Starting /dee2/code/volunteer_pipeline.sh SRR12666458 current disk space = 1543100395520 free memory = 1598640140 SRR12666458 SRAfilesize 50030e608af8c7abe53ce5701b514b18 SRR12666458.sra SRR12666458.sra file validated SRR12666458 is paired end SRR12666458 is conventional basespace SRR12666458 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666458_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 49 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.38 37.0 37.0 37.0 37.0 37.0 2 36.344 37.0 37.0 37.0 37.0 37.0 3 36.4945 37.0 37.0 37.0 37.0 37.0 4 36.515 37.0 37.0 37.0 37.0 37.0 5 36.5775 37.0 37.0 37.0 37.0 37.0 6 36.5515 37.0 37.0 37.0 37.0 37.0 7 36.509 37.0 37.0 37.0 37.0 37.0 8 36.588 37.0 37.0 37.0 37.0 37.0 9 36.5765 37.0 37.0 37.0 37.0 37.0 10-14 36.5593 37.0 37.0 37.0 37.0 37.0 15-19 36.595 37.0 37.0 37.0 37.0 37.0 20-24 36.5036 37.0 37.0 37.0 37.0 37.0 25-29 36.4577 37.0 37.0 37.0 37.0 37.0 30-34 36.413199999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.419799999999995 37.0 37.0 37.0 37.0 37.0 40-44 36.3732 37.0 37.0 37.0 37.0 37.0 45-49 36.323699999999995 37.0 37.0 37.0 37.0 37.0 50-54 36.3685 37.0 37.0 37.0 37.0 37.0 55-59 36.3207 37.0 37.0 37.0 37.0 37.0 60-64 36.3068 37.0 37.0 37.0 37.0 37.0 65-69 36.2394 37.0 37.0 37.0 37.0 37.0 70-74 36.2992 37.0 37.0 37.0 37.0 37.0 75-79 36.24550000000001 37.0 37.0 37.0 37.0 37.0 80-84 36.20119999999999 37.0 37.0 37.0 37.0 37.0 85-89 36.1968 37.0 37.0 37.0 37.0 37.0 90-94 36.2138 37.0 37.0 37.0 37.0 37.0 95-99 36.105999999999995 37.0 37.0 37.0 37.0 37.0 100-104 36.1566 37.0 37.0 37.0 37.0 37.0 105-109 36.1484 37.0 37.0 37.0 37.0 37.0 110-114 36.02120000000001 37.0 37.0 37.0 37.0 37.0 115-119 35.993399999999994 37.0 37.0 37.0 37.0 37.0 120-124 35.978699999999996 37.0 37.0 37.0 37.0 37.0 125-129 35.96169999999999 37.0 37.0 37.0 37.0 37.0 130-134 35.93730000000001 37.0 37.0 37.0 37.0 37.0 135-139 35.9332 37.0 37.0 37.0 37.0 37.0 140-144 35.714800000000004 37.0 37.0 37.0 37.0 37.0 145-149 35.6655 37.0 37.0 37.0 37.0 37.0 150-151 35.45225 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 1.0 21 0.0 22 0.0 23 3.0 24 4.0 25 3.0 26 5.0 27 9.0 28 10.0 29 23.0 30 25.0 31 40.0 32 64.0 33 83.0 34 131.0 35 317.0 36 2818.0 37 464.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 42.8 11.525 8.774999999999999 36.9 2 22.64764764764765 17.167167167167165 34.45945945945946 25.725725725725724 3 22.05 20.974999999999998 25.874999999999996 31.1 4 25.474999999999998 29.549999999999997 19.8 25.174999999999997 5 25.775 32.85 22.225 19.15 6 21.6 34.425 23.3 20.674999999999997 7 16.5 21.525 41.949999999999996 20.025000000000002 8 20.45 22.2 28.15 29.2 9 21.825 21.25 30.0 26.924999999999997 10-14 22.215 26.845000000000002 25.595000000000002 25.345000000000002 15-19 22.314999999999998 25.81 25.795 26.08 20-24 23.05 26.47 25.174999999999997 25.305 25-29 23.225 25.929999999999996 25.180000000000003 25.665 30-34 22.645 26.33 25.53 25.495 35-39 22.68 25.71 25.840000000000003 25.77 40-44 22.650000000000002 26.085 25.955000000000002 25.31 45-49 23.080000000000002 26.115 25.335 25.47 50-54 22.655 26.095000000000002 25.624999999999996 25.624999999999996 55-59 23.080000000000002 26.040000000000003 25.224999999999998 25.655 