Starting /dee2/code/volunteer_pipeline.sh SRR7172098 current disk space = 3087136276480 free memory = 1449567336 SRR7172098 SRAfilesize b2c029ebc37c62b4590f063248f40e9e SRR7172098.sra SRR7172098.sra file validated SRR7172098 is paired end SRR7172098 is conventional basespace SRR7172098 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7172098_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 42 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 31.68775 33.0 33.0 34.0 32.0 34.0 2 32.8765 33.0 33.0 34.0 31.0 34.0 3 32.47325 33.0 33.0 34.0 31.0 34.0 4 31.973 33.0 31.0 33.0 31.0 34.0 5 32.73575 33.0 33.0 33.0 32.0 34.0 6 37.12075 38.0 37.0 38.0 36.0 38.0 7 37.38525 38.0 38.0 38.0 36.0 38.0 8 37.55475 38.0 38.0 38.0 37.0 38.0 9 37.61125 38.0 38.0 38.0 38.0 38.0 10-14 37.674350000000004 38.0 38.0 38.0 38.0 38.0 15-19 37.6686 38.0 38.0 38.0 38.0 38.0 20-24 37.64885 38.0 38.0 38.0 38.0 38.0 25-29 37.54165 38.0 38.0 38.0 38.0 38.0 30-34 37.4662 38.0 38.0 38.0 38.0 38.0 35-39 37.40305 38.0 38.0 38.0 38.0 38.0 40-44 37.36560000000001 38.0 38.0 38.0 37.8 38.0 45-49 37.36375 38.0 38.0 38.0 37.8 38.0 50-54 37.2171 38.0 38.0 38.0 37.0 38.0 55-59 37.1616 38.0 38.0 38.0 37.0 38.0 60-64 37.1213 38.0 38.0 38.0 36.8 38.0 65-69 37.0788 38.0 38.0 38.0 36.8 38.0 70-74 37.0055 38.0 38.0 38.0 36.0 38.0 75-79 36.742900000000006 38.0 38.0 38.0 36.0 38.0 80-84 36.64275 38.0 38.0 38.0 36.0 38.0 85-89 36.4832 38.0 38.0 38.0 35.2 38.0 90-94 36.3575 38.0 38.0 38.0 34.6 38.0 95-99 36.289300000000004 38.0 38.0 38.0 34.6 38.0 100-104 36.173 38.0 38.0 38.0 34.2 38.0 105-109 35.9451 38.0 38.0 38.0 33.8 38.0 110-114 35.82365 38.0 37.8 38.0 33.6 38.0 115-119 35.6122 38.0 37.2 38.0 32.6 38.0 120-124 35.56170000000001 38.0 37.2 38.0 32.6 38.0 125-129 35.2909 38.0 37.0 38.0 31.0 38.0 130-134 35.091499999999996 38.0 36.0 38.0 29.8 38.0 135-139 34.707 38.0 36.0 38.0 28.0 38.0 140-144 34.5481 38.0 35.6 38.0 27.4 38.0 145-149 34.01585 38.0 35.0 38.0 24.0 38.0 150-151 30.506749999999997 36.5 29.0 38.0 8.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 3.0 7 3.0 8 7.0 9 1.0 10 2.0 11 2.0 12 2.0 13 2.0 14 1.0 15 7.0 16 2.0 17 3.0 18 11.0 19 28.0 20 2.0 21 6.0 22 10.0 23 6.0 24 3.0 25 16.0 26 7.0 27 8.0 28 10.0 29 28.0 30 33.0 31 37.0 32 46.0 33 74.0 34 120.0 35 201.0 36 628.0 37 2691.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.906639004149376 18.62033195020747 16.519709543568464 29.953319502074688 2 20.27027027027027 23.2982982982983 38.66366366366366 17.76776776776777 3 17.575 30.375000000000004 30.2 21.85 4 19.85 35.225 26.3 18.625 5 20.625 35.425000000000004 27.1 16.85 6 16.025 37.425000000000004 27.250000000000004 19.3 7 13.075000000000001 22.3 46.1 18.525 8 18.05 23.425 30.599999999999998 27.925 9 17.849999999999998 23.825 33.2 25.124999999999996 10-14 18.89 31.624999999999996 26.724999999999998 22.759999999999998 15-19 18.845 30.42 28.4 22.335 20-24 19.189999999999998 30.875000000000004 27.73 22.205 25-29 19.439999999999998 29.92 28.139999999999997 22.5 30-34 