Starting /dee2/code/volunteer_pipeline.sh SRR12671344 current disk space = 3049405255680 free memory = 1478625000 SRR12671344 SRAfilesize a97b6960ebb2efd722ae87dccd50cb7f SRR12671344.sra SRR12671344.sra file validated SRR12671344 is paired end SRR12671344 is conventional basespace SRR12671344 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671344_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 36.5965 37.0 37.0 37.0 37.0 37.0 2 36.44675 37.0 37.0 37.0 37.0 37.0 3 36.523 37.0 37.0 37.0 37.0 37.0 4 36.525 37.0 37.0 37.0 37.0 37.0 5 36.6435 37.0 37.0 37.0 37.0 37.0 6 36.6535 37.0 37.0 37.0 37.0 37.0 7 36.53 37.0 37.0 37.0 37.0 37.0 8 36.575 37.0 37.0 37.0 37.0 37.0 9 36.5945 37.0 37.0 37.0 37.0 37.0 10-14 36.6393 37.0 37.0 37.0 37.0 37.0 15-19 36.6047 37.0 37.0 37.0 37.0 37.0 20-24 36.584900000000005 37.0 37.0 37.0 37.0 37.0 25-29 36.5495 37.0 37.0 37.0 37.0 37.0 30-34 36.5454 37.0 37.0 37.0 37.0 37.0 35-39 36.503 37.0 37.0 37.0 37.0 37.0 40-44 36.4614 37.0 37.0 37.0 37.0 37.0 45-49 36.4466 37.0 37.0 37.0 37.0 37.0 50-54 36.4259 37.0 37.0 37.0 37.0 37.0 55-59 36.4358 37.0 37.0 37.0 37.0 37.0 60-64 36.3905 37.0 37.0 37.0 37.0 37.0 65-69 36.3894 37.0 37.0 37.0 37.0 37.0 70-74 36.3601 37.0 37.0 37.0 37.0 37.0 75-79 36.3373 37.0 37.0 37.0 37.0 37.0 80-84 36.323699999999995 37.0 37.0 37.0 37.0 37.0 85-89 36.27419999999999 37.0 37.0 37.0 37.0 37.0 90-94 36.260299999999994 37.0 37.0 37.0 37.0 37.0 95-99 36.241499999999995 37.0 37.0 37.0 37.0 37.0 100-104 36.233 37.0 37.0 37.0 37.0 37.0 105-109 36.243700000000004 37.0 37.0 37.0 37.0 37.0 110-114 36.1221 37.0 37.0 37.0 37.0 37.0 115-119 36.148900000000005 37.0 37.0 37.0 37.0 37.0 120-124 36.1644 37.0 37.0 37.0 37.0 37.0 125-129 36.1088 37.0 37.0 37.0 37.0 37.0 130-134 36.0484 37.0 37.0 37.0 37.0 37.0 135-139 36.0575 37.0 37.0 37.0 37.0 37.0 140-144 35.9647 37.0 37.0 37.0 37.0 37.0 145-149 35.9465 37.0 37.0 37.0 37.0 37.0 150-151 35.91125 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 21 3.0 22 1.0 23 1.0 24 2.0 25 5.0 26 5.0 27 7.0 28 7.0 29 17.0 30 18.0 31 32.0 32 41.0 33 68.0 34 100.0 35 275.0 36 2931.0 37 487.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 52.0 11.25 4.5249999999999995 32.225 2 19.09887359198999 11.439299123904881 38.02252816020025 31.439299123904878 3 17.65 17.925 29.099999999999998 35.325 4 22.25 24.75 24.7 28.299999999999997 5 23.724999999999998 31.8 23.799999999999997 20.674999999999997 6 19.275000000000002 35.9 23.7 21.125 7 14.799999999999999 25.6 41.9 17.7 8 16.1 25.025 34.300000000000004 24.575 9 17.675 21.8 35.475 25.05 10-14 19.7 29.515 27.834999999999997 22.95 15-19 20.150000000000002 27.92 27.805000000000003 24.125 20-24 20.255000000000003 28.29 27.339999999999996 24.115000000000002 25-29 20.205000000000002 28.51 28.02 23.265 30-34 20.485 28.050000000000004 27.735 23.73 35-39 20.51 27.815 28.12 23.555 40-44 19.605 29.04 27.325 24.03 45-49 20.585 28.415000000000003 27.46 23.54 50-54 20.255000000000003 28.62 27.405 23.72 55-59 19.744999999999997 28.249999999999996 27.58 24.425 