Starting /dee2/code/volunteer_pipeline.sh SRR12768914 current disk space = 3057345908736 free memory = 1510702420 SRR12768914 SRAfilesize 463113376083353d3cedad6c4c3274c7 SRR12768914.sra SRR12768914.sra file validated SRR12768914 is paired end SRR12768914 is conventional basespace SRR12768914 read1 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12768914_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.76175 37.0 37.0 37.0 37.0 37.0 2 36.5355 37.0 37.0 37.0 37.0 37.0 3 36.4565 37.0 37.0 37.0 37.0 37.0 4 35.995 37.0 37.0 37.0 37.0 37.0 5 35.3915 37.0 37.0 37.0 37.0 37.0 6 35.6445 37.0 37.0 37.0 37.0 37.0 7 35.4175 37.0 37.0 37.0 37.0 37.0 8 35.4235 37.0 37.0 37.0 37.0 37.0 9 35.0645 37.0 37.0 37.0 25.0 37.0 10-14 35.2432 37.0 37.0 37.0 29.8 37.0 15-19 35.9722 37.0 37.0 37.0 37.0 37.0 20-24 35.880100000000006 37.0 37.0 37.0 37.0 37.0 25-29 35.843 37.0 37.0 37.0 37.0 37.0 30-34 35.397 37.0 37.0 37.0 32.2 37.0 35-39 35.5997 37.0 37.0 37.0 34.6 37.0 40-44 35.8776 37.0 37.0 37.0 37.0 37.0 45-49 35.7072 37.0 37.0 37.0 37.0 37.0 50-54 35.7753 37.0 37.0 37.0 37.0 37.0 55-59 35.7033 37.0 37.0 37.0 37.0 37.0 60-64 35.6642 37.0 37.0 37.0 37.0 37.0 65-69 35.569300000000005 37.0 37.0 37.0 37.0 37.0 70-74 35.3495 37.0 37.0 37.0 37.0 37.0 75-79 35.0104 37.0 37.0 37.0 25.0 37.0 80-84 34.2 37.0 37.0 37.0 25.0 37.0 85-89 33.3496 37.0 37.0 37.0 16.6 37.0 90-94 32.3552 37.0 37.0 37.0 11.0 37.0 95-99 30.9882 37.0 25.0 37.0 11.0 37.0 100-104 29.915100000000002 37.0 25.0 37.0 11.0 37.0 105-109 29.523499999999995 37.0 25.0 37.0 11.0 37.0 110-114 29.55 37.0 25.0 37.0 11.0 37.0 115-119 29.639499999999998 37.0 25.0 37.0 11.0 37.0 120-124 30.620800000000003 37.0 25.0 37.0 11.0 37.0 125-129 31.274 37.0 25.0 37.0 11.0 37.0 130-134 31.966500000000003 37.0 32.2 37.0 11.0 37.0 135-139 32.404700000000005 37.0 37.0 37.0 11.0 37.0 140-144 33.016200000000005 37.0 37.0 37.0 11.0 37.0 145-149 33.6305 37.0 37.0 37.0 22.2 37.0 150 33.9635 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 2.0 23 10.0 24 15.0 25 20.0 26 38.0 27 46.0 28 68.0 29 78.0 30 117.0 31 214.0 32 390.0 33 850.0 34 1180.0 35 382.0 36 561.0 37 29.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 1.5761821366024518 94.17062797097825 2.476857643232424 1.77633224918689 2 1.275 2.9250000000000003 6.375 89.425 3 12.475 70.95 9.875 6.7 4 18.575 35.725 32.175 13.525 5 31.75 24.0 29.75 14.499999999999998 6 30.125 24.3 30.8 14.774999999999999 7 24.125 27.425 31.5 16.950000000000003 8 24.7 25.45 31.225 18.625 9 27.85 26.325 30.775000000000002 15.049999999999999 10-14 25.669999999999998 24.545 32.015 17.77 15-19 25.085 25.490000000000002 31.295 18.13 20-24 24.845 25.074999999999996 31.269999999999996 18.81 25-29 23.849999999999998 27.02 31.080000000000002 18.05 30-34 25.009999999999998 27.67 29.48 17.84 35-39 24.77 28.33 28.849999999999998 18.05 40-44 25.575 29.475 27.375 17.575 45-49 25.75 29.82 25.575 18.855 50-54 26.384999999999998 29.965000000000003 24.240000000000002 19.41 55-59 24.91 29.985 23.885 21.22 60-64 24.335 30.34 22.925 22.400000000000002 65-69 22.795 31.2 22.814999999999998 23.189999999999998 70-74 21.595 31.819999999999997 24.055 22.53 75-79 20.599999999999998 31.540000000000003 24.740000000000002 23.119999999999997 80-84 21.525 31.135 24.915000000000003 22.425 85-89 20.395 29.01 27.37 23.225 90-94 21.12 