19.314999999999998 30.235 27.839999999999996 22.61 35-39 19.39 30.665 27.415 22.53 40-44 20.080000000000002 30.43 27.775 21.715 45-49 20.43 30.29 27.625 21.654999999999998 50-54 19.98 30.404999999999998 26.729999999999997 22.884999999999998 55-59 19.12 30.395 27.939999999999998 22.545 60-64 19.155 29.830000000000002 28.575 22.439999999999998 65-69 19.925 30.225 27.555000000000003 22.295 70-74 19.45 30.409999999999997 27.894999999999996 22.245 75-79 19.935 30.415 26.71 22.939999999999998 80-84 19.545 29.87 27.63 22.955000000000002 85-89 19.869999999999997 29.205 28.095 22.830000000000002 90-94 20.695 29.54 27.815 21.95 95-99 20.005 28.84 28.685 22.470000000000002 100-104 20.43 29.310000000000002 27.474999999999998 22.785 105-109 20.205000000000002 29.349999999999998 27.77 22.675 110-114 20.119999999999997 29.64 26.955000000000002 23.285 115-119 20.03 29.07 27.694999999999997 23.205000000000002 120-124 21.17 29.445 26.474999999999998 22.91 125-129 20.71 29.270000000000003 27.51 22.509999999999998 130-134 21.05 29.56 26.775 22.615 135-139 21.055 29.765000000000004 26.07 23.11 140-144 21.5 29.085 26.58 22.835 145-149 21.37 29.49 25.724999999999998 23.415 150-151 22.025 28.225 26.700000000000003 23.05 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 4.0 1 2.0 2 0.0 3 1.0 4 3.0 5 3.5 6 2.0 7 1.5 8 1.5 9 0.5 10 1.5 11 1.5 12 0.0 13 0.0 14 0.0 15 0.0 16 1.0 17 1.0 18 0.0 19 1.0 20 2.0 21 2.0 22 2.0 23 3.0 24 5.0 25 5.5 26 8.0 27 12.5 28 18.0 29 24.0 30 30.5 31 54.0 32 80.5 33 111.0 34 128.5 35 153.5 36 184.5 37 198.0 38 204.0 39 213.5 40 206.0 41 198.0 42 200.5 43 182.5 44 192.5 45 200.0 46 180.5 47 165.5 48 154.5 49 149.5 50 123.0 51 88.5 52 93.5 53 92.0 54 69.0 55 55.5 56 46.0 57 36.5 58 28.5 59 19.0 60 11.5 61 6.5 62 7.5 63 7.5 64 4.5 65 4.0 66 4.5 67 3.0 68 1.0 69 0.0 70 1.0 71 1.0 72 0.5 73 1.0 74 0.5 75 0.5 76 1.0 77 0.5 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 3.5999999999999996 2 0.1 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 90.925 #Duplication Level Percentage of deduplicated Percentage of total 1 95.24333241682706 86.6 2 2.8320043992301347 5.1499999999999995 3 1.0173219686554853 2.775 4 0.27495188342040144 1.0 5 0.21996150673632117 1.0 6 0.08248556502612042 0.44999999999999996 7 0.10998075336816059 0.7000000000000001 8 0.13747594171020072 1.0 9 0.0 0.0 >10 0.08248556502612042 1.325 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACGTCTAGGTATCTCGTAT 28 0.7000000000000001 TruSeq Adapter, Index 11 (97% over 38bp) GTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGA 13 0.325 No Hit GGAAGCTATACTATATAGGTGGCTATCTATCCCTACCAAGGCTTATATTG 12 0.3 No Hit AAAATATCTAAGTGCTGGGGTTATGAGTAGGGATGAGCATAAACCAACAA 8 0.2 No Hit TGGCTATCTATCCCTACCAAGGCTTATATTGAAGTATAAACCAATGAGAG 8 0.2 No Hit GCCTTATGTGATAGATGCCTCTTTAAAATATCTAAGTGCTGGGGTTATGA 8 0.2 No Hit GTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGGGAA 8 0.2 No Hit TTTTTTTTTAAGGGTAAAACGCAAGCACCGGCTGTCGAGTTGTACGGCCG 8 0.2 No Hit GTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGGGAAGCTATAC 7 0.17500000000000002 No Hit GTTGGAACTCTACCAATTGGAGCTTTCTTAGCTGTCTTAGCAGTAGTTTA 7 0.17500000000000002 No Hit CTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGATGAGCATAAACCA 7 0.17500000000000002 No Hit GCAGTTTCCAGAAACGTGTATCACATCTAGGCATGGAATCTTATGCCAGC 7 0.17500000000000002 No Hit TGGAACTCTACCAATTGGAGCTTTCTTAGCTGTCTTAGCAGTAGTTTATA 6 0.15 No Hit CTTTGATATTCTCTGCATCCTATTTAGGGCTATTGATATTTAACAAATAT 6 0.15 No Hit GCCTCTTTAAAATATCTAAGTGCTGGGGTTATGAGTAGGGATGAGCATAA 6 0.15 No Hit GGAACAGTCGCATGACGAGGCAGTTTCCAGAAACGTGTATCACATCTAGG 5 0.125 No Hit GGATGTTGTTGTTAGACACTTCTTTTTGTCTTTAAATATAAGGCGTGGTA 5 0.125 No Hit TTTTTTTGGATTTTTTCCGCTTTGATATTCTCTGCATCCTATTTAGGGCT 5 0.125 No Hit CTTACAAGTCCGCTCCTCGGGGAGCTTGATTGATAATTCTGTATAAGGTG 5 0.125 No Hit GGGGTTATGAGTAGGGATGAGCATAAACCAACAACTCTCAAAGAAGATGG 5 0.125 No Hit GTCGAGACTGAAAAGCTATAACCCGCAGACCCGAGCGAAAGCGGCGGTCC 5 0.125 No Hit CTTTAATCCTCTCACTCCACAAATTCATAAGCTTCACCATTTTACTTCAC 5 0.125 No Hit GGGGAACAGTCGCATGACGAGGCAGTTTCCAGAAACGTGTATCACATCTA 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.037500000000000006 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.0625 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1375 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.225 0.0 0.0 0.0 0.0 90-91 0.25 0.0 0.0 0.0 0.0 92-93 0.32499999999999996 0.0 0.0 0.0 0.0 94-95 0.3625 0.0 0.0 0.0 0.0 96-97 0.4625 0.0 0.0 0.0 0.0 98-99 0.5875 0.0 0.0 0.0 0.0 100-101 0.7625 0.0 0.0 0.0 0.0 102-103 1.075 0.0 0.0 0.0 0.0 104-105 1.3375 0.0 0.0 0.0 0.0 106-107 1.5499999999999998 0.0 0.0 0.0 0.0 108-109 1.9125 0.0 0.0 0.0 0.0 110-111 2.2 0.0 0.0 0.0 0.0 112-113 2.5875000000000004 0.0 0.0 0.0 0.0 114-115 2.95 0.0 0.0 0.0 0.0 116-117 3.475 0.0 0.0 0.0 0.0 118-119 3.8 0.0 0.0 0.0 0.0 120-121 4.1875 0.0 0.0 0.0 0.0 122-123 4.775 0.0 0.0 0.0 0.0 124-125 5.2625 0.0 0.0 0.0 0.0 126-127 6.050000000000001 0.0 0.0 0.0 0.0 128-129 6.6 0.0 0.0 0.0 0.0 130-131 7.1875 0.0 0.0 0.0 0.0 132-133 7.75 0.0 0.0 0.0 0.0 134-135 8.3875 0.0 0.0 0.0 0.0 136-137 9.0 0.0 0.0 0.0 0.0 138-139 9.75 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACAGTCG 10 0.006836113 144.9625 6 CAGTCGC 10 0.006836113 144.9625 7 >>END_MODULE SRR7172098 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7172098_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 33.2715 34.0 33.0 34.0 33.0 34.0 2 33.289 34.0 33.0 34.0 33.0 34.0 3 33.30325 34.0 33.0 34.0 33.0 34.0 4 33.26925 34.0 33.0 34.0 33.0 34.0 5 33.2635 34.0 33.0 34.0 33.0 34.0 6 37.388 38.0 38.0 38.0 38.0 38.0 7 37.4075 38.0 38.0 38.0 38.0 38.0 8 37.3945 38.0 38.0 38.0 38.0 38.0 9 37.39825 38.0 38.0 38.0 38.0 38.0 10-14 37.33845 38.0 38.0 38.0 38.0 38.0 15-19 37.33665 38.0 38.0 38.0 38.0 38.0 20-24 37.316199999999995 38.0 38.0 38.0 38.0 38.0 25-29 37.3395 38.0 38.0 38.0 38.0 38.0 30-34 37.28945 38.0 38.0 38.0 38.0 38.0 35-39 37.23655 38.0 38.0 38.0 37.4 38.0 40-44 37.2543 38.0 38.0 38.0 37.6 38.0 45-49 37.186099999999996 38.0 38.0 38.0 37.2 38.0 50-54 37.1925 