Starting /dee2/code/volunteer_pipeline.sh SRR12670124 current disk space = 3057404416000 free memory = 1136197776 SRR12670124 SRAfilesize f0c91514d0fdd877f0fc87480d89f605 SRR12670124.sra SRR12670124.sra file validated SRR12670124 is paired end SRR12670124 is conventional basespace SRR12670124 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670124_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 36.5595 37.0 37.0 37.0 37.0 37.0 2 36.4 37.0 37.0 37.0 37.0 37.0 3 36.577 37.0 37.0 37.0 37.0 37.0 4 36.6535 37.0 37.0 37.0 37.0 37.0 5 36.718 37.0 37.0 37.0 37.0 37.0 6 36.674 37.0 37.0 37.0 37.0 37.0 7 36.5435 37.0 37.0 37.0 37.0 37.0 8 36.595 37.0 37.0 37.0 37.0 37.0 9 36.5985 37.0 37.0 37.0 37.0 37.0 10-14 36.6281 37.0 37.0 37.0 37.0 37.0 15-19 36.6269 37.0 37.0 37.0 37.0 37.0 20-24 36.5737 37.0 37.0 37.0 37.0 37.0 25-29 36.5317 37.0 37.0 37.0 37.0 37.0 30-34 36.534000000000006 37.0 37.0 37.0 37.0 37.0 35-39 36.533 37.0 37.0 37.0 37.0 37.0 40-44 36.5064 37.0 37.0 37.0 37.0 37.0 45-49 36.49069999999999 37.0 37.0 37.0 37.0 37.0 50-54 36.4044 37.0 37.0 37.0 37.0 37.0 55-59 36.4369 37.0 37.0 37.0 37.0 37.0 60-64 36.4458 37.0 37.0 37.0 37.0 37.0 65-69 36.441 37.0 37.0 37.0 37.0 37.0 70-74 36.3568 37.0 37.0 37.0 37.0 37.0 75-79 36.327 37.0 37.0 37.0 37.0 37.0 80-84 36.2674 37.0 37.0 37.0 37.0 37.0 85-89 36.3223 37.0 37.0 37.0 37.0 37.0 90-94 36.314800000000005 37.0 37.0 37.0 37.0 37.0 95-99 36.2659 37.0 37.0 37.0 37.0 37.0 100-104 36.258300000000006 37.0 37.0 37.0 37.0 37.0 105-109 36.2539 37.0 37.0 37.0 37.0 37.0 110-114 36.221500000000006 37.0 37.0 37.0 37.0 37.0 115-119 36.2123 37.0 37.0 37.0 37.0 37.0 120-124 36.1108 37.0 37.0 37.0 37.0 37.0 125-129 35.981700000000004 37.0 37.0 37.0 37.0 37.0 130-134 35.9215 37.0 37.0 37.0 37.0 37.0 135-139 35.7069 37.0 37.0 37.0 37.0 37.0 140-144 35.5059 37.0 37.0 37.0 37.0 37.0 145-149 35.355599999999995 37.0 37.0 37.0 37.0 37.0 150-151 35.044 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 1.0 24 0.0 25 1.0 26 6.0 27 3.0 28 10.0 29 15.0 30 13.0 31 25.0 32 43.0 33 93.0 34 148.0 35 355.0 36 2895.0 37 391.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 40.400000000000006 11.075 5.8999999999999995 42.625 2 18.678017025538306 12.343515272909364 38.70806209313971 30.27040560841262 3 17.65 16.55 27.325 38.475 4 21.975 25.0 23.925 29.099999999999998 5 23.1 31.35 23.825 21.725 6 20.45 34.9 25.45 19.2 7 15.475 27.275 42.1 15.15 8 18.625 23.875 32.95 24.55 9 17.5 24.275 34.75 23.474999999999998 10-14 20.01 29.755 27.450000000000003 22.785 15-19 19.814999999999998 27.92 28.18 24.085 20-24 20.31 27.435 28.025 24.23 25-29 19.525000000000002 28.444999999999997 27.655 24.375 30-34 20.02 28.68 27.744999999999997 23.555 35-39 19.81 