Starting /dee2/code/volunteer_pipeline.sh SRR7171110 current disk space = 3085715075072 free memory = 1580022852 SRR7171110 SRAfilesize f596064f688e578599f7d5e159f73180 SRR7171110.sra SRR7171110.sra file validated SRR7171110 is paired end SRR7171110 is conventional basespace SRR7171110 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171110_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 43 >>END_MODULE >>Per base sequence quality fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 19.7735 18.0 18.0 18.0 18.0 32.0 2 27.19675 27.0 27.0 28.0 25.0 30.0 3 29.09275 29.0 27.0 31.0 27.0 33.0 4 31.52325 33.0 31.0 33.0 29.0 33.0 5 32.37475 33.0 33.0 33.0 32.0 33.0 6 36.326 38.0 36.0 38.0 34.0 38.0 7 36.93125 38.0 37.0 38.0 35.0 38.0 8 37.28725 38.0 38.0 38.0 36.0 38.0 9 37.48025 38.0 38.0 38.0 37.0 38.0 10-14 37.4321 38.0 38.0 38.0 37.0 38.0 15-19 37.47769999999999 38.0 38.0 38.0 37.0 38.0 20-24 37.455200000000005 38.0 38.0 38.0 37.0 38.0 25-29 37.4172 38.0 38.0 38.0 37.4 38.0 30-34 37.4237 38.0 38.0 38.0 37.4 38.0 35-39 37.2589 38.0 38.0 38.0 36.8 38.0 40-44 37.11665000000001 38.0 38.0 38.0 36.6 38.0 45-49 37.22765 38.0 38.0 38.0 37.0 38.0 50-54 36.515699999999995 38.0 38.0 38.0 33.4 38.0 55-59 36.7808 38.0 38.0 38.0 35.2 38.0 60-64 36.7743 38.0 38.0 38.0 34.8 38.0 65-69 36.79280000000001 38.0 38.0 38.0 35.0 38.0 70-74 36.56385 38.0 38.0 38.0 34.0 38.0 75-79 35.2918 38.0 37.8 38.0 31.2 38.0 80-84 34.69235 38.0 37.0 38.0 29.0 38.0 85-89 34.5001 38.0 37.0 38.0 28.2 38.0 90-94 34.2279 38.0 37.0 38.0 25.4 38.0 95-99 34.201499999999996 38.0 36.8 38.0 24.4 38.0 100-104 34.15125 38.0 36.4 38.0 25.0 38.0 105-109 34.03335 38.0 36.0 38.0 23.4 38.0 110-114 33.772800000000004 38.0 35.8 38.0 18.2 38.0 115-119 33.36775 38.0 35.0 38.0 15.0 38.0 120-124 33.299549999999996 38.0 35.0 38.0 15.0 38.0 125-129 32.99205 38.0 34.6 38.0 14.6 38.0 130-134 30.543650000000003 36.0 27.4 38.0 13.8 38.0 135-139 32.2032 38.0 33.2 38.0 13.4 38.0 140-144 31.641399999999997 38.0 32.2 38.0 13.0 38.0 145-149 30.79095 37.8 31.0 38.0 2.0 38.0 150-151 26.42825 34.0 16.5 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 5 1.0 6 0.0 7 2.0 8 0.0 9 3.0 10 2.0 11 2.0 12 4.0 13 3.0 14 8.0 15 8.0 16 13.0 17 15.0 18 73.0 19 123.0 20 9.0 21 5.0 22 7.0 23 6.0 24 11.0 25 11.0 26 20.0 27 15.0 28 27.0 29 30.0 30 49.0 31 43.0 32 86.0 33 125.0 34 207.0 35 429.0 36 1220.0 37 1443.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 15.091962711010328 45.60342655580751 13.983371126228269 25.321239606953895 2 21.45536384096024 19.779944986246562 32.50812703175794 26.25656414103526 3 17.875 22.825 32.925 26.375 4 20.75 27.224999999999998 24.9 27.125 5 24.175 31.574999999999996 26.200000000000003 18.05 6 21.175 32.675 28.050000000000004 18.099999999999998 7 12.5 27.250000000000004 43.675000000000004 16.575 8 17.05 28.199999999999996 30.65 24.099999999999998 9 20.9 24.45 31.0 23.65 10-14 19.825 31.435000000000002 24.740000000000002 24.0 15-19 19.835 29.385 27.495000000000005 23.285 20-24 19.665 30.470000000000002 27.07 22.795 25-29 19.68 28.985 27.625 23.71 30-34 18.83 29.675 27.310000000000002 24.185000000000002 35-39 19.755 30.06 27.47 22.715 40-44 19.24 29.195 26.515 25.05 45-49 20.615 29.28 27.16 22.945 50-54 21.224999999999998 27.744999999999997 26.665 24.365000000000002 