Starting /dee2/code/volunteer_pipeline.sh SRR12670157 current disk space = 3055069229056 free memory = 1499063856 SRR12670157 SRAfilesize fea6e4b774e15da9a35a24d6b120ce9a SRR12670157.sra SRR12670157.sra file validated SRR12670157 is paired end SRR12670157 is conventional basespace SRR12670157 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670157_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.559 37.0 37.0 37.0 37.0 37.0 2 36.42525 37.0 37.0 37.0 37.0 37.0 3 36.534 37.0 37.0 37.0 37.0 37.0 4 36.6395 37.0 37.0 37.0 37.0 37.0 5 36.626 37.0 37.0 37.0 37.0 37.0 6 36.665 37.0 37.0 37.0 37.0 37.0 7 36.5875 37.0 37.0 37.0 37.0 37.0 8 36.622 37.0 37.0 37.0 37.0 37.0 9 36.628 37.0 37.0 37.0 37.0 37.0 10-14 36.6114 37.0 37.0 37.0 37.0 37.0 15-19 36.5703 37.0 37.0 37.0 37.0 37.0 20-24 36.5477 37.0 37.0 37.0 37.0 37.0 25-29 36.507400000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.463800000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.48800000000001 37.0 37.0 37.0 37.0 37.0 40-44 36.4559 37.0 37.0 37.0 37.0 37.0 45-49 36.4223 37.0 37.0 37.0 37.0 37.0 50-54 36.4273 37.0 37.0 37.0 37.0 37.0 55-59 36.3869 37.0 37.0 37.0 37.0 37.0 60-64 36.3872 37.0 37.0 37.0 37.0 37.0 65-69 36.3582 37.0 37.0 37.0 37.0 37.0 70-74 36.3039 37.0 37.0 37.0 37.0 37.0 75-79 36.3228 37.0 37.0 37.0 37.0 37.0 80-84 36.3078 37.0 37.0 37.0 37.0 37.0 85-89 36.2815 37.0 37.0 37.0 37.0 37.0 90-94 36.22279999999999 37.0 37.0 37.0 37.0 37.0 95-99 36.1914 37.0 37.0 37.0 37.0 37.0 100-104 36.233700000000006 37.0 37.0 37.0 37.0 37.0 105-109 36.16759999999999 37.0 37.0 37.0 37.0 37.0 110-114 36.0845 37.0 37.0 37.0 37.0 37.0 115-119 36.1391 37.0 37.0 37.0 37.0 37.0 120-124 36.0438 37.0 37.0 37.0 37.0 37.0 125-129 35.971599999999995 37.0 37.0 37.0 37.0 37.0 130-134 35.9106 37.0 37.0 37.0 37.0 37.0 135-139 35.8408 37.0 37.0 37.0 37.0 37.0 140-144 35.6284 37.0 37.0 37.0 37.0 37.0 145-149 35.6626 37.0 37.0 37.0 37.0 37.0 150-151 35.38925 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 2.0 22 0.0 23 0.0 24 0.0 25 1.0 26 1.0 27 9.0 28 11.0 29 23.0 30 23.0 31 32.0 32 39.0 33 75.0 34 130.0 35 315.0 36 2980.0 37 358.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.275000000000006 12.3 4.2 40.225 2 18.459994983697015 12.590920491597693 39.75420115374968 29.194883370955605 3 16.425 16.35 30.049999999999997 37.175000000000004 4 21.075 26.525 24.7 27.700000000000003 5 22.85 32.324999999999996 23.974999999999998 20.849999999999998 6 20.474999999999998 32.9 24.975 21.65 7 14.35 26.575 42.175000000000004 16.900000000000002 8 16.8 27.400000000000002 33.074999999999996 22.725 9 16.7 21.05 37.95 24.3 10-14 19.915 29.675 27.250000000000004 23.16 15-19 19.775000000000002 28.804999999999996 27.62 23.799999999999997 20-24 19.805 28.945 27.875 23.375 25-29 20.305 28.395 27.779999999999998 23.52 30-34 19.975 27.785 28.544999999999998 23.695 35-39 20.31 28.455000000000002 28.08 23.155 40-44 19.725 28.310000000000002 28.185 23.78 45-49 20.47 28.744999999999997 27.334999999999997 23.45 50-54 19.81 28.18 28.395 23.615 55-59 20.14 28.18 