Starting /dee2/code/volunteer_pipeline.sh SRR12666464 current disk space = 1543068573696 free memory = 1600499368 SRR12666464 SRAfilesize f2956325320876052a150832977e9e1f SRR12666464.sra SRR12666464.sra file validated SRR12666464 is paired end SRR12666464 is conventional basespace SRR12666464 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666464_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 48 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.4345 37.0 37.0 37.0 37.0 37.0 2 36.25225 37.0 37.0 37.0 37.0 37.0 3 36.4855 37.0 37.0 37.0 37.0 37.0 4 36.5255 37.0 37.0 37.0 37.0 37.0 5 36.596 37.0 37.0 37.0 37.0 37.0 6 36.528 37.0 37.0 37.0 37.0 37.0 7 36.4945 37.0 37.0 37.0 37.0 37.0 8 36.5755 37.0 37.0 37.0 37.0 37.0 9 36.5705 37.0 37.0 37.0 37.0 37.0 10-14 36.5521 37.0 37.0 37.0 37.0 37.0 15-19 36.5613 37.0 37.0 37.0 37.0 37.0 20-24 36.5052 37.0 37.0 37.0 37.0 37.0 25-29 36.445499999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.4392 37.0 37.0 37.0 37.0 37.0 35-39 36.385000000000005 37.0 37.0 37.0 37.0 37.0 40-44 36.3655 37.0 37.0 37.0 37.0 37.0 45-49 36.3193 37.0 37.0 37.0 37.0 37.0 50-54 36.3233 37.0 37.0 37.0 37.0 37.0 55-59 36.3401 37.0 37.0 37.0 37.0 37.0 60-64 36.3697 37.0 37.0 37.0 37.0 37.0 65-69 36.289500000000004 37.0 37.0 37.0 37.0 37.0 70-74 36.2915 37.0 37.0 37.0 37.0 37.0 75-79 36.220600000000005 37.0 37.0 37.0 37.0 37.0 80-84 36.207800000000006 37.0 37.0 37.0 37.0 37.0 85-89 36.238800000000005 37.0 37.0 37.0 37.0 37.0 90-94 36.159299999999995 37.0 37.0 37.0 37.0 37.0 95-99 36.061099999999996 37.0 37.0 37.0 37.0 37.0 100-104 36.1357 37.0 37.0 37.0 37.0 37.0 105-109 36.181 37.0 37.0 37.0 37.0 37.0 110-114 36.1247 37.0 37.0 37.0 37.0 37.0 115-119 36.0219 37.0 37.0 37.0 37.0 37.0 120-124 35.9734 37.0 37.0 37.0 37.0 37.0 125-129 35.98309999999999 37.0 37.0 37.0 37.0 37.0 130-134 35.9544 37.0 37.0 37.0 37.0 37.0 135-139 35.928200000000004 37.0 37.0 37.0 37.0 37.0 140-144 35.71 37.0 37.0 37.0 37.0 37.0 145-149 35.7001 37.0 37.0 37.0 37.0 37.0 150-151 35.41475 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 1.0 23 3.0 24 2.0 25 2.0 26 7.0 27 4.0 28 14.0 29 24.0 30 29.0 31 42.0 32 44.0 33 95.0 34 146.0 35 321.0 36 2788.0 37 478.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.75 12.049999999999999 7.625 33.575 2 21.380345086271568 15.27881970492623 35.73393348337085 27.60690172543136 3 21.3 23.275000000000002 25.85 29.575000000000003 4 25.4 30.325000000000003 21.7 22.575 5 25.424999999999997 33.475 21.825 19.275000000000002 6 21.8 33.975 23.875 20.349999999999998 7 17.849999999999998 21.4 41.475 19.275000000000002 8 19.6 20.1 29.275000000000002 31.025000000000002 9 20.0 21.25 31.3 27.450000000000003 10-14 22.79 27.045 25.055 25.11 15-19 22.64 25.624999999999996 25.91 25.825 20-24 22.97 25.540000000000003 25.724999999999998 25.765 25-29 23.419999999999998 25.77 25.759999999999998 25.05 30-34 22.6 26.290000000000003 25.69 25.419999999999998 35-39 22.634999999999998 26.14 25.465 25.759999999999998 40-44 23.46 25.6 25.85 25.09 45-49 23.205000000000002 26.715 24.995 25.085 50-54 22.735 25.71 25.590000000000003 25.965 55-59 22.605 26.25 25.235000000000003 25.91 60-64 22.725 25.695 25.72 25.86 65-69 22.975 25.369999999999997 26.005 