55-59 18.43 27.950000000000003 29.220000000000002 24.4 60-64 19.355 26.895000000000003 29.84 23.91 65-69 19.335 31.790000000000003 26.44 22.435 70-74 19.195 33.22 25.564999999999998 22.02 75-79 19.255 32.39 25.669999999999998 22.685 80-84 19.7 31.419999999999998 26.064999999999998 22.814999999999998 85-89 20.200000000000003 30.185000000000002 26.035000000000004 23.580000000000002 90-94 20.01 29.580000000000002 25.945 24.465 95-99 20.544999999999998 28.799999999999997 26.840000000000003 23.815 100-104 20.735 29.104999999999997 25.97 24.19 105-109 20.865000000000002 28.384999999999998 26.515 24.235 110-114 20.695 29.32 26.105 23.880000000000003 115-119 20.724999999999998 30.5 25.21 23.565 120-124 20.865000000000002 31.305 24.34 23.49 125-129 20.990000000000002 30.955 24.51 23.544999999999998 130-134 21.345 30.020000000000003 24.759999999999998 23.875 135-139 20.895 30.12 24.975 24.01 140-144 20.605 29.755 25.195 24.445 145-149 20.84 30.09 24.29 24.779999999999998 150-151 20.575 30.625000000000004 24.224999999999998 24.575 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 2.0 1 1.5 2 2.0 3 2.5 4 3.5 5 3.5 6 1.5 7 1.0 8 0.5 9 1.0 10 1.5 11 0.5 12 1.0 13 1.5 14 0.5 15 1.5 16 2.0 17 1.0 18 1.0 19 1.5 20 3.0 21 3.5 22 2.0 23 2.0 24 5.0 25 9.0 26 11.5 27 17.0 28 21.5 29 24.5 30 36.5 31 52.0 32 67.5 33 86.5 34 102.0 35 122.5 36 133.0 37 151.5 38 179.5 39 171.0 40 184.0 41 195.5 42 180.5 43 200.5 44 214.0 45 188.5 46 166.0 47 158.0 48 145.5 49 128.0 50 122.5 51 130.5 52 135.0 53 133.0 54 120.5 55 100.5 56 73.5 57 50.0 58 43.5 59 32.5 60 21.5 61 17.5 62 13.0 63 8.5 64 2.5 65 0.0 66 1.0 67 1.0 68 0.5 69 0.5 70 0.5 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 0.775 2 0.025 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 90.85 #Duplication Level Percentage of deduplicated Percentage of total 1 95.87231700605393 87.1 2 3.2471106219042376 5.8999999999999995 3 0.4678040726472207 1.275 4 0.24766097963676387 0.8999999999999999 5 0.0550357732526142 0.25 6 0.0275178866263071 0.15 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0275178866263071 0.25 >50 0.0275178866263071 1.375 >100 0.0275178866263071 2.8000000000000003 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source AATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGATTCCATCTCGTAT 112 2.8000000000000003 TruSeq Adapter, Index 9 (97% over 35bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGATTCCATCTCGTAT 55 1.375 TruSeq Adapter, Index 7 (97% over 38bp) ATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGATTCCATCTCGTATG 10 0.25 TruSeq Adapter, Index 7 (97% over 37bp) AGATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGATTCCATCTCGTA 6 0.15 TruSeq Adapter, Index 7 (97% over 38bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACGAGATTCCATCTCGTAC 5 0.125 TruSeq Adapter, Index 7 (97% over 38bp) CTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCGACTA 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 0.15 0.0 0.0 0.0 0.0 2 0.175 0.0 0.0 0.0 0.0 3 0.175 0.0 0.0 0.0 0.0 4 0.175 0.0 0.0 0.0 0.0 5 0.175 0.0 0.0 0.0 0.0 6 0.175 0.0 0.0 0.0 0.0 7 0.175 0.0 0.0 0.0 0.0 8 0.175 0.0 0.0 0.0 0.0 9 0.175 0.0 0.0 0.0 0.0 10-11 0.175 0.0 0.0 0.0 0.0 12-13 0.175 0.0 0.0 0.0 0.0 14-15 0.175 0.0 0.0 0.0 0.0 16-17 0.175 0.0 0.0 0.0 0.0 18-19 