26.39 29.14 23.35 95-99 23.11 25.790000000000003 28.53 22.57 100-104 25.97 24.785 27.98 21.265 105-109 31.380000000000003 23.335 26.090000000000003 19.195 110-114 36.78 22.57 24.3 16.35 115-119 43.635000000000005 20.200000000000003 21.14 15.024999999999999 120-124 50.79 17.72 18.395 13.095 125-129 56.56 15.36 16.49 11.59 130-134 60.485 14.38 15.225 9.91 135-139 65.405 13.475000000000001 12.425 8.695 140-144 68.715 12.49 11.155 7.64 145-149 72.50999999999999 9.825000000000001 10.315000000000001 7.35 150 74.52499999999999 10.299999999999999 9.700000000000001 5.475 >>END_MODULE >>Per sequence GC content warn #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 0.5 8 1.0 9 0.5 10 1.0 11 3.0 12 3.0 13 1.0 14 0.0 15 1.5 16 2.0 17 2.0 18 4.5 19 3.0 20 2.5 21 5.0 22 6.0 23 7.0 24 6.0 25 6.5 26 7.0 27 6.5 28 8.0 29 11.5 30 16.0 31 21.0 32 21.0 33 30.0 34 40.0 35 47.0 36 62.5 37 74.0 38 98.5 39 122.5 40 151.0 41 178.5 42 227.0 43 300.0 44 330.5 45 327.0 46 321.5 47 335.5 48 319.5 49 252.5 50 197.0 51 160.5 52 102.5 53 61.5 54 41.0 55 22.0 56 15.0 57 9.0 58 8.0 59 5.0 60 4.0 61 3.5 62 2.5 63 1.5 64 1.0 65 0.5 66 0.5 67 0.5 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 0.075 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 85.9 #Duplication Level Percentage of deduplicated Percentage of total 1 90.9487776484284 78.125 2 6.519208381839348 11.200000000000001 3 1.3678696158323633 3.5249999999999995 4 0.3492433061699651 1.2 5 0.2037252619324796 0.8750000000000001 6 0.11641443538998836 0.6 7 0.2037252619324796 1.225 8 0.02910360884749709 0.2 9 0.08731082654249127 0.675 >10 0.17462165308498254 2.375 >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 ACGTGTTCTTTTGAAGATTGTTGTTCGATTGTTACCTGAGAAAAGAAGAT 19 0.475 No Hit ACAAGTAGGAGCTCGAATTTCCCCGATCGTTCAAAGATCGGAAGAGCACA 18 0.44999999999999996 No Hit ACATGTTAGTGCTCCATGATCTTGAGAAGGAAACCTTGTCATTCCTTCCA 17 0.42500000000000004 No Hit ACATCCCAATTTCAGACTGTGAGTAACCCTGTAAGGAGATCGGAAGAGCA 16 0.4 No Hit ACTATGCGACCAGATCTCTGATGCGGTGCTCGATGCTTGCCTTGAGCAGG 13 0.325 No Hit ACGTGTTGCTGTTGATATTTAATTTGGTAATTTGATGTCAATTTTCTGAT 12 0.3 No Hit ACAACGATCAAGAGCGACTGTGCTATTCCTGCAATTCTTGCAAAGCTGGT 9 0.22499999999999998 No Hit ACGTGTCATTTATCTGGTTTGATCAATTCTGAAGCTATTATTTGTTTCCA 9 0.22499999999999998 No Hit ACCATGTCTGTTGGTACGTGTGATCTTTGGTATTGTAATAAAAAAAATAG 9 0.22499999999999998 No Hit ACATCATTAGCAACTGAAATGGGAAGATTGGTCTCTGAAGGGTATGTGCT 8 0.2 No Hit ACAAACTATGTGACCAGATCTCTGATGCAGTGCTCGATGCCTGCCTTGAG 7 0.17500000000000002 No Hit ACATGGGAGACTGTCAAGCTTCTCAAGCCCAATGCCTAAGTCTTTGGGAT 7 0.17500000000000002 No Hit ACAATGTTGGTTTCAATGTTAAGAATGTTGCTGTCAAGGATCTCAAAGAT 7 0.17500000000000002 No Hit ACAAACTATGCGACCAGATCTCTGATGCGGTGCTCGATGCTTGCCTTGAG 7 0.17500000000000002 No Hit ACAGAATAACTTCTCTGAAGATGCTGAAACCGATATGGTCGATGAGATCG 7 0.17500000000000002 No Hit ACAAAAGAGGAACTAATGAAGGTGCTCTGACTAGAGTTGTCGCTAGATCG 7 0.17500000000000002 No Hit ACAGTCGGGGGCATTCGTATTTCATAGTCAGAGGTGAAATTCTTGGATTT 7 0.17500000000000002 No Hit ACATCCACTTTTGAAAGCTTCAGGAGCTGGAAGGATTGTCTTTGTGTCCT 6 0.15 No Hit ACAAACGTGTTGCTGTTGATATTTAATTTGGTAATTTGATGTCAATTTTC 6 0.15 No Hit ACCAAGGATCGCGGGTTGTTTGATTTCCTGGGGAAGAAAGAAGAAGAGAA 6 0.15 No Hit ACATGAAGACTGTGATGCTCTTTGGAATTCTAAATGGTGTTTCTATCGGA 6 0.15 No Hit ACAAAACTGTATGGAGTCTATTAAACTTCTATGCCTACGTGAAAAACCAC 5 0.125 No Hit ACATGGGATTTAATTTAATAAGGTTTTGGATGGGGGTGCGTGGGATAATA 