28.22 28.310000000000002 23.66 40-44 20.315 28.955 27.47 23.26 45-49 20.04 28.365000000000002 27.915 23.68 50-54 20.97 27.384999999999998 27.955000000000002 23.69 55-59 20.580000000000002 28.910000000000004 27.415 23.095 60-64 20.25 27.939999999999998 27.950000000000003 23.86 65-69 20.71 28.255000000000003 27.310000000000002 23.724999999999998 70-74 20.485 28.63 27.54 23.345 75-79 20.49 28.125 27.58 23.805 80-84 20.34 28.725 27.43 23.505000000000003 85-89 20.86 28.194999999999997 27.435 23.51 90-94 20.7 28.470000000000002 27.455000000000002 23.375 95-99 20.925 29.175 26.815 23.085 100-104 20.93 28.4 27.1 23.57 105-109 21.475 28.139999999999997 27.155 23.23 110-114 21.09 28.785 26.46 23.665 115-119 21.21 27.875 27.21 23.705000000000002 120-124 20.979999999999997 28.845 26.195 23.98 125-129 21.425 28.645 25.685000000000002 24.245 130-134 21.32 28.26 25.900000000000002 24.52 135-139 21.335 28.53 25.974999999999998 24.16 140-144 21.240000000000002 27.57 25.89 25.3 145-149 21.82 27.529999999999998 26.255 24.395 150-151 22.3875 26.437500000000004 25.137500000000003 26.0375 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.5 3 0.5 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 1.0 23 1.0 24 0.5 25 3.0 26 4.0 27 3.5 28 8.0 29 12.0 30 16.0 31 18.0 32 32.5 33 37.5 34 39.0 35 68.0 36 90.5 37 99.5 38 123.0 39 157.0 40 187.0 41 240.0 42 264.5 43 251.5 44 241.0 45 255.5 46 269.0 47 266.5 48 252.0 49 213.0 50 191.0 51 148.0 52 100.0 53 81.0 54 71.0 55 66.5 56 54.0 57 40.0 58 29.0 59 21.0 60 16.0 61 9.5 62 5.0 63 4.0 64 3.0 65 1.0 66 0.0 67 1.0 68 1.0 69 1.5 70 1.5 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 0.15 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 82.425 #Duplication Level Percentage of deduplicated Percentage of total 1 83.1968456172278 68.575 2 13.345465574764937 22.0 3 2.6387625113739763 6.525 4 0.6066120715802245 2.0 5 0.18198362147406735 0.75 6 0.030330603579011222 0.15 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 GTCCAATAGGTGGTGGCTTAGGTTTTGGAGCTTCAGCTACAGCTGGTTCT 6 0.15 No Hit TTCTTTTCTTCTGCTTCCTTGTGAATTACTGCTATTTTGTTCTTCATTTT 5 0.125 No Hit GTAGAACACCATCTTTTTTGCTCTTTTTTTTTCAAACAACCAAACAAAAT 5 0.125 No Hit CTTCAGTCTCACCACCGATTCTACATGACCCTTCAGTGTATGGAGTTCCC 5 0.125 No Hit GCCATGGTTATGGAAGTCAGGCGGCTCCAAACCACCATGCGAAGGCTAAA 5 0.125 No Hit CTTCTTGATTGGTAGAATGTCACCAGAAGCTGTAGCACTAAAATAAGCGA 5 0.125 No Hit GAGCCGTGAATAGATGCCAAGCTCACGCATCTCATTGGAAATGAAAAAAG 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 0.0 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 0.025 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 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.037500000000000006 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 