Starting /dee2/code/volunteer_pipeline.sh SRR12917542 current disk space = 3091833761792 free memory = 1381387784 SRR12917542 SRAfilesize fca681165d80876d434cc24b277b4525 SRR12917542.sra SRR12917542.sra file validated SRR12917542 is paired end SRR12917542 is conventional basespace SRR12917542 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12917542_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 36.58 37.0 37.0 37.0 37.0 37.0 2 36.4645 37.0 37.0 37.0 37.0 37.0 3 36.548 37.0 37.0 37.0 37.0 37.0 4 36.626 37.0 37.0 37.0 37.0 37.0 5 36.625 37.0 37.0 37.0 37.0 37.0 6 36.6675 37.0 37.0 37.0 37.0 37.0 7 36.493 37.0 37.0 37.0 37.0 37.0 8 36.5715 37.0 37.0 37.0 37.0 37.0 9 36.5695 37.0 37.0 37.0 37.0 37.0 10-14 36.6144 37.0 37.0 37.0 37.0 37.0 15-19 36.611399999999996 37.0 37.0 37.0 37.0 37.0 20-24 36.5336 37.0 37.0 37.0 37.0 37.0 25-29 36.5424 37.0 37.0 37.0 37.0 37.0 30-34 36.4756 37.0 37.0 37.0 37.0 37.0 35-39 36.4691 37.0 37.0 37.0 37.0 37.0 40-44 36.4709 37.0 37.0 37.0 37.0 37.0 45-49 36.4821 37.0 37.0 37.0 37.0 37.0 50-54 36.4191 37.0 37.0 37.0 37.0 37.0 55-59 36.3603 37.0 37.0 37.0 37.0 37.0 60-64 36.388099999999994 37.0 37.0 37.0 37.0 37.0 65-69 36.2963 37.0 37.0 37.0 37.0 37.0 70-74 36.3602 37.0 37.0 37.0 37.0 37.0 75-79 36.37949999999999 37.0 37.0 37.0 37.0 37.0 80-84 36.3123 37.0 37.0 37.0 37.0 37.0 85-89 36.3571 37.0 37.0 37.0 37.0 37.0 90-94 36.3129 37.0 37.0 37.0 37.0 37.0 95-99 36.2836 37.0 37.0 37.0 37.0 37.0 100-104 36.169200000000004 37.0 37.0 37.0 37.0 37.0 105-109 36.1792 37.0 37.0 37.0 37.0 37.0 110-114 36.17659999999999 37.0 37.0 37.0 37.0 37.0 115-119 36.0736 37.0 37.0 37.0 37.0 37.0 120-124 36.116899999999994 37.0 37.0 37.0 37.0 37.0 125-129 36.0672 37.0 37.0 37.0 37.0 37.0 130-134 35.9994 37.0 37.0 37.0 37.0 37.0 135-139 35.9195 37.0 37.0 37.0 37.0 37.0 140-144 35.785000000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.757799999999996 37.0 37.0 37.0 37.0 37.0 150-151 35.46325 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 1.0 24 4.0 25 1.0 26 3.0 27 8.0 28 11.0 29 11.0 30 17.0 31 24.0 32 36.0 33 73.0 34 128.0 35 316.0 36 3039.0 37 327.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 39.16416416416417 13.538538538538539 6.706706706706707 40.590590590590594 2 19.925 11.325000000000001 37.525 31.225 3 17.05 16.3 28.175 38.475 4 23.200000000000003 20.849999999999998 24.425 31.525 5 23.674999999999997 28.025 24.675 23.625 6 22.650000000000002 31.7 22.125 23.525 7 16.225 29.675 38.1 16.0 8 17.349999999999998 26.5 32.7 23.45 9 16.325 24.7 34.599999999999994 24.375 10-14 19.145 29.74 28.17 22.945 15-19 20.155 27.91 27.810000000000002 24.125 20-24 20.57 28.18 27.13 24.12 25-29 20.665 28.634999999999998 26.474999999999998 24.224999999999998 30-34 20.685000000000002 28.23 26.745 24.34 35-39 20.21 28.305000000000003 27.089999999999996 24.395 40-44 20.169999999999998 28.765 27.12 23.945 45-49 20.97 28.12 26.875 24.035 50-54 20.135 28.155 27.205000000000002 24.505 55-59 20.595 28.705000000000002 