60-64 23.724999999999998 25.955000000000002 25.455 24.865000000000002 65-69 22.755 25.52 25.5 26.224999999999998 70-74 23.25 25.064999999999998 25.97 25.715 75-79 23.595 25.990000000000002 24.654999999999998 25.759999999999998 80-84 23.27 25.52 25.385 25.825 85-89 23.01 26.340000000000003 24.82 25.83 90-94 23.055 25.8 25.305 25.840000000000003 95-99 23.49 25.430000000000003 25.31 25.77 100-104 24.0 25.71 24.83 25.46 105-109 24.060000000000002 25.455 25.014999999999997 25.47 110-114 23.62 25.874999999999996 25.430000000000003 25.074999999999996 115-119 23.810000000000002 25.52 25.369999999999997 25.3 120-124 24.025 25.490000000000002 24.84 25.645 125-129 22.985 26.295 24.740000000000002 25.979999999999997 130-134 24.02 25.509999999999998 24.935 25.535000000000004 135-139 24.060000000000002 25.374999999999996 24.4 26.165 140-144 23.345 25.695 25.335 25.624999999999996 145-149 23.919999999999998 25.95 24.23 25.900000000000002 150-151 23.8625 23.875 26.3625 25.900000000000002 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 0.5 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.5 12 0.5 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 0.0 23 0.5 24 0.5 25 0.5 26 1.5 27 1.5 28 3.5 29 6.0 30 9.0 31 11.0 32 18.0 33 33.5 34 34.5 35 34.5 36 55.0 37 67.0 38 77.0 39 88.5 40 107.0 41 141.5 42 157.0 43 177.5 44 200.5 45 207.5 46 232.0 47 234.5 48 197.0 49 183.0 50 177.0 51 164.0 52 158.5 53 133.5 54 100.5 55 95.0 56 95.0 57 74.5 58 67.0 59 72.0 60 72.0 61 62.5 62 57.0 63 57.5 64 49.5 65 48.5 66 48.0 67 38.0 68 30.5 69 28.0 70 24.5 71 21.0 72 14.5 73 7.0 74 5.5 75 5.5 76 5.0 77 3.5 78 1.5 79 1.0 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 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 0.1 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 92.07499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 92.09883247352701 84.8 2 7.276676622318762 13.4 3 0.5430355688297583 1.5 4 0.08145533532446375 0.3 5 0.0 0.0 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 pass >>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 0.0125 0.0 0.0 0.0 0.0 70-71 0.025 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 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.16249999999999998 0.0 0.0 0.0 0.0 88-89 0.2625 0.0 0.0 0.0 0.0 90-91 0.275 0.0 0.0 0.0 0.0 92-93 0.3125 0.0 0.0 0.0 0.0 94-95 0.325 0.0 0.0 0.0 0.0 96-97 0.38749999999999996 0.0 0.0 0.0 0.0 98-99 0.44999999999999996 0.0 0.0 0.0 0.0 100-101 0.5 0.0 0.0 0.0 0.0 102-103 0.6625000000000001 0.0 0.0 0.0 0.0 104-105 0.875 0.0 0.0 0.0 0.0 106-107 0.975 0.0 0.0 0.0 0.0 108-109 1.0499999999999998 0.0 0.0 0.0 0.0 110-111 1.1749999999999998 0.0 0.0 0.0 0.0 112-113 1.3624999999999998 0.0 0.0 0.0 0.0 114-115 1.6625 0.0 0.0 0.0 0.0 116-117 1.825 0.0 0.0 0.0 0.0 118-119 2.05 0.0 0.0 0.0 0.0 120-121 2.3 0.0 0.0 0.0 0.0 122-123 2.575 0.0 0.0 0.0 0.0 124-125 2.9625000000000004 0.0 0.0 0.0 0.0 126-127 3.3 0.0 0.0 0.0 0.0 128-129 3.6500000000000004 0.0 0.0 0.0 0.0 130-131 4.012499999999999 0.0 0.0 0.0 0.0 132-133 4.425 0.0 0.0 0.0 0.0 134-135 4.7625 0.0 0.0 0.0 0.0 136-137 5.2 0.0 0.0 0.0 0.0 138-139 5.5375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AATTCCT 10 0.006830828 145.0 8 GATGAAC 10 0.006830828 