Starting /dee2/code/volunteer_pipeline.sh SRR12670150 current disk space = 3056971804672 free memory = 1162266496 SRR12670150 SRAfilesize 3c96876bf254f8b2a9d513b2e0342c0f SRR12670150.sra SRR12670150.sra file validated SRR12670150 is paired end SRR12670150 is conventional basespace SRR12670150 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670150_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6315 37.0 37.0 37.0 37.0 37.0 2 36.468 37.0 37.0 37.0 37.0 37.0 3 36.6395 37.0 37.0 37.0 37.0 37.0 4 36.6565 37.0 37.0 37.0 37.0 37.0 5 36.648 37.0 37.0 37.0 37.0 37.0 6 36.632 37.0 37.0 37.0 37.0 37.0 7 36.4905 37.0 37.0 37.0 37.0 37.0 8 36.608 37.0 37.0 37.0 37.0 37.0 9 36.628 37.0 37.0 37.0 37.0 37.0 10-14 36.6192 37.0 37.0 37.0 37.0 37.0 15-19 36.5998 37.0 37.0 37.0 37.0 37.0 20-24 36.5437 37.0 37.0 37.0 37.0 37.0 25-29 36.5061 37.0 37.0 37.0 37.0 37.0 30-34 36.5484 37.0 37.0 37.0 37.0 37.0 35-39 36.5065 37.0 37.0 37.0 37.0 37.0 40-44 36.4486 37.0 37.0 37.0 37.0 37.0 45-49 35.9953 37.0 37.0 37.0 37.0 37.0 50-54 36.2201 37.0 37.0 37.0 37.0 37.0 55-59 35.789 37.0 37.0 37.0 37.0 37.0 60-64 35.6918 37.0 37.0 37.0 37.0 37.0 65-69 35.4247 37.0 37.0 37.0 37.0 37.0 70-74 35.684999999999995 37.0 37.0 37.0 37.0 37.0 75-79 36.2694 37.0 37.0 37.0 37.0 37.0 80-84 36.27309999999999 37.0 37.0 37.0 37.0 37.0 85-89 36.291999999999994 37.0 37.0 37.0 37.0 37.0 90-94 36.308299999999996 37.0 37.0 37.0 37.0 37.0 95-99 36.248599999999996 37.0 37.0 37.0 37.0 37.0 100-104 36.2873 37.0 37.0 37.0 37.0 37.0 105-109 36.249300000000005 37.0 37.0 37.0 37.0 37.0 110-114 36.1518 37.0 37.0 37.0 37.0 37.0 115-119 36.2029 37.0 37.0 37.0 37.0 37.0 120-124 36.0057 37.0 37.0 37.0 37.0 37.0 125-129 35.9925 37.0 37.0 37.0 37.0 37.0 130-134 35.8095 37.0 37.0 37.0 37.0 37.0 135-139 35.69199999999999 37.0 37.0 37.0 37.0 37.0 140-144 35.46900000000001 37.0 37.0 37.0 37.0 37.0 145-149 35.3277 37.0 37.0 37.0 34.6 37.0 150-151 35.137249999999995 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 19 1.0 20 0.0 21 0.0 22 0.0 23 2.0 24 4.0 25 1.0 26 7.0 27 10.0 28 13.0 29 19.0 30 24.0 31 28.0 32 36.0 33 90.0 34 293.0 35 376.0 36 2757.0 37 339.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 40.1 10.575 6.9 42.425000000000004 2 18.236472945891784 17.30961923847695 35.59619238476954 28.857715430861724 3 17.224999999999998 14.899999999999999 31.724999999999998 36.15 4 21.375 23.25 22.125 33.25 5 27.125 28.7 23.025000000000002 21.15 6 24.775 31.45 24.8 18.975 7 15.575 30.099999999999998 37.55 16.775000000000002 8 17.525 28.675 31.5 22.3 9 22.650000000000002 20.65 33.050000000000004 23.65 10-14 20.735 29.84 25.91 23.515 15-19 20.599999999999998 27.115000000000002 27.560000000000002 24.725 20-24 21.18 28.060000000000002 27.405 23.355 25-29 20.585 27.685 27.63 