Starting /dee2/code/volunteer_pipeline.sh SRR12671374 current disk space = 3053259304960 free memory = 1477133740 SRR12671374 SRAfilesize 488930f923ec5eec4eff4256afb3b585 SRR12671374.sra SRR12671374.sra file validated SRR12671374 is paired end SRR12671374 is conventional basespace SRR12671374 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671374_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.6825 37.0 37.0 37.0 37.0 37.0 2 36.472 37.0 37.0 37.0 37.0 37.0 3 36.6475 37.0 37.0 37.0 37.0 37.0 4 36.6195 37.0 37.0 37.0 37.0 37.0 5 36.6575 37.0 37.0 37.0 37.0 37.0 6 36.722 37.0 37.0 37.0 37.0 37.0 7 36.6345 37.0 37.0 37.0 37.0 37.0 8 36.6255 37.0 37.0 37.0 37.0 37.0 9 36.6685 37.0 37.0 37.0 37.0 37.0 10-14 36.6309 37.0 37.0 37.0 37.0 37.0 15-19 36.6134 37.0 37.0 37.0 37.0 37.0 20-24 36.60000000000001 37.0 37.0 37.0 37.0 37.0 25-29 36.5651 37.0 37.0 37.0 37.0 37.0 30-34 36.5578 37.0 37.0 37.0 37.0 37.0 35-39 36.5283 37.0 37.0 37.0 37.0 37.0 40-44 36.4758 37.0 37.0 37.0 37.0 37.0 45-49 36.4653 37.0 37.0 37.0 37.0 37.0 50-54 36.4372 37.0 37.0 37.0 37.0 37.0 55-59 36.38549999999999 37.0 37.0 37.0 37.0 37.0 60-64 36.45190000000001 37.0 37.0 37.0 37.0 37.0 65-69 36.383799999999994 37.0 37.0 37.0 37.0 37.0 70-74 36.3462 37.0 37.0 37.0 37.0 37.0 75-79 36.3156 37.0 37.0 37.0 37.0 37.0 80-84 36.317600000000006 37.0 37.0 37.0 37.0 37.0 85-89 36.278 37.0 37.0 37.0 37.0 37.0 90-94 36.2844 37.0 37.0 37.0 37.0 37.0 95-99 36.236000000000004 37.0 37.0 37.0 37.0 37.0 100-104 36.20790000000001 37.0 37.0 37.0 37.0 37.0 105-109 36.2436 37.0 37.0 37.0 37.0 37.0 110-114 36.0798 37.0 37.0 37.0 37.0 37.0 115-119 36.174600000000005 37.0 37.0 37.0 37.0 37.0 120-124 36.068200000000004 37.0 37.0 37.0 37.0 37.0 125-129 36.04440000000001 37.0 37.0 37.0 37.0 37.0 130-134 36.0533 37.0 37.0 37.0 37.0 37.0 135-139 36.037400000000005 37.0 37.0 37.0 37.0 37.0 140-144 35.8916 37.0 37.0 37.0 37.0 37.0 145-149 35.8372 37.0 37.0 37.0 37.0 37.0 150-151 35.7375 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 1.0 20 2.0 21 3.0 22 3.0 23 2.0 24 2.0 25 4.0 26 6.0 27 7.0 28 6.0 29 16.0 30 19.0 31 31.0 32 48.0 33 59.0 34 94.0 35 233.0 36 2961.0 37 502.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 43.3 11.35 7.000000000000001 38.35 2 19.62406015037594 11.954887218045112 35.18796992481203 33.23308270676692 3 17.150000000000002 17.775 27.825 37.25 4 23.125 24.4 23.25 29.225 5 23.150000000000002 30.175 24.425 22.25 6 20.549999999999997 33.35 23.724999999999998 22.375 7 13.925 27.224999999999998 42.25 16.6 8 15.65 25.2 34.275 24.875 9 16.675 24.425 34.925 23.974999999999998 10-14 19.220000000000002 29.665000000000003 28.449999999999996 22.665 15-19 20.495 28.565 27.865000000000002 23.075000000000003 20-24 20.085 29.060000000000002 26.82 24.035 25-29 19.445 29.56 27.37 23.625 30-34 20.115 28.515 