5 0.125 No Hit ACATGATGTGTGCTGCTGATCCTCGCCATGGCAGATATCTCACAGCATCT 5 0.125 No Hit ACTATGTGACCAGATCTCTGATGCAGTGCTCGATGCCTGCCTTGAGCAGG 5 0.125 No Hit ACAGCAGGACGGTGGTCATGGAAGTCGAAATCCGCTAAGGAGTGTGTAAG 5 0.125 No Hit ACAATTATTTGGTTATGCCATTTTAGGATTTGCTCTAACGGAAGCAATCG 5 0.125 No Hit ACACGATGTATTTGTTGGCAAATGGAAACCTACCAAGAATGAGATCGGAA 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 0.025 0.0 0.0 0.0 0.0 2 0.025 0.0 0.0 0.0 0.0 3 0.075 0.0 0.0 0.0 0.0 4 0.15 0.0 0.0 0.0 0.0 5 0.15 0.0 0.0 0.0 0.0 6 0.175 0.0 0.0 0.0 0.0 7 0.2 0.0 0.0 0.0 0.0 8 0.225 0.0 0.0 0.0 0.0 9 0.225 0.0 0.0 0.0 0.0 10-11 0.3625 0.0 0.0 0.0 0.0 12-13 0.4 0.0 0.0 0.0 0.0 14-15 0.45 0.0 0.0 0.0 0.0 16-17 0.525 0.0 0.0 0.0 0.0 18-19 0.5875 0.0 0.0 0.0 0.0 20-21 0.6875 0.0 0.0 0.0 0.0 22-23 0.9875 0.0 0.0 0.0 0.0 24-25 1.1875 0.0 0.0 0.0 0.0 26-27 1.625 0.0 0.0 0.0 0.0 28-29 2.3875 0.0 0.0 0.0 0.0 30-31 3.675 0.0 0.0 0.0 0.0 32-33 5.4875 0.0 0.0 0.0 0.0 34-35 8.0875 0.0 0.0 0.0 0.0 36-37 10.425 0.0 0.0 0.0 0.0 38-39 12.8125 0.0 0.0 0.0 0.0 40-41 15.75 0.0 0.0 0.0 0.0 42-43 18.4875 0.0 0.0 0.0 0.0 44-45 21.475 0.0 0.0 0.0 0.0 46-47 25.5875 0.0 0.0 0.0 0.0 48-49 29.0 0.0 0.0 0.0 0.0 50-51 32.25 0.0 0.0 0.0 0.0 52-53 35.8 0.0 0.0 0.0 0.0 54-55 38.724999999999994 0.0 0.0 0.0 0.0 56-57 41.3 0.0 0.0 0.0 0.0 58-59 43.412499999999994 0.0 0.0 0.0 0.0 60-61 45.6625 0.0 0.0 0.0 0.0 62-63 47.9875 0.0 0.0 0.0 0.0 64-65 50.275 0.0 0.0 0.0 0.0 66-67 52.2625 0.0 0.0 0.0 0.0 68-69 54.1375 0.0 0.0 0.0 0.0 70-71 56.0375 0.0 0.0 0.0 0.0 72-73 58.0875 0.0 0.0 0.0 0.0 74-75 60.3875 0.0 0.0 0.0 0.0 76-77 61.95 0.0 0.0 0.0 0.0 78-79 63.125 0.0 0.0 0.0 0.0 80-81 64.0875 0.0 0.0 0.0 0.0 82-83 65.07499999999999 0.0 0.0 0.0 0.0 84-85 66.275 0.0 0.0 0.0 0.0 86-87 67.375 0.0 0.0 0.0 0.0 88-89 68.2625 0.0 0.0 0.0 0.0 90-91 69.175 0.0 0.0 0.0 0.0 92-93 69.875 0.0 0.0 0.0 0.0 94-95 70.69999999999999 0.0 0.0 0.0 0.0 96-97 71.6125 0.0 0.0 0.0 0.0 98-99 72.175 0.0 0.0 0.0 0.0 100-101 72.85 0.0 0.0 0.0 0.0 102-103 73.67500000000001 0.0 0.0 0.0 0.0 104-105 74.525 0.0 0.0 0.0 0.0 106-107 75.125 0.0 0.0 0.0 0.0 108-109 75.6625 0.0 0.0 0.0 0.0 110-111 76.1875 0.0 0.0 0.0 0.0 112-113 76.6875 0.0 0.0 0.0 0.0 114-115 77.125 0.0 0.0 0.0 0.0 116-117 77.65 0.0 0.0 0.0 0.0 118-119 78.1875 0.0 0.0 0.0 0.0 120-121 78.6125 0.0 0.0 0.0 0.0 122-123 78.9625 0.0 0.0 0.0 0.0 124-125 79.375 0.0 0.0 0.0 0.0 126-127 79.63749999999999 0.0 0.0 0.0 0.0 128-129 80.13749999999999 0.0 0.0 0.0 0.0 130-131 80.675 0.0 0.0 0.0 0.0 132-133 81.0875 0.0 0.0 0.0 0.0 134-135 81.4375 0.0 0.0 0.0 0.0 136-137 81.7125 0.0 0.0 0.0 0.0 138 82.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTTTTGA 10 0.006973645 144.0 8 ACATTTA 10 0.006973645 144.0 1 ACATTGG 10 0.006973645 144.0 1 AAGGTTG 10 0.006973645 144.0 3 ACAAGGA 10 0.006973645 144.0 1 GTTGGAG 10 0.006973645 144.0 6 ACGTGTT 10 0.006973645 144.0 1 ACAGTTT 10 0.006973645 144.0 1 TTTTTTT 90 0.0051234453 11.2 15-19 GGGGGGG 6580 0.0 5.4711246 140-144 >>END_MODULE SRR12768914 read2 length is 150 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12768914_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 150 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.516 37.0 37.0 37.0 37.0 37.0 2 36.267 37.0 37.0 37.0 37.0 37.0 3 36.273 37.0 37.0 37.0 37.0 37.0 4 36.399 37.0 37.0 37.0 37.0 