25.650000000000002 70-74 23.23 26.095000000000002 25.15 25.525 75-79 23.35 25.56 25.729999999999997 25.36 80-84 22.52 25.5 25.665 26.314999999999998 85-89 23.45 25.995 25.95 24.605 90-94 23.369999999999997 25.8 25.2 25.629999999999995 95-99 23.365 24.95 26.06 25.624999999999996 100-104 23.95 26.135 25.240000000000002 24.675 105-109 24.215 25.53 25.03 25.224999999999998 110-114 24.395 25.305 24.959999999999997 25.34 115-119 23.315 26.064999999999998 25.305 25.314999999999998 120-124 24.065 26.384999999999998 24.51 25.040000000000003 125-129 24.015 25.775 24.84 25.369999999999997 130-134 23.515 26.619999999999997 24.935 24.93 135-139 24.015 25.624999999999996 24.635 25.724999999999998 140-144 23.419999999999998 25.765 25.255 25.56 145-149 23.93 25.695 24.675 25.7 150-151 24.6625 26.3625 23.4125 25.5625 >>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 0.5 15 0.5 16 0.0 17 0.0 18 0.5 19 1.0 20 0.5 21 0.0 22 0.0 23 0.5 24 1.0 25 1.0 26 1.0 27 1.0 28 3.0 29 6.5 30 7.5 31 10.0 32 12.5 33 21.0 34 29.0 35 43.0 36 54.5 37 61.0 38 78.0 39 88.5 40 120.0 41 164.5 42 173.5 43 179.0 44 199.0 45 216.0 46 232.5 47 216.0 48 177.5 49 169.5 50 193.0 51 173.5 52 142.0 53 135.5 54 119.5 55 110.0 56 94.5 57 77.0 58 72.0 59 72.0 60 63.5 61 62.0 62 58.0 63 45.5 64 44.5 65 47.5 66 48.0 67 43.5 68 35.0 69 28.0 70 21.0 71 13.5 72 9.5 73 6.5 74 5.0 75 5.0 76 3.0 77 0.5 78 0.5 79 0.5 80 0.5 81 0.5 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 0.025 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 92.27499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 92.22432945001354 85.1 2 7.233811975074506 13.350000000000001 3 0.5147656461663506 1.425 4 0.0 0.0 5 0.0270929287455974 0.125 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 TCGTGCTGCCACATTTGTAGCAACCAAAACAAGAAACTTCCCGCTCCTGA 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.025 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 0.05 0.0 0.0 0.0 0.0 76-77 0.05 0.0 0.0 0.0 0.0 78-79 0.1 0.0 0.0 0.0 0.0 80-81 0.1 0.0 0.0 0.0 0.0 82-83 0.1 0.0 0.0 0.0 0.0 84-85 0.1125 0.0 0.0 0.0 0.0 86-87 0.125 0.0 0.0 0.0 0.0 88-89 0.175 0.0 0.0 0.0 0.0 90-91 0.2375 0.0 0.0 0.0 0.0 92-93 0.32499999999999996 0.0 0.0 0.0 0.0 94-95 0.4 0.0 0.0 0.0 0.0 96-97 0.5125 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 0.825 0.0 0.0 0.0 0.0 104-105 0.9375 0.0 0.0 0.0 0.0 106-107 1.025 0.0 0.0 0.0 0.0 108-109 1.15 0.0 0.0 0.0 0.0 110-111 1.375 0.0 0.0 0.0 0.0 112-113 1.5375 0.0 0.0 0.0 0.0 114-115 1.8125 0.0 0.0 0.0 0.0 116-117 2.125 0.0 0.0 0.0 0.0 118-119 2.525 0.0 0.0 0.0 0.0 120-121 2.8375000000000004 0.0 0.0 0.0 0.0 122-123 3.175 0.0 0.0 0.0 0.0 124-125 3.6375 0.0 0.0 0.0 0.0 126-127 4.2125 0.0 0.0 0.0 0.0 128-129 4.550000000000001 0.0 0.0 0.0 0.0 130-131 4.887499999999999 0.0 0.0 0.0 0.0 132-133 5.225 0.0 0.0 0.0 0.0 134-135 5.525 0.0 0.0 0.0 0.0 136-137 5.925 0.0 0.0 0.0 0.0 138-139 6.425000000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGTCCTG 10 0.006830828 145.0 145 >>END_MODULE SRR12666464 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666464_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.088 37.0 37.0 37.0 37.0 37.0 2 35.9645 37.0 37.0 37.0 37.0 37.0 3 36.1315 37.0 37.0 37.0 37.0 37.0 4 36.305 37.0 37.0 37.0 