38.0 38.0 38.0 37.0 38.0 55-59 37.157849999999996 38.0 38.0 38.0 37.0 38.0 60-64 37.11715 38.0 38.0 38.0 37.0 38.0 65-69 37.04880000000001 38.0 38.0 38.0 36.6 38.0 70-74 37.049899999999994 38.0 38.0 38.0 37.0 38.0 75-79 36.963550000000005 38.0 38.0 38.0 36.4 38.0 80-84 36.576950000000004 38.0 38.0 38.0 35.6 38.0 85-89 36.484449999999995 38.0 38.0 38.0 35.2 38.0 90-94 36.4543 38.0 38.0 38.0 35.2 38.0 95-99 36.330799999999996 38.0 38.0 38.0 35.0 38.0 100-104 36.32935 38.0 38.0 38.0 34.4 38.0 105-109 36.1933 38.0 38.0 38.0 34.0 38.0 110-114 36.08895 38.0 38.0 38.0 34.0 38.0 115-119 35.9793 38.0 38.0 38.0 33.4 38.0 120-124 35.76695 38.0 37.6 38.0 33.4 38.0 125-129 35.4858 38.0 36.6 38.0 32.2 38.0 130-134 35.21265 38.0 36.0 38.0 30.6 38.0 135-139 34.91075 38.0 36.0 38.0 28.6 38.0 140-144 34.5445 38.0 35.4 38.0 27.8 38.0 145-149 33.864599999999996 38.0 34.4 38.0 24.0 38.0 150-151 30.005625000000002 36.0 28.0 38.0 7.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 9.0 3 7.0 4 1.0 5 0.0 6 0.0 7 1.0 8 1.0 9 2.0 10 3.0 11 2.0 12 1.0 13 1.0 14 0.0 15 1.0 16 3.0 17 3.0 18 6.0 19 7.0 20 27.0 21 4.0 22 5.0 23 6.0 24 8.0 25 6.0 26 9.0 27 23.0 28 27.0 29 26.0 30 22.0 31 42.0 32 56.0 33 71.0 34 109.0 35 165.0 36 489.0 37 2857.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.225 16.05 17.925 25.8 2 24.275 23.400000000000002 33.375 18.95 3 21.425 24.975 32.15 21.45 4 25.074999999999996 33.6 21.025 20.3 5 25.224999999999998 35.875 21.0 17.9 6 19.85 36.475 23.625 20.05 7 17.849999999999998 17.275 41.825 23.05 8 21.7 23.225 26.325 28.749999999999996 9 22.35 23.974999999999998 28.999999999999996 24.675 10-14 23.66 28.349999999999998 26.1 21.89 15-19 23.855 27.975 27.889999999999997 20.28 20-24 24.005000000000003 28.4 27.089999999999996 20.505000000000003 25-29 24.47 28.23 27.389999999999997 19.91 30-34 23.015 27.639999999999997 28.525 20.82 35-39 23.32 27.295 28.005000000000003 21.38 40-44 24.11 27.700000000000003 28.525 19.665 45-49 23.035 26.605 29.425 20.935000000000002 50-54 22.31 27.005000000000003 28.810000000000002 21.875 55-59 23.724999999999998 26.700000000000003 29.005 20.57 60-64 22.55 28.17 28.610000000000003 20.669999999999998 65-69 22.939999999999998 27.975 28.799999999999997 20.285 70-74 22.42 28.715000000000003 27.939999999999998 20.925 75-79 22.305 28.18 28.705000000000002 20.810000000000002 80-84 23.04 28.765 28.53 19.665 85-89 22.91 28.384999999999998 28.73 19.975 90-94 22.755 29.07 28.595 19.580000000000002 95-99 22.68 28.665000000000003 28.38 20.275000000000002 100-104 23.015 28.415000000000003 28.13 20.44 105-109 23.445 27.97 28.355000000000004 20.23 110-114 23.47 29.205 27.555000000000003 19.77 115-119 23.125 29.544999999999998 28.325 19.005 120-124 22.900000000000002 28.975 28.12 20.005 125-129 23.16 28.765 28.64 19.435 130-134 23.76 28.665000000000003 28.46 19.115 135-139 23.905 28.29 28.38 19.425 140-144 24.715 28.07 28.255000000000003 18.96 145-149 25.665 27.694999999999997 27.925 18.715 150-151 25.874999999999996 28.000000000000004 