Starting /dee2/code/volunteer_pipeline.sh SRR12666601 current disk space = 1541220093952 free memory = 1602119004 SRR12666601 SRAfilesize 7824db9d49649cd847a17b0dee45d544 SRR12666601.sra SRR12666601.sra file validated SRR12666601 is paired end SRR12666601 is conventional basespace SRR12666601 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666601_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 36.485 37.0 37.0 37.0 37.0 37.0 2 36.2765 37.0 37.0 37.0 37.0 37.0 3 36.3875 37.0 37.0 37.0 37.0 37.0 4 36.524 37.0 37.0 37.0 37.0 37.0 5 36.54 37.0 37.0 37.0 37.0 37.0 6 36.504 37.0 37.0 37.0 37.0 37.0 7 36.413 37.0 37.0 37.0 37.0 37.0 8 36.5425 37.0 37.0 37.0 37.0 37.0 9 36.547 37.0 37.0 37.0 37.0 37.0 10-14 36.572199999999995 37.0 37.0 37.0 37.0 37.0 15-19 36.5587 37.0 37.0 37.0 37.0 37.0 20-24 36.5358 37.0 37.0 37.0 37.0 37.0 25-29 36.5107 37.0 37.0 37.0 37.0 37.0 30-34 36.4448 37.0 37.0 37.0 37.0 37.0 35-39 36.4329 37.0 37.0 37.0 37.0 37.0 40-44 36.421499999999995 37.0 37.0 37.0 37.0 37.0 45-49 36.34760000000001 37.0 37.0 37.0 37.0 37.0 50-54 36.325300000000006 37.0 37.0 37.0 37.0 37.0 55-59 36.2996 37.0 37.0 37.0 37.0 37.0 60-64 36.3221 37.0 37.0 37.0 37.0 37.0 65-69 36.3228 37.0 37.0 37.0 37.0 37.0 70-74 36.2438 37.0 37.0 37.0 37.0 37.0 75-79 36.28189999999999 37.0 37.0 37.0 37.0 37.0 80-84 36.2 37.0 37.0 37.0 37.0 37.0 85-89 36.2295 37.0 37.0 37.0 37.0 37.0 90-94 36.1356 37.0 37.0 37.0 37.0 37.0 95-99 36.071000000000005 37.0 37.0 37.0 37.0 37.0 100-104 36.1299 37.0 37.0 37.0 37.0 37.0 105-109 36.113 37.0 37.0 37.0 37.0 37.0 110-114 35.998200000000004 37.0 37.0 37.0 37.0 37.0 115-119 35.9755 37.0 37.0 37.0 37.0 37.0 120-124 35.9679 37.0 37.0 37.0 37.0 37.0 125-129 35.9465 37.0 37.0 37.0 37.0 37.0 130-134 35.9898 37.0 37.0 37.0 37.0 37.0 135-139 35.9008 37.0 37.0 37.0 37.0 37.0 140-144 35.746500000000005 37.0 37.0 37.0 37.0 37.0 145-149 35.576800000000006 37.0 37.0 37.0 37.0 37.0 150-151 35.34375 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 17 1.0 18 0.0 19 0.0 20 1.0 21 1.0 22 1.0 23 1.0 24 0.0 25 4.0 26 5.0 27 4.0 28 14.0 29 23.0 30 22.0 31 49.0 32 52.0 33 88.0 34 142.0 35 321.0 36 2826.0 37 445.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 46.925 11.774999999999999 7.124999999999999 34.175 2 23.65 16.55 34.449999999999996 25.35 3 19.6 23.7 25.724999999999998 30.975 4 25.35 28.775000000000002 21.475 24.4 5 24.45 33.074999999999996 22.075 20.4 6 20.974999999999998 34.699999999999996 23.674999999999997 20.65 7 16.325 22.55 40.325 20.8 8 19.85 22.400000000000002 28.075 29.675 9 19.650000000000002 21.15 31.3 27.900000000000002 10-14 22.845 26.125 25.14 25.89 15-19 23.145 25.275 26.015 25.564999999999998 20-24 22.314999999999998 26.27 26.265 25.15 25-29 22.57 25.124999999999996 26.169999999999998 26.135 30-34 22.509999999999998 26.075 25.865 25.55 35-39 22.985 25.885 25.21 25.919999999999998 40-44 22.525000000000002 26.165 25.515 25.795 45-49 22.895 25.635 25.335 26.135 