37.0 37.0 5 36.272 37.0 37.0 37.0 37.0 37.0 6 36.15 37.0 37.0 37.0 37.0 37.0 7 36.282 37.0 37.0 37.0 37.0 37.0 8 36.291 37.0 37.0 37.0 37.0 37.0 9 36.327 37.0 37.0 37.0 37.0 37.0 10-14 36.2484 37.0 37.0 37.0 37.0 37.0 15-19 36.1957 37.0 37.0 37.0 37.0 37.0 20-24 36.2038 37.0 37.0 37.0 37.0 37.0 25-29 36.1591 37.0 37.0 37.0 37.0 37.0 30-34 36.1709 37.0 37.0 37.0 37.0 37.0 35-39 36.151599999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.124700000000004 37.0 37.0 37.0 37.0 37.0 45-49 36.067899999999995 37.0 37.0 37.0 37.0 37.0 50-54 36.072900000000004 37.0 37.0 37.0 37.0 37.0 55-59 36.0333 37.0 37.0 37.0 37.0 37.0 60-64 36.0043 37.0 37.0 37.0 37.0 37.0 65-69 35.974900000000005 37.0 37.0 37.0 37.0 37.0 70-74 35.9815 37.0 37.0 37.0 37.0 37.0 75-79 35.9773 37.0 37.0 37.0 37.0 37.0 80-84 35.931 37.0 37.0 37.0 37.0 37.0 85-89 35.8428 37.0 37.0 37.0 37.0 37.0 90-94 35.85640000000001 37.0 37.0 37.0 37.0 37.0 95-99 35.8391 37.0 37.0 37.0 37.0 37.0 100-104 35.883599999999994 37.0 37.0 37.0 37.0 37.0 105-109 35.812400000000004 37.0 37.0 37.0 37.0 37.0 110-114 35.8155 37.0 37.0 37.0 37.0 37.0 115-119 35.7523 37.0 37.0 37.0 37.0 37.0 120-124 35.7958 37.0 37.0 37.0 37.0 37.0 125-129 35.786100000000005 37.0 37.0 37.0 37.0 37.0 130-134 35.7588 37.0 37.0 37.0 37.0 37.0 135-139 35.5858 37.0 37.0 37.0 37.0 37.0 140-144 35.4787 37.0 37.0 37.0 37.0 37.0 145-149 35.5559 37.0 37.0 37.0 37.0 37.0 150-151 35.246 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 4.0 13 4.0 14 4.0 15 5.0 16 1.0 17 4.0 18 1.0 19 2.0 20 6.0 21 3.0 22 3.0 23 4.0 24 8.0 25 6.0 26 12.0 27 11.0 28 9.0 29 11.0 30 27.0 31 33.0 32 48.0 33 94.0 34 183.0 35 430.0 36 2654.0 37 433.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 50.3 17.4 7.5 24.8 2 27.525 21.175 29.549999999999997 21.75 3 24.525 23.1 28.799999999999997 23.575 4 26.700000000000003 30.15 19.950000000000003 23.200000000000003 5 27.375 35.375 18.525 18.725 6 22.925 34.300000000000004 20.424999999999997 22.35 7 21.4 17.224999999999998 37.35 24.025 8 22.075 20.0 24.375 33.550000000000004 9 23.575 21.825 25.575 29.025000000000002 10-14 26.055 25.295 23.78 24.87 15-19 25.605 25.369999999999997 24.385 24.64 20-24 25.080000000000002 25.585 24.91 24.425 25-29 25.615 25.259999999999998 24.695 24.43 30-34 25.55 25.569999999999997 25.0 23.880000000000003 35-39 25.5 25.215 24.34 24.945 40-44 25.259999999999998 24.975 25.569999999999997 24.195 45-49 25.36 25.345000000000002 24.5 24.795 50-54 25.629999999999995 25.900000000000002 24.595 23.875 55-59 25.83 25.445 24.59 24.135 60-64 25.540000000000003 25.869999999999997 24.555 24.035 65-69 25.45 24.765 25.735000000000003 24.05 70-74 25.5 25.195 25.014999999999997 24.29 75-79 26.025 25.88 24.825 23.27 80-84 25.779999999999998 25.435000000000002 25.22 23.565 85-89 25.590000000000003 25.974999999999998 24.740000000000002 23.695 90-94 25.915 25.455 25.06 23.57 95-99 25.64 25.615 24.925 23.82 100-104 25.955000000000002 25.52 25.045 23.48 105-109 25.645 25.83 24.85 23.674999999999997 110-114 25.895000000000003 25.885 25.165 23.055 115-119 25.965 25.935000000000002 24.665 23.435 120-124 26.02 26.009999999999998 24.82 23.150000000000002 125-129 26.305 26.340000000000003 24.665 22.689999999999998 130-134 26.395000000000003 