27.537499999999998 18.587500000000002 >>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 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 1.0 18 1.0 19 0.5 20 0.5 21 0.5 22 0.5 23 1.0 24 0.5 25 1.5 26 3.0 27 2.5 28 6.0 29 9.5 30 14.5 31 30.0 32 45.5 33 51.5 34 66.0 35 91.0 36 107.0 37 152.5 38 219.5 39 235.0 40 225.5 41 199.5 42 188.0 43 201.5 44 205.5 45 219.5 46 213.5 47 202.5 48 216.0 49 183.0 50 144.5 51 128.5 52 112.0 53 104.5 54 87.0 55 71.5 56 64.5 57 50.0 58 35.0 59 32.5 60 21.5 61 15.0 62 10.5 63 6.0 64 4.0 65 3.5 66 2.5 67 1.0 68 0.5 69 1.5 70 1.5 71 1.5 72 2.0 73 0.5 74 0.0 75 0.0 76 0.0 77 0.5 78 1.5 79 1.0 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 0.0 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 89.525 #Duplication Level Percentage of deduplicated Percentage of total 1 95.47612398771292 85.475 2 2.541189611840268 4.55 3 0.8936051382295448 2.4 4 0.3351019268360793 1.2 5 0.2513264451270595 1.125 6 0.1117006422786931 0.6 7 0.1117006422786931 0.7000000000000001 8 0.05585032113934655 0.4 9 0.027925160569673275 0.22499999999999998 >10 0.1954761239877129 3.325 >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 GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGTCTAGGTGTGTAGATCT 34 0.8500000000000001 Illumina Single End PCR Primer 1 (96% over 32bp) GAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCC 29 0.7250000000000001 No Hit GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 21 0.525 No Hit TGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTC 14 0.35000000000000003 No Hit CTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCT 13 0.325 No Hit GGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCAAAACAATCAC 12 0.3 No Hit CTTCAATATAAGCCTTGGTAGGGATAGATAGCCACCTATATAGTATAGCT 10 0.25 No Hit GCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGG 9 0.22499999999999998 No Hit GTTTTACTAGGCTAGACTAGCGTACGAGCACTATGGTCAGTAATTCCTGG 8 0.2 No Hit CCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGT 8 0.2 No Hit GCCACCTATATAGTATAGCTTCCCATCTTCTTTGAGAGTTGTTGGTTTAT 7 0.17500000000000002 No Hit CTCTCATTGGTTTATACTTCAATATAAGCCTTGGTAGGGATAGATAGCCA 7 0.17500000000000002 No Hit ACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTC 7 0.17500000000000002 No Hit GGAGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTAC 7 0.17500000000000002 No Hit ATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTACTATGT 6 0.15 No Hit TAGGGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGT 6 0.15 No Hit TCCATTTCCGCCCAAGCTGCTCACAGTATACGGGCGTCGGCATCCAGACC 6 0.15 No Hit GTTGGTTTATGCTCATCCCTACTCATAACCCCAGCACTTAGATATTTTAA 6 0.15 No Hit AAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCT 5 0.125 No Hit GTCCGAATGGCACAAAGCTTGTTCCGTTAGCTGGCATAAGATTCCATGCC 5 0.125 No Hit CTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGGTTTTCA 5 0.125 No Hit AGTATTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTACTA 5 0.125 No Hit TTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTACTATGTTG 5 