28.23 23.45 60-64 20.305 28.07 28.01 23.615 65-69 20.02 28.494999999999997 28.044999999999998 23.44 70-74 20.8 27.88 28.000000000000004 23.32 75-79 20.31 28.575 27.655 23.46 80-84 20.565 29.26 26.965 23.21 85-89 20.69 28.765 27.11 23.435 90-94 20.235 28.605000000000004 27.555000000000003 23.605 95-99 20.985 28.325 27.625 23.064999999999998 100-104 20.674999999999997 28.544999999999998 27.57 23.21 105-109 21.255 27.689999999999998 27.325 23.73 110-114 20.685000000000002 28.884999999999998 26.905 23.525 115-119 21.235 28.725 25.955000000000002 24.085 120-124 21.425 27.555000000000003 27.26 23.76 125-129 20.200000000000003 28.57 27.11 24.12 130-134 20.830000000000002 28.73 26.625 23.815 135-139 20.995 27.47 26.474999999999998 25.06 140-144 21.224999999999998 26.790000000000003 27.675 24.310000000000002 145-149 21.240000000000002 26.805 27.615000000000002 24.34 150-151 21.0 26.137500000000003 27.3 25.5625 >>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 0.5 11 0.5 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 0.5 21 0.5 22 0.5 23 1.0 24 1.5 25 2.5 26 9.0 27 14.0 28 10.0 29 10.5 30 19.0 31 20.5 32 26.0 33 52.0 34 62.5 35 65.5 36 88.5 37 108.5 38 141.5 39 172.5 40 178.0 41 216.5 42 240.5 43 272.0 44 275.0 45 251.0 46 255.0 47 232.0 48 220.5 49 205.0 50 175.0 51 146.5 52 135.0 53 104.0 54 62.0 55 53.5 56 50.5 57 39.5 58 25.0 59 15.0 60 15.5 61 12.5 62 6.0 63 2.5 64 1.0 65 2.0 66 1.5 67 0.0 68 0.0 69 0.0 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 0.0 2 0.325 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 81.5 #Duplication Level Percentage of deduplicated Percentage of total 1 82.45398773006136 67.2 2 13.83435582822086 22.55 3 2.6687116564417175 6.525 4 0.7361963190184049 2.4 5 0.2147239263803681 0.8750000000000001 6 0.09202453987730061 0.44999999999999996 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 CCTGTACTTCCACATGACATTCAAAGCGAGGAGATTTCTACCCATGAACT 6 0.15 No Hit TTCAACGAAGCCTTGACTTGAAACCTACCACTGGATTTTGATGCTGACAT 6 0.15 No Hit GCTGCATATACAGAGAGTTTAGAGAACAAATGAGTGAGCTATCCAGGCAA 6 0.15 No Hit CAATGCCATAATAACCAGCAGGAACATTATGGGATACAATATTTTTGGTT 5 0.125 No Hit CTCCAACTTCTTTCGCAACATCTACCATGGCCTTTGCAATAACAGGGCGT 5 0.125 No Hit GCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGC 5 0.125 No Hit GCCCAGATTAGCAAGCCAGTCTTACCCCCAGCATAGACATCGCCAGTTGG 5 0.125 No Hit TCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACAC 5 0.125 No Hit CTCATTGAACCTTCAAATTGTTCTAGCGAGGGAATAAGAAATCACAACAT 5 0.125 No Hit GTCGCAGTGAGCCAATGCCAATGACAGGGGAGCTGGCCCTCGGACAACTC 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.15000000000000002 0.0 0.0 0.0 0.0 68-69 0.21250000000000002 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.38749999999999996 0.0 0.0 0.0 0.0 74-75 0.5125 0.0 0.0 0.0 0.0 76-77 0.5874999999999999 0.0 0.0 0.0 0.0 78-79 0.6625000000000001 0.0 0.0 0.0 0.0 80-81 0.8125 0.0 0.0 0.0 0.0 82-83 0.9625 0.0 0.0 0.0 0.0 84-85 1.25 0.0 0.0 0.0 0.0 86-87 1.575 0.0 0.0 0.0 0.0 88-89 1.75 0.0 0.0 0.0 0.0 90-91 2.05 0.0 0.0 0.0 0.0 92-93 2.5 0.0 0.0 0.0 0.0 94-95 2.9875 0.0 