26.484999999999996 24.215 60-64 20.39 28.57 26.775 24.265 65-69 21.05 28.455000000000002 27.07 23.425 70-74 21.529999999999998 27.694999999999997 27.084999999999997 23.69 75-79 20.755000000000003 27.644999999999996 27.155 24.445 80-84 20.990000000000002 28.410000000000004 26.724999999999998 23.875 85-89 20.965 28.115000000000002 26.915 24.005000000000003 90-94 20.65 27.845 26.735 24.77 95-99 20.835 27.735 27.155 24.275 100-104 20.415 28.494999999999997 27.195000000000004 23.895 105-109 21.15 28.15 26.340000000000003 24.36 110-114 21.310000000000002 27.839999999999996 26.529999999999998 24.32 115-119 21.42 27.845 26.384999999999998 24.349999999999998 120-124 21.485000000000003 27.555000000000003 26.905 24.055 125-129 20.755000000000003 27.55 26.840000000000003 24.855 130-134 21.555 27.525 26.919999999999998 24.0 135-139 21.715 27.02 26.505000000000003 24.759999999999998 140-144 21.385 27.095000000000002 27.05 24.47 145-149 20.87 27.43 27.034999999999997 24.665 150-151 22.162499999999998 27.450000000000003 25.6 24.7875 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.5 16 0.5 17 1.0 18 4.0 19 3.0 20 0.0 21 2.0 22 2.0 23 1.0 24 3.0 25 6.5 26 9.5 27 9.0 28 8.5 29 11.5 30 18.5 31 22.0 32 28.5 33 37.0 34 41.5 35 51.5 36 76.0 37 89.5 38 105.0 39 130.0 40 145.5 41 177.0 42 207.5 43 204.0 44 226.5 45 253.0 46 239.0 47 258.0 48 274.5 49 255.5 50 228.5 51 192.5 52 156.5 53 117.5 54 84.5 55 75.5 56 66.0 57 53.0 58 41.0 59 27.0 60 18.0 61 12.0 62 7.5 63 5.5 64 4.0 65 3.0 66 2.5 67 1.0 68 1.0 69 0.5 70 0.0 71 0.0 72 0.0 73 0.5 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 0.1 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 89.125 #Duplication Level Percentage of deduplicated Percentage of total 1 89.95792426367461 80.175 2 8.49929873772791 15.15 3 1.150070126227209 3.075 4 0.16830294530154277 0.6 5 0.22440392706872372 1.0 6 0.0 0.0 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 CCGCCAGGGTACCCCTGGTCACCAGTTGCGTTGGCAAAATTCTCAGCAGT 5 0.125 No Hit CCCCAGGAAGTAAAGCTTGGTTCCAATCCGATGATGACGAAGATGACGAC 5 0.125 No Hit GCCCCTTCCATTACAAATTATATTAAAATGGTATATCCAAAGCATCTATG 5 0.125 No Hit GTTCCATCATAAGGGAAGGACATGAGGCCCTTAATTCCACCACAGGCGCT 5 0.125 No Hit GTCATGGTAATAAGTACATTTTCTGCCTGCATCTTCTCTGTATGGAGGTG 5 0.125 No Hit GCACTGCACTTGACGAGTGTTGTCGAATCCAATGATACGGATAAAGGAGT 5 0.125 No Hit CACATTCTCTTGCTCCTTGACAAGCATGTTTCCGTACTCAAAGAGCTTCT 5 0.125 No Hit GCCTCCTTTTCACATTGTGTACAGAGGTCTGGGAAAGGTGCATTGGCATG 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 0.025 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 0.025 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 0.1 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0125 0.0 78-79 0.175 0.0 0.0 0.025 0.0 80-81 0.175 0.0 0.0 0.025 0.0 82-83 0.225 0.0 0.0 0.025 0.0 84-85 0.275 0.0 0.0 0.025 0.0 86-87 0.3125 0.0 0.0 0.025 0.0 88-89 0.36250000000000004 0.0 0.0 0.025 0.0 90-91 0.4125 0.0 0.0 0.025 0.0 92-93 0.5125 0.0 0.0 0.025 0.0 94-95 0.5875 0.0 0.0 0.025 0.0 96-97 0.65 0.0 0.0 0.025 0.0 98-99 