37.0 5 36.6385 37.0 37.0 37.0 37.0 37.0 6 36.12 37.0 37.0 37.0 37.0 37.0 7 36.576 37.0 37.0 37.0 37.0 37.0 8 36.6105 37.0 37.0 37.0 37.0 37.0 9 36.474 37.0 37.0 37.0 37.0 37.0 10-14 36.4816 37.0 37.0 37.0 37.0 37.0 15-19 36.5153 37.0 37.0 37.0 37.0 37.0 20-24 36.4495 37.0 37.0 37.0 37.0 37.0 25-29 36.335899999999995 37.0 37.0 37.0 37.0 37.0 30-34 36.199 37.0 37.0 37.0 37.0 37.0 35-39 36.173 37.0 37.0 37.0 37.0 37.0 40-44 36.116699999999994 37.0 37.0 37.0 37.0 37.0 45-49 36.13869999999999 37.0 37.0 37.0 37.0 37.0 50-54 36.069399999999995 37.0 37.0 37.0 37.0 37.0 55-59 35.9591 37.0 37.0 37.0 37.0 37.0 60-64 35.9966 37.0 37.0 37.0 37.0 37.0 65-69 35.9668 37.0 37.0 37.0 37.0 37.0 70-74 35.91610000000001 37.0 37.0 37.0 37.0 37.0 75-79 35.6553 37.0 37.0 37.0 37.0 37.0 80-84 35.3435 37.0 37.0 37.0 37.0 37.0 85-89 34.93730000000001 37.0 37.0 37.0 29.8 37.0 90-94 34.1003 37.0 37.0 37.0 25.0 37.0 95-99 33.4647 37.0 37.0 37.0 16.6 37.0 100-104 32.87330000000001 37.0 37.0 37.0 11.0 37.0 105-109 32.4467 37.0 37.0 37.0 11.0 37.0 110-114 32.3849 37.0 37.0 37.0 11.0 37.0 115-119 32.59080000000001 37.0 37.0 37.0 11.0 37.0 120-124 32.585 37.0 37.0 37.0 11.0 37.0 125-129 32.753699999999995 37.0 37.0 37.0 11.0 37.0 130-134 32.479200000000006 37.0 37.0 37.0 11.0 37.0 135-139 32.6838 37.0 37.0 37.0 11.0 37.0 140-144 32.8594 37.0 37.0 37.0 11.0 37.0 145-149 32.898399999999995 37.0 37.0 37.0 11.0 37.0 150 33.0505 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 18 3.0 19 1.0 20 6.0 21 9.0 22 12.0 23 17.0 24 15.0 25 13.0 26 17.0 27 13.0 28 18.0 29 77.0 30 82.0 31 141.0 32 161.0 33 290.0 34 506.0 35 1400.0 36 1116.0 37 103.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 16.400000000000002 22.8 35.75 25.05 2 16.75 30.75 20.175 32.324999999999996 3 13.600000000000001 24.2 39.7 22.5 4 17.925 28.65 28.7 24.725 5 18.925 31.374999999999996 26.200000000000003 23.5 6 16.150000000000002 30.875000000000004 28.799999999999997 24.175 7 17.575 27.950000000000003 27.075 27.400000000000002 8 17.849999999999998 33.575 26.700000000000003 21.875 9 17.2 31.075000000000003 28.425 23.3 10-14 18.93 30.630000000000003 25.64 24.8 15-19 18.345 30.85 26.669999999999998 24.135 20-24 18.275 31.28 25.900000000000002 24.545 25-29 17.615 31.215 25.974999999999998 25.195 30-34 19.885 29.145 27.62 23.35 35-39 20.979999999999997 29.599999999999998 27.200000000000003 22.220000000000002 40-44 21.59 29.13 26.715 22.564999999999998 45-49 22.905 28.560000000000002 27.29 21.245 50-54 23.335 28.000000000000004 27.165 21.5 55-59 23.275000000000002 27.705000000000002 27.155 21.865000000000002 60-64 24.02 28.455000000000002 27.08 20.445 65-69 24.21 27.315 27.46 21.015 70-74 25.740000000000002 25.259999999999998 28.439999999999998 20.560000000000002 75-79 27.16 24.45 27.3 21.09 80-84 26.91 23.43 28.410000000000004 21.25 85-89 26.295 24.575 28.044999999999998 21.085 90-94 27.939999999999998 25.424999999999997 26.700000000000003 19.935 95-99 29.330000000000002 25.685000000000002 26.634999999999998 18.35 100-104 33.145 26.1 25.380000000000003 15.375 105-109 38.800000000000004 23.62 23.0 14.580000000000002 110-114 46.18 20.849999999999998 20.48 12.49 115-119 51.190000000000005 18.725 18.475 11.61 120-124 55.06999999999999 17.51 16.835 10.585 125-129 59.330000000000005 16.45 15.465000000000002 8.755 130-134 63.415 14.975 