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.2 0.0 0.0 0.0 0.0 72-73 0.4 0.0 0.0 0.0 0.0 74-75 0.6 0.0 0.0 0.0 0.0 76-77 0.7125 0.0 0.0 0.0 0.0 78-79 0.8374999999999999 0.0 0.0 0.0 0.0 80-81 0.9375 0.0 0.0 0.0 0.0 82-83 1.0875 0.0 0.0 0.0 0.0 84-85 1.4125 0.0 0.0 0.0 0.0 86-87 1.875 0.0 0.0 0.0 0.0 88-89 2.45 0.0 0.0 0.0 0.0 90-91 2.85 0.0 0.0 0.0 0.0 92-93 3.4 0.0 0.0 0.0 0.0 94-95 3.825 0.0 0.0 0.0 0.0 96-97 4.550000000000001 0.0 0.0 0.0 0.0 98-99 5.2 0.0 0.0 0.0 0.0 100-101 5.8625 0.0 0.0 0.0 0.0 102-103 6.425 0.0 0.0 0.0 0.0 104-105 7.0125 0.0 0.0 0.0 0.0 106-107 7.925 0.0 0.0 0.0 0.0 108-109 8.6 0.0 0.0 0.0 0.0 110-111 9.4375 0.0 0.0 0.0 0.0 112-113 10.2375 0.0 0.0 0.0 0.0 114-115 10.9625 0.0 0.0 0.0 0.0 116-117 12.075 0.0 0.0 0.0 0.0 118-119 12.825 0.0 0.0 0.0 0.0 120-121 13.6625 0.0 0.0 0.0 0.0 122-123 14.5 0.0 0.0 0.0 0.0 124-125 15.6375 0.0 0.0 0.0 0.0 126-127 16.925 0.0 0.0 0.0 0.0 128-129 18.112499999999997 0.0 0.0 0.0 0.0 130-131 19.025 0.0 0.0 0.0 0.0 132-133 19.8875 0.0 0.0 0.0 0.0 134-135 20.9 0.0 0.0 0.0 0.0 136-137 21.7625 0.0 0.0 0.0 0.0 138-139 22.725 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GAAGTTC 10 0.006830828 145.0 145 AGCTGTC 10 0.006830828 145.0 4 AAAAAAA 35 0.0035366106 20.714287 115-119 >>END_MODULE SRR12670124 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12670124_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 36.3645 37.0 37.0 37.0 37.0 37.0 2 36.2565 37.0 37.0 37.0 37.0 37.0 3 36.3625 37.0 37.0 37.0 37.0 37.0 4 36.3355 37.0 37.0 37.0 37.0 37.0 5 36.258 37.0 37.0 37.0 37.0 37.0 6 36.333 37.0 37.0 37.0 37.0 37.0 7 36.2845 37.0 37.0 37.0 37.0 37.0 8 36.368 37.0 37.0 37.0 37.0 37.0 9 36.435 37.0 37.0 37.0 37.0 37.0 10-14 36.3923 37.0 37.0 37.0 37.0 37.0 15-19 36.4176 37.0 37.0 37.0 37.0 37.0 20-24 36.389599999999994 37.0 37.0 37.0 37.0 37.0 25-29 36.3657 37.0 37.0 37.0 37.0 37.0 30-34 36.306 37.0 37.0 37.0 37.0 37.0 35-39 36.2978 37.0 37.0 37.0 37.0 37.0 40-44 36.280499999999996 37.0 37.0 37.0 37.0 37.0 45-49 36.299 37.0 37.0 37.0 37.0 37.0 50-54 36.2291 37.0 37.0 37.0 37.0 37.0 55-59 36.1953 37.0 37.0 37.0 37.0 37.0 60-64 36.1825 37.0 37.0 37.0 37.0 37.0 65-69 36.191 37.0 37.0 37.0 37.0 37.0 70-74 36.0987 37.0 37.0 37.0 37.0 37.0 75-79 36.1048 37.0 37.0 37.0 37.0 37.0 80-84 36.122099999999996 37.0 37.0 37.0 37.0 37.0 85-89 36.0603 37.0 37.0 37.0 37.0 37.0 90-94 36.076100000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.983000000000004 37.0 37.0 37.0 37.0 37.0 100-104 35.9685 37.0 37.0 37.0 37.0 37.0 105-109 35.9704 37.0 37.0 37.0 37.0 37.0 110-114 35.9057 37.0 37.0 37.0 37.0 37.0 115-119 35.9005 37.0 37.0 37.0 37.0 37.0 120-124 35.7415 37.0 37.0 37.0 37.0 37.0 125-129 35.67960000000001 