0.7124999999999999 0.0 0.0 0.025 0.0 100-101 0.8 0.0 0.0 0.025 0.0 102-103 0.875 0.0 0.0 0.025 0.0 104-105 1.025 0.0 0.0 0.025 0.0 106-107 1.175 0.0 0.0 0.025 0.0 108-109 1.275 0.0 0.0 0.025 0.0 110-111 1.425 0.0 0.0 0.025 0.0 112-113 1.525 0.0 0.0 0.025 0.0 114-115 1.675 0.0 0.0 0.025 0.0 116-117 1.8624999999999998 0.0 0.0 0.025 0.0 118-119 2.05 0.0 0.0 0.025 0.0 120-121 2.2375 0.0 0.0 0.025 0.0 122-123 2.4125 0.0 0.0 0.025 0.0 124-125 2.6125 0.0 0.0 0.025 0.0 126-127 2.7625 0.0 0.0 0.025 0.0 128-129 2.9625 0.0 0.0 0.025 0.0 130-131 3.2249999999999996 0.0 0.0 0.025 0.0 132-133 3.4625 0.0 0.0 0.025 0.0 134-135 3.6875 0.0 0.0 0.025 0.0 136-137 3.825 0.0 0.0 0.025 0.0 138-139 3.9375 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR12917542 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12917542_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 36.256 37.0 37.0 37.0 37.0 37.0 2 36.209 37.0 37.0 37.0 37.0 37.0 3 36.1955 37.0 37.0 37.0 37.0 37.0 4 36.1865 37.0 37.0 37.0 37.0 37.0 5 36.1605 37.0 37.0 37.0 37.0 37.0 6 36.1605 37.0 37.0 37.0 37.0 37.0 7 36.1885 37.0 37.0 37.0 37.0 37.0 8 36.2825 37.0 37.0 37.0 37.0 37.0 9 36.271 37.0 37.0 37.0 37.0 37.0 10-14 36.269 37.0 37.0 37.0 37.0 37.0 15-19 36.2018 37.0 37.0 37.0 37.0 37.0 20-24 36.13420000000001 37.0 37.0 37.0 37.0 37.0 25-29 36.044200000000004 37.0 37.0 37.0 37.0 37.0 30-34 36.072599999999994 37.0 37.0 37.0 37.0 37.0 35-39 35.9713 37.0 37.0 37.0 37.0 37.0 40-44 35.9718 37.0 37.0 37.0 37.0 37.0 45-49 35.89960000000001 37.0 37.0 37.0 37.0 37.0 50-54 35.9177 37.0 37.0 37.0 37.0 37.0 55-59 35.8514 37.0 37.0 37.0 37.0 37.0 60-64 35.8688 37.0 37.0 37.0 37.0 37.0 65-69 35.810700000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.8228 37.0 37.0 37.0 37.0 37.0 75-79 35.7734 37.0 37.0 37.0 37.0 37.0 80-84 35.7316 37.0 37.0 37.0 37.0 37.0 85-89 35.7664 37.0 37.0 37.0 37.0 37.0 90-94 35.8369 37.0 37.0 37.0 37.0 37.0 95-99 35.722899999999996 37.0 37.0 37.0 37.0 37.0 100-104 35.7726 37.0 37.0 37.0 37.0 37.0 105-109 35.6157 37.0 37.0 37.0 37.0 37.0 110-114 35.6635 37.0 37.0 37.0 37.0 37.0 115-119 35.579 37.0 37.0 37.0 37.0 37.0 120-124 35.456500000000005 37.0 37.0 37.0 34.6 37.0 125-129 35.491600000000005 37.0 37.0 37.0 37.0 37.0 130-134 35.4103 37.0 37.0 37.0 34.6 37.0 135-139 35.424800000000005 37.0 37.0 37.0 37.0 37.0 140-144 35.23909999999999 37.0 37.0 37.0 27.4 37.0 145-149 35.1292 37.0 37.0 37.0 29.8 37.0 150-151 34.56625 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 3.0 15 0.0 16 1.0 17 4.0 18 2.0 19 1.0 20 6.0 21 4.0 22 3.0 23 4.0 24 4.0 25 10.0 26 9.0 27 12.0 28 11.0 29 20.0 30 27.0 31 32.0 32 68.0 33 110.0 34 234.0 35 687.0 36 2601.0 37 145.