50-54 22.355 26.279999999999998 24.955 26.41 55-59 23.26 25.77 25.174999999999997 25.795 60-64 23.080000000000002 25.765 24.955 26.200000000000003 65-69 23.145 25.865 24.875 26.115 70-74 24.245 25.895000000000003 24.490000000000002 25.369999999999997 75-79 23.745 25.6 25.52 25.135 80-84 23.419999999999998 26.295 24.515 25.77 85-89 23.674999999999997 25.945 24.575 25.805 90-94 22.98 25.729999999999997 24.959999999999997 26.33 95-99 24.435000000000002 25.419999999999998 25.0 25.145 100-104 23.755000000000003 25.575 25.115 25.555 105-109 23.95 24.985 25.69 25.374999999999996 110-114 23.275000000000002 25.75 25.41 25.564999999999998 115-119 23.565 25.405 25.46 25.569999999999997 120-124 23.724999999999998 25.6 24.805 25.869999999999997 125-129 23.585 26.07 24.68 25.665 130-134 24.26 25.555 24.38 25.805 135-139 23.419999999999998 25.259999999999998 25.4 25.919999999999998 140-144 24.495 25.86 24.305 25.34 145-149 23.69 25.119999999999997 24.645 26.545 150-151 24.1875 24.125 25.662499999999998 26.025 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 0.0 26 0.0 27 0.5 28 1.0 29 4.5 30 7.0 31 6.0 32 13.0 33 22.5 34 28.5 35 34.5 36 46.5 37 65.5 38 80.5 39 97.5 40 119.5 41 142.0 42 170.0 43 179.0 44 183.0 45 190.0 46 198.5 47 203.0 48 204.0 49 204.0 50 191.5 51 171.0 52 156.0 53 144.0 54 124.5 55 121.5 56 109.5 57 85.0 58 83.5 59 77.5 60 66.5 61 56.0 62 40.5 63 48.0 64 50.5 65 46.0 66 48.5 67 37.5 68 31.0 69 32.0 70 25.5 71 20.0 72 12.5 73 6.5 74 6.5 75 5.5 76 1.5 77 0.5 78 0.5 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 0.0 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 91.25 #Duplication Level Percentage of deduplicated Percentage of total 1 91.26027397260273 83.275 2 7.972602739726027 14.549999999999999 3 0.684931506849315 1.875 4 0.08219178082191782 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 0.0 0.0 0.0 0.0 0.0 70-71 0.025 0.0 0.0 0.0 0.0 72-73 0.025 0.0 0.0 0.0 0.0 74-75 0.025 0.0 0.0 0.0 0.0 76-77 0.025 0.0 0.0 0.0 0.0 78-79 0.05 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.05 0.0 0.0 0.0 0.0 84-85 0.075 0.0 0.0 0.0 0.0 86-87 0.1125 0.0 0.0 0.0 0.0 88-89 0.1625 0.0 0.0 0.0 0.0 90-91 0.2 0.0 0.0 0.0 0.0 92-93 0.21250000000000002 0.0 0.0 0.0 0.0 94-95 0.3625 0.0 0.0 0.0 0.0 96-97 0.44999999999999996 0.0 0.0 0.0 0.0 98-99 0.5 0.0 0.0 0.0 0.0 100-101 0.6875 0.0 0.0 0.0 0.0 102-103 0.8500000000000001 0.0 0.0 0.0 0.0 104-105 0.975 0.0 0.0 0.0 0.0 106-107 1.0625 0.0 0.0 0.0 0.0 108-109 1.2000000000000002 0.0 0.0 0.0 0.0 110-111 1.475 0.0 0.0 0.0 0.0 112-113 1.725 0.0 0.0 0.0 0.0 114-115 2.1624999999999996 0.0 0.0 0.0 0.0 116-117 2.5125 0.0 0.0 0.0 0.0 118-119 2.875 0.0 0.0 0.0 0.0 120-121 3.3 0.0 0.0 0.0 0.0 122-123 3.8625 0.0 0.0 0.0 0.0 124-125 4.35 0.0 0.0 0.0 0.0 126-127 4.775 0.0 0.0 0.0 0.0 128-129 5.2875 0.0 0.0 0.0 0.0 130-131 5.8125 0.0 0.0 0.0 0.0 132-133 6.275 0.0 0.0 0.0 0.0 134-135 6.775 0.0 0.0 0.0 0.0 136-137 7.175 0.0 0.0 0.0 0.0 138-139 