37.0 37.0 37.0 37.0 37.0 130-134 35.3902 37.0 37.0 37.0 32.2 37.0 135-139 35.2804 37.0 37.0 37.0 37.0 37.0 140-144 35.106700000000004 37.0 37.0 37.0 27.4 37.0 145-149 34.756299999999996 37.0 37.0 37.0 25.0 37.0 150-151 34.4165 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 2.0 14 0.0 15 1.0 16 2.0 17 0.0 18 2.0 19 3.0 20 0.0 21 0.0 22 2.0 23 5.0 24 5.0 25 6.0 26 3.0 27 13.0 28 9.0 29 6.0 30 25.0 31 29.0 32 52.0 33 105.0 34 197.0 35 573.0 36 2684.0 37 275.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.075 23.875 10.85 28.199999999999996 2 26.35 27.900000000000002 30.325000000000003 15.425 3 19.675 29.349999999999998 31.85 19.125 4 23.400000000000002 32.95 24.7 18.95 5 23.799999999999997 36.6 21.675 17.925 6 19.650000000000002 41.55 22.2 16.6 7 20.4 22.825 38.074999999999996 18.7 8 20.7 26.450000000000003 28.549999999999997 24.3 9 22.325 25.2 30.65 21.825 10-14 23.135 29.455 25.895000000000003 21.515 15-19 23.39 28.415000000000003 27.22 20.974999999999998 20-24 23.385 28.410000000000004 27.694999999999997 20.51 25-29 22.8 28.560000000000002 28.04 20.599999999999998 30-34 22.79 28.28 27.97 20.96 35-39 22.725 28.665000000000003 27.775 20.835 40-44 23.325000000000003 27.955000000000002 28.065 20.655 45-49 23.11 27.245 28.465 21.18 50-54 23.06 27.26 28.7 20.979999999999997 55-59 23.46 27.71 27.805000000000003 21.025 60-64 23.255 27.915 28.035 20.794999999999998 65-69 23.935000000000002 27.61 27.58 20.875 70-74 23.59 29.595 26.295 20.52 75-79 23.155 27.685 28.01 21.15 80-84 23.035 28.15 27.365000000000002 21.45 85-89 24.44 27.150000000000002 27.195000000000004 21.215 90-94 24.44 27.415 27.750000000000004 20.395 95-99 23.74 28.544999999999998 27.284999999999997 20.43 100-104 24.855 27.544999999999998 27.034999999999997 20.565 105-109 25.22 28.03 26.43 20.32 110-114 25.169999999999998 28.16 26.43 20.24 115-119 25.545 28.244999999999997 26.8 19.41 120-124 25.985000000000003 28.595 26.07 19.35 125-129 26.38 27.655 26.645000000000003 19.32 130-134 27.189999999999998 28.189999999999998 25.759999999999998 18.86 135-139 27.455000000000002 28.075 25.89 18.58 140-144 28.115000000000002 27.92 25.415 18.55 145-149 29.9 27.04 24.815 18.245 150-151 30.8 26.7625 25.624999999999996 16.8125 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.5 7 0.5 8 0.5 9 0.5 10 0.0 11 0.5 12 1.0 13 0.5 14 0.0 15 0.0 16 0.0 17 0.5 18 0.5 19 0.0 20 0.5 21 1.0 22 1.5 23 1.0 24 0.5 25 1.5 26 3.5 27 8.5 28 14.5 29 10.0 30 9.0 31 17.0 32 28.5 33 44.5 34 51.0 35 65.0 36 82.5 37 104.5 38 139.0 39 175.0 40 195.5 41 228.5 42 251.0 43 275.0 44 272.5 45 253.5 46 263.5 47 253.5 48 234.5 49 193.5 50 168.5 51 134.5 52 97.5 53 84.0 54 76.5 55 67.5 56 41.5 57 29.0 58 27.5 59 25.5 60 20.5 61 12.5 62 9.5 