Starting /dee2/code/volunteer_pipeline.sh SRR12670102 current disk space = 3057635459072 free memory = 1236603708 SRR12670102 SRAfilesize adcb9215d05b1c900f534c7e91ef3f09 SRR12670102.sra SRR12670102.sra file validated SRR12670102 is paired end SRR12670102 is conventional basespace SRR12670102 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670102_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.674 37.0 37.0 37.0 37.0 37.0 2 36.478 37.0 37.0 37.0 37.0 37.0 3 36.647 37.0 37.0 37.0 37.0 37.0 4 36.708 37.0 37.0 37.0 37.0 37.0 5 36.68 37.0 37.0 37.0 37.0 37.0 6 36.6595 37.0 37.0 37.0 37.0 37.0 7 36.5905 37.0 37.0 37.0 37.0 37.0 8 36.6365 37.0 37.0 37.0 37.0 37.0 9 36.6185 37.0 37.0 37.0 37.0 37.0 10-14 36.6444 37.0 37.0 37.0 37.0 37.0 15-19 36.6275 37.0 37.0 37.0 37.0 37.0 20-24 36.57 37.0 37.0 37.0 37.0 37.0 25-29 36.5312 37.0 37.0 37.0 37.0 37.0 30-34 36.5433 37.0 37.0 37.0 37.0 37.0 35-39 36.5317 37.0 37.0 37.0 37.0 37.0 40-44 36.4572 37.0 37.0 37.0 37.0 37.0 45-49 36.4521 37.0 37.0 37.0 37.0 37.0 50-54 36.386300000000006 37.0 37.0 37.0 37.0 37.0 55-59 36.376000000000005 37.0 37.0 37.0 37.0 37.0 60-64 36.4134 37.0 37.0 37.0 37.0 37.0 65-69 36.3712 37.0 37.0 37.0 37.0 37.0 70-74 36.3675 37.0 37.0 37.0 37.0 37.0 75-79 36.36300000000001 37.0 37.0 37.0 37.0 37.0 80-84 36.39640000000001 37.0 37.0 37.0 37.0 37.0 85-89 36.3482 37.0 37.0 37.0 37.0 37.0 90-94 36.3144 37.0 37.0 37.0 37.0 37.0 95-99 36.320499999999996 37.0 37.0 37.0 37.0 37.0 100-104 36.3277 37.0 37.0 37.0 37.0 37.0 105-109 36.3349 37.0 37.0 37.0 37.0 37.0 110-114 36.2267 37.0 37.0 37.0 37.0 37.0 115-119 36.274 37.0 37.0 37.0 37.0 37.0 120-124 36.153499999999994 37.0 37.0 37.0 37.0 37.0 125-129 36.11030000000001 37.0 37.0 37.0 37.0 37.0 130-134 36.065999999999995 37.0 37.0 37.0 37.0 37.0 135-139 35.9498 37.0 37.0 37.0 37.0 37.0 140-144 35.8419 37.0 37.0 37.0 37.0 37.0 145-149 35.7779 37.0 37.0 37.0 37.0 37.0 150-151 35.493 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 0.0 24 2.0 25 2.0 26 2.0 27 4.0 28 9.0 29 16.0 30 18.0 31 36.0 32 43.0 33 62.0 34 115.0 35 279.0 36 2949.0 37 462.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 38.324999999999996 10.75 8.175 42.75 2 20.476190476190474 13.258145363408522 34.76190476190476 31.50375939849624 3 19.275000000000002 15.4 28.15 37.175000000000004 4 22.15 24.099999999999998 23.05 30.7 5 23.849999999999998 28.225 25.25 22.675 6 22.275 32.05 23.35 22.325 7 16.125 27.224999999999998 40.150000000000006 16.5 8 17.05 28.375 30.599999999999998 23.974999999999998 9 17.849999999999998 23.75 34.300000000000004 24.099999999999998 10-14 19.71 29.67 27.725 22.895 15-19 20.59 28.084999999999997 27.139999999999997 24.185000000000002 20-24 19.98 27.855 28.060000000000002 24.104999999999997 25-29 20.419999999999998 