0.0 0.0 0.0 96-97 3.3375 0.0 0.0 0.0 0.0 98-99 3.6875 0.0 0.0 0.0 0.0 100-101 4.0875 0.0 0.0 0.0 0.0 102-103 4.8875 0.0 0.0 0.0 0.0 104-105 5.75 0.0 0.0 0.0 0.0 106-107 6.4625 0.0 0.0 0.0 0.0 108-109 7.074999999999999 0.0 0.0 0.0 0.0 110-111 7.7 0.0 0.0 0.0 0.0 112-113 8.5125 0.0 0.0 0.0 0.0 114-115 9.3625 0.0 0.0 0.0 0.0 116-117 10.149999999999999 0.0 0.0 0.0 0.0 118-119 11.037500000000001 0.0 0.0 0.0 0.0 120-121 11.8 0.0 0.0 0.0 0.0 122-123 12.587499999999999 0.0 0.0 0.0 0.0 124-125 13.5375 0.0 0.0 0.0 0.0 126-127 14.825 0.0 0.0 0.0 0.0 128-129 15.9875 0.0 0.0 0.0 0.0 130-131 16.775 0.0 0.0 0.0 0.0 132-133 17.5375 0.0 0.0 0.0 0.0 134-135 18.425 0.0 0.0 0.0 0.0 136-137 19.4125 0.0 0.0 0.0 0.0 138-139 20.5625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAAAAGT 10 0.006830828 145.0 8 CTCAGCC 10 0.006830828 145.0 1 CACTAAT 10 0.006830828 145.0 3 TCACTAA 10 0.006830828 145.0 2 TTGGATA 10 0.006830828 145.0 9 CTTGCTT 25 8.7132835E-4 87.0 2 >>END_MODULE SRR12670157 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670157_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.397 37.0 37.0 37.0 37.0 37.0 2 36.109 37.0 37.0 37.0 37.0 37.0 3 36.262 37.0 37.0 37.0 37.0 37.0 4 36.202 37.0 37.0 37.0 37.0 37.0 5 36.341 37.0 37.0 37.0 37.0 37.0 6 36.3425 37.0 37.0 37.0 37.0 37.0 7 36.2655 37.0 37.0 37.0 37.0 37.0 8 36.3615 37.0 37.0 37.0 37.0 37.0 9 36.24 37.0 37.0 37.0 37.0 37.0 10-14 36.31 37.0 37.0 37.0 37.0 37.0 15-19 36.3231 37.0 37.0 37.0 37.0 37.0 20-24 36.2804 37.0 37.0 37.0 37.0 37.0 25-29 36.2385 37.0 37.0 37.0 37.0 37.0 30-34 36.187799999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.164699999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.1551 37.0 37.0 37.0 37.0 37.0 45-49 36.1796 37.0 37.0 37.0 37.0 37.0 50-54 36.1329 37.0 37.0 37.0 37.0 37.0 55-59 36.0793 37.0 37.0 37.0 37.0 37.0 60-64 36.0757 37.0 37.0 37.0 37.0 37.0 65-69 36.0674 37.0 37.0 37.0 37.0 37.0 70-74 36.0423 37.0 37.0 37.0 37.0 37.0 75-79 36.0184 37.0 37.0 37.0 37.0 37.0 80-84 35.951800000000006 37.0 37.0 37.0 37.0 37.0 85-89 35.9782 37.0 37.0 37.0 37.0 37.0 90-94 35.911 37.0 37.0 37.0 37.0 37.0 95-99 35.891000000000005 37.0 37.0 37.0 37.0 37.0 100-104 35.8401 37.0 37.0 37.0 37.0 37.0 105-109 35.7598 37.0 37.0 37.0 37.0 37.0 110-114 35.7299 37.0 37.0 37.0 37.0 37.0 115-119 35.7829 37.0 37.0 37.0 37.0 37.0 120-124 35.593599999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.474000000000004 37.0 37.0 37.0 37.0 37.0 130-134 35.2737 37.0 37.0 37.0 34.6 37.0 135-139 35.2288 37.0 37.0 37.0 32.2 37.0 140-144 35.0222 37.0 37.0 37.0 25.0 37.0 145-149 34.8015 37.0 37.0 37.0 25.0 37.0 150-151 34.275000000000006 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 3.0 13 2.0 14 2.0 15 1.0 16 0.0 17 1.0 18 1.0 19 1.0 20 3.0 21 2.0 22 3.0 23 7.0 24 9.0 25 7.0 26 9.0 27 11.0 28 12.0 29 20.0 30 25.0 31 42.0 32 54.0 33 107.0 34 223.0 35 546.0 36 2633.0 37 276.