63 5.5 64 2.5 65 2.0 66 1.0 67 0.5 68 0.5 69 0.0 70 0.5 71 0.5 72 0.0 73 0.0 74 0.0 75 0.5 76 0.5 77 0.0 78 0.5 79 0.5 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.5 87 0.5 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.5 95 1.0 96 0.5 97 0.0 98 0.0 99 0.5 100 1.5 >>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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 82.22500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 83.55123137731833 68.7 2 12.921860747947706 21.25 3 2.5235633931286103 6.225 4 0.6688963210702341 2.1999999999999997 5 0.18242626938279113 0.75 6 0.09121313469139557 0.44999999999999996 7 0.030404378230465188 0.17500000000000002 8 0.0 0.0 9 0.0 0.0 >10 0.030404378230465188 0.25 >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 AGAGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAA 10 0.25 No Hit AGAACACATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATC 7 0.17500000000000002 No Hit AGAGACAGGCGCACAGACAACATGGCTAGCTGCAACATGGCATCAGCTGC 6 0.15 No Hit ATTCATACTCCAAGTCTTTTAGTTCATCCATTTAAGCTTAATCAATCAAT 6 0.15 No Hit CAAAACCACATATAGAGGGTGTAATAGCTAAGTAGCCTGTAAGAGATGGC 6 0.15 No Hit AGAACATTGCATGGGCTGCAAGCACCAGACACAAAGATGTTCACAGAGCG 5 0.125 No Hit AAGCAGCCTTGAAACTATTCCGATTTTGTTTGGTTGTTTGAAAAAAAAAG 5 0.125 No Hit GAAAAACTTGAGAAGAAAAAGGCAGAATATGTGGAGAAAATGAAGAACAA 5 0.125 No Hit GGATGATGCTGGTGTTTTGTACTGTGCAATTGGCTCTGTTGTTTGGTTCT 5 0.125 No Hit CATGACCGGGACTTTTTGGTAAGAAACCTGAAGTCATTTGATGTGCCGAT 5 0.125 No Hit AGAGCAAATTCTTTGAGACATTTGCAGCTCCATTCACCAAGAGAGGATTG 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 0.0 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 0.025 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 0.025 0.0 0.0 0.0 0.0 42-43 0.025 0.0 0.0 0.0 0.0 44-45 0.037500000000000006 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 0.05 0.0 0.0 0.0 0.0 52-53 0.05 0.0 0.0 0.0 0.0 54-55 0.05 0.0 0.0 0.0 0.0 56-57 0.05 0.0 0.0 0.0 0.0 58-59 0.075 0.0 0.0 0.0 0.0 60-61 0.075 0.0 0.0 0.0 0.0 62-63 0.075 0.0 0.0 0.0 0.0 64-65 0.075 0.0 0.0 0.0 0.0 66-67 0.1 0.0 0.0 0.0 0.0 68-69 0.125 0.0 0.0 0.0 0.0 70-71 0.2 0.0 0.0 0.0 0.0 72-73 0.4 0.0 0.0 0.0 0.0 74-75 0.6 0.0 0.0 0.0 0.0 76-77 0.7125 0.0 0.0 0.0 0.0 78-79 0.8374999999999999 0.0 0.0 0.0 0.0 80-81 0.9375 0.0 0.0 0.0 0.0 82-83 1.0875 0.0 0.0 0.0 0.0 84-85 1.4125 0.0 0.0 0.0 0.0 86-87 1.875 0.0 0.0 0.0 0.0 88-89 2.45 0.0 0.0 0.0 0.0 90-91 2.85 0.0 0.0 0.0 0.0 92-93 3.4 0.0 0.0 0.0 0.0 94-95 3.825 0.0 0.0 0.0 0.0 96-97 4.550000000000001 0.0 0.0 0.0 0.0 98-99 5.2 0.0 0.0 0.0 0.0 100-101 5.8625 0.0 0.0 0.0 0.0 102-103 6.425 0.0 0.0 0.0 0.0 104-105 7.025 0.0 0.0 0.0 0.0 106-107 7.949999999999999 0.0 0.0 0.0 0.0 108-109 8.675 0.0 0.0 0.0 0.0 110-111 9.5375 