24.099999999999998 30-34 19.415 26.974999999999998 27.62 25.990000000000002 35-39 20.415 27.639999999999997 28.98 22.965 40-44 19.79 28.299999999999997 26.86 25.05 45-49 21.0 27.145000000000003 28.335 23.52 50-54 21.32 25.995 27.529999999999998 25.155 55-59 19.885 25.765 29.315 25.035 60-64 20.615 26.13 29.475 23.78 65-69 20.955 29.87 26.775 22.400000000000002 70-74 24.905 26.435 26.93 21.73 75-79 24.705 26.540000000000003 26.284999999999997 22.470000000000002 80-84 24.84 26.755000000000003 25.985000000000003 22.42 85-89 25.5 27.315 25.215 21.97 90-94 25.535000000000004 26.645000000000003 25.25 22.57 95-99 25.665 27.029999999999998 25.374999999999996 21.93 100-104 25.480000000000004 27.815 24.775 21.93 105-109 25.35 26.974999999999998 24.615000000000002 23.06 110-114 25.605 26.965 24.759999999999998 22.67 115-119 25.324999999999996 26.784999999999997 24.7 23.189999999999998 120-124 25.695 25.919999999999998 24.740000000000002 23.645 125-129 25.069999999999997 25.874999999999996 25.72 23.335 130-134 25.505 26.055 24.959999999999997 23.48 135-139 25.765 24.985 25.040000000000003 24.21 140-144 26.784999999999997 24.515 25.22 23.48 145-149 27.13 24.625 25.019999999999996 23.225 150-151 27.4125 24.45 25.025 23.1125 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 3.0 1 1.5 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 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 1.5 25 2.5 26 4.5 27 5.5 28 5.0 29 6.0 30 11.0 31 18.5 32 21.5 33 27.0 34 39.5 35 49.0 36 64.5 37 90.0 38 109.0 39 128.5 40 172.0 41 204.5 42 239.0 43 251.5 44 226.0 45 231.0 46 243.5 47 242.5 48 229.5 49 215.5 50 194.0 51 158.0 52 137.0 53 115.5 54 86.0 55 72.0 56 59.5 57 38.5 58 30.5 59 29.5 60 18.0 61 8.0 62 3.0 63 5.5 64 17.5 65 55.0 66 70.5 67 38.5 68 13.5 69 3.5 70 0.0 71 1.0 72 2.0 73 1.0 74 0.0 75 0.0 76 0.0 77 0.5 78 0.5 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 0.2 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 79.75 #Duplication Level Percentage of deduplicated Percentage of total 1 84.45141065830721 67.35 2 12.163009404388715 19.400000000000002 3 2.5391849529780566 6.075 4 0.658307210031348 2.1 5 0.12539184952978058 0.5 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.031347962382445145 1.0250000000000001 >50 0.0 0.0 >100 0.031347962382445145 3.55 >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 GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTTATGCATCTCGTAT 142 3.55 TruSeq Adapter, Index 2 (97% over 37bp) GATCGGAAGAGCACACGTCTGAACTCCAGTCACCGTTATGCATCGCGTAT 41 1.0250000000000001 TruSeq Adapter, Index 2 (97% over 37bp) GAGGACTTTTAATGCCATCTATTGGCTTGGAATCAGGCAGCTCAGATGAA 5 0.125 No Hit CCTTCTTTGAGCTCCGTTAATTTAAAGATAAAAAACAAACTAAATGGAAC 5 0.125 No Hit CATGAACAGAGATACAGCAGCAATCCAGACTGCAGTATAAACAGCTTTTC 5 0.125 No