145.0 5 >>END_MODULE SRR12666458 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666458_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 50 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.1045 37.0 37.0 37.0 37.0 37.0 2 35.908 37.0 37.0 37.0 37.0 37.0 3 36.206 37.0 37.0 37.0 37.0 37.0 4 36.2745 37.0 37.0 37.0 37.0 37.0 5 36.326 37.0 37.0 37.0 37.0 37.0 6 36.1415 37.0 37.0 37.0 37.0 37.0 7 36.2515 37.0 37.0 37.0 37.0 37.0 8 36.3195 37.0 37.0 37.0 37.0 37.0 9 36.2595 37.0 37.0 37.0 37.0 37.0 10-14 36.343 37.0 37.0 37.0 37.0 37.0 15-19 36.2655 37.0 37.0 37.0 37.0 37.0 20-24 36.18769999999999 37.0 37.0 37.0 37.0 37.0 25-29 36.217 37.0 37.0 37.0 37.0 37.0 30-34 36.1639 37.0 37.0 37.0 37.0 37.0 35-39 36.1639 37.0 37.0 37.0 37.0 37.0 40-44 36.1006 37.0 37.0 37.0 37.0 37.0 45-49 36.076100000000004 37.0 37.0 37.0 37.0 37.0 50-54 36.046400000000006 37.0 37.0 37.0 37.0 37.0 55-59 36.088800000000006 37.0 37.0 37.0 37.0 37.0 60-64 35.9797 37.0 37.0 37.0 37.0 37.0 65-69 36.0317 37.0 37.0 37.0 37.0 37.0 70-74 36.005700000000004 37.0 37.0 37.0 37.0 37.0 75-79 36.0055 37.0 37.0 37.0 37.0 37.0 80-84 35.9377 37.0 37.0 37.0 37.0 37.0 85-89 35.9203 37.0 37.0 37.0 37.0 37.0 90-94 35.912400000000005 37.0 37.0 37.0 37.0 37.0 95-99 35.9757 37.0 37.0 37.0 37.0 37.0 100-104 35.921 37.0 37.0 37.0 37.0 37.0 105-109 35.87060000000001 37.0 37.0 37.0 37.0 37.0 110-114 35.851400000000005 37.0 37.0 37.0 37.0 37.0 115-119 35.796299999999995 37.0 37.0 37.0 37.0 37.0 120-124 35.783500000000004 37.0 37.0 37.0 37.0 37.0 125-129 35.8233 37.0 37.0 37.0 37.0 37.0 130-134 35.7762 37.0 37.0 37.0 37.0 37.0 135-139 35.6899 37.0 37.0 37.0 37.0 37.0 140-144 35.563199999999995 37.0 37.0 37.0 37.0 37.0 145-149 35.541199999999996 37.0 37.0 37.0 37.0 37.0 150-151 35.1785 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 11 1.0 12 0.0 13 2.0 14 2.0 15 3.0 16 1.0 17 1.0 18 1.0 19 2.0 20 4.0 21 2.0 22 10.0 23 4.0 24 5.0 25 6.0 26 6.0 27 12.0 28 21.0 29 22.0 30 19.0 31 36.0 32 57.0 33 98.0 34 157.0 35 446.0 36 2632.0 37 450.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.35 16.925 10.674999999999999 30.049999999999997 2 27.224999999999998 21.825 29.599999999999998 21.349999999999998 3 24.85 24.349999999999998 27.500000000000004 23.3 4 27.325 30.95 19.225 22.5 5 26.375 35.05 17.65 20.925 6 20.875 36.0 20.8 22.325 7 22.15 17.150000000000002 36.425000000000004 24.275 8 23.775 20.75 23.05 32.425 9 23.599999999999998 20.925 27.375 28.1 10-14 26.11 25.705 22.59 25.595000000000002 15-19 25.885 25.224999999999998 24.43 24.46 20-24 25.35 25.055 24.62 24.975 25-29 25.39 24.935 24.605 25.069999999999997 30-34 25.81 24.83 25.264999999999997 24.095 35-39 25.705 25.180000000000003 23.985 25.130000000000003 40-44 25.77 25.485000000000003 24.145 24.6 45-49 25.415 25.324999999999996 24.455 24.805 50-54 26.125 25.480000000000004 24.86 23.535 55-59 26.185000000000002 25.285000000000004 24.485 24.044999999999998 60-64 26.009999999999998 25.53 24.4 24.060000000000002 65-69 26.150000000000002 25.11 25.025 23.715 70-74 26.68 25.255 24.295 23.77 75-79 25.490000000000002 25.115 25.785000000000004 23.61 80-84 25.580000000000002 25.235000000000003 24.625 24.560000000000002 85-89 26.035000000000004 24.93 24.654999999999998 