27.82 27.235 24.525 30-34 20.4 28.89 27.025 23.685000000000002 35-39 20.39 28.455000000000002 26.935 24.22 40-44 21.09 28.1 27.215 23.595 45-49 20.91 27.810000000000002 27.74 23.54 50-54 20.39 27.82 27.61 24.18 55-59 20.69 27.744999999999997 27.465 24.099999999999998 60-64 21.005 27.284999999999997 27.865000000000002 23.845 65-69 20.765 27.99 27.165 24.08 70-74 21.215 27.29 26.97 24.525 75-79 20.72 27.205000000000002 27.63 24.445 80-84 20.66 27.925 27.665 23.75 85-89 20.61 27.185 28.07 24.135 90-94 21.375 27.63 27.279999999999998 23.715 95-99 20.87 27.935 26.965 24.23 100-104 21.175 27.71 26.56 24.555 105-109 21.32 27.32 26.88 24.48 110-114 21.85 27.515 26.645000000000003 23.990000000000002 115-119 22.009999999999998 28.035 26.029999999999998 23.925 120-124 21.875 28.4 25.679999999999996 24.044999999999998 125-129 21.560000000000002 28.110000000000003 25.515 24.815 130-134 22.055 28.904999999999998 25.35 23.69 135-139 21.705 28.32 25.509999999999998 24.465 140-144 22.15 27.57 25.169999999999998 25.11 145-149 22.134999999999998 28.15 25.865 23.849999999999998 150-151 22.4875 27.200000000000003 24.875 25.4375 >>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 0.5 10 0.5 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 0.5 20 0.5 21 0.5 22 1.0 23 1.5 24 3.0 25 4.0 26 3.0 27 2.5 28 4.5 29 9.5 30 12.5 31 16.5 32 24.0 33 29.5 34 37.5 35 58.5 36 81.0 37 98.5 38 124.5 39 146.0 40 161.5 41 180.0 42 203.5 43 246.5 44 266.0 45 254.0 46 264.5 47 252.0 48 218.0 49 213.0 50 209.5 51 176.0 52 131.0 53 116.0 54 111.5 55 96.5 56 73.5 57 50.0 58 37.0 59 31.0 60 22.5 61 9.0 62 2.5 63 3.0 64 2.5 65 1.5 66 2.5 67 2.5 68 1.0 69 0.5 70 1.0 71 0.5 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 0.25 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 79.875 #Duplication Level Percentage of deduplicated Percentage of total 1 81.62754303599374 65.2 2 13.77151799687011 22.0 3 3.286384976525822 7.875 4 0.8763693270735524 2.8000000000000003 5 0.18779342723004694 0.75 6 0.12519561815336464 0.6 7 0.06259780907668232 0.35000000000000003 8 0.03129890453834116 0.2 9 0.03129890453834116 0.22499999999999998 >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 CGTCCCGAGAGCCAAGCACTGCTCCTTCCTGGCCAGCTTGAGCAAGTTAG 9 0.22499999999999998 No Hit CTGCTCAATCCTATACAAGTTAAAGCGGTCCTCGTACGTGATCAAATTCA 8 0.2 No Hit CCCTGGTGCTTTGAGCTCACAGCTTTTACCACTAGATAATGGACCCAAAT 7 0.17500000000000002 No Hit CGGATGATAATGATACAGAAACAGCGACACAGTAACGATCTATACTTTTA 7 0.17500000000000002 No Hit GGCCAGAAGAGTCTTCCCAGTACCTGGAGGTCCAACAAGAAGAACACCTT 6 0.15 No Hit GCCTTTTACTTCTATGGCTACATGTATTTTCCCTGTCCGAATTTGTTGGC 6 0.15 No Hit CTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAAC 6 0.15 No Hit GCTGTTATATTATGTTTGGCGGCGAAATCAATCATCTCTTGTGTCTCCTT 6 0.15 No Hit