Hit CCAGAAACCACTGAAGAGAACAATGAAACCATATGCTTCCAAAATCATGC 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 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.07500000000000001 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.2 0.0 0.0 0.0 0.0 56-57 0.225 0.0 0.0 0.0 0.0 58-59 0.2625 0.0 0.0 0.0 0.0 60-61 0.3125 0.0 0.0 0.0 0.0 62-63 0.5 0.0 0.0 0.0 0.0 64-65 0.625 0.0 0.0 0.0 0.0 66-67 0.725 0.0 0.0 0.0 0.0 68-69 0.825 0.0 0.0 0.0 0.0 70-71 0.8875 0.0 0.0 0.0 0.0 72-73 1.0625 0.0 0.0 0.0 0.0 74-75 1.325 0.0 0.0 0.0 0.0 76-77 1.5875 0.0 0.0 0.0 0.0 78-79 1.9249999999999998 0.0 0.0 0.0 0.0 80-81 2.3 0.0 0.0 0.0 0.0 82-83 2.875 0.0 0.0 0.0 0.0 84-85 3.4875 0.0 0.0 0.0 0.0 86-87 4.324999999999999 0.0 0.0 0.0 0.0 88-89 5.0 0.0 0.0 0.0 0.0 90-91 5.9 0.0 0.0 0.0 0.0 92-93 6.8625 0.0 0.0 0.0 0.0 94-95 7.825 0.0 0.0 0.0 0.0 96-97 8.75 0.0 0.0 0.0 0.0 98-99 9.625 0.0 0.0 0.0 0.0 100-101 10.5125 0.0 0.0 0.0 0.0 102-103 11.649999999999999 0.0 0.0 0.0 0.0 104-105 12.675 0.0 0.0 0.0 0.0 106-107 13.7875 0.0 0.0 0.0 0.0 108-109 14.525 0.0 0.0 0.0 0.0 110-111 15.4375 0.0 0.0 0.0 0.0 112-113 16.5625 0.0 0.0 0.0 0.0 114-115 17.674999999999997 0.0 0.0 0.0 0.0 116-117 18.6875 0.0 0.0 0.0 0.0 118-119 19.8 0.0 0.0 0.0 0.0 120-121 20.6875 0.0 0.0 0.0 0.0 122-123 21.7125 0.0 0.0 0.0 0.0 124-125 22.675 0.0 0.0 0.0 0.0 126-127 23.6125 0.0 0.0 0.0 0.0 128-129 24.5375 0.0 0.0 0.0 0.0 130-131 25.737499999999997 0.0 0.0 0.0 0.0 132-133 26.7625 0.0 0.0 0.0 0.0 134-135 27.8125 0.0 0.0 0.0 0.0 136-137 28.8125 0.0 0.0 0.0 0.0 138-139 30.1125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAGCACA 150 3.4143748E-5 29.000002 9 GAAGAGC 155 4.27173E-5 28.064516 6 AAGAGCA 160 5.3055614E-5 27.1875 7 CGGAAGA 160 5.3055614E-5 27.1875 4 GGAAGAG 160 5.3055614E-5 27.1875 5 TCGGAAG 165 6.5446795E-5 26.363638 3 AGAGCAC 165 6.5446795E-5 26.363638 8 ATCGGAA 165 6.5446795E-5 26.363638 2 GATCGGA 160 0.0018216907 22.65625 1 CTTGAAA 55 0.0025160722 15.818182 60-64 TGCTTGA 60 0.004491891 14.500001 60-64 GCTTGAA 65 0.0076375785 13.384615 60-64 CTCGTAT 65 0.0076375785 13.384615 40-44 >>END_MODULE SRR12670150 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670150_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.3465 37.0 37.0 37.0 37.0 37.0 2 36.3125 37.0 37.0 37.0 37.0 37.0 3 36.1715 37.0 37.0 37.0 37.0 37.0 4 36.1805 37.0 37.0 37.0 37.0 37.0 5 36.2635 37.0 37.0 37.0 37.0 37.0 6 36.299 37.0 37.0 37.0 37.0 37.0 7 36.1485 37.0 37.0 37.0 37.0 37.0 8 36.056 37.0 37.0 37.0 37.0 37.0 9 36.1195 37.0 37.0 37.0 37.0 37.0 10-14 35.9437 37.0 37.0 37.0 37.0 37.0 15-19 35.9549 37.0 37.0 37.0 37.0 37.0 20-24 35.7967 37.0 37.0 37.0 37.0 37.0 25-29 35.4389 37.0 37.0 37.0 37.0 37.0 30-34 35.349599999999995 37.0 37.0 37.0 37.0 37.0 35-39 35.297 37.0 37.0 37.0 37.0 37.0 40-44 