24.38 90-94 25.635 25.480000000000004 24.895 23.990000000000002 95-99 26.135 25.515 24.27 24.08 100-104 25.855 25.424999999999997 24.64 24.08 105-109 25.645 25.06 24.865000000000002 24.43 110-114 26.32 26.215 24.455 23.01 115-119 26.745 25.415 24.099999999999998 23.74 120-124 26.51 25.66 24.310000000000002 23.52 125-129 26.529999999999998 25.645 24.52 23.305 130-134 26.889999999999997 25.055 24.795 23.26 135-139 27.0 25.635 24.79 22.575 140-144 27.139999999999997 25.55 25.080000000000002 22.23 145-149 27.205000000000002 25.740000000000002 24.285 22.770000000000003 150-151 27.125 25.8625 24.7875 22.225 >>END_MODULE >>Per sequence GC content fail #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 0.0 11 1.0 12 1.0 13 0.0 14 0.0 15 0.0 16 0.5 17 0.5 18 0.5 19 0.5 20 0.0 21 0.5 22 1.0 23 1.5 24 1.0 25 0.0 26 0.0 27 0.5 28 1.0 29 3.0 30 5.5 31 6.0 32 7.5 33 11.5 34 20.5 35 30.5 36 33.5 37 48.5 38 78.5 39 100.0 40 111.5 41 125.5 42 155.5 43 178.5 44 186.0 45 186.5 46 189.0 47 187.5 48 189.5 49 174.0 50 154.0 51 156.5 52 149.5 53 139.0 54 125.0 55 106.0 56 94.0 57 98.5 58 89.5 59 78.0 60 69.5 61 62.5 62 71.5 63 76.5 64 70.0 65 58.0 66 56.5 67 58.0 68 56.0 69 46.5 70 34.0 71 25.5 72 18.0 73 18.5 74 17.0 75 9.5 76 5.0 77 3.5 78 1.5 79 1.0 80 0.5 81 0.5 82 1.0 83 1.0 84 0.5 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.5 93 0.5 94 0.0 95 1.0 96 1.0 97 0.0 98 0.0 99 0.0 100 2.5 >>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 92.175 #Duplication Level Percentage of deduplicated Percentage of total 1 92.37862761052345 85.15 2 6.91619202603743 12.75 3 0.5966910767561703 1.6500000000000001 4 0.08136696501220504 0.3 5 0.0 0.0 6 0.027122321670735017 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 GGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGGG 6 0.15 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 0.0125 0.0 0.0 0.0 0.0 70-71 0.025 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 0.075 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.125 0.0 0.0 0.0 0.0 86-87 0.16249999999999998 0.0 0.0 0.0 0.0 88-89 0.2625 0.0 0.0 0.0 0.0 90-91 0.275 0.0 0.0 0.0 0.0 92-93 0.3125 0.0 0.0 0.0 0.0 94-95 0.325 0.0 0.0 0.0 0.0 96-97 0.375 0.0 0.0 0.0 0.0 98-99 0.42500000000000004 0.0 0.0 0.0 0.0 100-101 0.475 0.0 0.0 0.0 0.0 102-103 0.6375 0.0 0.0 0.0 0.0 104-105 0.85 0.0 0.0 0.0 0.0 106-107 0.95 0.0 0.0 0.0 0.0 108-109 1.025 0.0 0.0 0.0 0.0 110-111 1.15 0.0 0.0 0.0 0.0 112-113 1.3375 0.0 0.0 0.0 0.0 114-115 1.6375 0.0 0.0 0.0 0.0 116-117 1.8 0.0 0.0 0.0 0.0 118-119 2.0375 0.0 0.0 0.0 0.0 120-121 2.3125 0.0 0.0 0.0 0.0 122-123 2.5999999999999996 0.0 0.0 0.0 0.0 124-125 2.9875 0.0 0.0 0.0 0.0 126-127 3.3499999999999996 0.0 0.0 0.0 0.0 128-129 3.7 0.0 0.0 0.0 0.0 130-131 4.0625 0.0 0.0 0.0 0.0 132-133 4.475 0.0 0.0 0.0 0.0 134-135 4.7875 0.0 0.0 0.0 0.0 136-137 5.225 0.0 0.0 0.0 0.0 138-139 5.5625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra Read 1714322 spots for SRR12666458.sra Written 1714322 spots for SRR12666458.sra Read 1714316 spots for SRR12666458.sra Written 1714316 spots for SRR12666458.sra SRR ids: ['SRR12666458.