27.644999999999996 23.724999999999998 35-39 19.61 28.03 28.155 24.205 40-44 19.37 29.78 27.165 23.685000000000002 45-49 20.41 28.73 27.54 23.32 50-54 19.555 28.98 27.439999999999998 24.025 55-59 19.785 29.025000000000002 27.655 23.535 60-64 19.845 28.560000000000002 28.175 23.419999999999998 65-69 19.495 29.360000000000003 27.355 23.79 70-74 20.285 28.904999999999998 27.615000000000002 23.195 75-79 19.805 28.794999999999998 27.63 23.77 80-84 19.64 28.48 27.96 23.919999999999998 85-89 20.0 28.849999999999998 27.185 23.965 90-94 20.035 28.425 27.084999999999997 24.455 95-99 20.11 27.99 27.49 24.41 100-104 20.49 28.415000000000003 27.634999999999998 23.46 105-109 20.105 28.52 27.685 23.69 110-114 20.855 28.68 27.195000000000004 23.27 115-119 20.53 28.46 27.26 23.75 120-124 20.830000000000002 27.584999999999997 27.405 24.18 125-129 20.345 27.725 27.715 24.215 130-134 20.995 27.775 27.63 23.599999999999998 135-139 20.355 28.565 27.04 24.04 140-144 21.12 28.225 26.72 23.935000000000002 145-149 21.01 28.365000000000002 26.669999999999998 23.955000000000002 150-151 21.25 27.6125 27.400000000000002 23.7375 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 1.0 1 1.0 2 1.0 3 0.5 4 0.0 5 1.0 6 1.5 7 0.5 8 1.0 9 1.0 10 0.0 11 0.5 12 0.5 13 0.5 14 0.5 15 0.0 16 0.0 17 0.0 18 0.5 19 1.0 20 1.5 21 2.5 22 2.0 23 2.0 24 2.5 25 4.0 26 4.0 27 5.0 28 15.0 29 15.5 30 22.5 31 35.0 32 45.0 33 61.0 34 69.0 35 76.0 36 83.0 37 111.5 38 141.0 39 151.0 40 172.5 41 205.5 42 215.5 43 231.5 44 245.5 45 232.0 46 237.5 47 245.5 48 229.5 49 209.5 50 191.0 51 163.0 52 124.5 53 96.0 54 85.0 55 62.5 56 46.5 57 39.0 58 26.0 59 23.5 60 20.0 61 12.0 62 6.5 63 3.5 64 2.0 65 2.0 66 2.0 67 2.5 68 2.5 69 1.0 70 1.5 71 0.5 72 0.5 73 1.0 74 0.5 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 83.525 #Duplication Level Percentage of deduplicated Percentage of total 1 84.52559114037713 70.6 2 12.062256809338521 20.150000000000002 3 2.843460041903622 7.124999999999999 4 0.38910505836575876 1.3 5 0.08979347500748279 0.375 6 0.08979347500748279 0.44999999999999996 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >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 GCATTTTTGCTTTTTTGCCACCAACAAAGTTGCACAGGTACATCACACCC 6 0.15 No Hit GTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGAC 6 0.15 No Hit GCAGATTTTGGTATTAATGAATCTAGAAAATTACAGCATTATTCCATTCT 6 0.15 No Hit GTGCAGCCAAGAGGGAGTCTTCACAGGTGTTGTGCAGCACTATAGTGTTT 5 0.125 No Hit ACCAGCTTCAGTTGAGTTTTTCTTCATCTCCTCTCCAAACTTGTCCTTCC 5 0.125 No Hit GGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGA 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.0625 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.125 0.0 0.0 0.0 0.0 82-83 0.125 0.0 0.0 0.0 0.0 84-85 0.225 0.0 0.0 0.0 0.0 86-87 0.275 0.0 0.0 0.0 0.0 88-89 0.275 0.0 0.0 0.0 0.0 90-91 0.3125 0.0 