25.82 24.779999999999998 23.005 135-139 26.52 26.334999999999997 24.505 22.64 140-144 26.700000000000003 26.265 24.715 22.32 145-149 27.32 26.215 24.47 21.995 150-151 27.9375 25.4375 23.425 23.200000000000003 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 5 0.0 6 0.0 7 0.5 8 0.5 9 0.0 10 0.0 11 2.0 12 2.0 13 0.0 14 0.5 15 1.0 16 0.5 17 0.0 18 1.0 19 1.0 20 0.0 21 0.0 22 1.0 23 1.0 24 1.0 25 2.0 26 2.0 27 2.5 28 5.0 29 6.5 30 6.5 31 7.5 32 12.0 33 18.5 34 20.0 35 22.5 36 33.0 37 54.5 38 84.0 39 111.0 40 120.5 41 119.0 42 126.0 43 151.0 44 179.0 45 186.5 46 200.0 47 219.5 48 204.0 49 176.5 50 154.0 51 144.5 52 147.0 53 135.5 54 129.5 55 113.5 56 94.0 57 95.0 58 89.5 59 88.0 60 82.5 61 77.0 62 80.5 63 70.0 64 63.0 65 63.0 66 50.0 67 44.0 68 44.0 69 37.5 70 30.5 71 24.0 72 18.5 73 8.5 74 5.5 75 7.0 76 5.0 77 2.0 78 1.0 79 1.5 80 1.5 81 0.5 82 0.5 83 1.0 84 0.5 85 0.5 86 0.5 87 0.5 88 1.0 89 0.5 90 0.0 91 0.0 92 0.5 93 0.5 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.5 100 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 0.0 150-151 0.0 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 92.05 #Duplication Level Percentage of deduplicated Percentage of total 1 92.2324823465508 84.89999999999999 2 7.0342205323193925 12.950000000000001 3 0.6518196632265073 1.7999999999999998 4 0.027159152634437803 0.1 5 0.05431830526887561 0.25 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 AATGAAAGCTAGTTCATCAGTCAAGCATCTTGCTCTTCCTTGTAACCGTG 5 0.125 No Hit GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 5 0.125 No Hit >>END_MODULE >>Adapter Content warn #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 0.0125 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 0.05 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.075 0.0 0.0 0.0 0.0 74-75 0.075 0.0 0.0 0.0 0.0 76-77 0.075 0.0 0.0 0.0 0.0 78-79 0.125 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 0.1375 0.0 0.0 0.0 0.0 86-87 0.15 0.0 0.0 0.0 0.0 88-89 0.2 0.0 0.0 0.0 0.0 90-91 0.2625 0.0 0.0 0.0 0.0 92-93 0.35 0.0 0.0 0.0 0.0 94-95 0.42500000000000004 0.0 0.0 0.0 0.0 96-97 0.5375000000000001 0.0 0.0 0.0 0.0 98-99 0.6625000000000001 0.0 0.0 0.0 0.0 100-101 0.7125 0.0 0.0 0.0 0.0 102-103 0.85 0.0 0.0 0.0 0.0 104-105 0.9624999999999999 0.0 0.0 0.0 0.0 106-107 1.0499999999999998 0.0 0.0 0.0 0.0 108-109 1.175 0.0 0.0 0.0 0.0 110-111 1.4 0.0 0.0 0.0 0.0 112-113 1.575 0.0 0.0 0.0 0.0 114-115 1.8875000000000002 0.0 0.0 0.0 0.0 116-117 2.2375 0.0 0.0 0.0 0.0 118-119 2.6375 0.0 0.0 0.0 0.0 120-121 2.9625000000000004 0.0 0.0 0.0 0.0 122-123 3.35 0.0 0.0 0.0 0.0 124-125 3.8375000000000004 0.0 0.0 0.0 0.0 126-127 4.387499999999999 0.0 0.0 0.0 0.0 128-129 4.725 0.0 0.0 0.0 0.0 130-131 5.074999999999999 0.0 0.0 0.0 0.0 132-133 5.45 0.0 0.0 0.0 0.0 134-135 5.737500000000001 0.0 0.0 0.0 0.0 136-137 6.1 0.0 0.0 0.0 0.0 138-139 6.625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCATTCA 10 0.006830828 145.0 145 TGAATCA 10 0.006830828 145.0 3 >>END_MODULE Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309800 spots for SRR12666464.sra Written 1309800 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra Read 1309799 spots for SRR12666464.sra Written 1309799 spots for SRR12666464.sra SRR ids: ['SRR12666464.