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 35.85 26.974999999999998 10.424999999999999 26.75 2 28.249999999999996 24.625 30.925000000000004 16.2 3 19.275000000000002 28.050000000000004 32.925 19.75 4 23.849999999999998 33.95 23.400000000000002 18.8 5 25.900000000000002 35.55 21.15 17.4 6 19.975 40.925 21.125 17.974999999999998 7 20.3 23.3 37.375 19.025 8 21.0 26.275 28.175 24.55 9 22.275 23.775 28.749999999999996 25.2 10-14 22.689999999999998 28.92 26.43 21.959999999999997 15-19 22.7 28.615000000000002 26.889999999999997 21.795 20-24 22.805 28.88 26.795 21.52 25-29 23.565 27.845 27.450000000000003 21.14 30-34 23.31 28.22 26.919999999999998 21.55 35-39 23.575 27.54 26.525 22.36 40-44 23.044999999999998 28.03 27.095000000000002 21.83 45-49 22.745 27.525 27.700000000000003 22.03 50-54 23.32 27.685 27.150000000000002 21.845 55-59 23.005 27.810000000000002 27.310000000000002 21.875 60-64 23.985 26.790000000000003 26.75 22.475 65-69 24.005000000000003 27.295 27.075 21.625 70-74 24.235 27.084999999999997 26.200000000000003 22.48 75-79 23.150000000000002 27.79 26.795 22.264999999999997 80-84 24.060000000000002 26.935 26.61 22.395 85-89 23.845 27.425 25.965 22.765 90-94 24.79 27.38 25.790000000000003 22.040000000000003 95-99 23.865 27.98 26.584999999999997 21.57 100-104 24.23 27.165 27.229999999999997 21.375 105-109 24.0 26.83 27.83 21.34 110-114 24.145 27.245 27.41 21.2 115-119 24.095 27.315 26.985 21.605 120-124 24.4 27.639999999999997 26.779999999999998 21.18 125-129 25.1 27.33 26.040000000000003 21.529999999999998 130-134 25.085 26.88 26.72 21.315 135-139 24.185000000000002 27.365000000000002 27.445000000000004 21.005 140-144 24.505 27.32 26.615 21.560000000000002 145-149 24.84 27.51 25.924999999999997 21.725 150-151 24.837500000000002 28.012500000000003 26.775 20.375 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.5 8 0.5 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.0 19 0.5 20 1.0 21 1.0 22 1.0 23 1.5 24 3.5 25 2.5 26 2.5 27 4.5 28 7.5 29 8.5 30 8.5 31 13.5 32 15.0 33 21.5 34 31.0 35 48.5 36 74.5 37 103.5 38 118.0 39 133.0 40 159.5 41 191.0 42 240.5 43 237.0 44 238.5 45 275.0 46 269.5 47 254.5 48 248.0 49 234.0 50 196.5 51 158.0 52 135.5 53 111.0 54 100.5 55 84.5 56 64.0 57 56.0 58 38.5 59 24.5 60 22.5 61 15.0 62 6.5 63 6.0 64 4.0 65 2.5 66 2.0 67 2.0 68 1.5 69 1.5 70 1.0 71 0.0 72 0.0 73 0.0 74 0.5 75 1.0 76 1.0 77 1.0 78 0.5 79 0.0 80 0.0 81 0.5 82 0.5 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 1.0 89 1.0 90 0.0 91 0.5 92 0.5 93 0.5 94 0.5 95 1.0 96 1.0 97 1.0 98 1.5 99 0.5 100 1.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140-144 0.0 145-149 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 89.0 #Duplication Level Percentage of deduplicated Percentage of total 1 90.53370786516854 80.575 2 7.837078651685394 13.950000000000001 3 0.9831460674157303 2.625 4 0.25280898876404495 0.8999999999999999 5 0.3089887640449438 1.375 6 0.02808988764044944 0.15 7 0.0 0.0 8 0.02808988764044944 0.2 9 0.02808988764044944 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 AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 9 0.22499999999999998 No Hit GGGCAGTAGTCTTAAACCATACTCTAAAATCTTCTTATAATTCCAGTTGT 8 0.2 No Hit AGGGAGCACTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTA 6 0.15 No Hit GTTCGAGACTCTTTCTTACCTTCCAGATCTCACAGAGGAGGAATTGGCCA 