0.125 No Hit CCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCCTCCTATGG 5 0.125 No Hit GCGGTGTACACCCTTTTGAGCAATGATTGCACAACCTGCGATCACCTTAT 5 0.125 No Hit GTTTCCTCCTATGGTTTTCAAAACAATCACCATCATGCTATTAATGATAT 5 0.125 No Hit TTTGCACTTGTGGTAACGGTATTTGCATTATTGATGGTTTTTACTATGTT 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.037500000000000006 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.0625 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1375 0.0 0.0 0.0 0.0 86-87 0.2 0.0 0.0 0.0 0.0 88-89 0.225 0.0 0.0 0.0 0.0 90-91 0.25 0.0 0.0 0.0 0.0 92-93 0.32499999999999996 0.0 0.0 0.0 0.0 94-95 0.3625 0.0 0.0 0.0 0.0 96-97 0.4625 0.0 0.0 0.0 0.0 98-99 0.5875 0.0 0.0 0.0 0.0 100-101 0.7375 0.0 0.0 0.0 0.0 102-103 1.025 0.0 0.0 0.0 0.0 104-105 1.2625000000000002 0.0 0.0 0.0 0.025 106-107 1.4875 0.0 0.0 0.0 0.025 108-109 1.85 0.0 0.0 0.0 0.025 110-111 2.1125 0.0 0.0 0.0 0.025 112-113 2.45 0.0 0.0 0.0 0.025 114-115 2.8 0.0 0.0 0.0 0.025 116-117 3.2625 0.0 0.0 0.0 0.025 118-119 3.575 0.0 0.0 0.0 0.025 120-121 3.9499999999999997 0.0 0.0 0.0 0.025 122-123 4.574999999999999 0.0 0.0 0.0 0.025 124-125 5.05 0.0 0.0 0.0 0.025 126-127 5.9125 0.0 0.0 0.0 0.025 128-129 6.45 0.0 0.0 0.0 0.025 130-131 7.0 0.0 0.0 0.0 0.025 132-133 7.5625 0.0 0.0 0.0 0.025 134-135 8.175 0.0 0.0 0.0 0.025 136-137 8.7875 0.0 0.0 0.0 0.025 138-139 9.5625 0.0 0.0 0.0 0.025 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGGAAAT 10 0.006830828 145.0 1 >>END_MODULE Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389938 spots for SRR7172098.sra Written 389938 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra Read 389921 spots for SRR7172098.sra Written 389921 spots for SRR7172098.sra SRR ids: ['SRR7172098.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_g88cydtf SRR7172098.sra spots: 7798437 blocks: [[1, 389921], [389922, 779842], [779843, 1169763], [1169764, 1559684], [1559685, 1949605], [1949606, 2339526], [2339527, 2729447], [2729448, 3119368], [3119369, 3509289], [3509290, 3899210], [3899211, 4289131], [4289132, 4679052], [4679053, 5068973], [5068974, 5458894], [5458895, 5848815], [5848816, 6238736], [6238737, 6628657], [6628658, 7018578], [7018579, 7408499], [7408500, 7798437]] SRR7172098 file size 2625233 SRR7172098 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 SRR7172098 SRR7172098_1.fastq SRR7172098_2.fastq Input file: SRR7172098_1.fastq Paired file: SRR7172098_2.fastq trimmed: SRR7172098-trimmed-pair1.fastq, SRR7172098-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 Fri Feb 14 04:40:23 2025 >> started Fri Feb 14 04:40:32 2025 >> done (8.432s) 7798437 read pairs processed; of these: 12536 ( 0.16%) short read pairs filtered out after trimming by size control 48799 ( 0.63%) empty read pairs filtered out after trimming by size control 7737102 (99.21%) read pairs available; of these: 4021065 (51.97%) trimmed read pairs available after processing 3716037 (48.03%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 2 0.00% 20 3 0.00% 21 7 