GGGGCTTGACATGGATGCAGCGCACACAGCTGCCATCAAAGATGCACTCA 5 0.125 No Hit GATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGCAGTAATCTCGTAT 5 0.125 TruSeq Adapter, Index 9 (97% over 39bp) CACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCC 5 0.125 No Hit CCCAAATTAACGCCTGTGAATCATCCCCAGCAGTACAAATATGGCATGAA 5 0.125 No Hit GGCAGAAACAATGAGATGAATCTAATAATGAATGGCAGGTAGACCAGAAA 5 0.125 No Hit CTGCTGTACTGGAGTCCTCTGTATTACTGTTCTGAAATGGGGAACGTCCA 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 0.0125 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.0875 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.1875 0.0 0.0 0.0 0.0 72-73 0.2875 0.0 0.0 0.0 0.0 74-75 0.35 0.0 0.0 0.0 0.0 76-77 0.4 0.0 0.0 0.0 0.0 78-79 0.5125 0.0 0.0 0.0 0.0 80-81 0.575 0.0 0.0 0.0 0.0 82-83 0.7875 0.0 0.0 0.0 0.0 84-85 1.025 0.0 0.0 0.0 0.0 86-87 1.2125 0.0 0.0 0.0 0.0 88-89 1.5375 0.0 0.0 0.0 0.0 90-91 1.7999999999999998 0.0 0.0 0.0 0.0 92-93 2.1125 0.0 0.0 0.0 0.0 94-95 2.5999999999999996 0.0 0.0 0.0 0.0 96-97 3.0625 0.0 0.0 0.0 0.0 98-99 3.6625 0.0 0.0 0.0 0.0 100-101 4.175 0.0 0.0 0.0 0.0 102-103 4.875 0.0 0.0 0.0 0.0 104-105 5.5 0.0 0.0 0.0 0.0 106-107 6.0875 0.0 0.0 0.0 0.0 108-109 6.6375 0.0 0.0 0.0 0.0 110-111 7.325 0.0 0.0 0.0 0.0 112-113 8.025 0.0 0.0 0.0 0.0 114-115 8.8125 0.0 0.0 0.0 0.0 116-117 9.6625 0.0 0.0 0.0 0.0 118-119 10.4875 0.0 0.0 0.0 0.0 120-121 11.15 0.0 0.0 0.0 0.0 122-123 12.375 0.0 0.0 0.0 0.0 124-125 13.0875 0.0 0.0 0.0 0.0 126-127 13.9375 0.0 0.0 0.0 0.0 128-129 14.9125 0.0 0.0 0.0 0.0 130-131 15.712499999999999 0.0 0.0 0.0 0.0 132-133 16.637500000000003 0.0 0.0 0.0 0.0 134-135 17.674999999999997 0.0 0.0 0.0 0.0 136-137 18.525 0.0 0.0 0.0 0.0 138-139 19.8125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CACGAGC 45 0.008957279 48.333332 145 GTCACGA 55 0.0025160722 15.818182 140-144 AGTCACG 55 0.0025160722 15.818182 140-144 CACGTCT 65 0.0076375785 13.384615 125-129 CTGAACT 65 0.0076375785 13.384615 130-134 TCTGAAC 65 0.0076375785 13.384615 130-134 >>END_MODULE SRR12670102 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670102_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 45 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.3965 37.0 37.0 37.0 37.0 37.0 2 36.333 37.0 37.0 37.0 37.0 37.0 3 36.29 37.0 37.0 37.0 37.0 37.0 4 36.256 37.0 37.0 37.0 37.0 37.0 5 36.3935 37.0 37.0 37.0 37.0 37.0 6 36.401 37.0 37.0 37.0 37.0 37.0 7 36.3635 37.0 37.0 37.0 37.0 37.0 8 36.298 37.0 37.0 37.0 37.0 37.0 9 36.4155 37.0 37.0 37.0 37.0 37.0 10-14 36.381899999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.3784 37.0 37.0 37.0 37.0 37.0 20-24 36.333000000000006 37.0 37.0 37.0 37.0 37.0 25-29 36.318200000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.2614 37.0 37.0 37.0 37.0 37.0 35-39 36.283699999999996 37.0 