0.0 0.0 0.0 92-93 0.44999999999999996 0.0 0.0 0.0 0.0 94-95 0.5 0.0 0.0 0.0 0.0 96-97 0.55 0.0 0.0 0.0 0.0 98-99 0.6375 0.0 0.0 0.0 0.0 100-101 0.6875 0.0 0.0 0.0 0.0 102-103 0.725 0.0 0.0 0.0 0.0 104-105 0.8375 0.0 0.0 0.0 0.0 106-107 0.95 0.0 0.0 0.0 0.0 108-109 1.0625 0.0 0.0 0.0 0.0 110-111 1.2125 0.0 0.0 0.0 0.0 112-113 1.3875 0.0 0.0 0.0 0.0 114-115 1.6124999999999998 0.0 0.0 0.0 0.0 116-117 1.7374999999999998 0.0 0.0 0.0 0.0 118-119 1.9 0.0 0.0 0.0 0.0 120-121 2.0 0.0 0.0 0.0 0.0 122-123 2.325 0.0 0.0 0.0 0.0 124-125 2.55 0.0 0.0 0.0 0.0 126-127 2.7125 0.0 0.0 0.0 0.0 128-129 2.9000000000000004 0.0 0.0 0.0 0.0 130-131 3.0875 0.0 0.0 0.0 0.0 132-133 3.4 0.0 0.0 0.0 0.0 134-135 3.6375 0.0 0.0 0.0 0.0 136-137 3.9875 0.0 0.0 0.0 0.0 138-139 4.35 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12671374 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671374_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 36.1265 37.0 37.0 37.0 37.0 37.0 2 35.756 37.0 37.0 37.0 37.0 37.0 3 36.12 37.0 37.0 37.0 37.0 37.0 4 36.0395 37.0 37.0 37.0 37.0 37.0 5 36.2355 37.0 37.0 37.0 37.0 37.0 6 36.1345 37.0 37.0 37.0 37.0 37.0 7 36.017 37.0 37.0 37.0 37.0 37.0 8 36.1875 37.0 37.0 37.0 37.0 37.0 9 36.184 37.0 37.0 37.0 37.0 37.0 10-14 36.200599999999994 37.0 37.0 37.0 37.0 37.0 15-19 36.144400000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.1322 37.0 37.0 37.0 37.0 37.0 25-29 36.1076 37.0 37.0 37.0 37.0 37.0 30-34 36.066 37.0 37.0 37.0 37.0 37.0 35-39 36.0565 37.0 37.0 37.0 37.0 37.0 40-44 36.074 37.0 37.0 37.0 37.0 37.0 45-49 36.019600000000004 37.0 37.0 37.0 37.0 37.0 50-54 35.9757 37.0 37.0 37.0 37.0 37.0 55-59 35.9589 37.0 37.0 37.0 37.0 37.0 60-64 35.971000000000004 37.0 37.0 37.0 37.0 37.0 65-69 35.964800000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.8899 37.0 37.0 37.0 37.0 37.0 75-79 35.9219 37.0 37.0 37.0 37.0 37.0 80-84 35.862300000000005 37.0 37.0 37.0 37.0 37.0 85-89 35.8835 37.0 37.0 37.0 37.0 37.0 90-94 35.8362 37.0 37.0 37.0 37.0 37.0 95-99 35.7703 37.0 37.0 37.0 37.0 37.0 100-104 35.781499999999994 37.0 37.0 37.0 37.0 37.0 105-109 35.720400000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.7 37.0 37.0 37.0 37.0 37.0 115-119 35.756899999999995 37.0 37.0 37.0 37.0 37.0 120-124 35.670100000000005 37.0 37.0 37.0 37.0 37.0 125-129 35.6447 37.0 37.0 37.0 37.0 37.0 130-134 35.561099999999996 37.0 37.0 37.0 37.0 37.0 135-139 35.532599999999995 37.0 37.0 37.0 37.0 37.0 140-144 35.5687 37.0 37.0 37.0 37.0 37.0 145-149 35.476099999999995 37.0 37.0 37.0 34.6 37.0 150-151 35.32 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 2.0 16 1.0 17 0.0 18 0.0 19 2.0 20 0.0 21 2.0 22 3.0 23 7.0 24 6.0 25 12.0 26 8.0 27 13.0 28 14.0 29 22.0 30 19.0 31 23.0 32 53.0 33 95.0 34 203.0 35 631.0 36 2676.0 37 200.