0.00% 22 4 0.00% 23 5 0.00% 24 15 0.00% 25 8 0.00% 26 6 0.00% 27 7 0.00% 28 7 0.00% 29 6 0.00% 30 13 0.00% 31 6 0.00% 32 5 0.00% 33 11 0.00% 34 9 0.00% 35 10 0.00% 36 8 0.00% 37 6 0.00% 38 8 0.00% 39 3 0.00% 40 6 0.00% 41 11 0.00% 42 7 0.00% 43 11 0.00% 44 15 0.00% 45 17 0.00% 46 13 0.00% 47 27 0.00% 48 17 0.00% 49 25 0.00% 50 36 0.00% 51 46 0.00% 52 28 0.00% 53 61 0.00% 54 50 0.00% 55 60 0.00% 56 77 0.00% 57 74 0.00% 58 81 0.00% 59 106 0.00% 60 97 0.00% 61 123 0.00% 62 119 0.00% 63 139 0.00% 64 147 0.00% 65 170 0.00% 66 182 0.00% 67 200 0.00% 68 223 0.00% 69 234 0.00% 70 292 0.00% 71 317 0.00% 72 403 0.01% 73 426 0.01% 74 568 0.01% 75 847 0.01% 76 1986 0.03% 77 1802 0.02% 78 1025 0.01% 79 941 0.01% 80 986 0.01% 81 1248 0.02% 82 1496 0.02% 83 1649 0.02% 84 2310 0.03% 85 2828 0.04% 86 3443 0.04% 87 4260 0.06% 88 4572 0.06% 89 4624 0.06% 90 4884 0.06% 91 4823 0.06% 92 5404 0.07% 93 5428 0.07% 94 5864 0.08% 95 6185 0.08% 96 6664 0.09% 97 6768 0.09% 98 7183 0.09% 99 7857 0.10% 100 8401 0.11% 101 8988 0.12% 102 9793 0.13% 103 10092 0.13% 104 10945 0.14% 105 12002 0.16% 106 12679 0.16% 107 13680 0.18% 108 14281 0.18% 109 14868 0.19% 110 15586 0.20% 111 16625 0.21% 112 17593 0.23% 113 20163 0.26% 114 20473 0.26% 115 21255 0.27% 116 21803 0.28% 117 21501 0.28% 118 22309 0.29% 119 22990 0.30% 120 23917 0.31% 121 24982 0.32% 122 25494 0.33% 123 26659 0.34% 124 27255 0.35% 125 28478 0.37% 126 29748 0.38% 127 30053 0.39% 128 31057 0.40% 129 32739 0.42% 130 33178 0.43% 131 34089 0.44% 132 36166 0.47% 133 37248 0.48% 134 38582 0.50% 135 39692 0.51% 136 42450 0.55% 137 42876 0.55% 138 45163 0.58% 139 47106 0.61% 140 49909 0.65% 141 52139 0.67% 142 57093 0.74% 143 61237 0.79% 144 68465 0.88% 145 78377 1.01% 146 96958 1.25% 147 128684 1.66% 148 198860 2.57% 149 405680 5.24% 150 1731069 22.37% 151 3716037 48.03% 7737102 reads passed initial QC criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=2.27 fanout-score-rank=32 prefix-density=0.41 prefix-fanout=2.2 sequence=ACCTGCAATGATTGTCTC criterion=fanout-score sequence-density=0.03 sequence-density-rank=24 fanout-score=286.44 fanout-score-rank=1 prefix-density=0.45 prefix-fanout=22.2 sequence=TCATCATCACCACCATCACCATCCCTGATTGATCTTTGATTCACAACAAGACCAACCAACCGTACAATGTTTACATAACTTGGGATAATCTCACAAGAAAGAAAGATCAATACAAAACTAGTCAGCTCAGGATGTTCCAGGCACGGTAGAACCGTAGAACCATAACAACAAGAGACATATTGCAGATGAGTACTGAAAAACAAAACACAGTACGTATTTACATGGGCAACCTTGGTTGAAGGCAACCTCATCAACGATGCTCGCTCTTCGTCTCTCCACTGTACATCCAGTCATAGACAGTGGGTGTGTTAGGCTGTGGCTTGTCAAAAACATGAGCACCAATATTCTTAGTAGCAAGGTTGCTACCAGGGTGGAACACGCTCCTCCAAACATTGCTACGCGCCGACACTGGGGTTGTAGGGGTCACTGGTGTCGTCGGTGTCCCTGGAGTTCCTGGCATAGTCATGGACCTCTGAAACTTATTAAC criterion=sequence-density sequence-density=0.83 sequence-density-rank=1 fanout-score=3.11 fanout-score-rank=22 prefix-density=1.26 prefix-fanout=2.0 sequence=CTGCAAGTGCGG criterion=fanout-score sequence-density=0.01 sequence-density-rank=27 fanout-score=25.29 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=1.0 