37.0 37.0 37.0 37.0 40-44 36.24979999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.2436 37.0 37.0 37.0 37.0 37.0 50-54 36.199 37.0 37.0 37.0 37.0 37.0 55-59 36.132799999999996 37.0 37.0 37.0 37.0 37.0 60-64 36.1529 37.0 37.0 37.0 37.0 37.0 65-69 36.106399999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.0719 37.0 37.0 37.0 37.0 37.0 75-79 36.1083 37.0 37.0 37.0 37.0 37.0 80-84 35.9895 37.0 37.0 37.0 37.0 37.0 85-89 36.0585 37.0 37.0 37.0 37.0 37.0 90-94 36.0524 37.0 37.0 37.0 37.0 37.0 95-99 36.0103 37.0 37.0 37.0 37.0 37.0 100-104 35.9353 37.0 37.0 37.0 37.0 37.0 105-109 35.945800000000006 37.0 37.0 37.0 37.0 37.0 110-114 35.9151 37.0 37.0 37.0 37.0 37.0 115-119 35.8866 37.0 37.0 37.0 37.0 37.0 120-124 35.826499999999996 37.0 37.0 37.0 37.0 37.0 125-129 35.7099 37.0 37.0 37.0 37.0 37.0 130-134 35.5375 37.0 37.0 37.0 34.6 37.0 135-139 35.4525 37.0 37.0 37.0 37.0 37.0 140-144 35.2505 37.0 37.0 37.0 37.0 37.0 145-149 35.029500000000006 37.0 37.0 37.0 29.8 37.0 150-151 34.88375 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 4.0 14 3.0 15 3.0 16 0.0 17 1.0 18 1.0 19 1.0 20 5.0 21 2.0 22 3.0 23 5.0 24 3.0 25 7.0 26 4.0 27 12.0 28 8.0 29 16.0 30 24.0 31 26.0 32 45.0 33 64.0 34 182.0 35 520.0 36 2769.0 37 291.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.55 23.075000000000003 12.575 27.800000000000004 2 26.924999999999997 26.85 29.575000000000003 16.650000000000002 3 22.650000000000002 27.725 29.925 19.7 4 23.95 32.5 24.2 19.35 5 26.3 33.375 22.625 17.7 6 22.25 38.550000000000004 22.05 17.150000000000002 7 21.349999999999998 22.7 36.199999999999996 19.75 8 24.425 24.8 25.95 24.825 9 22.725 23.125 30.425 23.724999999999998 10-14 24.27 28.405 25.840000000000003 21.485000000000003 15-19 23.445 28.155 26.634999999999998 21.765 20-24 23.805 28.125 26.58 21.490000000000002 25-29 24.19 28.060000000000002 26.889999999999997 20.86 30-34 23.445 26.815 28.060000000000002 21.68 35-39 23.794999999999998 27.67 27.439999999999998 21.095 40-44 24.205 28.075 27.025 20.695 45-49 23.46 27.595 27.49 21.455 50-54 23.665 28.01 27.29 21.035 55-59 24.72 27.205000000000002 26.655 21.42 60-64 23.45 27.205000000000002 27.534999999999997 21.81 65-69 24.895 26.57 27.800000000000004 20.735 70-74 24.625 27.72 26.825 20.830000000000002 75-79 24.12 27.565 26.55 21.765 80-84 24.505 27.515 26.915 21.065 85-89 24.705 27.77 26.39 21.135 90-94 24.245 28.565 26.55 20.64 95-99 24.335 27.295 27.284999999999997 21.085 100-104 25.645 27.735 26.584999999999997 20.035 105-109 24.755 27.944999999999997 26.450000000000003 20.849999999999998 110-114 26.224999999999998 26.91 26.474999999999998 20.39 115-119 26.700000000000003 27.765 26.43 19.105 120-124 27.22 28.03 25.624999999999996 19.125 125-129 27.37 27.805000000000003 25.395 19.43 130-134 