0.0 0.0 0.0 0.0 112-113 10.3125 0.0 0.0 0.0 0.0 114-115 11.0375 0.0 0.0 0.0 0.0 116-117 12.2125 0.0 0.0 0.0 0.0 118-119 13.025 0.0 0.0 0.0 0.0 120-121 13.8875 0.0 0.0 0.0 0.0 122-123 14.7625 0.0 0.0 0.0 0.0 124-125 15.9 0.0 0.0 0.0 0.0 126-127 17.1625 0.0 0.0 0.0 0.0 128-129 18.3375 0.0 0.0 0.0 0.0 130-131 19.25 0.0 0.0 0.0 0.0 132-133 20.1125 0.0 0.0 0.0 0.0 134-135 21.1125 0.0 0.0 0.0 0.0 136-137 21.9875 0.0 0.0 0.0 0.0 138-139 22.9375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AGCCTCA 10 0.006830828 145.0 9 AACCAAG 10 0.006830828 145.0 6 CAGCCTC 10 0.006830828 145.0 8 >>END_MODULE Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550934 spots for SRR12670124.sra Written 550934 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra Read 550920 spots for SRR12670124.sra Written 550920 spots for SRR12670124.sra SRR ids: ['SRR12670124.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_a77scj5j SRR12670124.sra spots: 11018414 blocks: [[1, 550920], [550921, 1101840], [1101841, 1652760], [1652761, 2203680], [2203681, 2754600], [2754601, 3305520], [3305521, 3856440], [3856441, 4407360], [4407361, 4958280], [4958281, 5509200], [5509201, 6060120], [6060121, 6611040], [6611041, 7161960], [7161961, 7712880], [7712881, 8263800], [8263801, 8814720], [8814721, 9365640], [9365641, 9916560], [9916561, 10467480], [10467481, 11018414]] SRR12670124 file size 3722838 SRR12670124 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 SRR12670124 SRR12670124_1.fastq SRR12670124_2.fastq Input file: SRR12670124_1.fastq Paired file: SRR12670124_2.fastq trimmed: SRR12670124-trimmed-pair1.fastq, SRR12670124-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 00:19:07 2025 >> started Tue Feb 11 00:19:18 2025 >> done (11.896s) 11018414 read pairs processed; of these: 51 ( 0.00%) short read pairs filtered out after trimming by size control 3485 ( 0.03%) empty read pairs filtered out after trimming by size control 11014878 (99.97%) read pairs available; of these: 2871272 (26.07%) trimmed read pairs available after processing 8143606 (73.93%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 5 0.00% 20 2 0.00% 21 19 0.00% 22 18 0.00% 23 30 0.00% 24 28 0.00% 25 31 0.00% 26 40 0.00% 27 26 0.00% 28 46 0.00% 29 58 0.00% 30 48 0.00% 31 55 0.00% 32 69 0.00% 33 76 0.00% 34 88 0.00% 35 79 0.00% 36 100 0.00% 37 109 0.00% 38 94 0.00% 39 139 0.00% 40 151 0.00% 41 133 0.00% 42 150 0.00% 43 155 0.00% 44 170 0.00% 45 167 0.00% 46 206 0.00% 47 232 0.00% 48 272 0.00% 49 337 0.00% 50 419 0.00% 51 415 0.00% 52 485 0.00% 53 494 0.00% 54 510 0.00% 55 596 0.01% 56 639 0.01% 57 734 0.01% 58 830 0.01% 59 995 0.01% 60 1202 0.01% 61 1323 0.01% 62 1556 0.01% 63 1758 0.02% 64 1809 0.02% 65 1991 0.02% 66 