0.175 0.0 0.0 0.0 0.0 20-21 0.175 0.0 0.0 0.0 0.0 22-23 0.175 0.0 0.0 0.0 0.0 24-25 0.175 0.0 0.0 0.0 0.0 26-27 0.175 0.0 0.0 0.0 0.0 28-29 0.175 0.0 0.0 0.0 0.0 30-31 0.175 0.0 0.0 0.0 0.0 32-33 0.175 0.0 0.0 0.0 0.0 34-35 0.175 0.0 0.0 0.0 0.0 36-37 0.175 0.0 0.0 0.0 0.0 38-39 0.175 0.0 0.0 0.0 0.0 40-41 0.175 0.0 0.0 0.0 0.0 42-43 0.175 0.0 0.0 0.0 0.0 44-45 0.2 0.0 0.0 0.0 0.0 46-47 0.2 0.0 0.0 0.0 0.0 48-49 0.2 0.0 0.0 0.0 0.0 50-51 0.225 0.0 0.0 0.0 0.0 52-53 0.275 0.0 0.0 0.0 0.0 54-55 0.275 0.0 0.0 0.0 0.0 56-57 0.275 0.0 0.0 0.0 0.0 58-59 0.2875 0.0 0.0 0.0 0.0 60-61 0.3125 0.0 0.0 0.0 0.0 62-63 0.3625 0.0 0.0 0.0 0.0 64-65 0.375 0.0 0.0 0.0 0.0 66-67 0.4375 0.0 0.0 0.0 0.0 68-69 0.45 0.0 0.0 0.0 0.0 70-71 0.5 0.0 0.0 0.0 0.0 72-73 0.55 0.0 0.0 0.0 0.0 74-75 0.5625 0.0 0.0 0.0 0.0 76-77 0.6 0.0 0.0 0.0 0.0 78-79 0.7 0.0 0.0 0.0 0.0 80-81 0.825 0.0 0.0 0.0 0.0 82-83 1.0625 0.0 0.0 0.0 0.0 84-85 1.2625000000000002 0.0 0.0 0.0 0.0 86-87 1.45 0.0 0.0 0.0 0.0 88-89 1.7125 0.0 0.0 0.0 0.0 90-91 1.875 0.0 0.0 0.0 0.0 92-93 2.275 0.0 0.0 0.0 0.0 94-95 2.7125 0.0 0.0 0.0 0.0 96-97 3.0625 0.0 0.0 0.0 0.0 98-99 3.55 0.0 0.0 0.0 0.0 100-101 3.975 0.0 0.0 0.0 0.0 102-103 4.4125 0.0 0.0 0.0 0.0 104-105 4.9 0.0 0.0 0.0 0.0 106-107 5.525 0.0 0.0 0.0 0.0 108-109 6.0625 0.0 0.0 0.0 0.0 110-111 6.775 0.0 0.0 0.0 0.0 112-113 7.5375 0.0 0.0 0.0 0.0 114-115 8.3125 0.0 0.0 0.0 0.0 116-117 9.100000000000001 0.0 0.0 0.0 0.0 118-119 10.087499999999999 0.0 0.0 0.0 0.0 120-121 10.8 0.0 0.0 0.0 0.0 122-123 11.625 0.0 0.0 0.0 0.0 124-125 12.45 0.0 0.0 0.0 0.0 126-127 13.25 0.0 0.0 0.0 0.0 128-129 14.075 0.0 0.0 0.0 0.0 130-131 14.8875 0.0 0.0 0.0 0.0 132-133 15.8625 0.0 0.0 0.0 0.0 134-135 16.625 0.0 0.0 0.0 0.0 136-137 17.425 0.0 0.0 0.0 0.0 138-139 18.112499999999997 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCGTCTT 20 0.00593511 29.0 50-54 TCTGCTT 20 0.00593511 29.0 55-59 GCTTGAA 20 0.00593511 29.0 60-64 CGTCTTC 20 0.00593511 29.0 50-54 AAAAAAA 220 9.906216E-9 10.545455 65-69 >>END_MODULE SRR7171110 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171110_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 32.78325 33.0 33.0 34.0 32.0 34.0 2 32.59525 34.0 33.0 34.0 32.0 34.0 3 32.807 34.0 33.0 34.0 32.0 34.0 4 32.73225 34.0 33.0 34.0 32.0 34.0 5 32.82825 34.0 33.0 34.0 32.0 34.0 6 36.91525 38.0 38.0 38.0 37.0 38.0 7 36.873 38.0 38.0 38.0 37.0 38.0 8 36.90025 38.0 38.0 38.0 37.0 38.0 9 36.92825 38.0 38.0 38.0 37.0 38.0 10-14 36.9071 38.0 38.0 38.0 36.8 38.0 15-19 36.809900000000006 38.0 38.0 38.0 36.8 38.0 20-24 35.6962 38.0 37.2 38.0 29.0 38.0 25-29 36.2763 38.0 38.0 38.0 34.0 38.0 30-34 36.61345 38.0 38.0 38.0 35.4 38.0 35-39 36.7534 38.0 38.0 38.0 36.4 38.0 40-44 36.80915 38.0 38.0 38.0 36.6 38.0 45-49 36.78885 38.0 38.0 38.0 36.4 38.0 50-54 36.77289999999999 38.0 38.0 38.0 36.6 38.0 55-59 36.6685 38.0 38.0 38.0 35.8 38.0 60-64 36.6029 38.0 38.0 38.0 35.8 38.0 65-69 36.56915 38.0 38.0 38.0 36.0 38.0 70-74 36.63975 38.0 38.0 38.0 36.0 38.0 75-79 36.24735 38.0 37.8 38.0 33.6 38.0 80-84 33.241550000000004 37.8 34.2 38.0 21.6 38.0 85-89 34.593650000000004 38.0 38.0 38.0 28.4 38.0 90-94 34.57065 38.0 38.0 38.0 28.6 38.0 95-99 34.3357 38.0 37.8 38.0 25.4 38.0 100-104 34.2522 38.0 37.4 38.0 24.2 38.0 105-109 32.9052 37.8 33.6 38.0 17.4 38.0 110-114 33.6575 38.0 35.8 38.0 16.2 38.0 115-119 32.882600000000004 38.0 34.2 38.0 14.6 38.0 120-124 33.197799999999994 38.0 35.0 38.0 14.8 38.0 125-129 32.92685 38.0 35.0 38.0 14.0 38.0 130-134 32.682399999999994 38.0 34.4 38.0 13.6 38.0 135-139 32.2508 38.0 33.0 38.0 13.0 38.0 140-144 30.458949999999998 36.8 28.6 38.0 4.2 38.0 145-149 29.233150000000002 36.0 27.4 38.0 2.0 38.0 150-151 25.158 33.0 15.0 37.