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_n05xhpgh SRR12666458.sra spots: 34286326 blocks: [[1, 1714316], [1714317, 3428632], [3428633, 5142948], [5142949, 6857264], [6857265, 8571580], [8571581, 10285896], [10285897, 12000212], [12000213, 13714528], [13714529, 15428844], [15428845, 17143160], [17143161, 18857476], [18857477, 20571792], [20571793, 22286108], [22286109, 24000424], [24000425, 25714740], [25714741, 27429056], [27429057, 29143372], [29143373, 30857688], [30857689, 32572004], [32572005, 34286326]] SRR12666458 file size 11630293 SRR12666458 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 SRR12666458 SRR12666458_1.fastq SRR12666458_2.fastq Input file: SRR12666458_1.fastq Paired file: SRR12666458_2.fastq trimmed: SRR12666458-trimmed-pair1.fastq, SRR12666458-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 13:31:34 2024 >> started Sat Dec 7 13:32:11 2024 >> done (37.697s) 34286326 read pairs processed; of these: 68 ( 0.00%) short read pairs filtered out after trimming by size control 15919 ( 0.05%) empty read pairs filtered out after trimming by size control 34270339 (99.95%) read pairs available; of these: 2947657 ( 8.60%) trimmed read pairs available after processing 31322682 (91.40%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 19 0.00% 19 11 0.00% 20 15 0.00% 21 19 0.00% 22 26 0.00% 23 28 0.00% 24 21 0.00% 25 42 0.00% 26 35 0.00% 27 42 0.00% 28 50 0.00% 29 45 0.00% 30 36 0.00% 31 52 0.00% 32 68 0.00% 33 59 0.00% 34 63 0.00% 35 60 0.00% 36 71 0.00% 37 68 0.00% 38 96 0.00% 39 82 0.00% 40 91 0.00% 41 80 0.00% 42 119 0.00% 43 99 0.00% 44 83 0.00% 45 115 0.00% 46 120 0.00% 47 120 0.00% 48 119 0.00% 49 152 0.00% 50 146 0.00% 51 146 0.00% 52 186 0.00% 53 213 0.00% 54 212 0.00% 55 232 0.00% 56 208 0.00% 57 244 0.00% 58 280 0.00% 59 272 0.00% 60 317 0.00% 61 427 0.00% 62 411 0.00% 63 494 0.00% 64 432 0.00% 65 460 0.00% 66 567 0.00% 67 596 0.00% 68 693 0.00% 69 791 0.00% 70 963 0.00% 71 1031 0.00% 72 1254 0.00% 73 1368 0.00% 74 1585 0.00% 75 1682 0.00% 76 1721 0.01% 77 1983 0.01% 78 2173 0.01% 79 2500 0.01% 80 2792 0.01% 81 3235 0.01% 82 3722 0.01% 83 4186 0.01% 84 4743 0.01% 85 5035 0.01% 86 5602 0.02% 87 5990 0.02% 88 6705 0.02% 89 7139 0.02% 90 7908 0.02% 91 8972 0.03% 92 9821 0.03% 93 11186 0.03% 94 12215 0.04% 95 13288 0.04% 96 14054 0.04% 97 14561 0.04% 98 15187 0.04% 99 16059 0.05% 100 17219 0.05% 101 18566 0.05% 102 20544 0.06% 103 22203 0.06% 104 23381 0.07% 105 25087 0.07% 106 26188 0.08% 107 26716 0.08% 108 27941 0.08% 109 28687 0.08% 110 29629 0.09% 111 31822 0.09% 112 34083 0.10% 113 35530 0.10% 114 38226 0.11% 115 39384 0.11% 116 40330 0.12% 117 41755 0.12% 118 42417 0.12% 119 42658 0.12% 120 44144 0.13% 121 46561 0.14% 122 48056 0.14% 123 50610 0.15% 124 52849 0.15% 125 55471 0.16% 126 56621 0.17% 127 57637 0.17% 128 57872 0.17% 129 59291 0.17% 130 59632 0.17% 131 60433 0.18% 132 62981 0.18% 133 65161 0.19% 134 67732 0.20% 135 70928 0.21% 136 72773 0.21% 137 73363 0.21% 138 74416 0.22% 139 75479 0.22% 140 74983 0.22% 141 76048 0.22% 142 77816 0.23% 143 79155 0.23% 144 83273 0.24% 145 85875 0.25% 146 88248 0.26% 147 89627 0.26% 148 89835 0.26% 149 90219 0.26% 150 90109 0.26% 151 31322682 91.40% 34270339 reads passed initial QC criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=4.76 fanout-score-rank=25 prefix-density=0.26 