5 0.125 No Hit CTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTATGATCTCA 5 0.125 No Hit CCAATACACTGTCAACAACCAGATGGTTAATGCTACCCTCATGAACATTG 5 0.125 No Hit ATTTTCGCTGACAATCAAATATGTACTTCCATTGCACATGAACTTCCTTT 5 0.125 No Hit ATAGAACACGAAAATTGCTTACTACCTTTCATTCCCTGTTTCAGAAACCT 5 0.125 No Hit CTCATCGGCAGCCGTTGCCACCGTCAACCGCACCCCGGCACAAGCCAACA 5 0.125 No Hit CCATGGTACGGACCAGACCGTGTTAAATACTTGGGCCCGTTCTCTGGTGA 5 0.125 No Hit AGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGCTTCCTCTGTGATT 5 0.125 No Hit CTTCAAGGGCAGTAGTCTTAAACCATACTCTAAAATCTTCTTATAATTCC 5 0.125 No Hit CAAGCTTGGAGCGGCATCCCCTGGTTCGAGGCTGGTGCTGACCCTGGTGC 5 0.125 No Hit GAATATGGTCCCGCCATACGATAAGACTAAGTACGCTGGAGTTGGGGCAG 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 0.025 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 0.025 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 0.1 0.0 0.0 0.0 0.0 76-77 0.125 0.0 0.0 0.0 0.0 78-79 0.175 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.225 0.0 0.0 0.0 0.0 84-85 0.275 0.0 0.0 0.0 0.0 86-87 0.3125 0.0 0.0 0.0 0.0 88-89 0.36250000000000004 0.0 0.0 0.0 0.0 90-91 0.4125 0.0 0.0 0.0 0.0 92-93 0.5125 0.0 0.0 0.0 0.0 94-95 0.5875 0.0 0.0 0.0 0.0 96-97 0.65 0.0 0.0 0.0 0.0 98-99 0.7124999999999999 0.0 0.0 0.0 0.0 100-101 0.8 0.0 0.0 0.0 0.0 102-103 0.875 0.0 0.0 0.0 0.0 104-105 1.025 0.0 0.0 0.0 0.0 106-107 1.175 0.0 0.0 0.0 0.0 108-109 1.275 0.0 0.0 0.0 0.0 110-111 1.425 0.0 0.0 0.0 0.0 112-113 1.525 0.0 0.0 0.0 0.0 114-115 1.675 0.0 0.0 0.0 0.0 116-117 1.8624999999999998 0.0 0.0 0.0 0.0 118-119 2.05 0.0 0.0 0.0 0.0 120-121 2.2375 0.0 0.0 0.0 0.0 122-123 2.4125 0.0 0.0 0.0 0.0 124-125 2.6125 0.0 0.0 0.0 0.0 126-127 2.7625 0.0 0.0 0.0 0.0 128-129 2.9625 0.0 0.0 0.0 0.0 130-131 3.2249999999999996 0.0 0.0 0.0 0.0 132-133 3.4625 0.0 0.0 0.0 0.0 134-135 3.6875 0.0 0.0 0.0 0.0 136-137 3.825 0.0 0.0 0.0 0.0 138-139 3.9375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCCAGTC 10 0.006830828 145.0 145 AGGGAGC 10 0.006830828 145.0 1 GAGCACT 10 0.006830828 145.0 4 GCACTGC 10 0.006830828 145.0 6 GGAGCAC 10 0.006830828 145.0 3 AATGAAG 10 0.006830828 145.0 6 >>END_MODULE Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543733 spots for SRR12917542.sra Written 543733 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra Read 543730 spots for SRR12917542.sra Written 543730 spots for SRR12917542.sra SRR ids: ['SRR12917542.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_gl1zyslk SRR12917542.sra spots: 10874603 blocks: [[1, 543730], [543731, 1087460], [1087461, 1631190], [1631191, 2174920], [2174921, 2718650], [2718651, 3262380], [3262381, 3806110], [3806111, 4349840], [4349841, 4893570], [4893571, 5437300], [5437301, 5981030], [5981031, 6524760], [6524761, 7068490], [7068491, 7612220], [7612221, 8155950], [8155951, 8699680], [8699681, 9243410], [9243411, 9787140], [9787141, 10330870], [10330871, 10874603]] SRR12917542 file size 3673965 SRR12917542 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 