13.514999999999999 8.094999999999999 135-139 67.415 11.790000000000001 13.235 7.5600000000000005 140-144 70.045 11.62 11.76 6.575 145-149 72.08 10.43 11.125 6.365 150 73.45 9.75 10.625 6.175 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 11.0 1 7.0 2 3.5 3 3.5 4 2.5 5 3.5 6 3.5 7 2.5 8 1.5 9 0.5 10 1.0 11 2.0 12 1.5 13 0.0 14 0.0 15 0.5 16 3.5 17 5.5 18 3.5 19 2.0 20 2.5 21 4.0 22 5.5 23 3.5 24 3.0 25 7.5 26 9.5 27 7.5 28 5.5 29 7.0 30 8.5 31 14.5 32 19.5 33 25.0 34 34.5 35 50.5 36 57.5 37 69.5 38 87.0 39 95.5 40 119.5 41 140.5 42 165.0 43 203.0 44 263.0 45 299.0 46 294.0 47 309.5 48 327.5 49 302.5 50 253.0 51 210.5 52 156.0 53 115.0 54 92.0 55 63.5 56 41.5 57 24.0 58 12.0 59 6.0 60 4.5 61 4.0 62 2.5 63 2.0 64 4.0 65 3.0 66 2.5 67 3.5 68 2.0 69 1.0 70 0.5 71 0.5 72 0.5 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 0.5 100 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 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 150 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.425 #Duplication Level Percentage of deduplicated Percentage of total 1 90.316849274504 76.25 2 7.1957358602309744 12.15 3 1.2733195143618596 3.225 4 0.32573289902280134 1.0999999999999999 5 0.26650873556411014 1.125 6 0.059224163458691144 0.3 7 0.11844832691738229 0.7000000000000001 8 0.08883624518803672 0.6 9 0.11844832691738229 0.8999999999999999 >10 0.23689665383476458 3.65 >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 TTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTTT 21 0.525 No Hit AGTTCACAATCCAAAGCCTAATCAGAAAATTGACATCAAATTACCAAATT 21 0.525 No Hit TGGAAGGAATGACAAGGTTTCCTTCTCAAGATCATGGAGCACTAACATGT 20 0.5 No Hit TCTTTTCTCAGGTAACAATCGAACAACAATCTTCAAAAGAACACGTGATC 20 0.5 No Hit TTGAACGATCGGGGAAATTCGAGCTCCTACTTGTGATCGTCGGACTGTAG 19 0.475 No Hit CCTGCTCAAGGCAAGCATCGAGCACCGCATCAGAGATCTGGTCGCATAGT 19 0.475 No Hit CCTTACAGGGTTACTCACAGTCTGAAATTGGGATGTGATCGTCGGACTGT 16 0.4 No Hit CTGGGTCCTGCTCAAGGCAGGCATCGAGCACTGCATCAGAGATCTGGTCA 10 0.25 No Hit ATTTTTTTTATTACAATACCAAAGATCACACGTACCAACAGACATGGTGA 9 0.22499999999999998 No Hit AAATGGAAACAAATAATAGCTTCAGAATTGATCAAACCAGATAAATGACA 9 0.22499999999999998 No Hit AGCTGCTCCCGCACCTATTAATTTAGCACCTTCTAACATTCTCTTTTTTC 9 0.22499999999999998 No Hit TAGCACATACCCTTCAGAGACCAATCTTCCCATTTCAGTTGCTAATGATG 9 0.22499999999999998 No Hit ATCAAGCCAATCCCAAAGACTTAGGCATTGGGCTTGAGAAGCTTGACAGT 8 0.2 No Hit TCGTCTTTCATAAATCCAAGAATTTCACCTCTGACTATGAAATACGAATG 8 0.2 No Hit TAATGACCGAGACCTTCCTCCAACTCTTCCTCAGGTTGGCTAGCAAACCA 8 0.2 No Hit ATGAAACCTCTGGTGCACTTTACGTGGTTTTTCACGTAGGCATAGAAGTT 7 0.17500000000000002 No Hit AGCGACAACTCTAGTCAGAGCACCTTCATTAGTTCCTCTTTTGTGATCGT 7 0.17500000000000002 No Hit TTGAGATCCTTGACAGCAACATTCTTAACATTGAAACCAACATTGTGATC 7 0.17500000000000002 No Hit CATCGACCATATCGGTTTCAGCATCTTCAGAGAAGTTATTCTGTGATCGT 7 0.17500000000000002 No Hit AAGGGGCCACCCACCCATTCCCCTTAGCCCTCTCACTCCCTAAGCTAAGG 6 0.15 No Hit CACGCCGCAAATAGAGGACACAAAGACAATCCTTCCAGCTCCTGAAGCTT 6 0.15 No Hit GCGTCGCTCCAATCATGGCATATCCACTTCATGAAAACGGCATCTGCTTT 5 0.125 No Hit AACTACCAGCAAATAGGCAATAGCTAAAACAGTCCTTGTGATCGTCGGAC 5 0.125 No Hit GCTCATTTTGCCACGAAACATTGCAGATGCTGTGAGATATCTGCCATGGC 5 0.125 No Hit TACACACTCCTTAGCGGATTTCGACTTCCATGACCACCGTCCTGCTGTGA 5 0.125 No Hit TTTCCTCAGCCATACTGATCAAAATCACAATATGAACCTAATGAAGAAAA 5 0.125 No Hit CCGATAGAAACACCATTTAGAATTCCAAAGAGCATCACAGTCTTCATGTG 