7.5875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TTCTGGT 10 0.006830828 145.0 2 TCACCAT 10 0.006830828 145.0 2 >>END_MODULE SRR12666601 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666601_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 36.0135 37.0 37.0 37.0 37.0 37.0 3 36.0505 37.0 37.0 37.0 37.0 37.0 4 36.23 37.0 37.0 37.0 37.0 37.0 5 36.203 37.0 37.0 37.0 37.0 37.0 6 36.146 37.0 37.0 37.0 37.0 37.0 7 36.207 37.0 37.0 37.0 37.0 37.0 8 36.2645 37.0 37.0 37.0 37.0 37.0 9 36.378 37.0 37.0 37.0 37.0 37.0 10-14 36.2488 37.0 37.0 37.0 37.0 37.0 15-19 36.202200000000005 37.0 37.0 37.0 37.0 37.0 20-24 36.208600000000004 37.0 37.0 37.0 37.0 37.0 25-29 36.1486 37.0 37.0 37.0 37.0 37.0 30-34 36.172399999999996 37.0 37.0 37.0 37.0 37.0 35-39 36.1078 37.0 37.0 37.0 37.0 37.0 40-44 36.0594 37.0 37.0 37.0 37.0 37.0 45-49 36.0729 37.0 37.0 37.0 37.0 37.0 50-54 36.02910000000001 37.0 37.0 37.0 37.0 37.0 55-59 36.06779999999999 37.0 37.0 37.0 37.0 37.0 60-64 35.936 37.0 37.0 37.0 37.0 37.0 65-69 35.931799999999996 37.0 37.0 37.0 37.0 37.0 70-74 35.9296 37.0 37.0 37.0 37.0 37.0 75-79 35.9273 37.0 37.0 37.0 37.0 37.0 80-84 35.95399999999999 37.0 37.0 37.0 37.0 37.0 85-89 35.898399999999995 37.0 37.0 37.0 37.0 37.0 90-94 35.908300000000004 37.0 37.0 37.0 37.0 37.0 95-99 35.845200000000006 37.0 37.0 37.0 37.0 37.0 100-104 35.825199999999995 37.0 37.0 37.0 37.0 37.0 105-109 35.821000000000005 37.0 37.0 37.0 37.0 37.0 110-114 35.7783 37.0 37.0 37.0 37.0 37.0 115-119 35.7131 37.0 37.0 37.0 37.0 37.0 120-124 35.7012 37.0 37.0 37.0 37.0 37.0 125-129 35.7654 37.0 37.0 37.0 37.0 37.0 130-134 35.685100000000006 37.0 37.0 37.0 37.0 37.0 135-139 35.5625 37.0 37.0 37.0 37.0 37.0 140-144 35.4508 37.0 37.0 37.0 37.0 37.0 145-149 35.350699999999996 37.0 37.0 37.0 37.0 37.0 150-151 34.900999999999996 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 2.0 13 3.0 14 7.0 15 1.0 16 1.0 17 4.0 18 0.0 19 0.0 20 2.0 21 2.0 22 8.0 23 7.0 24 7.0 25 9.0 26 14.0 27 11.0 28 14.0 29 18.0 30 35.0 31 40.0 32 56.0 33 96.0 34 182.0 35 401.0 36 2600.0 37 480.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 45.9 17.549999999999997 8.4 28.15 2 28.575 20.9 30.025000000000002 20.5 3 23.150000000000002 23.225 30.625000000000004 23.0 4 27.400000000000002 29.525000000000002 20.025000000000002 23.05 5 26.85 33.275 18.35 21.525 6 22.275 36.35 19.15 22.225 7 22.6 16.825000000000003 36.449999999999996 24.125 8 23.0 20.974999999999998 24.45 31.574999999999996 9 24.2 21.3 26.275 28.225 10-14 25.759999999999998 25.53 23.505000000000003 25.205 15-19 25.965 25.05 24.2 24.785 20-24 25.83 25.585 23.79 24.795 25-29 25.275 25.645 24.065 25.014999999999997 30-34 25.855 25.525 24.154999999999998 24.465 35-39 26.21 25.16 24.65 23.98 40-44 24.995 25.64 24.335 25.03 45-49 26.235000000000003 25.590000000000003 24.0 24.175 50-54 25.96 25.025 24.82 24.195 55-59 26.040000000000003 25.465 24.37 24.125 60-64 26.56 25.295 24.41 23.735 65-69 26.25 