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.225 24.65 7.925 25.2 2 26.974999999999998 25.525 32.300000000000004 15.2 3 18.95 27.474999999999998 34.300000000000004 19.275000000000002 4 22.175 34.075 24.175 19.575 5 23.775 38.625 23.175 14.424999999999999 6 20.625 37.8 22.575 19.0 7 20.150000000000002 21.55 39.375 18.925 8 20.625 25.900000000000002 29.799999999999997 23.674999999999997 9 19.775000000000002 24.8 31.75 23.674999999999997 10-14 23.830000000000002 30.020000000000003 26.505000000000003 19.645000000000003 15-19 22.84 28.34 27.49 21.33 20-24 22.915 28.28 28.01 20.794999999999998 25-29 22.545 28.754999999999995 28.599999999999998 20.1 30-34 22.33 28.999999999999996 28.27 20.4 35-39 22.735 28.265 28.305000000000003 20.695 40-44 23.015 28.804999999999996 27.965 20.215 45-49 23.035 27.665 28.435 20.865000000000002 50-54 22.415 28.525 28.235 20.825 55-59 22.869999999999997 28.139999999999997 28.294999999999998 20.695 60-64 22.66 28.305000000000003 27.884999999999998 21.15 65-69 23.5 28.050000000000004 27.92 20.53 70-74 23.14 28.744999999999997 27.395000000000003 20.72 75-79 23.415 28.965000000000003 26.445 21.175 80-84 24.005000000000003 28.68 27.065 20.25 85-89 23.625 28.65 27.11 20.615 90-94 23.165 28.015 27.655 21.165 95-99 23.915 28.375 26.86 20.849999999999998 100-104 24.095 28.655 26.99 20.26 105-109 24.16 27.955000000000002 27.810000000000002 20.075000000000003 110-114 25.14 28.525 26.51 19.825 115-119 25.180000000000003 28.144999999999996 26.775 19.900000000000002 120-124 26.13 28.365000000000002 26.584999999999997 18.92 125-129 26.169999999999998 28.415000000000003 26.31 19.105 130-134 26.529999999999998 27.925 26.495 19.05 135-139 27.205000000000002 27.525 26.490000000000002 18.78 140-144 27.29 26.705000000000002 27.0 19.005 145-149 28.660000000000004 26.555 26.729999999999997 18.055 150-151 28.962500000000002 26.1 26.05 18.8875 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.5 8 0.5 9 0.0 10 0.0 11 0.5 12 0.5 13 0.5 14 0.5 15 0.5 16 1.0 17 0.5 18 1.0 19 2.0 20 1.5 21 1.0 22 0.5 23 0.5 24 2.0 25 3.5 26 3.5 27 5.5 28 7.5 29 9.5 30 12.5 31 24.5 32 45.0 33 51.5 34 47.0 35 59.5 36 92.5 37 128.0 38 144.5 39 164.5 40 200.5 41 242.0 42 261.0 43 265.0 44 280.5 45 277.5 46 252.5 47 229.0 48 219.5 49 197.0 50 164.0 51 138.0 52 112.0 53 84.0 54 64.5 55 51.0 56 38.5 57 30.5 58 27.0 59 20.5 60 9.5 61 7.0 62 6.5 63 3.0 64 1.0 65 1.0 66 1.0 67 0.5 68 0.5 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 0.5 95 0.5 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 0.0 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 81.825 #Duplication Level Percentage of deduplicated Percentage of total 1 83.07363275282616 67.975 2 13.229453101130462 21.65 3 2.6886648334860985 6.6000000000000005 4 0.7638252367858234 2.5 5 0.09165902841429881 0.375 6 0.09165902841429881 0.44999999999999996 7 0.030553009471432937 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.030553009471432937 0.27499999999999997 >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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 11 0.27499999999999997 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 7 0.17500000000000002 No Hit ATTTACATCACAAGAATCCCAGACTTTTTCCCGGGATGCATTTGAGATTA 