60-64 20.68 28.43 27.560000000000002 23.330000000000002 65-69 19.939999999999998 28.544999999999998 27.735 23.78 70-74 20.555 28.625 27.355 23.465 75-79 20.44 28.560000000000002 27.38 23.62 80-84 20.419999999999998 28.694999999999997 27.21 23.674999999999997 85-89 19.85 28.435 27.405 24.310000000000002 90-94 19.825 28.935 27.355 23.885 95-99 20.515 28.084999999999997 27.905 23.494999999999997 100-104 20.455000000000002 28.205000000000002 27.075 24.265 105-109 20.825 27.800000000000004 27.865000000000002 23.51 110-114 20.150000000000002 28.03 28.065 23.755000000000003 115-119 20.865000000000002 28.185 27.255000000000003 23.695 120-124 20.93 28.365000000000002 26.974999999999998 23.73 125-129 20.78 28.375 27.435 23.41 130-134 21.745 27.405 27.095000000000002 23.755000000000003 135-139 21.66 28.720000000000002 26.88 22.74 140-144 21.12 28.7 26.66 23.52 145-149 20.5 28.785 26.75 23.965 150-151 21.15 28.825 26.3625 23.6625 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.0 8 1.0 9 1.5 10 1.5 11 1.0 12 0.5 13 1.0 14 0.5 15 0.0 16 0.0 17 0.5 18 1.5 19 1.0 20 1.5 21 2.5 22 3.5 23 4.0 24 2.0 25 1.5 26 4.0 27 8.5 28 13.0 29 17.0 30 16.0 31 17.5 32 28.0 33 40.5 34 56.0 35 71.0 36 82.5 37 100.0 38 127.0 39 154.0 40 176.0 41 194.0 42 233.0 43 259.5 44 255.0 45 244.0 46 248.5 47 256.5 48 235.5 49 224.5 50 200.5 51 141.5 52 108.5 53 96.0 54 79.5 55 74.0 56 61.5 57 47.5 58 34.0 59 20.0 60 14.0 61 8.5 62 6.5 63 5.0 64 2.0 65 3.5 66 3.0 67 0.0 68 3.0 69 3.5 70 0.5 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.0 77 0.0 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.125 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 79.975 #Duplication Level Percentage of deduplicated Percentage of total 1 81.11909971866208 64.875 2 14.348233823069709 22.95 3 3.376055017192873 8.1 4 0.8127539856205065 2.6 5 0.25007814942169426 1.0 6 0.06251953735542357 0.3 7 0.03125976867771178 0.17500000000000002 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 ATTCTTAATCTCCTTCACCTTCAGGAGTGCAGCTTGATCAGGATCCTTTG 7 0.17500000000000002 No Hit GGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGA 6 0.15 No Hit GTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACC 6 0.15 No Hit ATCTGCTGTTTCTCACGCTTGGCAAATTGTTTGGAATCTTTGCATGGGGT 5 0.125 No Hit GTCAAATTGGGACCAATACTGGCAATGCCAATAAGAATGCTAGCTGCTGC 5 0.125 No Hit GCCAATTCTGGAAGTGTTTTGTTGAGATATTTTGGAGACAAGTAATCCAA 5 0.125 No Hit GCTCACCCTCGCGGGATCGCGACCCTTTGTCCCGGCCATTGTAGCACGTG 5 0.125 No Hit GTAAGGAGACTTGTTAGTGAAGCAAAAACGGTGGACTCCTTTCTGATGTG 5 0.125 No Hit TTTTTTTTTTTACACTAATTATAAGACTTCATTAAAACCACACCAGAGGC 5 0.125 No Hit GCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATTAGCCT 5 0.125 No Hit CCCTCTTGTACTCTTGTGAGGTTGCCAAAAACGCAGCATGAGGACCACCA 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 70-71 0.037500000000000006 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.1375 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.3375 0.0 0.0 0.0 0.0 84-85 0.35 0.0 0.0 0.0 0.0 86-87 0.4375 0.0 0.0 0.0 0.0 88-89 0.475 0.0 0.0 0.0 0.0 