sequence=CCGGCGCACGCCACAGGCGTCATACTTCCCAAGAAGCGGCCATAGCCCAGATGCGAGGTGGAAAAGTCACACTAGAGCGACACCAACATCGTTACGCTTACACACCGGACGCTTGGATCAGTGGGAAGTGCTCACGCGCGGAGCCCACTGGGCGAACAGCAACGTTATAACGGCCACTCAGTGGTTCGTCACGCGCAGCCCCGGGTTCGTCCCCTATAAGGGCCTAGTACCTTTCGAGCCCCGCGCGTACTAGGCAGATAAGAACCCTCCAGCTCGGGGCCTCAAACCGATATTCCATGTGGGCCAACTGCCATGTTGTGTCCAGTCGCTATCGGAGTAGCCGCGCTGGTGCCACACGACTACAACCCTCGTAATAGGGCTGCGTGCGTCCTAAATACACTCGCTGTTGAGATACTAAAATTATCTGTGGATTGCCGGCATTGAGCCCACGGTAAACCCCAAATACATAAGTGTATAATGTCTCGGACCCGTCGCAACGGTTGTTAATATG SRR7172098 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 04:41:42 Started mapping on | Feb 14 04:41:42 Finished on | Feb 14 04:48:01 Mapping speed, Million of reads per hour | 73.49 Number of input reads | 7737102 Average input read length | 292 UNIQUE READS: Uniquely mapped reads number | 5045698 Uniquely mapped reads % | 65.21% Average mapped length | 290.60 Number of splices: Total | 3503339 Number of splices: Annotated (sjdb) | 3409413 Number of splices: GT/AG | 3433026 Number of splices: GC/AG | 46780 Number of splices: AT/AC | 3081 Number of splices: Non-canonical | 20452 Mismatch rate per base, % | 0.43% Deletion rate per base | 0.05% Deletion average length | 2.55 Insertion rate per base | 0.03% Insertion average length | 2.17 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 139438 % of reads mapped to multiple loci | 1.80% Number of reads mapped to too many loci | 42730 % of reads mapped to too many loci | 0.55% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 32.22% % of reads unmapped: other | 0.21% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2561750 2561750 2561750 N_multimapping 139438 139438 139438 N_noFeature 162191 4963400 184458 N_ambiguous 84167 412 23935 UnstrandedReadsAssigned:4799340 PositiveStrandReadsAssigned:81886 NegativeStrandReadsAssigned:4837305 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=147 echo kmer=143 SRR7172098 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: SRR7172098-trimmed-pair1.fastq SRR7172098-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 7,737,102 reads, 4,845,744 reads pseudoaligned [quant] estimated average fragment length: 209.031 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,105 rounds 52401 SRR7172098.ke.tsv 34699 SRR7172098.se.tsv 87100 total ==> SRR7172098.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1809.97 402 37.8139 Potri.005G024800.1.v4.1 1035 826.969 55 11.3232 Potri.004G059700.1.v4.1 961 752.981 17 3.84381 Potri.007G009000.2.v4.1 1416 1207.97 0 0 Potri.003G141000.2.v4.1 2943 2734.97 248 15.4382 Potri.016G087400.1.v4.1 270 90.089 258 487.579 Potri.015G069301.1.v4.1 564 357.152 0 0 Potri.010G195200.1.v4.1 1773 1564.97 355 38.6206 Potri.012G127500.1.v4.1 977 768.975 2478 548.638 ==> SRR7172098.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 34 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 990 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 321 Potri.001G452600.v4.1 188 SRR7172098 completed mapping pipeline successfully