6 0.15 No Hit CTCGAAAGAATTGTTGGGTCAGATGATTCTGCCTTCAGTGGAATAGACCT 6 0.15 No Hit GCTTCTTGTTGAGAAGAGAGTAGAGAGGGCAGGAGCGAAGATCAGAGAAA 6 0.15 No Hit GTTGTGCCATGGAACCAGGCCGAGAAGAAGTTCATCTGCCCCTGCCACGG 5 0.125 No Hit GGATGATCATGCTTCACCTGTCAACGTTGAGAAGGAGATGGTGCTTCTAA 5 0.125 No Hit ATTTGTGAGAGATTTCATTTTTCCTTGCTTGCGAGCAGGTGCCATCTATG 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 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.15000000000000002 0.0 0.0 0.0 0.0 68-69 0.21250000000000002 0.0 0.0 0.0 0.0 70-71 0.275 0.0 0.0 0.0 0.0 72-73 0.38749999999999996 0.0 0.0 0.0 0.0 74-75 0.5125 0.0 0.0 0.0 0.0 76-77 0.5874999999999999 0.0 0.0 0.0 0.0 78-79 0.675 0.0 0.0 0.0 0.0 80-81 0.8375 0.0 0.0 0.0 0.0 82-83 0.9875 0.0 0.0 0.0 0.0 84-85 1.275 0.0 0.0 0.0 0.0 86-87 1.6125 0.0 0.0 0.0 0.0 88-89 1.8 0.0 0.0 0.0 0.0 90-91 2.0875000000000004 0.0 0.0 0.0 0.0 92-93 2.55 0.0 0.0 0.0 0.0 94-95 3.05 0.0 0.0 0.0 0.0 96-97 3.425 0.0 0.0 0.0 0.0 98-99 3.7875 0.0 0.0 0.0 0.0 100-101 4.2 0.0 0.0 0.0 0.0 102-103 4.9875 0.0 0.0 0.0 0.0 104-105 5.8625 0.0 0.0 0.0 0.0 106-107 6.5875 0.0 0.0 0.0 0.0 108-109 7.199999999999999 0.0 0.0 0.0 0.0 110-111 7.8125 0.0 0.0 0.0 0.0 112-113 8.6875 0.0 0.0 0.0 0.0 114-115 9.5625 0.0 0.0 0.0 0.0 116-117 10.350000000000001 0.0 0.0 0.0 0.0 118-119 11.2375 0.0 0.0 0.0 0.0 120-121 12.037500000000001 0.0 0.0 0.0 0.0 122-123 12.837499999999999 0.0 0.0 0.0 0.0 124-125 13.774999999999999 0.0 0.0 0.0 0.0 126-127 15.0875 0.0 0.0 0.0 0.0 128-129 16.2625 0.0 0.0 0.0 0.0 130-131 17.0625 0.0 0.0 0.0 0.0 132-133 17.8125 0.0 0.0 0.0 0.0 134-135 18.7 0.0 0.0 0.0 0.0 136-137 19.7 0.0 0.0 0.0 0.0 138-139 20.8125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GATACAC 10 0.006830828 145.0 7 TAAGATA 10 0.006830828 145.0 4 CTCTAAG 10 0.006830828 145.0 1 TCTGTGG 10 0.006830828 145.0 3 AAGATAC 10 0.006830828 145.0 5 TTGAAAC 10 0.006830828 145.0 7 ATACACT 10 0.006830828 145.0 8 GGAAAAG 10 0.006830828 145.0 1 AGATACA 10 0.006830828 145.0 6 >>END_MODULE Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782951 spots for SRR12670157.sra Written 782951 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra Read 782942 spots for SRR12670157.sra Written 782942 spots for SRR12670157.sra SRR ids: ['SRR12670157.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_mln48nku SRR12670157.sra spots: 15658849 blocks: [[1, 782942], [782943, 1565884], [1565885, 2348826], [2348827, 3131768], [3131769, 3914710], [3914711, 4697652], [4697653, 5480594], [5480595, 6263536], [6263537, 7046478], [7046479, 7829420], [7829421, 8612362], [8612363, 9395304], [9395305, 10178246], [10178247, 10961188], [10961189, 11744130], [11744131, 12527072], [12527073, 13310014], [13310015, 14092956], [14092957, 14875898], [14875899, 15658849]] SRR12670157 file size 5299861 SRR12670157 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 SRR12670157 SRR12670157_1.fastq SRR12670157_2.fastq Input file: SRR12670157_1.fastq Paired file: SRR12670157_2.fastq trimmed: SRR12670157-trimmed-pair1.fastq, SRR12670157-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 