35.3568 37.0 37.0 37.0 37.0 37.0 45-49 35.162099999999995 37.0 37.0 37.0 37.0 37.0 50-54 35.1154 37.0 37.0 37.0 37.0 37.0 55-59 35.219 37.0 37.0 37.0 37.0 37.0 60-64 35.388099999999994 37.0 37.0 37.0 37.0 37.0 65-69 35.2527 37.0 37.0 37.0 34.6 37.0 70-74 34.969500000000004 37.0 37.0 37.0 27.4 37.0 75-79 34.938599999999994 37.0 37.0 37.0 29.8 37.0 80-84 35.0705 37.0 37.0 37.0 32.2 37.0 85-89 35.2793 37.0 37.0 37.0 37.0 37.0 90-94 35.5331 37.0 37.0 37.0 37.0 37.0 95-99 35.6038 37.0 37.0 37.0 37.0 37.0 100-104 35.5991 37.0 37.0 37.0 37.0 37.0 105-109 35.5771 37.0 37.0 37.0 37.0 37.0 110-114 35.422200000000004 37.0 37.0 37.0 37.0 37.0 115-119 35.3361 37.0 37.0 37.0 37.0 37.0 120-124 34.92209999999999 37.0 37.0 37.0 27.4 37.0 125-129 34.551500000000004 37.0 37.0 37.0 25.0 37.0 130-134 34.156000000000006 37.0 37.0 37.0 25.0 37.0 135-139 33.7559 37.0 37.0 37.0 19.4 37.0 140-144 33.4735 37.0 37.0 37.0 13.8 37.0 145-149 33.135099999999994 37.0 37.0 37.0 11.0 37.0 150-151 32.763000000000005 37.0 37.0 37.0 11.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 4.0 14 2.0 15 4.0 16 4.0 17 1.0 18 5.0 19 3.0 20 13.0 21 15.0 22 14.0 23 15.0 24 17.0 25 22.0 26 27.0 27 42.0 28 31.0 29 50.0 30 70.0 31 75.0 32 124.0 33 189.0 34 260.0 35 520.0 36 2231.0 37 262.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.35 20.125 10.575 28.95 2 30.25 24.4 29.349999999999998 16.0 3 26.474999999999998 24.85 30.075000000000003 18.6 4 27.950000000000003 31.35 22.125 18.575 5 28.525 34.125 20.325 17.025000000000002 6 24.975 36.125 23.225 15.675 7 24.875 21.7 35.475 17.95 8 25.3 24.025 27.625 23.05 9 26.125 22.7 30.425 20.75 10-14 26.784999999999997 27.965 25.11 20.14 15-19 27.224999999999998 27.35 25.979999999999997 19.445 20-24 26.58 27.375 26.3 19.744999999999997 25-29 26.46 27.725 26.135 19.68 30-34 26.005 26.875 26.825 20.294999999999998 35-39 26.775 26.619999999999997 26.224999999999998 20.380000000000003 40-44 26.424999999999997 26.919999999999998 26.200000000000003 20.455000000000002 45-49 26.115 26.955000000000002 27.0 19.93 50-54 26.115 26.169999999999998 26.889999999999997 20.825 55-59 26.700000000000003 26.384999999999998 26.825 20.09 60-64 26.840000000000003 26.419999999999998 26.695 20.044999999999998 65-69 26.935 26.400000000000002 25.965 20.7 70-74 27.089999999999996 27.1 25.919999999999998 19.89 75-79 26.474999999999998 27.295 26.150000000000002 20.080000000000002 80-84 27.58 26.924999999999997 25.55 19.945 85-89 27.944999999999997 26.640000000000004 25.525 19.89 90-94 27.91 27.025 25.055 20.01 95-99 29.049999999999997 26.995 24.51 19.445 100-104 29.73 26.590000000000003 24.29 19.39 105-109 30.175 26.795 24.474999999999998 18.555 110-114 30.570000000000004 26.525 24.425 18.48 115-119 31.624999999999996 25.91 24.560000000000002 