90-91 0.5874999999999999 0.0 0.0 0.0 0.0 92-93 0.6625000000000001 0.0 0.0 0.0 0.0 94-95 0.675 0.0 0.0 0.0 0.0 96-97 0.7 0.0 0.0 0.0 0.0 98-99 0.8 0.0 0.0 0.0 0.0 100-101 0.9874999999999999 0.0 0.0 0.0 0.0 102-103 1.1 0.0 0.0 0.0 0.0 104-105 1.225 0.0 0.0 0.0 0.0 106-107 1.35 0.0 0.0 0.0 0.0 108-109 1.4375 0.0 0.0 0.0 0.0 110-111 1.5 0.0 0.0 0.0 0.0 112-113 1.6 0.0 0.0 0.0 0.0 114-115 1.7000000000000002 0.0 0.0 0.0 0.0 116-117 1.85 0.0 0.0 0.0 0.0 118-119 1.9874999999999998 0.0 0.0 0.0 0.0 120-121 2.1125 0.0 0.0 0.0 0.0 122-123 2.3625 0.0 0.0 0.0 0.0 124-125 2.6375 0.0 0.0 0.0 0.0 126-127 2.9125 0.0 0.0 0.0 0.0 128-129 3.325 0.0 0.0 0.0 0.0 130-131 3.5625 0.0 0.0 0.0 0.0 132-133 3.7375 0.0 0.0 0.0 0.0 134-135 4.075 0.0 0.0 0.0 0.0 136-137 4.3 0.0 0.0 0.0 0.0 138-139 4.6125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GCAAACA 10 0.006830828 145.0 2 >>END_MODULE SRR12671344 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12671344_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 36.145 37.0 37.0 37.0 37.0 37.0 2 35.885 37.0 37.0 37.0 37.0 37.0 3 36.068 37.0 37.0 37.0 37.0 37.0 4 36.189 37.0 37.0 37.0 37.0 37.0 5 36.1675 37.0 37.0 37.0 37.0 37.0 6 36.2585 37.0 37.0 37.0 37.0 37.0 7 36.2485 37.0 37.0 37.0 37.0 37.0 8 36.253 37.0 37.0 37.0 37.0 37.0 9 36.198 37.0 37.0 37.0 37.0 37.0 10-14 36.2027 37.0 37.0 37.0 37.0 37.0 15-19 36.221799999999995 37.0 37.0 37.0 37.0 37.0 20-24 36.1173 37.0 37.0 37.0 37.0 37.0 25-29 36.116200000000006 37.0 37.0 37.0 37.0 37.0 30-34 36.1016 37.0 37.0 37.0 37.0 37.0 35-39 36.0458 37.0 37.0 37.0 37.0 37.0 40-44 36.044999999999995 37.0 37.0 37.0 37.0 37.0 45-49 35.9999 37.0 37.0 37.0 37.0 37.0 50-54 35.955400000000004 37.0 37.0 37.0 37.0 37.0 55-59 35.9292 37.0 37.0 37.0 37.0 37.0 60-64 35.8702 37.0 37.0 37.0 37.0 37.0 65-69 35.969 37.0 37.0 37.0 37.0 37.0 70-74 35.90560000000001 37.0 37.0 37.0 37.0 37.0 75-79 35.932 37.0 37.0 37.0 37.0 37.0 80-84 35.8016 37.0 37.0 37.0 37.0 37.0 85-89 35.8977 37.0 37.0 37.0 37.0 37.0 90-94 35.847300000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.7303 37.0 37.0 37.0 37.0 37.0 100-104 35.7474 37.0 37.0 37.0 37.0 37.0 105-109 35.6808 37.0 37.0 37.0 37.0 37.0 110-114 35.614599999999996 37.0 37.0 37.0 37.0 37.0 115-119 35.7011 37.0 37.0 37.0 37.0 37.0 120-124 35.669000000000004 37.0 37.0 37.0 37.0 37.0 125-129 35.5329 37.0 37.0 37.0 37.0 37.0 130-134 35.4219 37.0 37.0 37.0 34.6 37.0 135-139 35.3387 37.0 37.0 37.0 32.2 37.0 140-144 35.469500000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.3677 37.0 37.0 37.0 34.6 37.0 150-151 35.159 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 1.0 15 2.0 16 3.0 17 2.0 18 0.0 19 0.0 20 3.0 21 4.0 22 1.0 23 5.0 24 4.0 25 8.0 26 12.0 27 15.0 28 15.0 29 23.0 30 23.0 31 41.0 32 77.0 33 113.0 34 200.0 35 585.0 36 2616.0 37 245.