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 26.0 3 10.0 4 2.0 5 4.0 6 3.0 7 2.0 8 0.0 9 0.0 10 1.0 11 6.0 12 14.0 13 3.0 14 4.0 15 8.0 16 8.0 17 8.0 18 20.0 19 34.0 20 150.0 21 13.0 22 4.0 23 10.0 24 8.0 25 11.0 26 24.0 27 16.0 28 22.0 29 28.0 30 51.0 31 52.0 32 67.0 33 109.0 34 198.0 35 322.0 36 970.0 37 1792.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.375 18.45 17.125 24.05 2 28.4 27.250000000000004 26.474999999999998 17.875 3 23.525 25.95 31.624999999999996 18.9 4 24.68734367183592 31.015507753876935 21.935967983991997 22.36118059029515 5 30.890445222611305 32.44122061030515 20.31015507753877 16.358179089544773 6 25.474999999999998 33.95 21.975 18.6 7 20.525 24.075 35.949999999999996 19.45 8 23.225 28.925 24.099999999999998 23.75 9 27.400000000000002 25.05 25.874999999999996 21.675 10-14 25.759999999999998 27.63 24.46 22.15 15-19 26.05 25.91 27.025 21.015 20-24 27.115000000000002 27.800000000000004 25.805 19.28 25-29 25.365 29.74 25.36 19.535 30-34 25.224999999999998 26.295 27.915 20.565 35-39 23.105 26.52 27.625 22.75 40-44 26.064999999999998 25.929999999999996 28.744999999999997 19.259999999999998 45-49 24.4 27.944999999999997 27.685 19.97 50-54 25.064999999999998 25.75 28.155 21.029999999999998 55-59 26.369999999999997 25.405 27.860000000000003 20.365 60-64 23.965 26.534999999999997 27.52 21.98 65-69 22.759999999999998 26.915 29.75 20.575 70-74 23.200000000000003 31.22 26.255 19.325 75-79 22.145 31.81 26.5 19.545 80-84 23.5 30.325000000000003 26.61 19.564999999999998 85-89 23.695 30.285 26.515 19.505 90-94 23.955000000000002 29.744999999999997 26.985 19.314999999999998 95-99 23.974999999999998 29.294999999999998 27.185 19.545 100-104 25.205 28.165000000000003 27.02 19.61 105-109 25.019999999999996 28.51 26.455000000000002 20.015 110-114 24.84 28.595 26.93 19.634999999999998 115-119 25.05 29.445 26.52 18.985 120-124 25.155 29.53 25.979999999999997 19.335 125-129 25.22 29.310000000000002 26.465 19.005 130-134 26.025 28.57 26.314999999999998 19.09 135-139 26.455000000000002 28.08 26.71 18.755 140-144 26.255 28.03 26.724999999999998 18.990000000000002 145-149 26.915 27.735 26.43 18.92 150-151 26.737499999999997 29.049999999999997 26.4625 17.75 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 0.5 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.5 14 0.5 15 0.5 16 0.5 17 0.5 18 0.5 19 1.0 20 3.0 21 2.0 22 0.0 23 1.0 24 2.0 25 3.5 26 5.5 27 9.0 28 11.0 29 13.0 30 20.5 31 24.5 32 31.5 33 42.0 34 57.5 35 72.5 36 96.0 37 117.5 38 135.5 39 161.0 40 189.5 41 198.5 42 199.0 43 198.5 44 187.0 45 208.0 46 203.5 47 193.5 48 196.5 49 179.0 50 176.0 51 158.0 52 146.0 53 155.5 54 149.0 55 116.5 56 84.5 57 63.5 58 48.0 59 42.0 60 27.0 61 19.5 62 21.0 63 13.0 64 4.5 65 2.0 66 1.0 67 1.5 68 1.0 69 0.5 70 0.5 71 0.0 72 0.0 73 0.5 74 0.5 75 0.0 76 0.5 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 