07:19:50 2025 >> started Tue Feb 11 07:29:21 2025 >> done (571.153s) 15658849 read pairs processed; of these: 120 ( 0.00%) short read pairs filtered out after trimming by size control 2728 ( 0.02%) empty read pairs filtered out after trimming by size control 15656001 (99.98%) read pairs available; of these: 3717578 (23.75%) trimmed read pairs available after processing 11938423 (76.25%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 21 0.00% 20 27 0.00% 21 31 0.00% 22 35 0.00% 23 57 0.00% 24 47 0.00% 25 87 0.00% 26 74 0.00% 27 100 0.00% 28 113 0.00% 29 131 0.00% 30 131 0.00% 31 114 0.00% 32 120 0.00% 33 141 0.00% 34 146 0.00% 35 167 0.00% 36 159 0.00% 37 192 0.00% 38 183 0.00% 39 213 0.00% 40 253 0.00% 41 249 0.00% 42 270 0.00% 43 250 0.00% 44 232 0.00% 45 312 0.00% 46 355 0.00% 47 359 0.00% 48 401 0.00% 49 520 0.00% 50 600 0.00% 51 649 0.00% 52 682 0.00% 53 748 0.00% 54 832 0.01% 55 895 0.01% 56 985 0.01% 57 1063 0.01% 58 1343 0.01% 59 1531 0.01% 60 1793 0.01% 61 2029 0.01% 62 2144 0.01% 63 2363 0.02% 64 2602 0.02% 65 2872 0.02% 66 3025 0.02% 67 3506 0.02% 68 3839 0.02% 69 4598 0.03% 70 5052 0.03% 71 5988 0.04% 72 6687 0.04% 73 7283 0.05% 74 7748 0.05% 75 8493 0.05% 76 9193 0.06% 77 9967 0.06% 78 10632 0.07% 79 11953 0.08% 80 12897 0.08% 81 14638 0.09% 82 16315 0.10% 83 17244 0.11% 84 19015 0.12% 85 20627 0.13% 86 21386 0.14% 87 22195 0.14% 88 23680 0.15% 89 24772 0.16% 90 26354 0.17% 91 28700 0.18% 92 29762 0.19% 93 32142 0.21% 94 33983 0.22% 95 35760 0.23% 96 36672 0.23% 97 37666 0.24% 98 38179 0.24% 99 39077 0.25% 100 40803 0.26% 101 41502 0.27% 102 44510 0.28% 103 45703 0.29% 104 46847 0.30% 105 48441 0.31% 106 49572 0.32% 107 49595 0.32% 108 49755 0.32% 109 51255 0.33% 110 50940 0.33% 111 52101 0.33% 112 53708 0.34% 113 54453 0.35% 114 56131 0.36% 115 57604 0.37% 116 58279 0.37% 117 58037 0.37% 118 59258 0.38% 119 58598 0.37% 120 60153 0.38% 121 60745 0.39% 122 60898 0.39% 123 61596 0.39% 124 63544 0.41% 125 63276 0.40% 126 65217 0.42% 127 64491 0.41% 128 64071 0.41% 129 63724 0.41% 130 64355 0.41% 131 63699 0.41% 132 64657 0.41% 133 65931 0.42% 134 65597 0.42% 135 66245 0.42% 136 67320 0.43% 137 67304 0.43% 138 66535 0.42% 139 68077 0.43% 140 66675 0.43% 141 66665 0.43% 142 66804 0.43% 143 67497 0.43% 144 68310 0.44% 145 68951 0.44% 146 68254 0.44% 147 67859 0.43% 148 68575 0.44% 149 67051 0.43% 150 68750 0.44% 151 11938423 76.25% 15656001 reads passed initial QC criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=21 prefix-density=0.51 prefix-fanout=2.0 sequence=TGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTG criterion=fanout-score sequence-density=0.02 sequence-density-rank=27 fanout-score=179.59 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=16.1 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=1.04 sequence-density-rank=1 fanout-score=2.05 fanout-score-rank=25 prefix-density=1.04 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=100.10 fanout-score-rank=1 prefix-density=0.08 prefix-fanout=7.8 