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 39.7 25.324999999999996 10.025 24.95 2 26.700000000000003 26.8 31.525 14.975 3 19.925 28.95 31.574999999999996 19.55 4 23.5 34.675 23.225 18.6 5 26.0 35.85 21.75 16.400000000000002 6 21.25 38.95 22.225 17.575 7 20.4 22.650000000000002 38.525 18.425 8 20.45 24.275 28.999999999999996 26.275 9 21.75 24.175 29.625 24.45 10-14 23.21 29.494999999999997 26.21 21.085 15-19 23.51 28.665000000000003 27.11 20.715 20-24 23.23 28.549999999999997 27.125 21.095 25-29 23.01 28.455000000000002 27.91 20.625 30-34 23.145 28.04 27.905 20.91 35-39 23.175 28.310000000000002 27.37 21.145 40-44 22.8 28.335 27.98 20.885 45-49 23.45 27.68 27.800000000000004 21.07 50-54 23.16 28.605000000000004 27.075 21.16 55-59 23.205000000000002 27.889999999999997 28.189999999999998 20.715 60-64 22.46 27.36 28.555000000000003 21.625 65-69 23.724999999999998 28.110000000000003 27.450000000000003 20.715 70-74 23.735 28.34 26.915 21.01 75-79 24.075 27.575 27.63 20.72 80-84 23.22 28.449999999999996 27.565 20.765 85-89 24.125 27.534999999999997 27.589999999999996 20.75 90-94 24.05 27.650000000000002 27.235 21.065 95-99 24.43 27.405 27.51 20.655 100-104 23.56 27.884999999999998 27.47 21.085 105-109 23.57 27.455000000000002 27.939999999999998 21.035 110-114 23.185 27.639999999999997 28.315 20.86 115-119 24.385 28.525 26.729999999999997 20.36 120-124 23.805 28.09 27.6 20.505000000000003 125-129 24.224999999999998 27.255000000000003 27.99 20.53 130-134 24.605 27.834999999999997 27.375 20.185 135-139 24.89 26.634999999999998 28.395 20.080000000000002 140-144 24.44 28.025 27.555000000000003 19.98 145-149 24.62246224622462 27.912791279127912 27.057705770577055 20.407040704070408 150-151 24.2 28.262500000000003 27.1625 20.375 >>END_MODULE >>Per sequence GC content pass #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 0.5 9 0.5 10 0.0 11 1.0 12 1.5 13 1.5 14 2.0 15 1.5 16 0.5 17 0.5 18 0.5 19 1.0 20 1.0 21 0.0 22 0.0 23 0.5 24 3.5 25 4.5 26 3.5 27 5.5 28 8.0 29 12.0 30 17.5 31 25.5 32 27.0 33 33.5 34 58.5 35 71.0 36 79.0 37 111.0 38 132.0 39 163.5 40 202.5 41 214.0 42 226.0 43 252.0 44 263.0 45 258.5 46 257.5 47 257.0 48 231.5 49 195.0 50 167.0 51 138.0 52 120.0 53 93.5 54 75.5 55 67.5 56 55.0 57 42.5 58 27.5 59 23.5 60 21.0 61 12.0 62 6.5 63 3.0 64 2.5 65 1.5 66 1.0 67 0.5 68 1.0 69 1.0 70 0.5 71 0.5 72 0.5 73 0.5 74 0.5 75 0.5 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 0.5 86 0.5 87 0.0 88 0.0 89 0.0 90 0.5 91 0.5 92 0.5 93 1.0 94 1.5 95 1.0 96 0.0 97 0.5 98 0.5 99 0.0 100 2.0 >>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 0.01 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 84.075 #Duplication Level Percentage of deduplicated Percentage of total 1 85.34046981861432 71.75 2 11.507582515611062 19.35 3 2.4382991376746954 6.15 4 0.44603033006244425 1.5 5 0.17841213202497772 0.75 6 