SRR12917542 SRR12917542_1.fastq SRR12917542_2.fastq Input file: SRR12917542_1.fastq Paired file: SRR12917542_2.fastq trimmed: SRR12917542-trimmed-pair1.fastq, SRR12917542-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 Thu Feb 13 12:37:50 2025 >> started Thu Feb 13 12:38:03 2025 >> done (13.168s) 10874603 read pairs processed; of these: 27 ( 0.00%) short read pairs filtered out after trimming by size control 5099 ( 0.05%) empty read pairs filtered out after trimming by size control 10869477 (99.95%) read pairs available; of these: 653709 ( 6.01%) trimmed read pairs available after processing 10215768 (93.99%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 5 0.00% 20 3 0.00% 21 4 0.00% 22 14 0.00% 23 8 0.00% 24 10 0.00% 25 13 0.00% 26 9 0.00% 27 17 0.00% 28 7 0.00% 29 7 0.00% 30 7 0.00% 31 16 0.00% 32 16 0.00% 33 15 0.00% 34 13 0.00% 35 9 0.00% 36 12 0.00% 37 13 0.00% 38 16 0.00% 39 14 0.00% 40 29 0.00% 41 19 0.00% 42 28 0.00% 43 17 0.00% 44 18 0.00% 45 19 0.00% 46 23 0.00% 47 30 0.00% 48 20 0.00% 49 26 0.00% 50 46 0.00% 51 55 0.00% 52 73 0.00% 53 72 0.00% 54 64 0.00% 55 71 0.00% 56 87 0.00% 57 89 0.00% 58 87 0.00% 59 112 0.00% 60 143 0.00% 61 161 0.00% 62 194 0.00% 63 265 0.00% 64 260 0.00% 65 283 0.00% 66 375 0.00% 67 325 0.00% 68 412 0.00% 69 457 0.00% 70 560 0.01% 71 550 0.01% 72 671 0.01% 73 803 0.01% 74 878 0.01% 75 885 0.01% 76 1068 0.01% 77 1066 0.01% 78 1170 0.01% 79 1337 0.01% 80 1390 0.01% 81 1553 0.01% 82 1787 0.02% 83 1964 0.02% 84 2059 0.02% 85 2237 0.02% 86 2442 0.02% 87 2497 0.02% 88 2672 0.02% 89 2688 0.02% 90 2944 0.03% 91 3042 0.03% 92 3168 0.03% 93 3347 0.03% 94 3791 0.03% 95 4167 0.04% 96 4163 0.04% 97 4408 0.04% 98 4533 0.04% 99 4664 0.04% 100 4799 0.04% 101 4737 0.04% 102 5043 0.05% 103 5323 0.05% 104 5694 0.05% 105 5912 0.05% 106 6066 0.06% 107 6484 0.06% 108 6563 0.06% 109 6744 0.06% 110 6678 0.06% 111 6971 0.06% 112 7038 0.06% 113 7285 0.07% 114 7519 0.07% 115 8023 0.07% 116 8420 0.08% 117 8920 0.08% 118 9330 0.09% 119 9089 0.08% 120 9620 0.09% 121 9729 0.09% 122 9760 0.09% 123 10189 0.09% 124 10585 0.10% 125 10693 0.10% 126 11548 0.11% 127 11493 0.11% 128 11822 0.11% 129 12151 0.11% 130 12790 0.12% 131 12680 0.12% 132 13052 0.12% 133 13352 0.12% 134 13536 0.12% 135 13811 0.13% 136 14382 0.13% 137 14831 0.14% 138 15434 0.14% 139 16136 0.15% 140 15919 0.15% 141 16602 0.15% 142 16892 0.16% 143 16857 0.16% 144 17252 0.16% 145 17603 0.16% 146 18132 0.17% 147 18522 0.17% 148 19233 0.18% 149 19486 0.18% 150 20384 0.19% 151 10215768 93.99% 10869477 reads passed initial QC criterion=sequence-density sequence-density=1.05 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=21 prefix-density=1.06 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=25 fanout-score=14.54 fanout-score-rank=1 prefix-density=0.04 prefix-fanout=1.9 sequence=AAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCGGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTG criterion=sequence-density sequence-density=1.18 