25.835 24.16 23.755000000000003 70-74 26.55 25.185000000000002 24.915000000000003 23.35 75-79 26.44 25.64 23.94 23.98 80-84 25.919999999999998 25.85 24.42 23.810000000000002 85-89 26.490000000000002 25.264999999999997 24.565 23.68 90-94 26.595000000000002 25.374999999999996 24.16 23.87 95-99 26.255 25.264999999999997 24.66 23.82 100-104 25.55 25.115 25.705 23.630000000000003 105-109 26.695 25.124999999999996 24.86 23.32 110-114 26.415 25.805 24.295 23.485 115-119 26.555 26.19 24.315 22.939999999999998 120-124 26.915 25.16 24.490000000000002 23.435 125-129 27.29 25.25 24.654999999999998 22.805 130-134 26.595000000000002 25.619999999999997 24.93 22.855 135-139 27.544999999999998 25.53 24.265 22.66 140-144 27.415 25.835 24.81 21.94 145-149 27.74 25.779999999999998 24.995 21.485000000000003 150-151 27.9125 26.0125 24.0375 22.037499999999998 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.0 5 0.5 6 0.5 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 1.0 17 1.0 18 0.0 19 0.0 20 0.5 21 0.5 22 0.0 23 1.0 24 2.0 25 1.0 26 0.5 27 1.5 28 4.5 29 4.0 30 2.5 31 4.5 32 7.5 33 16.5 34 21.0 35 22.5 36 33.0 37 44.5 38 62.0 39 86.0 40 104.0 41 122.5 42 150.0 43 175.0 44 194.0 45 193.0 46 181.0 47 176.5 48 179.5 49 183.5 50 160.5 51 155.5 52 160.0 53 138.0 54 135.5 55 128.5 56 103.5 57 102.5 58 101.0 59 102.5 60 91.0 61 72.5 62 73.5 63 66.5 64 58.5 65 57.0 66 56.5 67 49.5 68 45.0 69 42.5 70 35.5 71 24.5 72 16.5 73 14.0 74 8.0 75 2.0 76 1.5 77 1.0 78 1.5 79 2.5 80 1.5 81 0.0 82 1.0 83 1.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.5 91 1.0 92 0.5 93 0.0 94 0.5 95 1.0 96 1.0 97 0.5 98 0.5 99 1.5 100 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 91.4 #Duplication Level Percentage of deduplicated Percentage of total 1 91.54814004376368 83.675 2 7.576586433260394 13.850000000000001 3 0.7932166301969366 2.175 4 0.08205689277899343 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 0.025 0.0 0.0 24-25 0.0 0.0 0.05 0.0 0.0 26-27 0.0 0.0 0.05 0.0 0.0 28-29 0.0 0.0 0.05 0.0 0.0 30-31 0.0 0.0 0.05 0.0 0.0 32-33 0.0 0.0 0.05 0.0 0.0 34-35 0.0 0.0 0.05 0.0 0.0 36-37 0.0 0.0 0.05 0.0 0.0 38-39 0.0 0.0 0.05 0.0 0.0 40-41 0.0 0.0 0.05 0.0 0.0 42-43 0.0 0.0 0.05 0.0 0.0 44-45 0.0 0.0 0.05 0.0 0.0 46-47 0.0 0.0 0.05 0.0 0.0 48-49 0.0 0.0 0.05 0.0 0.0 50-51 0.0 0.0 0.05 0.0 0.0 52-53 0.0 0.0 0.05 0.0 0.0 54-55 0.0 0.0 0.05 0.0 0.0 56-57 0.0 0.0 0.05 0.0 0.0 58-59 0.0 0.0 0.05 0.0 0.0 60-61 0.0 0.0 0.05 0.0 0.0 62-63 0.0 0.0 0.05 0.0 0.0 64-65 0.0 0.0 0.05 0.0 0.0 66-67 0.0 0.0 0.05 0.0 0.0 68-69 0.0 0.0 0.05 0.0 0.0 70-71 0.025 0.0 0.05 0.0 0.0 72-73 0.025 0.0 0.05 0.0 0.0 74-75 0.025 0.0 0.05 0.0 0.0 76-77 0.025 0.0 0.05 0.0 0.0 78-79 0.05 0.0 0.05 0.0 0.0 80-81 0.05 0.0 0.05 0.0 0.0 82-83 0.05 0.0 0.05 0.0 0.0 84-85 0.075 0.0 0.05 0.0 0.0 86-87 0.1125 0.0 0.05 0.0 0.0 88-89 0.1625 0.0 0.05 0.0 0.0 90-91 0.2 0.0 0.05 0.0 0.0 92-93 0.21250000000000002 0.0 0.05 0.0 0.0 94-95 0.3625 0.0 0.05 0.0 0.0 