0.05947071067499256 0.3 7 0.0 0.0 8 0.02973535533749628 0.2 9 0.0 0.0 >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 AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 8 0.2 No Hit ATTTGAGTTGCTCACATCATTGGTACGAAGGTGGTGACAACATGGCCATT 6 0.15 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 No Hit CTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTATGATCTCA 5 0.125 No Hit ATCTGTTCTGGTTGATTTCCTTGTTGGGGCCGGTATTAAGCCAACGTCAA 5 0.125 No Hit GTGGAGTTGACCAACTAGTTGAGATCATTAAGGTTCTGGGAACACCAACC 5 0.125 No Hit GCTGTTGTAGACGATGATTTCTTGCAGAAATATGACATCAAGCTGAACAA 5 0.125 No Hit TGTGGTGGAAGGGTCTAAAATTCTCAGATTTTATGTACGTAACAAAGCGT 5 0.125 No Hit CTCAGAGAGAGAGAGAGAGAGAGACAGAGAGAATGGCCACCACAGCAGCC 5 0.125 No Hit >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.037500000000000006 0.0 0.0 0.0 0.0 70-71 0.05 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.0625 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.075 0.0 0.0 0.0 0.0 80-81 0.15 0.0 0.0 0.0 0.0 82-83 0.15 0.0 0.0 0.0 0.0 84-85 0.25 0.0 0.0 0.0 0.0 86-87 0.3 0.0 0.0 0.0 0.0 88-89 0.3 0.0 0.0 0.0 0.0 90-91 0.3375 0.0 0.0 0.0 0.0 92-93 0.475 0.0 0.0 0.0 0.0 94-95 0.525 0.0 0.0 0.0 0.0 96-97 0.575 0.0 0.0 0.0 0.0 98-99 0.6625 0.0 0.0 0.0 0.0 100-101 0.7124999999999999 0.0 0.0 0.0 0.0 102-103 0.75 0.0 0.0 0.0 0.0 104-105 0.8625 0.0 0.0 0.0 0.0 106-107 0.975 0.0 0.0 0.0 0.0 108-109 1.0875 0.0 0.0 0.0 0.0 110-111 1.2375 0.0 0.0 0.0 0.0 112-113 1.4125 0.0 0.0 0.0 0.0 114-115 1.6625 0.0 0.0 0.0 0.0 116-117 1.7875 0.0 0.0 0.0 0.0 118-119 1.975 0.0 0.0 0.0 0.0 120-121 2.075 0.0 0.0 0.0 0.0 122-123 2.4000000000000004 0.0 0.0 0.0 0.0 124-125 2.625 0.0 0.0 0.0 0.0 126-127 2.7750000000000004 0.0 0.0 0.0 0.0 128-129 2.95 0.0 0.0 0.0 0.0 130-131 3.15 0.0 0.0 0.0 0.0 132-133 3.475 0.0 0.0 0.0 0.0 134-135 3.7125 0.0 0.0 0.0 0.0 136-137 4.0625 0.0 0.0 0.0 0.0 138-139 4.425000000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra Read 849133 spots for SRR12671374.sra Written 849133 spots for SRR12671374.sra Read 849115 spots for SRR12671374.sra Written 849115 spots for SRR12671374.sra SRR ids: ['SRR12671374.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_vzaj6nwr SRR12671374.sra spots: 16982318 blocks: [[1, 849115], [849116, 1698230], [1698231, 2547345], [2547346, 3396460], [3396461, 4245575], [4245576, 5094690], [5094691, 5943805], [5943806, 6792920], [6792921, 7642035], [7642036, 8491150], [8491151, 9340265], [9340266, 10189380], [10189381, 11038495], [11038496, 11887610], [11887611, 12736725], [12736726, 13585840], [13585841, 14434955], [14434956, 15284070], [15284071, 16133185], [16133186, 16982318]] SRR12671374 file size 5749634 SRR12671374 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 SRR12671374 SRR12671374_1.fastq SRR12671374_2.fastq Input file: SRR12671374_1.fastq Paired file: SRR12671374_2.fastq trimmed: SRR12671374-trimmed-pair1.fastq, SRR12671374-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 20:19:43 2025 >> started Tue Feb 11 20:20:01 2025 >> done (18.707s) 16982318 read pairs processed; of these: 34 ( 0.00%) short read pairs filtered out after trimming by size control 8206 ( 0.05%) empty read pairs filtered out after trimming by size control 16974078 (99.95%) read pairs available; of these: 1123459 ( 6.62%) trimmed read pairs available after processing 15850619 (93.38%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 4 0.00% 20 4 0.00% 21 1 0.00% 22 5 0.00% 23 7 0.00% 24 9 0.00% 25 13 0.00% 26 12 0.00% 27 14 0.00% 28 9 0.00% 29 16 0.00% 30 14 0.00% 31 11 0.00% 32 19 0.00% 33 16 0.00% 34 10 0.00% 35 21 0.00% 36 15 0.00% 37 15 0.00% 38 25 0.00% 39 26 0.00% 40 28 0.00% 41 26 0.00% 42 24 0.00% 43 17 0.00% 44 17 0.00% 45 28 0.00% 46 34 0.00% 47 39 0.00% 48 59 0.00% 49 46 0.00% 50 45 0.00% 51 60 0.00% 52 73 0.00% 53 84 0.00% 54 70 0.00% 55 85 0.00% 56 99 0.00% 57 101 0.00% 58 129 0.00% 59 145 0.00% 60 178 0.00% 61 186 0.00% 62 228 0.00% 63 227 0.00% 64 246 0.00% 65 321 0.00% 66 350 0.00% 67 369 0.00% 68 400 0.00% 69 477 0.00% 70 558 0.00% 71 637 0.00% 72 719 0.00% 73 836 0.00% 74 914 0.01% 75 1049 0.01% 76 1162 0.01% 77 1177 0.01% 78 1413 0.01% 79 1477 0.01% 80 1749 0.01% 81 1940 0.01% 82 2193 0.01% 83 2357 0.01% 84 2515 0.01% 85 2972 0.02% 86 3140 0.02% 87 3511 0.02% 88 3630 0.02% 89 3719 0.02% 90 4179 0.02% 91 4444 0.03% 92 4621 0.03% 93 5187 0.03% 94 5552 0.03% 95 5941 0.04% 96 6365 0.04% 97 6705 0.04% 98 6891 0.04% 99 7391 0.04% 100 7820 0.05% 101 7709 0.05% 102 8310 0.05% 103 8627 0.05% 104 9078 0.05% 105 9753 0.06% 106 10135 0.06% 107 10687 0.06% 108 10940 0.06% 109 11356 0.07% 110 11600 0.07% 111 11919 0.07% 112 12302 0.07% 113 12706 0.07% 114 13934 0.08% 115 13950 0.08% 116 14954 0.09% 117 15479 0.09% 118 15786 0.09% 119 16168 0.10% 120 16782 0.10% 121 17048 0.10% 122 17857 0.11% 123 18499 0.11% 124 18606 0.11% 125 19098 0.11% 126 20057 0.12% 127 20472 0.12% 128 20976 0.12% 129 22049 0.13% 130 22244 0.13% 131 22906 0.13% 132 23479 0.14% 133 23864 0.14% 134 24222 0.14% 135 24921 0.15% 136 25345 0.15% 137 26318 0.16% 138 27117 0.16% 139 28236 0.17% 140 28979 0.17% 141 29198 0.17% 142 29885 0.18% 143 30294 0.18% 144 31151 0.18% 145 31212 0.18% 146 32220 0.19% 147 32961 0.19% 148 34507 0.20% 149 34267 0.20% 150 36070 0.21% 151 15850619 93.38% 16974078 reads passed initial QC criterion=sequence-density sequence-density=0.43 sequence-density-rank=1 fanout-score=2.33 fanout-score-rank=23 prefix-density=0.45 prefix-fanout=2.2 sequence=TGAGATGCCTCAGTGCATCCAAACATGGGTAG criterion=fanout-score sequence-density=0.01 sequence-density-rank=32 fanout-score=326.39 fanout-score-rank=1 prefix-density=0.25 prefix-fanout=11.7 