17.904999999999998 120-124 32.615 25.6 24.240000000000002 17.544999999999998 125-129 33.300000000000004 25.485000000000003 24.195 17.02 130-134 33.85 24.595 24.82 16.735 135-139 34.805 24.445 24.4 16.35 140-144 36.67 23.51 23.65 16.17 145-149 38.17 23.145 23.745 14.940000000000001 150-151 38.05 24.25 22.400000000000002 15.299999999999999 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 1.0 10 1.0 11 0.5 12 0.5 13 0.0 14 1.0 15 1.5 16 0.5 17 0.0 18 0.5 19 0.5 20 0.0 21 1.0 22 2.5 23 2.0 24 1.0 25 0.5 26 2.0 27 3.5 28 6.0 29 6.5 30 7.0 31 13.0 32 17.5 33 25.5 34 37.0 35 55.5 36 74.5 37 95.0 38 125.0 39 153.0 40 169.5 41 196.5 42 226.0 43 238.5 44 255.5 45 258.5 46 257.0 47 248.5 48 237.5 49 211.0 50 175.5 51 158.0 52 131.5 53 100.5 54 82.0 55 68.5 56 43.5 57 31.0 58 24.5 59 14.5 60 9.5 61 6.0 62 4.5 63 4.0 64 3.5 65 2.5 66 2.0 67 2.0 68 1.5 69 1.5 70 1.5 71 1.5 72 1.0 73 0.5 74 1.0 75 3.5 76 3.0 77 3.0 78 4.0 79 2.0 80 2.0 81 2.0 82 2.5 83 2.0 84 0.5 85 0.0 86 1.5 87 1.5 88 2.0 89 4.0 90 3.5 91 4.0 92 3.5 93 4.5 94 6.5 95 5.5 96 8.5 97 11.5 98 17.0 99 27.5 100 42.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 81.575 #Duplication Level Percentage of deduplicated Percentage of total 1 84.64603125957709 69.05 2 11.952191235059761 19.5 3 2.451731535396874 6.0 4 0.7355194606190621 2.4 5 0.09193993257738277 0.375 6 0.030646644192460923 0.15 7 0.030646644192460923 0.17500000000000002 8 0.0 0.0 9 0.030646644192460923 0.22499999999999998 >10 0.0 0.0 >50 0.030646644192460923 2.125 >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 fail #Sequence Count Percentage Possible Source GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 85 2.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTGGG 9 0.22499999999999998 No Hit AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 7 0.17500000000000002 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGTG 6 0.15 No Hit ATGCAATTCTTCATGAAACGCCAGAATTTTAAGGGAACTATTTCATTTGG 5 0.125 No Hit GTGAAATCAAGGGAAACATGGCAAGGTCAATCAGTCAAAATGGAGCTCTG 5 0.125 No Hit CTTGAGACCATATGAAAAGAGAGATCATGCACTGTTAGTTCCATTTAGTT 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 0.025 0.0 0.0 0.0 0.0 4 0.025 0.0 0.0 0.0 0.0 5 0.025 0.0 0.0 0.0 0.0 6 0.025 0.0 0.0 0.0 0.0 7 0.025 0.0 0.0 0.0 0.0 8 0.025 0.0 0.0 0.0 0.0 9 0.025 0.0 0.0 0.0 0.0 10-11 0.025 0.0 0.0 0.0 0.0 12-13 0.025 0.0 0.0 0.0 0.0 14-15 0.025 0.0 0.0 0.0 0.0 16-17 0.025 0.0 0.0 0.0 0.0 18-19 0.025 0.0 0.0 0.0 0.0 20-21 0.025 0.0 0.0 0.0 0.0 22-23 0.025 0.0 0.0 0.0 0.0 24-25 0.025 0.0 0.0 0.0 0.0 26-27 0.025 0.0 0.0 0.0 0.0 28-29 0.025 0.0 0.0 0.0 0.0 30-31 0.025 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 0.037500000000000006 0.0 0.0 0.0 0.0 42-43 0.05 0.0 0.0 0.0 0.0 44-45 0.05 0.0 0.0 0.0 0.0 46-47 0.05 0.0 0.0 0.0 0.0 48-49 0.05 