prefix-fanout=3.3 sequence=GATCTCGCCGAAG criterion=fanout-score sequence-density=0.03 sequence-density-rank=31 fanout-score=199.82 fanout-score-rank=1 prefix-density=0.40 prefix-fanout=16.3 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.40 sequence-density-rank=1 fanout-score=2.25 fanout-score-rank=36 prefix-density=0.41 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.02 sequence-density-rank=37 fanout-score=753.75 fanout-score-rank=1 prefix-density=0.80 prefix-fanout=18.8 sequence=GCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGACCACCAAGTACTACTGCACCGTCATTGATGCCCCTGGACACCGTGACTTCATCAAGAACATGATTACCGGTACCTCCCAGGCTGACTGTGCCGTGCTTATCATTGACTCCACGACTGGAGGTTTTGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCATGCCCTCCTTGCTTTCACTCTTGGAGTGAAGCAGATGATCTGCTGCTGCAACAAGATGGA SRR12666458 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 13:33:27 Started mapping on | Dec 07 13:33:27 Finished on | Dec 07 13:36:55 Mapping speed, Million of reads per hour | 593.14 Number of input reads | 34270339 Average input read length | 298 UNIQUE READS: Uniquely mapped reads number | 32553891 Uniquely mapped reads % | 94.99% Average mapped length | 296.97 Number of splices: Total | 35255499 Number of splices: Annotated (sjdb) | 33061550 Number of splices: GT/AG | 34746940 Number of splices: GC/AG | 399336 Number of splices: AT/AC | 25799 Number of splices: Non-canonical | 83424 Mismatch rate per base, % | 0.31% Deletion rate per base | 0.02% Deletion average length | 2.51 Insertion rate per base | 0.02% Insertion average length | 2.24 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 479232 % of reads mapped to multiple loci | 1.40% Number of reads mapped to too many loci | 45502 % of reads mapped to too many loci | 0.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 2.66% % of reads unmapped: other | 0.82% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1237216 1237216 1237216 N_multimapping 479232 479232 479232 N_noFeature 1181460 31735612 1454576 N_ambiguous 650402 4774 107389 UnstrandedReadsAssigned:30722029 PositiveStrandReadsAssigned:813505 NegativeStrandReadsAssigned:30991926 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12666458 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: SRR12666458-trimmed-pair1.fastq SRR12666458-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 34,270,339 reads, 31,355,386 reads pseudoaligned [quant] estimated average fragment length: 288.097 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,210 rounds 52973 SRR12666458.ke.tsv 35125 SRR12666458.se.tsv 88098 total ==> SRR12666458.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 649.899 0 0 PNS24247 1044 756.903 190.53 12.351 PNS24249 1928 1640.9 232.992 6.96688 PNS24246 1044 756.903 190.53 12.351 PNS24248 1044 756.903 190.53 12.351 PNS24244 1471 1183.9 237.417 9.83956 PNS24243 293 90.7392 2 1.08147 KQK14069 1603 1315.9 7113.11 265.225 KQK14071 474 222.931 128.971 28.3858 ==> SRR12666458.se.tsv <== BRADI_1g14170v3 7959 BRADI_1g53295v3 575 BRADI_1g59795v3 1037 BRADI_1g07683v3 0 BRADI_1g00485v3 128 BRADI_1g20270v3 2485 BRADI_1g74790v3 63 BRADI_1g09890v3 0 BRADI_1g77505v3 201 BRADI_1g48960v3 0 SRR12666458 completed mapping pipeline successfully