0.0 2 0.0 3 0.0 4 0.05 5 0.05 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 90.85 #Duplication Level Percentage of deduplicated Percentage of total 1 97.02806824435883 88.14999999999999 2 2.0363236103467255 3.6999999999999997 3 0.4678040726472207 1.275 4 0.1926252063841497 0.7000000000000001 5 0.0825536598789213 0.375 6 0.0275178866263071 0.15 7 0.0275178866263071 0.17500000000000002 8 0.0550357732526142 0.4 9 0.0275178866263071 0.22499999999999998 >10 0.0275178866263071 0.375 >50 0.0 0.0 >100 0.0275178866263071 4.475 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences fail #Sequence Count Percentage Possible Source GATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGCCTCTATGTGTAGATCT 179 4.475 Illumina Single End PCR Primer 1 (96% over 32bp) CTCAGATTGAACGCTGGCGGCAGGCCTAACACATGCAAGTCGAACGGTAA 15 0.375 No Hit GCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAG 9 0.22499999999999998 No Hit GGCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTC 8 0.2 No Hit GGGAAACCGAGTCTTAACTGGGCGTTAAGTTGCAGGGTATAGACCCGAAA 8 0.2 No Hit GGGAACTCAAAGGAGACTGCCAGTGATAAACTGGAGGAAGGTGGGGATGA 7 0.17500000000000002 No Hit AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGCCTCTATGTGTAGATC 6 0.15 Illumina Single End PCR Primer 1 (96% over 33bp) GATCGGAAGAGCGTCGTGTAGGTAAAGAGTGTGCCTCTATGTGTAGATCT 5 0.125 Illumina Single End PCR Primer 1 (96% over 32bp) GCTGAAAGCCCTAACTTAATGGACGGGAGGTATCCCAATAGGAGGTTTCC 5 0.125 No Hit GCTGCTCACAGTATACGGGCGTCGGCATCCAGACCGTCGGCTGATCGTGG 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 0.15 0.0 0.0 0.0 0.0 2 0.175 0.0 0.0 0.0 0.0 3 0.175 0.0 0.0 0.0 0.0 4 0.175 0.0 0.0 0.0 0.0 5 0.175 0.0 0.0 0.0 0.0 6 0.175 0.0 0.0 0.0 0.0 7 0.175 0.0 0.0 0.0 0.0 8 0.175 0.0 0.0 0.0 0.0 9 0.175 0.0 0.0 0.0 0.0 10-11 0.175 0.0 0.0 0.0 0.0 12-13 0.175 0.0 0.0 0.0 0.0 14-15 0.175 0.0 0.0 0.0 0.0 16-17 0.175 0.0 0.0 0.0 0.0 18-19 0.175 0.0 0.0 0.0 0.0 20-21 0.175 0.0 0.0 0.0 0.0 22-23 0.175 0.0 0.0 0.0 0.0 24-25 0.175 0.0 0.0 0.0 0.0 26-27 0.175 0.0 0.0 0.0 0.0 28-29 0.175 0.0 0.0 0.0 0.0 30-31 0.175 0.0 0.0 0.0 0.0 32-33 0.175 0.0 0.0 0.0 0.0 34-35 0.175 0.0 0.0 0.0 0.0 36-37 0.175 0.0 0.0 0.0 0.0 38-39 0.175 0.0 0.0 0.0 0.0 40-41 0.175 0.0 0.0 0.0 0.0 42-43 0.175 0.0 0.0 0.0 0.0 44-45 0.175 0.0 0.0 0.0 0.0 46-47 0.175 0.0 0.0 0.0 0.0 48-49 0.175 0.0 0.0 0.0 0.0 50-51 0.2 0.0 0.0 0.0 0.0 52-53 0.25 0.0 0.0 0.0 0.0 54-55 0.25 0.0 0.0 0.0 0.0 56-57 0.25 0.0 0.0 0.0 0.0 58-59 0.2625 0.0 0.0 0.0 0.0 60-61 0.2875 0.0 0.0 0.0 0.0 62-63 0.3375 0.0 0.0 0.0 0.0 64-65 0.35 0.0 0.0 0.0 0.0 66-67 0.4125 0.0 0.0 0.0 0.0 68-69 0.425 0.0 0.0 0.0 0.0 70-71 0.475 0.0 0.0 0.0 0.0 72-73 0.525 0.0 0.0 0.0 0.0 74-75 0.5375000000000001 0.0 0.0 0.0 0.0 76-77 0.575 0.0 0.0 0.0 0.0 78-79 0.65 0.0 0.0 0.0 0.0 80-81 0.7749999999999999 0.0 0.0 0.0 0.0 82-83 1.0125 0.0 0.0 0.0 0.0 84-85 1.2125 0.0 0.0 0.0 0.0 86-87 1.375 0.0 0.0 0.0 0.0 88-89 1.6375 0.0 0.0 0.0 0.0 90-91 1.775 0.0 0.0 0.0 0.0 92-93 2.1375 0.0 0.0 0.0 0.0 94-95 2.5375 0.0 0.0 0.0 0.0 96-97 2.8875 0.0 0.0 0.0 0.0 98-99 3.3375 0.0 0.0 0.0 0.0 100-101 3.6625 0.0 0.0 0.0 0.0 102-103 4.0625 0.0 0.0 0.0 0.0 104-105 4.45 0.0 0.0 0.0 0.0 106-107 5.05 0.0 0.0 0.0 0.0 108-109 5.5625 0.0 0.0 0.0 0.0 110-111 6.275 0.0 0.0 0.0 0.0 112-113 7.0375 0.0 0.0 0.0 0.0 114-115 