0.0 0.0 0.0 0.0 50-51 0.07500000000000001 0.0 0.0 0.0 0.0 52-53 0.1 0.0 0.0 0.0 0.0 54-55 0.2 0.0 0.0 0.0 0.0 56-57 0.225 0.0 0.0 0.0 0.0 58-59 0.2625 0.0 0.0 0.0 0.0 60-61 0.3125 0.0 0.0 0.0 0.0 62-63 0.5 0.0 0.0 0.0 0.0 64-65 0.625 0.0 0.0 0.0 0.0 66-67 0.725 0.0 0.0 0.0 0.0 68-69 0.825 0.0 0.0 0.0 0.0 70-71 0.8875 0.0 0.0 0.0 0.0 72-73 1.0625 0.0 0.0 0.0 0.0 74-75 1.325 0.0 0.0 0.0 0.0 76-77 1.5875 0.0 0.0 0.0 0.0 78-79 1.9249999999999998 0.0 0.0 0.0 0.0 80-81 2.325 0.0 0.0 0.0 0.0 82-83 2.9000000000000004 0.0 0.0 0.0 0.0 84-85 3.525 0.0 0.0 0.0 0.0 86-87 4.375 0.0 0.0 0.0 0.0 88-89 5.05 0.0 0.0 0.0 0.0 90-91 5.9375 0.0 0.0 0.0 0.0 92-93 6.875 0.0 0.0 0.0 0.0 94-95 7.887499999999999 0.0 0.0 0.0 0.0 96-97 8.825 0.0 0.0 0.0 0.0 98-99 9.6625 0.0 0.0 0.0 0.0 100-101 10.5125 0.0 0.0 0.0 0.0 102-103 11.6375 0.0 0.0 0.0 0.0 104-105 12.65 0.0 0.0 0.0 0.0 106-107 13.7625 0.0 0.0 0.0 0.0 108-109 14.525 0.0 0.0 0.0 0.0 110-111 15.4375 0.0 0.0 0.0 0.0 112-113 16.5625 0.0 0.0 0.0 0.0 114-115 17.7125 0.0 0.0 0.0 0.0 116-117 18.737499999999997 0.0 0.0 0.0 0.0 118-119 19.9 0.0 0.0 0.0 0.0 120-121 20.75 0.0 0.0 0.0 0.0 122-123 21.7875 0.0 0.0 0.0 0.0 124-125 22.725 0.0 0.0 0.0 0.0 126-127 23.6375 0.0 0.0 0.0 0.0 128-129 24.5625 0.0 0.0 0.0 0.0 130-131 25.775 0.0 0.0 0.0 0.0 132-133 26.8125 0.0 0.0 0.0 0.0 134-135 27.8625 0.0 0.0 0.0 0.0 136-137 28.9 0.0 0.0 0.0 0.0 138-139 30.2125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AAAAAAA 20 0.00593511 29.0 140-144 >>END_MODULE Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra Read 482014 spots for SRR12670150.sra Written 482014 spots for SRR12670150.sra SRR ids: ['SRR12670150.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_jks7u358 SRR12670150.sra spots: 9640280 blocks: [[1, 482014], [482015, 964028], [964029, 1446042], [1446043, 1928056], [1928057, 2410070], [2410071, 2892084], [2892085, 3374098], [3374099, 3856112], [3856113, 4338126], [4338127, 4820140], [4820141, 5302154], [5302155, 5784168], [5784169, 6266182], [6266183, 6748196], [6748197, 7230210], [7230211, 7712224], [7712225, 8194238], [8194239, 8676252], [8676253, 9158266], [9158267, 9640280]] SRR12670150 file size 3255191 SRR12670150 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 SRR12670150 SRR12670150_1.fastq SRR12670150_2.fastq Input file: SRR12670150_1.fastq Paired file: SRR12670150_2.fastq trimmed: SRR12670150-trimmed-pair1.fastq, SRR12670150-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Feb 11 02:30:13 2025 >> started Tue Feb 11 02:36:13 2025 >> done (359.754s) 9640280 read pairs processed; of these: 100 ( 0.00%) short read pairs filtered out after trimming by size control 381830 ( 3.96%) empty read pairs filtered out after trimming by size control 9258350 (96.04%) read pairs available; of