96-97 0.44999999999999996 0.0 0.05 0.0 0.0 98-99 0.5 0.0 0.05 0.0 0.0 100-101 0.6875 0.0 0.05 0.0 0.0 102-103 0.8625 0.0 0.05 0.0 0.0 104-105 1.025 0.0 0.05 0.0 0.0 106-107 1.125 0.0 0.05 0.0 0.0 108-109 1.275 0.0 0.05 0.0 0.0 110-111 1.55 0.0 0.05 0.0 0.0 112-113 1.7999999999999998 0.0 0.05 0.0 0.0 114-115 2.25 0.0 0.05 0.0 0.0 116-117 2.5875 0.0 0.05 0.0 0.0 118-119 2.95 0.0 0.05 0.0 0.0 120-121 3.375 0.0 0.05 0.0 0.0 122-123 3.9625000000000004 0.0 0.05 0.0 0.0 124-125 4.475 0.0 0.05 0.0 0.0 126-127 4.8875 0.0 0.05 0.0 0.0 128-129 5.3875 0.0 0.05 0.0 0.0 130-131 5.95 0.0 0.05 0.0 0.0 132-133 6.425000000000001 0.0 0.05 0.0 0.0 134-135 6.925000000000001 0.0 0.05 0.0 0.0 136-137 7.3375 0.0 0.05 0.0 0.0 138-139 7.762499999999999 0.0 0.05 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CGCCGCC 10 0.006830828 145.0 6 GGACAAG 20 0.00593511 29.0 15-19 GGGGGGG 40 0.0076550315 18.125 140-144 >>END_MODULE Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446746 spots for SRR12666601.sra Written 1446746 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra Read 1446736 spots for SRR12666601.sra Written 1446736 spots for SRR12666601.sra SRR ids: ['SRR12666601.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_hz3d5x1w SRR12666601.sra spots: 28934730 blocks: [[1, 1446736], [1446737, 2893472], [2893473, 4340208], [4340209, 5786944], [5786945, 7233680], [7233681, 8680416], [8680417, 10127152], [10127153, 11573888], [11573889, 13020624], [13020625, 14467360], [14467361, 15914096], [15914097, 17360832], [17360833, 18807568], [18807569, 20254304], [20254305, 21701040], [21701041, 23147776], [23147777, 24594512], [24594513, 26041248], [26041249, 27487984], [27487985, 28934730]] SRR12666601 file size 9811586 SRR12666601 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 SRR12666601 SRR12666601_1.fastq SRR12666601_2.fastq Input file: SRR12666601_1.fastq Paired file: SRR12666601_2.fastq trimmed: SRR12666601-trimmed-pair1.fastq, SRR12666601-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 17:36:49 2024 >> started Sat Dec 7 17:37:23 2024 >> done (34.062s) 28934730 read pairs processed; of these: 68 ( 0.00%) short read pairs filtered out after trimming by size control 13429 ( 0.05%) empty read pairs filtered out after trimming by size control 28921233 (99.95%) read pairs available; of these: 3095907 (10.70%) trimmed read pairs available after processing 25825326 (89.30%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 11 0.00% 19 7 0.00% 20 10 0.00% 21 15 0.00% 22 11 0.00% 23 21 0.00% 24 11 0.00% 25 23 0.00% 26 20 0.00% 27 14 0.00% 28 25 0.00% 29 28 0.00% 30 25 0.00% 31 20 0.00% 32 26 0.00% 33 28 0.00% 34 34 0.00% 35 45 0.00% 36 38 0.00% 37 41 0.00% 38 53 0.00% 39 49 0.00% 40 45 0.00% 41 56 0.00% 42 63 0.00% 43 54 0.00% 44 67 0.00% 45 63 0.00% 46 58 0.00% 47 72 0.00% 48 85 0.00% 49 85 0.00% 50 103 0.00% 51 98 0.00% 52 110 0.00% 53 112 0.00% 54 110 0.00% 55 131 0.00% 56 122 0.00% 57 159 0.00% 