5 0.125 No Hit CCCAGTGAGCGGGATCGACCTTGCACTTCTCAAAGAAGTCAACAAGGAGC 5 0.125 No Hit TTTCCTCAGCCATACTGATCAAAATCACAATATGAACCTAATCAAGAAAA 5 0.125 No Hit CATTCTTGGTAGGTTTCCATTTGCCAACAAATACATCGTGTGATCGTCGG 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 0.025 0.0 0.0 2 0.0 0.0 0.025 0.0 0.0 3 0.0 0.0 0.075 0.0 0.0 4 0.0 0.0 0.15 0.0 0.0 5 0.0 0.0 0.15 0.0 0.0 6 0.0 0.0 0.175 0.0 0.0 7 0.0 0.0 0.2 0.0 0.0 8 0.0 0.0 0.225 0.0 0.0 9 0.0 0.0 0.225 0.0 0.0 10-11 0.0 0.0 0.3625 0.0 0.0 12-13 0.0 0.0 0.4 0.0 0.0 14-15 0.0 0.0 0.45 0.0 0.0 16-17 0.0 0.0 0.525 0.0 0.0 18-19 0.0 0.0 0.5875 0.0 0.0 20-21 0.0 0.0 0.6875 0.0 0.0 22-23 0.0 0.0 0.9875 0.0 0.0 24-25 0.0 0.0 1.2125 0.0 0.0 26-27 0.0 0.0 1.6625 0.0 0.0 28-29 0.0 0.0 2.425 0.0 0.0 30-31 0.0 0.0 3.6875 0.0 0.0 32-33 0.0 0.0 5.4875 0.0 0.0 34-35 0.0 0.0 8.1 0.0 0.0 36-37 0.0 0.0 10.45 0.0 0.0 38-39 0.0 0.0 12.8375 0.0 0.0 40-41 0.0 0.0 15.725000000000001 0.0 0.0 42-43 0.0 0.0 18.45 0.0 0.0 44-45 0.0 0.0 21.35 0.0 0.0 46-47 0.0 0.0 25.4 0.0 0.0 48-49 0.0 0.0 28.675 0.0 0.0 50-51 0.0 0.0 31.8375 0.0 0.0 52-53 0.0 0.0 35.375 0.0 0.0 54-55 0.0 0.0 38.2875 0.0 0.0 56-57 0.0 0.0 40.8625 0.0 0.0 58-59 0.0 0.0 42.95 0.0 0.0 60-61 0.0 0.0 45.212500000000006 0.0 0.0 62-63 0.0 0.0 47.537499999999994 0.0 0.0 64-65 0.0 0.0 49.712500000000006 0.0 0.0 66-67 0.0 0.0 51.7 0.0 0.0 68-69 0.0 0.0 53.55 0.0 0.0 70-71 0.0 0.0 55.425 0.0 0.0 72-73 0.0 0.0 57.35 0.0 0.0 74-75 0.0 0.0 59.5875 0.0 0.0 76-77 0.0 0.0 61.150000000000006 0.0 0.0 78-79 0.0 0.0 62.3 0.0 0.0 80-81 0.0 0.0 63.2375 0.0 0.0 82-83 0.0 0.0 64.225 0.0 0.0 84-85 0.0 0.0 65.425 0.0 0.0 86-87 0.0 0.0 66.5 0.0 0.0 88-89 0.0 0.0 67.4125 0.0 0.0 90-91 0.0 0.0 68.325 0.0 0.0 92-93 0.0 0.0 69.025 0.0 0.0 94-95 0.0 0.0 69.8625 0.0 0.0 96-97 0.0 0.0 70.7375 0.0 0.0 98-99 0.0 0.0 71.3 0.0 0.0 100-101 0.0 0.0 71.975 0.0 0.0 102-103 0.0 0.0 72.80000000000001 0.0 0.0 104-105 0.0 0.0 73.625 0.0 0.0 106-107 0.0 0.0 74.175 0.0 0.0 108-109 0.0 0.0 74.7125 0.0 0.0 110-111 0.0 0.0 75.275 0.0 0.0 112-113 0.0 0.0 75.76249999999999 0.0 0.0 114-115 0.0 0.0 76.1625 0.0 0.0 116-117 0.0 0.0 76.675 0.0 0.0 118-119 0.0 0.0 77.2125 0.0 0.0 120-121 0.0 0.0 77.625 0.0 0.0 122-123 0.0 0.0 77.9375 0.0 0.0 124-125 0.0 0.0 78.375 0.0 0.0 126-127 0.0 0.0 78.63749999999999 0.0 0.0 128-129 0.0 0.0 79.15 0.0 0.0 130-131 0.0 0.0 79.675 0.0 0.0 132-133 0.0 0.0 80.1125 0.0 0.0 134-135 0.0 0.0 80.4875 0.0 0.0 136-137 0.0 0.0 80.80000000000001 0.0 0.0 138 0.0 0.0 81.1 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCAGGTA 10 0.006973645 144.0 8 TTTCTCA 10 0.006973645 144.0 4 CATCCCT 10 0.006973645 144.0 9 TTTTCTC 10 0.006973645 144.0 3 GGTTCAA 10 0.006973645 144.0 8 CTCAGGT 10 0.006973645 144.0 7 ATTCTCA 10 0.006973645 144.0 8 TCATCCC 10 0.006973645 144.0 8 TCTCAGG 10 0.006973645 144.0 6 >>END_MODULE Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291790 spots for SRR12768914.sra Written 2291790 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra Read 2291771 spots for SRR12768914.sra Written 2291771 spots for SRR12768914.sra SRR ids: ['SRR12768914.