these: 3189174 (34.45%) trimmed read pairs available after processing 6069176 (65.55%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 5 0.00% 20 7 0.00% 21 7 0.00% 22 14 0.00% 23 19 0.00% 24 17 0.00% 25 23 0.00% 26 45 0.00% 27 40 0.00% 28 57 0.00% 29 56 0.00% 30 60 0.00% 31 71 0.00% 32 76 0.00% 33 91 0.00% 34 94 0.00% 35 106 0.00% 36 121 0.00% 37 158 0.00% 38 154 0.00% 39 203 0.00% 40 280 0.00% 41 279 0.00% 42 270 0.00% 43 300 0.00% 44 353 0.00% 45 309 0.00% 46 395 0.00% 47 486 0.01% 48 576 0.01% 49 741 0.01% 50 819 0.01% 51 934 0.01% 52 1090 0.01% 53 1132 0.01% 54 1216 0.01% 55 1309 0.01% 56 1462 0.02% 57 1685 0.02% 58 2007 0.02% 59 2364 0.03% 60 2768 0.03% 61 3286 0.04% 62 3666 0.04% 63 4093 0.04% 64 4440 0.05% 65 4637 0.05% 66 5054 0.05% 67 5517 0.06% 68 6363 0.07% 69 7252 0.08% 70 8158 0.09% 71 9337 0.10% 72 10535 0.11% 73 11631 0.13% 74 12848 0.14% 75 13392 0.14% 76 14627 0.16% 77 15407 0.17% 78 16228 0.18% 79 17972 0.19% 80 19209 0.21% 81 21372 0.23% 82 23171 0.25% 83 25148 0.27% 84 26784 0.29% 85 28387 0.31% 86 29475 0.32% 87 30140 0.33% 88 30881 0.33% 89 31772 0.34% 90 33165 0.36% 91 34958 0.38% 92 36075 0.39% 93 38176 0.41% 94 39658 0.43% 95 41215 0.45% 96 41471 0.45% 97 42827 0.46% 98 42535 0.46% 99 42161 0.46% 100 43160 0.47% 101 43147 0.47% 102 43988 0.48% 103 45238 0.49% 104 46367 0.50% 105 46768 0.51% 106 47099 0.51% 107 47631 0.51% 108 47110 0.51% 109 46972 0.51% 110 46185 0.50% 111 45657 0.49% 112 46918 0.51% 113 46791 0.51% 114 47273 0.51% 115 48189 0.52% 116 48955 0.53% 117 49108 0.53% 118 48222 0.52% 119 48030 0.52% 120 47417 0.51% 121 47021 0.51% 122 47067 0.51% 123 47187 0.51% 124 47676 0.51% 125 47071 0.51% 126 47675 0.51% 127 47722 0.52% 128 46968 0.51% 129 46621 0.50% 130 46710 0.50% 131 45733 0.49% 132 44663 0.48% 133 45879 0.50% 134 44854 0.48% 135 44794 0.48% 136 45271 0.49% 137 45049 0.49% 138 44616 0.48% 139 45033 0.49% 140 44234 0.48% 141 43802 0.47% 142 43826 0.47% 143 42901 0.46% 144 43449 0.47% 145 43001 0.46% 146 42985 0.46% 147 42938 0.46% 148 43730 0.47% 149 42601 0.46% 150 42649 0.46% 151 6069176 65.55% 9258350 reads passed initial QC criterion=sequence-density sequence-density=0.58 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=18 prefix-density=0.58 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.02 sequence-density-rank=23 fanout-score=29.43 fanout-score-rank=1 prefix-density=0.09 prefix-fanout=7.1 sequence=ACCACACCAGAGGCCACAGACATGGCCAATACATAACAATGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGTA criterion=sequence-density sequence-density=0.77 sequence-density-rank=1 fanout-score=2.09 fanout-score-rank=23 prefix-density=0.78 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.13 sequence-density-rank=23 fanout-score=10.14 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=3.5 