sequence=AAGGATGGTAGAGTAGCATCCTTAGCGTTGCTGGTTTACTTTCCTAACAATCCTCAAAACCATTCTTCTTAGACTCTCTATACATTCCAAATAACCTAATTTGTACTGTATAGATATATAGTCTACGTCAAGCTTAAATAAATCCTCATTAACATGGCCCCAGGAGTGCCTATAGATGGGAATATTTTGGGTACCGGGAAGGTTTCCACAGTTAACACTGGCTATTCTAAGAGGGCCTACGTGACATTTTTAGCCGGCAACGGGGATTATGTTAAAGGGGTAGTTGGGTTGGCTAAGGGTTTGCGCAAGGTGAAGAGTGCATACCCTCTTGTCGTAGCAATCTTGCCGGATGTGCCCGAGGAACACCGTGACATTTTGAGGTCTCAAGGTTGCATTGTTCGTGAGATCGAGCCTATTTATCCACCTGAGAACCAGATTCAGTTTGCCATGGCCTACTACGTGATCAACTACTCCAAGCTCCGAATTTGGAATTTTGAGGAGTACAGCAAGA SRR12670157 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 07:33:32 Started mapping on | Feb 11 07:33:32 Finished on | Feb 11 07:35:07 Mapping speed, Million of reads per hour | 593.28 Number of input reads | 15656001 Average input read length | 287 UNIQUE READS: Uniquely mapped reads number | 14666938 Uniquely mapped reads % | 93.68% Average mapped length | 285.62 Number of splices: Total | 13964362 Number of splices: Annotated (sjdb) | 13623213 Number of splices: GT/AG | 13675137 Number of splices: GC/AG | 221656 Number of splices: AT/AC | 9187 Number of splices: Non-canonical | 58382 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.91 Insertion rate per base | 0.02% Insertion average length | 2.43 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 367746 % of reads mapped to multiple loci | 2.35% Number of reads mapped to too many loci | 40649 % of reads mapped to too many loci | 0.26% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.60% % of reads unmapped: other | 0.11% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 621317 621317 621317 N_multimapping 367746 367746 367746 N_noFeature 652553 14450206 744274 N_ambiguous 211580 782 86273 UnstrandedReadsAssigned:13802805 PositiveStrandReadsAssigned:215950 NegativeStrandReadsAssigned:13836391 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=142 echo kmer=137 SRR12670157 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: SRR12670157-trimmed-pair1.fastq SRR12670157-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 15,656,001 reads, 13,810,860 reads pseudoaligned [quant] estimated average fragment length: 214.633 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,048 rounds 52401 SRR12670157.ke.tsv 34699 SRR12670157.se.tsv 87100 total ==> SRR12670157.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1804.37 702 28.0626 Potri.005G024800.1.v4.1 1035 821.367 266 23.3593 Potri.004G059700.1.v4.1 961 747.434 12 1.15804 Potri.007G009000.2.v4.1 1416 1202.37 0 0 Potri.003G141000.2.v4.1 2943 2729.37 1201 31.7393 Potri.016G087400.1.v4.1 270 106.099 949 645.163 Potri.015G069301.1.v4.1 564 357.948 0 0 Potri.010G195200.1.v4.1 1773 1559.37 63 2.91412 Potri.012G127500.1.v4.1 977 763.406 137 12.9444 ==> SRR12670157.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 172 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 156 Potri.001G212900.v4.1 51 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 16 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 24 SRR12670157 completed mapping pipeline successfully