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 47.275 25.3 6.625 20.8 2 26.275 24.025 33.4 16.3 3 19.950000000000003 26.200000000000003 35.3 18.55 4 23.150000000000002 34.175 23.275000000000002 19.400000000000002 5 25.650000000000002 37.4 21.375 15.575 6 19.400000000000002 40.2 21.65 18.75 7 19.35 22.55 38.0 20.1 8 19.35 24.675 30.575000000000003 25.4 9 21.7 23.825 30.425 24.05 10-14 23.055 29.335 27.04 20.57 15-19 22.314999999999998 28.139999999999997 28.17 21.375 20-24 22.67 28.52 27.689999999999998 21.12 25-29 22.325 27.55 29.054999999999996 21.07 30-34 22.45 28.444999999999997 28.405 20.7 35-39 22.625 27.694999999999997 28.050000000000004 21.63 40-44 22.634999999999998 28.18 28.499999999999996 20.685000000000002 45-49 22.770000000000003 28.055000000000003 28.08 21.095 50-54 22.725 28.349999999999998 28.28 20.645 55-59 22.634999999999998 28.405 27.985 20.974999999999998 60-64 23.05 27.18 27.57 22.2 65-69 23.425 27.715 27.83 21.029999999999998 70-74 22.655 28.32 27.675 21.349999999999998 75-79 22.375 27.965 27.310000000000002 22.35 80-84 22.86 27.97 27.115000000000002 22.055 85-89 23.119999999999997 27.99 27.215 21.675 90-94 23.24 27.54 27.68 21.54 95-99 23.31 27.935 27.334999999999997 21.42 100-104 23.54 27.02 28.055000000000003 21.385 105-109 23.69 27.939999999999998 27.46 20.91 110-114 23.605 29.075 26.445 20.875 115-119 23.935000000000002 28.49 27.13 20.445 120-124 23.830000000000002 27.894999999999996 28.055000000000003 20.22 125-129 24.305 27.755000000000003 27.400000000000002 20.54 130-134 24.515 27.800000000000004 26.924999999999997 20.76 135-139 24.72 27.944999999999997 27.029999999999998 20.305 140-144 24.88 27.185 27.639999999999997 20.294999999999998 145-149 25.370074014802963 28.315663132626522 26.66533306661332 19.648929785957193 150-151 23.825 29.275000000000002 26.5 20.4 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.0 7 0.5 8 0.5 9 0.0 10 0.5 11 0.5 12 0.0 13 0.5 14 0.5 15 0.5 16 0.5 17 0.5 18 0.5 19 0.5 20 1.0 21 2.0 22 3.5 23 3.5 24 2.5 25 5.5 26 8.5 27 9.5 28 13.0 29 15.5 30 17.0 31 23.5 32 31.5 33 37.5 34 53.0 35 68.5 36 74.5 37 106.0 38 133.0 39 168.5 40 193.5 41 224.0 42 241.5 43 256.5 44 283.5 45 275.0 46 253.5 47 226.0 48 222.5 49 186.5 50 151.5 51 142.5 52 117.0 53 98.5 54 86.5 55 62.0 56 50.5 57 42.0 58 25.0 59 18.0 60 12.5 61 12.5 62 12.0 63 4.5 64 2.0 65 0.5 66 0.5 67 1.5 68 1.5 69 1.0 70 1.0 71 0.5 72 0.5 73 1.5 74 1.5 75 1.0 76 1.0 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 0.5 96 0.5 97 0.5 98 1.0 99 0.5 100 0.5 >>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 0.02 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 79.95 #Duplication Level Percentage of deduplicated Percentage of total 1 81.39462163852407 65.075 2 13.977485928705441 22.35 3 3.533458411507192 8.475000000000001 4 0.7817385866166353 2.5 5 0.18761726078799248 0.75 6 0.0 0.0 7 0.06253908692933083 0.35000000000000003 8 0.0 0.0 9 0.031269543464665414 0.22499999999999998 >10 0.031269543464665414 0.27499999999999997 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences warn #Sequence Count Percentage Possible Source AGAGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 11 0.27499999999999997 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 9 0.22499999999999998 