sequence-density-rank=1 fanout-score=2.11 fanout-score-rank=23 prefix-density=1.19 prefix-fanout=2.1 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=26 fanout-score=42.03 fanout-score-rank=1 prefix-density=0.13 prefix-fanout=5.8 sequence=ACAACTTCAAGGGCAGTAGTCTTAAACCATACTCTAAAATCTTCTTATAATTCCAGTTGTAATATTCTGCTAGCATATAATGGCTTCTTCAATGAGCTTGAAGCTGGCCTGTGCCATGCTTGTAGCGATGGTTGTTAGTGCACCACTAGCAGAAGCTGCCATCTCATGTGGCCAGGTGTCAAGCAGCTTGGCACAATGTATAACCTACCTCCAGAAGGGTGGGGCTGTGCCTGCAGCTTGCTGCAGTGGGTTGAAAGGACTTAATTCTGCAGCCACGACCACCGCCGACC SRR12917542 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 12:38:46 Started mapping on | Feb 13 12:38:47 Finished on | Feb 13 12:40:17 Mapping speed, Million of reads per hour | 434.78 Number of input reads | 10869477 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 10217271 Uniquely mapped reads % | 94.00% Average mapped length | 297.79 Number of splices: Total | 10257914 Number of splices: Annotated (sjdb) | 10109147 Number of splices: GT/AG | 10024458 Number of splices: GC/AG | 197035 Number of splices: AT/AC | 6638 Number of splices: Non-canonical | 29783 Mismatch rate per base, % | 0.37% Deletion rate per base | 0.03% Deletion average length | 3.02 Insertion rate per base | 0.02% Insertion average length | 2.41 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 259706 % of reads mapped to multiple loci | 2.39% Number of reads mapped to too many loci | 84897 % of reads mapped to too many loci | 0.78% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.68% % of reads unmapped: other | 0.15% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 392500 392500 392500 N_multimapping 259706 259706 259706 N_noFeature 218212 10043771 255575 N_ambiguous 217060 506 80612 UnstrandedReadsAssigned:9781999 PositiveStrandReadsAssigned:172994 NegativeStrandReadsAssigned:9881084 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12917542 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: SRR12917542-trimmed-pair1.fastq SRR12917542-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 10,869,477 reads, 9,920,354 reads pseudoaligned [quant] estimated average fragment length: 288.068 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 996 rounds 52401 SRR12917542.ke.tsv 34699 SRR12917542.se.tsv 87100 total ==> SRR12917542.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1730.93 188 8.04012 Potri.005G024800.1.v4.1 1035 747.932 257 25.4364 Potri.004G059700.1.v4.1 961 674.091 49 5.381 Potri.007G009000.2.v4.1 1416 1128.93 0 0 Potri.003G141000.2.v4.1 2943 2655.93 326 9.08627 Potri.016G087400.1.v4.1 270 74.1646 570 568.935 Potri.015G069301.1.v4.1 564 295.826 0 0 Potri.010G195200.1.v4.1 1773 1485.93 2 0.0996359 Potri.012G127500.1.v4.1 977 690.022 442 47.4181 ==> SRR12917542.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 144 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 130 Potri.001G212900.v4.1 0 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 SRR12917542 completed mapping pipeline successfully