/AG | 24125214 Number of splices: GC/AG | 304471 Number of splices: AT/AC | 15117 Number of splices: Non-canonical | 44899 Mismatch rate per base, % | 0.23% Deletion rate per base | 0.01% Deletion average length | 2.22 Insertion rate per base | 0.01% Insertion average length | 2.42 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 304622 % of reads mapped to multiple loci | 1.12% Number of reads mapped to too many loci | 55695 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.50% % of reads unmapped: other | 1.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1285413 1285413 1285413 N_multimapping 304622 304622 304622 N_noFeature 1090900 24903137 1327005 N_ambiguous 536341 3316 84445 UnstrandedReadsAssigned:23964396 PositiveStrandReadsAssigned:685184 NegativeStrandReadsAssigned:24180187 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12951318 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: SRR12951318-trimmed-pair1.fastq SRR12951318-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 27,181,672 reads, 24,597,201 reads pseudoaligned [quant] estimated average fragment length: 246.115 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,175 rounds 52973 SRR12951318.ke.tsv 35125 SRR12951318.se.tsv 88098 total ==> SRR12951318.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 691.413 0 0 PNS24247 1044 798.885 127.184 9.38725 PNS24249 1928 1682.88 368.281 12.9037 PNS24246 1044 798.885 127.184 9.38725 PNS24248 1044 798.885 127.184 9.38725 PNS24244 1471 1225.88 144.167 6.93433 PNS24243 293 109.63 1 0.537849 KQK14069 1603 1357.88 53720.4 2332.74 KQK14071 474 251.975 1000.49 234.123 ==> SRR12951318.se.tsv <== BRADI_1g14170v3 57605 BRADI_1g53295v3 307 BRADI_1g59795v3 922 BRADI_1g07683v3 0 BRADI_1g00485v3 21 BRADI_1g20270v3 1050 BRADI_1g74790v3 2040 BRADI_1g09890v3 0 BRADI_1g77505v3 339 BRADI_1g48960v3 0 SRR12951318 completed mapping pipeline successfully