No Hit GTGAGATATTCAAGAGAAATACGTTTAGAAATCAAGAGAGAGAGAGAGTT 7 0.17500000000000002 No Hit GGGAGCACTGCATAGCTTATAAGCTTGTAAGAGATGGCTTCCTCCTCTAT 7 0.17500000000000002 No Hit GTTCTTGTCACAAATCTTAAAACTGGATTCAGGAAAGGAGAATGGGACAG 5 0.125 No Hit ACTATCCATTGGCCTTGTTGTCGTGGGCGCGATTCTTCTTATTGGATACT 5 0.125 No Hit GCATGGCTGTCGTCAGCTCGTGCCGTAAGGTGTTGGGTTAAGTCCCGCAG 5 0.125 No Hit AGAACACATTCATACCCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 5 0.125 No Hit CTTACTATACCAAGCAACCTCTCCATGTTGAAGCCAAAACTTGGGGTCTC 5 0.125 No Hit GGAAGAATGCTTCTCTCATGATGTTAAATATGAAGGAGATACAGTTCATG 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 0.0125 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 0.025 0.0 0.0 0.0 0.0 70-71 0.037500000000000006 0.0 0.0 0.0 0.0 72-73 0.05 0.0 0.0 0.0 0.0 74-75 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.1375 0.0 0.0 0.0 0.0 80-81 0.175 0.0 0.0 0.0 0.0 82-83 0.3375 0.0 0.0 0.0 0.0 84-85 0.35 0.0 0.0 0.0 0.0 86-87 0.4375 0.0 0.0 0.0 0.0 88-89 0.475 0.0 0.0 0.0 0.0 90-91 0.5874999999999999 0.0 0.0 0.0 0.0 92-93 0.6625000000000001 0.0 0.0 0.0 0.0 94-95 0.675 0.0 0.0 0.0 0.0 96-97 0.7 0.0 0.0 0.0 0.0 98-99 0.8 0.0 0.0 0.0 0.0 100-101 0.9874999999999999 0.0 0.0 0.0 0.0 102-103 1.1 0.0 0.0 0.0 0.0 104-105 1.225 0.0 0.0 0.0 0.0 106-107 1.35 0.0 0.0 0.0 0.0 108-109 1.4375 0.0 0.0 0.0 0.0 110-111 1.5 0.0 0.0 0.0 0.0 112-113 1.6 0.0 0.0 0.0 0.0 114-115 1.7000000000000002 0.0 0.0 0.0 0.0 116-117 1.85 0.0 0.0 0.0 0.0 118-119 1.9874999999999998 0.0 0.0 0.0 0.0 120-121 2.1125 0.0 0.0 0.0 0.0 122-123 2.3625 0.0 0.0 0.0 0.0 124-125 2.6125 0.0 0.0 0.0 0.0 126-127 2.8625 0.0 0.0 0.0 0.0 128-129 3.2750000000000004 0.0 0.0 0.0 0.0 130-131 3.5125 0.0 0.0 0.0 0.0 132-133 3.6875 0.0 0.0 0.0 0.0 134-135 4.025 0.0 0.0 0.0 0.0 136-137 4.25 0.0 0.0 0.0 0.0 138-139 4.5625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCCTCTC 10 0.0068378756 144.95 2 TGGGTCT 10 0.0068378756 144.95 3 AGCAAGT 10 0.0068378756 144.95 6 AATGATG 10 0.0068378756 144.95 5 >>END_MODULE Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002502 spots for SRR12671344.sra Written 1002502 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra Read 1002484 spots for SRR12671344.sra Written 1002484 spots for SRR12671344.sra SRR ids: ['SRR12671344.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_9n_z7bcz SRR12671344.sra spots: 20049698 blocks: [[1, 1002484], [1002485, 2004968], [2004969, 3007452], [3007453, 4009936], [4009937, 5012420], [5012421, 6014904], [6014905, 7017388], [7017389, 8019872], [8019873, 9022356], [9022357, 10024840], [10024841, 11027324], [11027325, 12029808], [12029809, 13032292], [13032293, 14034776], [14034777, 15037260], [15037261, 16039744], [16039745, 17042228], [17042229, 18044712], [18044713, 19047196], [19047197, 20049698]] SRR12671344 file size 6792064 SRR12671344 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 SRR12671344 SRR12671344_1.fastq SRR12671344_2.fastq Input file: SRR12671344_1.fastq Paired file: SRR12671344_2.fastq trimmed: SRR12671344-trimmed-pair1.fastq, SRR12671344-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 17:29:50 2025 >> started Tue Feb 11 17:30:13 2025 >> done (22.506s) 20049698 read pairs processed; of these: 172 ( 0.00%) short read pairs filtered out after trimming by size control 3452 ( 0.02%) empty read pairs filtered out after trimming by size control 20046074 (99.98%) read pairs available; of these: 1083942 ( 5.41%) trimmed read pairs available after processing 18962132 (94.59%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 13 0.00% 19 11 0.00% 20 24 0.00% 21 25 0.00% 22 20 0.00% 23 30 0.00% 24 17 0.00% 25 37 0.00% 26 37 0.00% 27 23 0.00% 28 37 0.00% 29 34 0.00% 30 49 0.00% 31 38 0.00% 32 42 0.00% 33 26 0.00% 34 39 0.00% 35 23 0.00% 36 31 0.00% 37 37 0.00% 38 49 0.00% 39 54 0.00% 40 44 0.00% 41 41 0.00% 42 54 0.00% 43 49 0.00% 44 48 0.00% 45 36 0.00% 46 45 0.00% 47 70 0.00% 48 67 0.00% 49 80 0.00% 50 93 0.00% 51 82 0.00% 52 91 0.00% 53 137 0.00% 54 108 0.00% 55 122 0.00% 56 134 0.00% 57 147 0.00% 58 145 0.00% 59 192 0.00% 60 232 0.00% 61 271 0.00% 62 278 0.00% 63 343 0.00% 64 358 0.00% 65 359 0.00% 66 475 0.00% 67 501 0.00% 68 548 0.00% 69 705 0.00% 70 786 0.00% 71 777 0.00% 72 989 0.00% 73 1019 0.01% 74 1123 0.01% 75 1276 0.01% 76 1378 0.01% 77 1477 0.01% 78 1744 0.01% 79 1902 0.01% 80 2030 0.01% 81 2269 0.01% 82 2508 0.01% 83 2612 0.01% 84 2956 0.01% 85 3187 0.02% 86 3427 0.02% 87 3758 0.02% 88 3977 0.02% 89 4280 0.02% 90 4437 0.02% 91 4792 0.02% 92 5013 0.03% 93 5820 0.03% 94 5759 0.03% 95 6456 0.03% 96 6538 0.03% 97 6794 0.03% 98 7220 0.04% 99 7507 0.04% 100 7782 0.04% 101 8199 0.04% 102 8572 0.04% 103 8738 0.04% 104 9346 0.05% 105 9552 0.05% 106 9960 0.05% 107 10149 0.05% 108 10803 0.05% 109 11093 0.06% 110 11225 0.06% 111 11911 0.06% 112 12258 0.06% 113 12465 0.06% 114 13098 0.07% 115 13523 0.07% 116 14046 0.07% 117 14439 0.07% 118 15152 0.08% 119 15304 0.08% 120 16024 0.08% 121 16710 0.08% 122 16601 0.08% 123 17327 0.09% 124 17939 0.09% 125 18299 0.09% 126 19086 0.10% 127 19252 0.10% 128 20051 0.10% 129 20603 0.10% 130 21068 0.11% 131 21143 0.11% 132 21780 0.11% 133 22453 0.11% 134 22814 0.11% 135 23814 0.12% 136 24400 0.12% 137 25005 0.12% 138 25460 0.13% 139 26709 0.13% 140 26412 0.13% 141 26942 0.13% 142 27675 0.14% 143 28296 0.14% 144 29142 0.15% 145 29655 0.15% 146 30652 0.15% 147 31704 0.16% 148 32528 0.16% 149 32420 0.16% 150 34001 0.17% 151 18962132 94.59% 20046074 reads passed initial QC criterion=sequence-density sequence-density=0.58 sequence-density-rank=1 fanout-score=2.01 fanout-score-rank=17 prefix-density=0.59 prefix-fanout=2.0 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTT criterion=fanout-score sequence-density=0.01 sequence-density-rank=24 fanout-score=492.70 fanout-score-rank=1 prefix-density=0.24 prefix-fanout=16.5 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAG criterion=sequence-density sequence-density=1.58 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=27 prefix-density=1.58 prefix-fanout=2.0 