sequence=CAATGGCAGCAGCAACAATGGCCCTCTCCTCCCCTTCGCTAGCCGGAAAGGCGGTGAAGCTCAACCCCTCCTCCTCTGAGATCATGGGCAATGGCCGTGTCTCCATGAGGAAAACCACCAAGCCTGTTCCCTCCGGGAGCCCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGAGCCCCCATCCTACTTGACTGGTGAGTTCCCTGGTGACTACGGCTGGGACACTGCTGG SRR12670150 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 03:18:30 Started mapping on | Feb 11 03:18:51 Finished on | Feb 11 04:36:14 Mapping speed, Million of reads per hour | 7.18 Number of input reads | 9258350 Average input read length | 276 UNIQUE READS: Uniquely mapped reads number | 8699686 Uniquely mapped reads % | 93.97% Average mapped length | 275.40 Number of splices: Total | 7935709 Number of splices: Annotated (sjdb) | 7770710 Number of splices: GT/AG | 7767434 Number of splices: GC/AG | 135530 Number of splices: AT/AC | 4726 Number of splices: Non-canonical | 28019 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.80 Insertion rate per base | 0.02% Insertion average length | 2.40 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 218087 % of reads mapped to multiple loci | 2.36% Number of reads mapped to too many loci | 38287 % of reads mapped to too many loci | 0.41% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.99% % of reads unmapped: other | 0.28% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 340577 340577 340577 N_multimapping 218087 218087 218087 N_noFeature 276385 8554679 341478 N_ambiguous 139638 407 59470 UnstrandedReadsAssigned:8283663 PositiveStrandReadsAssigned:144600 NegativeStrandReadsAssigned:8298738 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=120 echo kmer=115 SRR12670150 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: SRR12670150-trimmed-pair1.fastq SRR12670150-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 9,258,350 reads, 8,335,314 reads pseudoaligned [quant] estimated average fragment length: 192.756 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,052 rounds 52401 SRR12670150.ke.tsv 34699 SRR12670150.se.tsv 87100 total ==> SRR12670150.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1826.24 247 16.322 Potri.005G024800.1.v4.1 1035 843.244 86 12.3078 Potri.004G059700.1.v4.1 961 769.319 5 0.78433 Potri.007G009000.2.v4.1 1416 1224.24 0 0 Potri.003G141000.2.v4.1 2943 2751.24 309.714 13.5852 Potri.016G087400.1.v4.1 270 120.021 340 341.867 Potri.015G069301.1.v4.1 564 379.788 0 0 Potri.010G195200.1.v4.1 1773 1581.24 25 1.90799 Potri.012G127500.1.v4.1 977 785.269 68 10.4502 ==> SRR12670150.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 227 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 194 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 1 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12670150 completed mapping pipeline successfully