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd__efq3tg9 SRR12666464.sra spots: 26195981 blocks: [[1, 1309799], [1309800, 2619598], [2619599, 3929397], [3929398, 5239196], [5239197, 6548995], [6548996, 7858794], [7858795, 9168593], [9168594, 10478392], [10478393, 11788191], [11788192, 13097990], [13097991, 14407789], [14407790, 15717588], [15717589, 17027387], [17027388, 18337186], [18337187, 19646985], [19646986, 20956784], [20956785, 22266583], [22266584, 23576382], [23576383, 24886181], [24886182, 26195981]] SRR12666464 file size 8880840 SRR12666464 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 SRR12666464 SRR12666464_1.fastq SRR12666464_2.fastq Input file: SRR12666464_1.fastq Paired file: SRR12666464_2.fastq trimmed: SRR12666464-trimmed-pair1.fastq, SRR12666464-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 Sat Dec 7 13:40:32 2024 >> started Sat Dec 7 13:41:09 2024 >> done (36.464s) 26195981 read pairs processed; of these: 55 ( 0.00%) short read pairs filtered out after trimming by size control 3556 ( 0.01%) empty read pairs filtered out after trimming by size control 26192370 (99.99%) read pairs available; of these: 2603939 ( 9.94%) trimmed read pairs available after processing 23588431 (90.06%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 5 0.00% 19 20 0.00% 20 8 0.00% 21 15 0.00% 22 59 0.00% 23 22 0.00% 24 14 0.00% 25 21 0.00% 26 23 0.00% 27 22 0.00% 28 33 0.00% 29 36 0.00% 30 27 0.00% 31 27 0.00% 32 37 0.00% 33 29 0.00% 34 39 0.00% 35 44 0.00% 36 38 0.00% 37 42 0.00% 38 43 0.00% 39 35 0.00% 40 39 0.00% 41 37 0.00% 42 64 0.00% 43 46 0.00% 44 47 0.00% 45 62 0.00% 46 58 0.00% 47 61 0.00% 48 46 0.00% 49 67 0.00% 50 69 0.00% 51 67 0.00% 52 68 0.00% 53 102 0.00% 54 71 0.00% 55 101 0.00% 56 101 0.00% 57 138 0.00% 58 123 0.00% 59 123 0.00% 60 168 0.00% 61 198 0.00% 62 209 0.00% 63 197 0.00% 64 249 0.00% 65 258 0.00% 66 307 0.00% 67 286 0.00% 68 368 0.00% 69 422 0.00% 70 490 0.00% 71 484 0.00% 72 641 0.00% 73 790 0.00% 74 765 0.00% 75 894 0.00% 76 1077 0.00% 77 1166 0.00% 78 1314 0.01% 79 1517 0.01% 80 1708 0.01% 81 2052 0.01% 82 2386 0.01% 83 2594 0.01% 84 3009 0.01% 85 3243 0.01% 86 3588 0.01% 87 4108 0.02% 88 4583 0.02% 89 5116 0.02% 90 5693 0.02% 91 6323 0.02% 92 7180 0.03% 93 7807 0.03% 94 8731 0.03% 95 9396 0.04% 96 10497 0.04% 97 11066 0.04% 98 11717 0.04% 99 12859 0.05% 100 13754 0.05% 101 14883 0.06% 102 16398 0.06% 103 18003 0.07% 104 18992 0.07% 105 20423 0.08% 106 21168 0.08% 107 22114 0.08% 108 23719 0.09% 109 24479 0.09% 110 25437 0.10% 111 27682 0.11% 112 28664 0.11% 113 30881 0.12% 114 32814 0.13% 115 34469 0.13% 116 35059 0.13% 117 36541 0.14% 118 36845 0.14% 119 38232 0.15% 120 39867 0.15% 121 41558 0.16% 122 43094 0.16% 123 45063 0.17% 124 47223 0.18% 125 48443 0.18% 126 50454 0.19% 127 51175 0.20% 128 52042 0.20% 129 53313 0.20% 130 54488 0.21% 131 55874 0.21% 132 57937 0.22% 133 59980 0.23% 134 61419 0.23% 135 64027 0.24% 136 66079 0.25% 137 66763 0.25% 138 67733 0.26% 139 68756 0.26% 140 68940 0.26% 141 71156 0.27% 142 72067 0.28% 143 73077 0.28% 144 77284 0.30% 145 78576 0.30% 146 80930 0.31% 147 80827 0.31% 148 82107 0.31% 149 81941 0.31% 150 83604 0.32% 151 23588431 90.06% 26192370 reads passed initial QC