2104 0.02% 67 2337 0.02% 68 2726 0.02% 69 3054 0.03% 70 3447 0.03% 71 3994 0.04% 72 4547 0.04% 73 5073 0.05% 74 5598 0.05% 75 6040 0.05% 76 6596 0.06% 77 7137 0.06% 78 7780 0.07% 79 8496 0.08% 80 9658 0.09% 81 10797 0.10% 82 11993 0.11% 83 13075 0.12% 84 14584 0.13% 85 15600 0.14% 86 16480 0.15% 87 17306 0.16% 88 17868 0.16% 89 19185 0.17% 90 20606 0.19% 91 22140 0.20% 92 23110 0.21% 93 25293 0.23% 94 26792 0.24% 95 28550 0.26% 96 29445 0.27% 97 30244 0.27% 98 30937 0.28% 99 32290 0.29% 100 32965 0.30% 101 33805 0.31% 102 35422 0.32% 103 36882 0.33% 104 38376 0.35% 105 39621 0.36% 106 40313 0.37% 107 40404 0.37% 108 40724 0.37% 109 41201 0.37% 110 41208 0.37% 111 41794 0.38% 112 43406 0.39% 113 43848 0.40% 114 45125 0.41% 115 46081 0.42% 116 46208 0.42% 117 46698 0.42% 118 47101 0.43% 119 46327 0.42% 120 47111 0.43% 121 47645 0.43% 122 47785 0.43% 123 48808 0.44% 124 49484 0.45% 125 49553 0.45% 126 50181 0.46% 127 50219 0.46% 128 49740 0.45% 129 49347 0.45% 130 49432 0.45% 131 48922 0.44% 132 49398 0.45% 133 50202 0.46% 134 49893 0.45% 135 50534 0.46% 136 50814 0.46% 137 49940 0.45% 138 49703 0.45% 139 51097 0.46% 140 49622 0.45% 141 49525 0.45% 142 49985 0.45% 143 49674 0.45% 144 50795 0.46% 145 50021 0.45% 146 50136 0.46% 147 50453 0.46% 148 51157 0.46% 149 49597 0.45% 150 49218 0.45% 151 8143606 73.93% 11014878 reads passed initial QC criterion=sequence-density sequence-density=0.43 sequence-density-rank=1 fanout-score=1.94 fanout-score-rank=28 prefix-density=0.44 prefix-fanout=1.9 sequence=CGGTAGACCCAACCTTTCTCCAACTCGAATTCCAAGCAAGGAACCCACTTCGAGCGAAGAAGGTAATCAATTTCCTTGGCCAATTCCTCCTCTGTGAGATCTGGAAGGTAAGAAAGAGTCTCGAACTTCTTCAATCCAGTTGGTGGCCACACCTGCATGCATTGAACTCGTCCACCATTGCTTGCAATGGAAGTAATGTCATT criterion=fanout-score sequence-density=0.03 sequence-density-rank=29 fanout-score=146.71 fanout-score-rank=1 prefix-density=0.26 prefix-fanout=14.6 sequence=TGAAGAAGACACAAAGATAAAGACACTCACGGACACTTTTGTTTGTTCACTCCACACCCACAAGTACAGAAGAACACAGATTATTTATCAGAAATTACATTATTAATCCACTCCCAATCCCACATCAAACATGATAGTTGATGTGCTTGCTTAATGACCGCATGTGCAGGTAGTGCAAGTGCAGCCAGTACCGCAGTTGCACTTGCCATCGTTCTCAGCTGCTGGCACCTCCATGACTACGGAGGAGACATAGTTCTTCTCAGTCTCGACGATGCCAGCAGTGTAGCTGCTTCCCTTCTTGACACACTGGGTCTTGTCAGCGCAGTCGCAGGTGTCGCAGGTGCTAGACATGATGATTGATTGATTAAGCTTAAATGGATGAACTAAAAGACTTGGAGTATGAATGTGTTCTCTGTGT criterion=sequence-density sequence-density=0.55 sequence-density-rank=1 fanout-score=2.25 fanout-score-rank=23 prefix-density=0.56 prefix-fanout=2.2 sequence=TGTAAGAGATGGCTTCCTC criterion=fanout-score sequence-density=0.01 sequence-density-rank=29 fanout-score=36.97 fanout-score-rank=1 prefix-density=0.06 prefix-fanout=4.2 