sequence=CTGCGACTGCGCTGACAAGACCCAGTGTGTCAAGAAGGGAAGCAGCTACACTGCTGGCATCGTCGAGACTGAGAAGAACTATGTCTCCTCCGTAGTCATGGAGGTGCCAGCAGCTGAGAACGATGGCAAGTGCAACTGCGGTACTGGCTGCACTTGCACTACCTGCACATGCGGTCATTAAGCAAGCACATCAACTATCATGTTTGATGTGGGATTGGGAGTGGATTAATAATGTAATTTCTGATAAATAATCTGTGTTCTTCTGTACTTGTGGGTGTGGAGTGAACAAACAAAAGTGTCCGTGAGTGTCTTTATCTTTGTGTCTTCTTCA criterion=fanout-score sequence-density=0.18 sequence-density-rank=21 fanout-score=11.23 fanout-score-rank=1 prefix-density=0.35 prefix-fanout=5.9 sequence=AAGAAAGCTTACCCTAAC SRR12671344 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 17:31:01 Started mapping on | Feb 11 17:31:01 Finished on | Feb 11 17:33:18 Mapping speed, Million of reads per hour | 526.76 Number of input reads | 20046074 Average input read length | 299 UNIQUE READS: Uniquely mapped reads number | 18497409 Uniquely mapped reads % | 92.27% Average mapped length | 297.69 Number of splices: Total | 18484608 Number of splices: Annotated (sjdb) | 18110930 Number of splices: GT/AG | 18123799 Number of splices: GC/AG | 296049 Number of splices: AT/AC | 11183 Number of splices: Non-canonical | 53577 Mismatch rate per base, % | 0.38% Deletion rate per base | 0.03% Deletion average length | 2.90 Insertion rate per base | 0.02% Insertion average length | 2.17 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 488859 % of reads mapped to multiple loci | 2.44% Number of reads mapped to too many loci | 139802 % of reads mapped to too many loci | 0.70% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.35% % of reads unmapped: other | 0.24% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1059806 1059806 1059806 N_multimapping 488859 488859 488859 N_noFeature 769496 18135248 879141 N_ambiguous 374216 1381 120868 UnstrandedReadsAssigned:17353697 PositiveStrandReadsAssigned:360780 NegativeStrandReadsAssigned:17497400 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12671344 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: SRR12671344-trimmed-pair1.fastq SRR12671344-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 20,046,074 reads, 17,490,495 reads pseudoaligned [quant] estimated average fragment length: 291.564 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,194 rounds 52401 SRR12671344.ke.tsv 34699 SRR12671344.se.tsv 87100 total ==> SRR12671344.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1727.44 627 16.4938 Potri.005G024800.1.v4.1 1035 744.436 270 16.4813 Potri.004G059700.1.v4.1 961 670.711 2 0.135503 Potri.007G009000.2.v4.1 1416 1125.44 0 0 Potri.003G141000.2.v4.1 2943 2652.44 1016 17.4062 Potri.016G087400.1.v4.1 270 73.9918 661.556 406.291 Potri.015G069301.1.v4.1 564 293.338 0 0 Potri.010G195200.1.v4.1 1773 1482.44 67 2.05378 Potri.012G127500.1.v4.1 977 686.55 101 6.68503 ==> SRR12671344.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 92 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 211 Potri.001G212900.v4.1 18 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 3 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12671344 completed mapping pipeline successfully