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=0.93 sequence-density-rank=1 fanout-score=2.12 fanout-score-rank=30 prefix-density=0.94 prefix-fanout=2.1 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=38 fanout-score=53.21 fanout-score-rank=1 prefix-density=0.20 prefix-fanout=1.9 sequence=AAGGAACTCAAACGCATAGCTTCCTACAAATACCCCAGCTAGCCAATACTCTCAACCACTAAACCCAAAGCTCAAAAAAAATCTTAACTGCACCCGCTCATCCAGCAATGGCAGCAGCAACAATGGCCCTCTC SRR12671374 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 20:20:48 Started mapping on | Feb 11 20:20:48 Finished on | Feb 11 20:22:59 Mapping speed, Million of reads per hour | 466.46 Number of input reads | 16974078 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 15809563 Uniquely mapped reads % | 93.14% Average mapped length | 297.53 Number of splices: Total | 15645924 Number of splices: Annotated (sjdb) | 15342129 Number of splices: GT/AG | 15338823 Number of splices: GC/AG | 258946 Number of splices: AT/AC | 9931 Number of splices: Non-canonical | 38224 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.82 Insertion rate per base | 0.02% Insertion average length | 2.19 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 373080 % of reads mapped to multiple loci | 2.20% Number of reads mapped to too many loci | 77291 % of reads mapped to too many loci | 0.46% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.04% % of reads unmapped: other | 0.17% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 791435 791435 791435 N_multimapping 373080 373080 373080 N_noFeature 499400 15530316 580737 N_ambiguous 292373 1144 93925 UnstrandedReadsAssigned:15017790 PositiveStrandReadsAssigned:278103 NegativeStrandReadsAssigned:15134901 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671374 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: SRR12671374-trimmed-pair1.fastq SRR12671374-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 16,974,078 reads, 15,170,272 reads pseudoaligned [quant] estimated average fragment length: 274.154 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,079 rounds 52401 SRR12671374.ke.tsv 34699 SRR12671374.se.tsv 87100 total ==> SRR12671374.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1744.85 482 14.7933 Potri.005G024800.1.v4.1 1035 761.846 142 9.98153 Potri.004G059700.1.v4.1 961 687.972 17 1.32329 Potri.007G009000.2.v4.1 1416 1142.85 0 0 Potri.003G141000.2.v4.1 2943 2669.85 763 15.3043 Potri.016G087400.1.v4.1 270 74.8965 717 512.665 Potri.015G069301.1.v4.1 564 303.679 0 0 Potri.010G195200.1.v4.1 1773 1499.85 66 2.35653 Potri.012G127500.1.v4.1 977 703.924 45 3.42344 ==> SRR12671374.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 206 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 304 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 5 SRR12671374 completed mapping pipeline successfully