sequence=GGGAAACTTACCAGGTCCAGACATAGTAAGGATTGACAGACTGAGAGCTCTTTCTTGATTCTATGGGTGGTGGTGCATGGCCGTTCTTAGTTGGTGGAGCGATTTGTCTGGTTAATTCCGTTAACGAACGAGACCTCAGCCTGCTAACTAGCTATGCGGAGGTGACCCTCCGCGGCCAGCTTCTTAGAGGGACTATGGCCTTCCAGGCCAAGGAAGTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCACGCGCGCTACACTGAT SRR12670124 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 00:20:00 Started mapping on | Feb 11 00:20:01 Finished on | Feb 11 00:21:12 Mapping speed, Million of reads per hour | 558.50 Number of input reads | 11014878 Average input read length | 285 UNIQUE READS: Uniquely mapped reads number | 10315982 Uniquely mapped reads % | 93.65% Average mapped length | 284.32 Number of splices: Total | 10063741 Number of splices: Annotated (sjdb) | 9840441 Number of splices: GT/AG | 9855335 Number of splices: GC/AG | 166455 Number of splices: AT/AC | 6133 Number of splices: Non-canonical | 35818 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.92 Insertion rate per base | 0.02% Insertion average length | 2.47 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 265443 % of reads mapped to multiple loci | 2.41% Number of reads mapped to too many loci | 96143 % of reads mapped to too many loci | 0.87% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.91% % of reads unmapped: other | 0.16% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 433453 433453 433453 N_multimapping 265443 265443 265443 N_noFeature 382048 10168766 438234 N_ambiguous 156638 545 65274 UnstrandedReadsAssigned:9777296 PositiveStrandReadsAssigned:146671 NegativeStrandReadsAssigned:9812474 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=137 echo kmer=133 SRR12670124 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: SRR12670124-trimmed-pair1.fastq SRR12670124-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 11,014,878 reads, 9,843,318 reads pseudoaligned [quant] estimated average fragment length: 211.097 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,055 rounds 52401 SRR12670124.ke.tsv 34699 SRR12670124.se.tsv 87100 total ==> SRR12670124.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1807.9 384 21.717 Potri.005G024800.1.v4.1 1035 824.903 160 19.8317 Potri.004G059700.1.v4.1 961 750.932 0 0 Potri.007G009000.2.v4.1 1416 1205.9 0 0 Potri.003G141000.2.v4.1 2943 2732.9 654 24.4679 Potri.016G087400.1.v4.1 270 107.945 410 388.351 Potri.015G069301.1.v4.1 564 361.212 0 0 Potri.010G195200.1.v4.1 1773 1562.9 36 2.35513 Potri.012G127500.1.v4.1 977 766.908 50 6.66608 ==> SRR12670124.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 123 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 140 Potri.001G212900.v4.1 3 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 1 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR12670124 completed mapping pipeline successfully