27.785 27.875 25.650000000000002 18.69 135-139 29.235 27.52 25.319999999999997 17.925 140-144 29.759999999999998 27.195000000000004 25.035 18.01 145-149 30.36 27.13 24.98 17.53 150-151 32.337500000000006 26.8125 23.974999999999998 16.875 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.5 6 0.5 7 0.0 8 2.0 9 2.5 10 0.5 11 0.5 12 1.0 13 1.0 14 1.0 15 1.5 16 1.5 17 1.0 18 1.0 19 0.5 20 0.0 21 0.5 22 1.0 23 0.5 24 0.0 25 1.5 26 2.5 27 1.5 28 2.0 29 3.5 30 6.0 31 16.5 32 19.5 33 13.5 34 20.0 35 39.0 36 59.5 37 82.5 38 117.0 39 135.5 40 171.0 41 198.5 42 219.5 43 278.0 44 289.5 45 272.0 46 273.0 47 267.0 48 243.0 49 229.0 50 197.0 51 151.5 52 129.5 53 125.5 54 117.5 55 90.5 56 61.5 57 40.0 58 28.5 59 20.0 60 13.0 61 8.0 62 6.0 63 4.0 64 2.0 65 0.5 66 1.0 67 0.5 68 0.5 69 0.5 70 0.0 71 1.0 72 1.5 73 0.5 74 0.0 75 0.0 76 0.5 77 1.0 78 0.5 79 0.5 80 0.5 81 0.0 82 0.0 83 0.0 84 0.5 85 0.5 86 0.5 87 0.5 88 1.0 89 1.0 90 0.5 91 0.5 92 0.5 93 0.5 94 0.5 95 0.5 96 0.5 97 1.0 98 1.0 99 3.0 100 4.0 >>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 80.525 #Duplication Level Percentage of deduplicated Percentage of total 1 82.17944737659111 66.175 2 13.505122632722758 21.75 3 3.0735796336541448 7.425 4 0.8692952499223843 2.8000000000000003 5 0.21732381248059607 0.8750000000000001 6 0.06209251785159888 0.3 7 0.0 0.0 8 0.06209251785159888 0.4 9 0.0 0.0 >10 0.03104625892579944 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 11 0.27499999999999997 No Hit CCATGAAGGTTGCTGCTGCAGAGGAAACAGCTGTCAAAGAGGCTCCGGTG 8 0.2 No Hit TCCTGTTTCTATATCCATGCAAAGATGTTGCAAGACCATCGTAACAGAGT 8 0.2 No Hit AGCTTGCCCAAATTCGGATACTCAGAGAGCTCAAGAGCAGAATTGAAAGG 6 0.15 No Hit TTTAGTTGCTCTATTGAAGTCTCATGGAAAGCTAGTTTTGGTCGGTGCTC 6 0.15 No Hit CAGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTA 5 0.125 No Hit TGGCTTGCCAGCAATGGCAAAGAAGGGAAGAGTGAGCTGTTCCATGGAGG 5 0.125 No Hit CTCCTTTCTCGACGCTCATCAGGAGGAATGGGTGGGCCTGGTGGTCCTGG 5 0.125 No Hit AGAGAACCTAAGCCAAAGATTCAGGTGCAGACCCTATTTTGCATTGCATT 5 0.125 No Hit GCTCCAACAGCGAGGCATAGAAGATAGTAGACAACTCAGCCCAGCATCAG 5 0.125 No Hit GTTGGATATTCGCTTCCCAACTCTTCCAGTGGTGGAATTGCAGAGGCATC 5 0.125 No Hit TTTACCCAACGGTGATTAAGTTGTCAAGGCAGATGTCTGATACTGTGGTT 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 0.0125 0.0 0.0 0.0 0.0 32-33 0.025 0.0 0.0 0.0 0.0 34-35 0.025 0.0 0.0 0.0 0.0 36-37 0.025 0.0 0.0 0.0 0.0 38-39 0.025 0.0 0.0 0.0 0.0 40-41 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.025 0.0 0.0 0.0 0.0 46-47 0.025 0.0 0.0 0.0 0.0 48-49 0.025 0.0 0.0 0.0 0.0 50-51 0.025 0.0 0.0 0.0 0.0 52-53 0.025 0.0 0.0 0.0 0.0 54-55 0.025 0.0 0.0 0.0 0.0 56-57 0.025 0.0 0.0 0.0 0.0 58-59 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.0875 0.0 0.0 0.0 0.0 66-67 0.175 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.1875 