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_uh9h_d7w SRR12768914.sra spots: 45835439 blocks: [[1, 2291771], [2291772, 4583542], [4583543, 6875313], [6875314, 9167084], [9167085, 11458855], [11458856, 13750626], [13750627, 16042397], [16042398, 18334168], [18334169, 20625939], [20625940, 22917710], [22917711, 25209481], [25209482, 27501252], [27501253, 29793023], [29793024, 32084794], [32084795, 34376565], [34376566, 36668336], [36668337, 38960107], [38960108, 41251878], [41251879, 43543649], [43543650, 45835439]] SRR12768914 file size 15465664 SRR12768914 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 SRR12768914 SRR12768914_1.fastq SRR12768914_2.fastq Input file: SRR12768914_1.fastq Paired file: SRR12768914_2.fastq trimmed: SRR12768914-trimmed-pair1.fastq, SRR12768914-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 Mon Feb 10 22:28:55 2025 >> started Mon Feb 10 22:30:04 2025 >> done (68.146s) 45835439 read pairs processed; of these: 181013 ( 0.39%) short read pairs filtered out after trimming by size control 8654 ( 0.02%) empty read pairs filtered out after trimming by size control 45645772 (99.59%) read pairs available; of these: 39259038 (86.01%) trimmed read pairs available after processing 6386734 (13.99%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 20612 0.05% 19 30272 0.07% 20 31360 0.07% 21 56453 0.12% 22 57694 0.13% 23 72568 0.16% 24 128758 0.28% 25 107039 0.23% 26 147699 0.32% 27 183253 0.40% 28 275594 0.60% 29 252360 0.55% 30 394740 0.86% 31 350836 0.77% 32 341830 0.75% 33 645440 1.41% 34 642473 1.41% 35 561632 1.23% 36 735920 1.61% 37 595883 1.31% 38 603453 1.32% 39 773569 1.69% 40 583491 1.28% 41 705123 1.54% 42 691318 1.51% 43 722280 1.58% 44 836137 1.83% 45 812331 1.78% 46 955401 2.09% 47 710889 1.56% 48 858356 1.88% 49 711909 1.56% 50 997913 2.19% 51 781606 1.71% 52 737966 1.62% 53 643538 1.41% 54 710186 1.56% 55 608174 1.33% 56 590831 1.29% 57 598329 1.31% 58 493392 1.08% 59 554974 1.22% 60 575441 1.26% 61 475534 1.04% 62 494447 1.08% 63 446720 0.98% 64 476504 1.04% 65 452341 0.99% 66 525613 1.15% 67 385317 0.84% 68 423508 0.93% 69 446382 0.98% 70 658054 1.44% 71 389795 0.85% 72 445723 0.98% 73 427013 0.94% 74 432148 0.95% 75 316713 0.69% 76 313513 0.69% 77 281483 0.62% 78 342161 0.75% 79 258618 0.57% 80 280340 0.61% 81 291914 0.64% 82 223582 0.49% 83 224635 0.49% 84 284476 0.62% 85 217915 0.48% 86 213561 0.47% 87 219597 0.48% 88 209830 0.46% 89 200144 0.44% 90 263328 0.58% 91 188246 0.41% 92 191700 0.42% 93 197109 0.43% 94 194853 0.43% 95 178869 0.39% 96 223157 0.49% 97 151936 0.33% 98 159658 0.35% 99 189906 0.42% 100 142271 0.31% 101 138567 0.30% 102 165839 0.36% 103 147147 0.32% 104 137104 0.30% 105 141022 0.31% 106 129153 0.28% 107 133497 0.29% 108 148155 0.32% 109 136160 0.30% 110 145709 0.32% 111 127368 0.28% 112 113769 0.25% 113 131315 0.29% 114 119705 0.26% 115 117087 0.26% 116 108298 0.24% 117 121540 0.27% 118 116764 0.26% 119 99509 0.22% 120 100913 0.22% 121 102067 0.22% 122 93237 0.20% 123 94012 0.21% 124 104641 0.23% 125 85437 0.19% 126 97807 0.21% 127 88594 0.19% 128 89065 0.20% 129 84123 0.18% 130 84299 0.18% 131 82946 0.18% 132 98416 0.22% 133 73332 0.16% 134 75767 0.17% 135 82793 0.18% 136 75277 0.16% 137 71846 0.16% 138 81724 0.18% 139 69124 0.15% 140 86887 0.19% 141 69661 0.15% 142 66931 0.15% 143 65189 0.14% 144 86979 0.19% 145 70187 0.15% 146 70689 0.15% 147 70228 0.15% 148 66799 0.15% 149 64723 0.14% 150 6386734 13.99% 45645772 reads passed initial QC criterion=sequence-density sequence-density=0.54 sequence-density-rank=1 