7.737500000000001 0.0 0.0 0.0 0.0 116-117 8.475000000000001 0.0 0.0 0.0 0.0 118-119 9.4375 0.0 0.0 0.0 0.0 120-121 10.2 0.0 0.0 0.0 0.0 122-123 11.075 0.0 0.0 0.0 0.0 124-125 11.95 0.0 0.0 0.0 0.0 126-127 12.912500000000001 0.0 0.0 0.0 0.0 128-129 13.7375 0.0 0.0 0.0 0.0 130-131 14.5875 0.0 0.0 0.0 0.0 132-133 15.5625 0.0 0.0 0.0 0.0 134-135 16.2125 0.0 0.0 0.0 0.0 136-137 16.775 0.0 0.0 0.0 0.0 138-139 17.3125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGATTTT 10 0.006830828 145.0 1 GAGCGTC 95 0.004191872 30.526318 9 GAAGAGC 95 0.004191872 30.526318 6 CGGAAGA 95 0.004191872 30.526318 4 GGAAGAG 95 0.004191872 30.526318 5 TGGTCGC 20 0.00593511 29.0 50-54 ATCTCGG 25 4.977651E-4 29.0 45-49 AAGAGCG 100 0.005388326 29.0 7 CCGTATC 20 0.00593511 29.0 60-64 CATTAAA 20 0.00593511 29.0 65-69 AGAGCGT 100 0.005388326 29.0 8 TCTCGGT 20 0.00593511 29.0 45-49 TCGCCGT 20 0.00593511 29.0 55-59 ATTAAAA 20 0.00593511 29.0 65-69 CGTATCA 20 0.00593511 29.0 60-64 ATCATTA 20 0.00593511 29.0 60-64 GGTGGTC 20 0.00593511 29.0 50-54 GTGGTCG 20 0.00593511 29.0 50-54 GCCGTAT 20 0.00593511 29.0 55-59 TCATTAA 20 0.00593511 29.0 65-69 >>END_MODULE Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607165 spots for SRR7171110.sra Written 607165 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra Read 607146 spots for SRR7171110.sra Written 607146 spots for SRR7171110.sra SRR ids: ['SRR7171110.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_471iz9ld SRR7171110.sra spots: 12142939 blocks: [[1, 607146], [607147, 1214292], [1214293, 1821438], [1821439, 2428584], [2428585, 3035730], [3035731, 3642876], [3642877, 4250022], [4250023, 4857168], [4857169, 5464314], [5464315, 6071460], [6071461, 6678606], [6678607, 7285752], [7285753, 7892898], [7892899, 8500044], [8500045, 9107190], [9107191, 9714336], [9714337, 10321482], [10321483, 10928628], [10928629, 11535774], [11535775, 12142939]] SRR7171110 file size 4093143 SRR7171110 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 SRR7171110 SRR7171110_1.fastq SRR7171110_2.fastq Input file: SRR7171110_1.fastq Paired file: SRR7171110_2.fastq trimmed: SRR7171110-trimmed-pair1.fastq, SRR7171110-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 05:54:34 2025 >> started Fri Feb 14 05:54:47 2025 >> done (13.625s) 12142939 read pairs processed; of these: 32555 ( 0.27%) short read pairs filtered out after trimming by size control 775578 ( 6.39%) empty read pairs filtered out after trimming by size control 11334806 (93.34%) read pairs available; of these: 7691115 (67.85%) trimmed read pairs available after processing 3643691 (32.15%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 37 0.00% 19 53 0.00% 20 43 0.00% 21 62 0.00% 22 34 0.00% 23 53 0.00% 24 51 0.00% 25 45 0.00% 26 74 0.00% 27 72 0.00% 28 52 0.00% 29 80 0.00% 30 90 0.00% 31 102 0.00% 32 127 0.00% 33 110 0.00% 34 101 0.00% 35 102 0.00% 36 149 0.00% 37 149 0.00% 38 165 0.00% 39 210 0.00% 40 250 0.00% 41 268 0.00% 42 299 0.00% 43 281 0.00% 44 314 0.00% 45 507 0.00% 46 586 0.01% 47 761 0.01% 48 800 0.01% 49 773 0.01% 50 926 0.01% 51 914 0.01% 52 1005 0.01% 53 936 0.01% 54 948 0.01% 55 1004 0.01% 56 1103 0.01% 57 1130 0.01% 58 1260 0.01% 59 1637 0.01% 60 1793 0.02% 61 2087 0.02% 62 2334 0.02% 63 2531 0.02% 64 2787 0.02% 65 3072 0.03% 66 2941 