0.0 0.0 0.0 0.0 72-73 0.2875 0.0 0.0 0.0 0.0 74-75 0.35 0.0 0.0 0.0 0.0 76-77 0.4 0.0 0.0 0.0 0.0 78-79 0.5125 0.0 0.0 0.0 0.0 80-81 0.575 0.0 0.0 0.0 0.0 82-83 0.7875 0.0 0.0 0.0 0.0 84-85 1.025 0.0 0.0 0.0 0.0 86-87 1.2125 0.0 0.0 0.0 0.0 88-89 1.5375 0.0 0.0 0.0 0.0 90-91 1.7999999999999998 0.0 0.0 0.0 0.0 92-93 2.1125 0.0 0.0 0.0 0.0 94-95 2.5875 0.0 0.0 0.0 0.0 96-97 3.0125 0.0 0.0 0.0 0.0 98-99 3.6125 0.0 0.0 0.0 0.0 100-101 4.15 0.0 0.0 0.0 0.0 102-103 4.875 0.0 0.0 0.0 0.0 104-105 5.5 0.0 0.0 0.0 0.0 106-107 6.0875 0.0 0.0 0.0 0.0 108-109 6.6625 0.0 0.0 0.0 0.0 110-111 7.35 0.0 0.0 0.0 0.0 112-113 8.0625 0.0 0.0 0.0 0.0 114-115 8.8625 0.0 0.0 0.0 0.0 116-117 9.7125 0.0 0.0 0.0 0.0 118-119 10.5375 0.0 0.0 0.0 0.0 120-121 11.225 0.0 0.0 0.0 0.0 122-123 12.45 0.0 0.0 0.0 0.0 124-125 13.1625 0.0 0.0 0.0 0.0 126-127 14.037500000000001 0.0 0.0 0.0 0.0 128-129 15.0125 0.0 0.0 0.0 0.0 130-131 15.8125 0.0 0.0 0.0 0.0 132-133 16.737499999999997 0.0 0.0 0.0 0.0 134-135 17.75 0.0 0.0 0.0 0.0 136-137 18.575000000000003 0.0 0.0 0.0 0.0 138-139 19.8625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TGTATGC 10 0.006830828 145.0 7 GTGAGCA 45 0.008957279 48.333332 145 GTGTGAG 55 0.0025160722 15.818182 140-144 AGTGTGA 60 0.004491891 14.500001 140-144 TCGTGTA 65 0.0076375785 13.384615 125-129 GTAGGGA 65 0.0076375785 13.384615 130-134 TAGGGAA 65 0.0076375785 13.384615 130-134 GGGGGGG 165 5.380233E-4 8.787879 140-144 >>END_MODULE Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605322 spots for SRR12670102.sra Written 605322 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra Read 605316 spots for SRR12670102.sra Written 605316 spots for SRR12670102.sra SRR ids: ['SRR12670102.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_5zpq8iuw SRR12670102.sra spots: 12106326 blocks: [[1, 605316], [605317, 1210632], [1210633, 1815948], [1815949, 2421264], [2421265, 3026580], [3026581, 3631896], [3631897, 4237212], [4237213, 4842528], [4842529, 5447844], [5447845, 6053160], [6053161, 6658476], [6658477, 7263792], [7263793, 7869108], [7869109, 8474424], [8474425, 9079740], [9079741, 9685056], [9685057, 10290372], [10290373, 10895688], [10895689, 11501004], [11501005, 12106326]] SRR12670102 file size 4092558 SRR12670102 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 SRR12670102 SRR12670102_1.fastq SRR12670102_2.fastq Input file: SRR12670102_1.fastq Paired file: SRR12670102_2.fastq trimmed: SRR12670102-trimmed-pair1.fastq, SRR12670102-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 22:40:57 2025 >> started Mon Feb 10 22:41:17 2025 >> done (19.248s) 12106326 read pairs processed; of these: 65 ( 0.00%) short read pairs filtered out after trimming by size control 22045 ( 0.18%) empty read pairs filtered out