fanout-score=1.72 fanout-score-rank=11 prefix-density=0.91 prefix-fanout=1.0 sequence=ATCTCTGATGCGGTGCTCGATGCTTGCCTTGAGCAGGACCCAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=41 fanout-score=64.74 fanout-score-rank=1 prefix-density=0.12 prefix-fanout=6.1 sequence=TTTTTCTTCATTTTACGTGTTCTTTTGAAGATTGTTGTTCGATTGTTACCTGAGAAAAGA criterion=sequence-density sequence-density=0.91 sequence-density-rank=1 fanout-score=2.32 fanout-score-rank=15 prefix-density=0.94 prefix-fanout=2.2 sequence=GCATCAGAGATCTGGTCGCATAGTTTGT criterion=fanout-score sequence-density=0.01 sequence-density-rank=34 fanout-score=94.62 fanout-score-rank=1 prefix-density=0.15 prefix-fanout=7.5 sequence=TTTTCTTTTCTCAGGTAACAATCGAACAACAATCTTCAAAAGAACACGTAAAATGAAGAAAA SRR12768914 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 22:30:36 Started mapping on | Feb 10 22:30:37 Finished on | Feb 10 22:33:42 Mapping speed, Million of reads per hour | 888.24 Number of input reads | 45645772 Average input read length | 152 UNIQUE READS: Uniquely mapped reads number | 37641086 Uniquely mapped reads % | 82.46% Average mapped length | 134.65 Number of splices: Total | 13565461 Number of splices: Annotated (sjdb) | 13323600 Number of splices: GT/AG | 13298257 Number of splices: GC/AG | 200916 Number of splices: AT/AC | 11038 Number of splices: Non-canonical | 55250 Mismatch rate per base, % | 0.19% Deletion rate per base | 0.02% Deletion average length | 2.04 Insertion rate per base | 0.01% Insertion average length | 1.58 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 1645583 % of reads mapped to multiple loci | 3.61% Number of reads mapped to too many loci | 291196 % of reads mapped to too many loci | 0.64% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 13.12% % of reads unmapped: other | 0.18% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 6359103 6359103 6359103 N_multimapping 1645583 1645583 1645583 N_noFeature 1805216 1908890 37240923 N_ambiguous 428002 131285 811 UnstrandedReadsAssigned:35407868 PositiveStrandReadsAssigned:35600911 NegativeStrandReadsAssigned:399352 Dataset is classified positive stranded MeadianReadLen=62 20thPercentileLength=43 echo kmer=39 SRR12768914 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: SRR12768914-trimmed-pair1.fastq SRR12768914-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 45,645,772 reads, 34,573,808 reads pseudoaligned [quant] estimated average fragment length: 66.4299 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,145 rounds 52401 SRR12768914.ke.tsv 34699 SRR12768914.se.tsv 87100 total ==> SRR12768914.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1952.57 901 20.2837 Potri.005G024800.1.v4.1 1035 969.57 273 12.3769 Potri.004G059700.1.v4.1 961 895.57 38 1.86515 Potri.007G009000.2.v4.1 1416 1350.57 0 0 Potri.003G141000.2.v4.1 2943 2877.57 711.568 10.8698 Potri.016G087400.1.v4.1 270 205.123 480 102.862 Potri.015G069301.1.v4.1 564 498.57 0 0 Potri.010G195200.1.v4.1 1773 1707.57 136 3.50098 Potri.012G127500.1.v4.1 977 911.57 2781 134.104 ==> SRR12768914.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1872 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 423 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 46 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 10 SRR12768914 completed mapping pipeline successfully