0.03% 67 2918 0.03% 68 3148 0.03% 69 3601 0.03% 70 4091 0.04% 71 4712 0.04% 72 6296 0.06% 73 8381 0.07% 74 12656 0.11% 75 26430 0.23% 76 74289 0.66% 77 96598 0.85% 78 31502 0.28% 79 16348 0.14% 80 14539 0.13% 81 13601 0.12% 82 14158 0.12% 83 14884 0.13% 84 17784 0.16% 85 17881 0.16% 86 19057 0.17% 87 20147 0.18% 88 21550 0.19% 89 22209 0.20% 90 22644 0.20% 91 24034 0.21% 92 24250 0.21% 93 27369 0.24% 94 28657 0.25% 95 30909 0.27% 96 30844 0.27% 97 30568 0.27% 98 30820 0.27% 99 32093 0.28% 100 34257 0.30% 101 33723 0.30% 102 36066 0.32% 103 38588 0.34% 104 40835 0.36% 105 43379 0.38% 106 42927 0.38% 107 42358 0.37% 108 43371 0.38% 109 46717 0.41% 110 47437 0.42% 111 46391 0.41% 112 47992 0.42% 113 52579 0.46% 114 52621 0.46% 115 55012 0.49% 116 54369 0.48% 117 53471 0.47% 118 54027 0.48% 119 53720 0.47% 120 54716 0.48% 121 54575 0.48% 122 56849 0.50% 123 59195 0.52% 124 59408 0.52% 125 59414 0.52% 126 60700 0.54% 127 61342 0.54% 128 61582 0.54% 129 63148 0.56% 130 64116 0.57% 131 64635 0.57% 132 66444 0.59% 133 69480 0.61% 134 72861 0.64% 135 76320 0.67% 136 77205 0.68% 137 82259 0.73% 138 85170 0.75% 139 88249 0.78% 140 91402 0.81% 141 98769 0.87% 142 105710 0.93% 143 116092 1.02% 144 131432 1.16% 145 152699 1.35% 146 186268 1.64% 147 242723 2.14% 148 358069 3.16% 149 672338 5.93% 150 2493929 22.00% 151 3643691 32.15% 11334806 reads passed initial QC criterion=sequence-density sequence-density=0.44 sequence-density-rank=1 fanout-score=2.31 fanout-score-rank=36 prefix-density=0.46 prefix-fanout=2.2 sequence=AGTTCCTTCACCCGAGTTCTCTCAAGCGCCTTGGTATTCTCTACCTGACCACCTGTGTCGGTTTGGGGTACGATTTGATGTTACCTGATGCTTAGAGGCTTTTCCTGGAAGCAGGGCATTTGTTGCTTCAGCACCGTAGTGCCTCGTCATCACGCCTCAGCCTTGATTTTCCGGATTTGCCTGGAAAACCAGCCTACACGCTTAAACCGGGACAACCGTCGCCCGGCCAACATAGCCTTCTCCGTCCCCCCTTCGCAGTAACACCAAGTACAGGAATATTAACCTGTTTCCCATCGACTACGCCTTTCGGCCTCGCCTTAGGGGTCGACTCACCCTGCCCCGATTAACGTTGGACAGGAACCCTTGGTCTTCCGGCGAGCGGGCTTTTCACCCGCTTTATCGTTACTTATGTCAGCATTCGCACTTCTGATACCTCCAGCATGCCTCACAGCACACCTTCGCAGGCTTACAGAACGCTCCCCTACCCAACAACGCATAAGCGTCGCTGCCG criterion=fanout-score sequence-density=0.01 sequence-density-rank=44 fanout-score=100.85 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=2.0 sequence=AGGTGATCCAACCGCAGGTTCCCCTACGGTTACCTTGTTACGACTTCACCCCAGTCATGAATCACAAAGTGGTAAGCGCCCTCCCGAAGGTTAAGCTACCTACTTCTTTTGCAACCCACTCCCATGGTGTGACGGGCGGTGTGTACAAGGCCCGGGAACGTATTCACCGTGGCATTCTGATCCACGATTACTAGCGATTCCGACTTCATGGAGTCGAGTTGCAGACTCCAATCCGGACTACGACGCACTTTATGAGGTCCGCTTGCTCTCGCGAGGTCGCTTCTCTTTGTATGCGCCATTGTAGCACGTGTGTAGCCCTGGTCGTAAGGGCCATGATGACTTGACGTCATCCCCACCTTCCTCCAGTTTATCACTGGCAGTCTCCTTTGAGTTCCCGGCCGGACCGCTGGCAACAAAGGATAAGGGTTGCGCTCGTTGCGGGACTTAACCCAACATTTCACAACACGAGCTGACGACAGCCATGCAGCACCTGTCTCACGGTTCCCGAAGG criterion=sequence-density sequence-density=1.22 sequence-density-rank=1 fanout-score=2.63 fanout-score-rank=27 prefix-density=1.36 prefix-fanout=2.3 sequence=GCTGACGAGTGGCGGACGGGTGAGTAATGTCTGGGAAACTGCCTGATGGAGGGGGATAACTACTGGAAACGGTAGCTAATACCGCATAACGTCGCAAGACCAAAGAGGGGGACCTTCGGGCCTCTTGCCATCGGATGTGCCCAGATGGGATTAGCTAGTAGGTGGGGTAACGGCTCACCTAGGCGACGATCCCTAGCTGGTCTGAGAGGATGACCAGCCACACTGGAACTGAGACACGGTCCAGACTCCTACGGGAGGCAGCAGTGGGGAATATTGCACAATGGGCGCAAGCCTGATGCAGCCATGCCGCGTGTATGAAGAAGGCCTTCGGGTTGTAAAGTACTTTCAGCGGGGAGGAAGGGAGTAAAGTTAATACCTTTGCTCATTGACGTTACCCGCAGAAGAAGCACCGGCTAACTCCGTGCCAGCAGCCGCGGTAATACGGAGGGTGCAAGCGTTAATCGGAATTACTGGGCGTAAAGCGCACGCAGGCGGTTTGTTAAGTCAGATG criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=24.84 fanout-score-rank=1 prefix-density=0.05 prefix-fanout=5.5 sequence=CAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATTTCATCGGCGGCCGTTGCCACAGTTAACCGCACCCCTGCACAGGCCAACATGGTTGCACCATTCAACGGCCTCAAGTCTACCTCAGCTTTCCCGGTCACCAGAAAGGCTAACAATGACATTACTTCCATTGCAAGCAATGGCGGAAGAGTTCAATGCATGCAGGTGTGGCCTCCAACTGGATTGAAGAAGTTCGAGACTCTTTCTTACCTTCCAGATCTCACTACTGAGCAATTGGCCCAGGAAATTGAGTACCTTCTTCGCAACAAGTGGGTTCCTTGCTTGGAATTCGAGTTGGAGAAAGGTTGGGTCTACCGCGAGCACCACCAGTCCCCAGGGTACTATGATGGACGCTACTGGACTATGTGGAAACTACCCATGTTTGGATGCACTGAGGCATCTCAGGTGCTGATTGAGCTCGAGGAGGCGAAGAAAGCTTACCCTAACTCCT SRR7171110 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 14 05:55:46 Started mapping on | Feb 14 05:55:46 Finished on | Feb 14 06:00:24 Mapping speed, Million of reads per hour | 146.78 Number of input reads | 11334806 Average input read length | 279 UNIQUE READS: Uniquely mapped reads number | 7738234 Uniquely mapped reads % | 68.27% Average mapped length | 281.97 Number of splices: Total | 4732232 Number of splices: Annotated (sjdb) | 4612067 Number of splices: GT/AG | 4620444 Number of splices: GC/AG | 86886 Number of splices: AT/AC | 5355 Number of splices: Non-canonical | 19547 Mismatch rate per base, % | 0.40% Deletion rate per base | 0.04% Deletion average length | 2.86 Insertion rate per base | 0.03% Insertion average length | 2.01 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 196999 % of reads mapped to multiple loci | 1.74% Number of reads mapped to too many loci | 47825 % of reads mapped to too many loci | 0.42% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 29.29% % of reads unmapped: other | 0.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 3420113 3420113 3420113 N_multimapping 196999 196999 196999 N_noFeature 260516 7511130 335560 N_ambiguous 209821 734 57605 UnstrandedReadsAssigned:7267897 PositiveStrandReadsAssigned:226370 NegativeStrandReadsAssigned:7345069 Dataset is classified negative stranded MeadianReadLen=150 20thPercentileLength=130 echo kmer=125 SRR7171110 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: SRR7171110-trimmed-pair1.fastq SRR7171110-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,334,806 reads, 7,447,197 reads pseudoaligned [quant] estimated average fragment length: 192.213 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,227 rounds 52401 SRR7171110.ke.tsv 34699 SRR7171110.se.tsv 87100 total ==> SRR7171110.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1826.79 213 12.9736 Potri.005G024800.1.v4.1 1035 843.787 55 7.25271 Potri.004G059700.1.v4.1 961 769.787 1 0.144544 Potri.007G009000.2.v4.1 1416 1224.79 0 0 Potri.003G141000.2.v4.1 2943 2751.79 396 16.0122 Potri.016G087400.1.v4.1 270 101.96 266 290.285 Potri.015G069301.1.v4.1 564 373.49 0 0 Potri.010G195200.1.v4.1 1773 1581.79 1 0.0703432 Potri.012G127500.1.v4.1 977 785.787 16 2.26561 ==> SRR7171110.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 199 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 334 Potri.001G212900.v4.1 4 Potri.001G182400.v4.1 2 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR7171110 completed mapping pipeline successfully