after trimming by size control 12084216 (99.82%) read pairs available; of these: 3006746 (24.88%) trimmed read pairs available after processing 9077470 (75.12%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 4 0.00% 20 7 0.00% 21 6 0.00% 22 19 0.00% 23 25 0.00% 24 21 0.00% 25 31 0.00% 26 43 0.00% 27 44 0.00% 28 50 0.00% 29 65 0.00% 30 60 0.00% 31 82 0.00% 32 86 0.00% 33 56 0.00% 34 81 0.00% 35 90 0.00% 36 105 0.00% 37 93 0.00% 38 95 0.00% 39 119 0.00% 40 140 0.00% 41 166 0.00% 42 139 0.00% 43 169 0.00% 44 172 0.00% 45 215 0.00% 46 209 0.00% 47 237 0.00% 48 318 0.00% 49 317 0.00% 50 367 0.00% 51 402 0.00% 52 467 0.00% 53 514 0.00% 54 478 0.00% 55 554 0.00% 56 612 0.01% 57 719 0.01% 58 793 0.01% 59 991 0.01% 60 1170 0.01% 61 1313 0.01% 62 1496 0.01% 63 1596 0.01% 64 1723 0.01% 65 1985 0.02% 66 2021 0.02% 67 2318 0.02% 68 2586 0.02% 69 2878 0.02% 70 3319 0.03% 71 4030 0.03% 72 4404 0.04% 73 4981 0.04% 74 5503 0.05% 75 6064 0.05% 76 6619 0.05% 77 7190 0.06% 78 7623 0.06% 79 8356 0.07% 80 9095 0.08% 81 10499 0.09% 82 11717 0.10% 83 13066 0.11% 84 14288 0.12% 85 15583 0.13% 86 16381 0.14% 87 16692 0.14% 88 17687 0.15% 89 18627 0.15% 90 19915 0.16% 91 21527 0.18% 92 22957 0.19% 93 24366 0.20% 94 26395 0.22% 95 27944 0.23% 96 28759 0.24% 97 29579 0.24% 98 29910 0.25% 99 30231 0.25% 100 31557 0.26% 101 32590 0.27% 102 34093 0.28% 103 35088 0.29% 104 36934 0.31% 105 38074 0.32% 106 39116 0.32% 107 39432 0.33% 108 39808 0.33% 109 40350 0.33% 110 40622 0.34% 111 41576 0.34% 112 43229 0.36% 113 43784 0.36% 114 45347 0.38% 115 46645 0.39% 116 47521 0.39% 117 48451 0.40% 118 47759 0.40% 119 47971 0.40% 120 48581 0.40% 121 49262 0.41% 122 50022 0.41% 123 51128 0.42% 124 51563 0.43% 125 52746 0.44% 126 53315 0.44% 127 52695 0.44% 128 52862 0.44% 129 52508 0.43% 130 53100 0.44% 131 52740 0.44% 132 53214 0.44% 133 54338 0.45% 134 55081 0.46% 135 55468 0.46% 136 55462 0.46% 137 56140 0.46% 138 55809 0.46% 139 56856 0.47% 140 55971 0.46% 141 55392 0.46% 142 56208 0.47% 143 56660 0.47% 144 57701 0.48% 145 58281 0.48% 146 58478 0.48% 147 57607 0.48% 148 59139 0.49% 149 58590 0.48% 150 58321 0.48% 151 9077470 75.12% 12084216 reads passed initial QC criterion=sequence-density sequence-density=0.52 sequence-density-rank=1 fanout-score=1.99 fanout-score-rank=30 prefix-density=0.51 prefix-fanout=2.0 sequence=GTGTTGTCGAATCC criterion=fanout-score sequence-density=0.11 sequence-density-rank=29 fanout-score=8.71 fanout-score-rank=1 prefix-density=0.69 prefix-fanout=1.4 sequence=GCTTGTAAGGAAGACATGGTGTTGATGTTGGTGGTTGGCTAGGTACGCAATATCG criterion=sequence-density sequence-density=1.09 sequence-density-rank=1 fanout-score=2.17 fanout-score-rank=23 prefix-density=1.10 prefix-fanout=2.2 