criterion=sequence-density sequence-density=0.22 sequence-density-rank=1 fanout-score=3.96 fanout-score-rank=26 prefix-density=0.26 prefix-fanout=3.3 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.03 sequence-density-rank=29 fanout-score=173.31 fanout-score-rank=1 prefix-density=0.37 prefix-fanout=14.2 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.38 sequence-density-rank=1 fanout-score=2.26 fanout-score-rank=34 prefix-density=0.39 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.04 sequence-density-rank=35 fanout-score=443.32 fanout-score-rank=1 prefix-density=0.82 prefix-fanout=21.7 sequence=CGCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR12666464 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 13:41:52 Started mapping on | Dec 07 13:41:52 Finished on | Dec 07 13:45:17 Mapping speed, Million of reads per hour | 459.96 Number of input reads | 26192370 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 24513330 Uniquely mapped reads % | 93.59% Average mapped length | 296.39 Number of splices: Total | 26392177 Number of splices: Annotated (sjdb) | 24782978 Number of splices: GT/AG | 26021403 Number of splices: GC/AG | 295842 Number of splices: AT/AC | 17143 Number of splices: Non-canonical | 57789 Mismatch rate per base, % | 0.36% Deletion rate per base | 0.03% Deletion average length | 2.94 Insertion rate per base | 0.02% Insertion average length | 2.52 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 382769 % of reads mapped to multiple loci | 1.46% Number of reads mapped to too many loci | 31836 % of reads mapped to too many loci | 0.12% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 4.11% % of reads unmapped: other | 0.72% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1296271 1296271 1296271 N_multimapping 382769 382769 382769 N_noFeature 873534 23894961 1085675 N_ambiguous 480740 3098 75192 UnstrandedReadsAssigned:23159056 PositiveStrandReadsAssigned:615271 NegativeStrandReadsAssigned:23352463 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12666464 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: 52,972 [index] number of k-mers: 66,720,672 [index] number of equivalence classes: 111,837 [quant] running in paired-end mode [quant] will process pair 1: SRR12666464-trimmed-pair1.fastq SRR12666464-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 26,192,370 reads, 23,640,260 reads pseudoaligned [quant] estimated average fragment length: 267.213 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,215 rounds 52973 SRR12666464.ke.tsv 35125 SRR12666464.se.tsv 88098 total ==> SRR12666464.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 670.598 0 0 PNS24247 1044 777.787 122.04 10.3109 PNS24249 1928 1661.79 155.589 6.15262 PNS24246 1044 777.787 122.04 10.3109 PNS24248 1044 777.787 122.04 10.3109 PNS24244 1471 1204.79 179.291 9.77923 PNS24243 293 94.1399 0 0 KQK14069 1603 1336.79 7221.54 354.996 KQK14071 474 234.814 134.336 37.5947 ==> SRR12666464.se.tsv <== BRADI_1g14170v3 8134 BRADI_1g53295v3 1024 BRADI_1g59795v3 154 BRADI_1g07683v3 0 BRADI_1g00485v3 93 BRADI_1g20270v3 1844 BRADI_1g74790v3 76 BRADI_1g09890v3 0 BRADI_1g77505v3 195 BRADI_1g48960v3 0 SRR12666464 completed mapping pipeline successfully