sequence=CCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAATCATCATGTCTAGCACCTGCGACACCTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCATTGTTATGTATTGGCCATGTCTGTGGCCTCTGGTGTGGTTTTAATGAAGTCTTATAATTAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=33 fanout-score=17.83 fanout-score-rank=1 prefix-density=0.03 prefix-fanout=3.7 sequence=ACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGC SRR12670102 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 22:42:04 Started mapping on | Feb 10 22:42:05 Finished on | Feb 10 22:44:11 Mapping speed, Million of reads per hour | 345.26 Number of input reads | 12084216 Average input read length | 286 UNIQUE READS: Uniquely mapped reads number | 11075759 Uniquely mapped reads % | 91.65% Average mapped length | 285.74 Number of splices: Total | 10602251 Number of splices: Annotated (sjdb) | 10375165 Number of splices: GT/AG | 10378414 Number of splices: GC/AG | 177600 Number of splices: AT/AC | 7513 Number of splices: Non-canonical | 38724 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.96 Insertion rate per base | 0.02% Insertion average length | 2.32 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 369097 % of reads mapped to multiple loci | 3.05% Number of reads mapped to too many loci | 48942 % of reads mapped to too many loci | 0.41% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.73% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 639360 639360 639360 N_multimapping 369097 369097 369097 N_noFeature 278422 10838844 344270 N_ambiguous 252904 648 81652 UnstrandedReadsAssigned:10544433 PositiveStrandReadsAssigned:236267 NegativeStrandReadsAssigned:10649837 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=141 echo kmer=137 SRR12670102 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: SRR12670102-trimmed-pair1.fastq SRR12670102-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,084,216 reads, 10,754,035 reads pseudoaligned [quant] estimated average fragment length: 204.634 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,099 rounds 52401 SRR12670102.ke.tsv 34699 SRR12670102.se.tsv 87100 total ==> SRR12670102.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1814.37 406 15.7448 Potri.005G024800.1.v4.1 1035 831.366 233 19.7197 Potri.004G059700.1.v4.1 961 757.378 0 0 Potri.007G009000.2.v4.1 1416 1212.37 0 0 Potri.003G141000.2.v4.1 2943 2739.37 593 15.2315 Potri.016G087400.1.v4.1 270 104.053 672 454.415 Potri.015G069301.1.v4.1 564 364.219 0 0 Potri.010G195200.1.v4.1 1773 1569.37 91 4.07994 Potri.012G127500.1.v4.1 977 773.366 91 8.27929 ==> SRR12670102.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 128 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 269 Potri.001G212900.v4.1 41 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12670102 completed mapping pipeline successfully