58 158 0.00% 59 212 0.00% 60 232 0.00% 61 297 0.00% 62 343 0.00% 63 306 0.00% 64 344 0.00% 65 419 0.00% 66 446 0.00% 67 450 0.00% 68 527 0.00% 69 678 0.00% 70 764 0.00% 71 897 0.00% 72 1011 0.00% 73 1269 0.00% 74 1344 0.00% 75 1493 0.01% 76 1615 0.01% 77 1790 0.01% 78 1972 0.01% 79 2335 0.01% 80 2626 0.01% 81 3080 0.01% 82 3594 0.01% 83 4296 0.01% 84 4796 0.02% 85 5032 0.02% 86 5557 0.02% 87 6004 0.02% 88 6465 0.02% 89 7320 0.03% 90 7905 0.03% 91 9084 0.03% 92 10373 0.04% 93 11457 0.04% 94 12992 0.04% 95 13736 0.05% 96 14381 0.05% 97 15137 0.05% 98 15790 0.05% 99 17018 0.06% 100 18203 0.06% 101 19863 0.07% 102 22239 0.08% 103 23609 0.08% 104 25602 0.09% 105 27352 0.09% 106 28322 0.10% 107 28450 0.10% 108 29572 0.10% 109 30710 0.11% 110 31868 0.11% 111 33937 0.12% 112 36605 0.13% 113 38753 0.13% 114 41177 0.14% 115 43369 0.15% 116 44016 0.15% 117 44851 0.16% 118 44979 0.16% 119 45910 0.16% 120 47624 0.16% 121 48866 0.17% 122 51151 0.18% 123 54509 0.19% 124 57369 0.20% 125 59685 0.21% 126 60710 0.21% 127 61027 0.21% 128 60941 0.21% 129 62458 0.22% 130 62559 0.22% 131 63467 0.22% 132 66315 0.23% 133 69567 0.24% 134 72127 0.25% 135 75266 0.26% 136 77286 0.27% 137 77626 0.27% 138 78286 0.27% 139 77364 0.27% 140 77022 0.27% 141 79210 0.27% 142 81104 0.28% 143 82396 0.28% 144 86475 0.30% 145 89266 0.31% 146 91294 0.32% 147 92417 0.32% 148 92791 0.32% 149 91327 0.32% 150 91322 0.32% 151 25825326 89.30% 28921233 reads passed initial QC criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=5.19 fanout-score-rank=25 prefix-density=0.23 prefix-fanout=4.0 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.04 sequence-density-rank=27 fanout-score=113.39 fanout-score-rank=1 prefix-density=0.36 prefix-fanout=13.2 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.36 sequence-density-rank=1 fanout-score=2.34 fanout-score-rank=31 prefix-density=0.37 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.07 sequence-density-rank=24 fanout-score=251.04 fanout-score-rank=1 prefix-density=0.83 prefix-fanout=19.9 sequence=CCGCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGC SRR12666601 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 17:38:13 Started mapping on | Dec 07 17:38:13 Finished on | Dec 07 17:40:28 Mapping speed, Million of reads per hour | 771.23 Number of input reads | 28921233 Average input read length | 297 UNIQUE READS: Uniquely mapped reads number | 27639196 Uniquely mapped reads % | 95.57% Average mapped length | 296.47 Number of splices: Total | 29850759 Number of splices: Annotated (sjdb) | 28054684 Number of splices: GT/AG | 29461394 Number of splices: GC/AG | 343305 Number of splices: AT/AC | 20839 Number of splices: Non-canonical | 25221 Mismatch rate per base, % | 0.11% Deletion rate per base | 0.00% Deletion average length | 1.46 Insertion rate per base | 0.00% Insertion average length | 1.20 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 356153 % of reads mapped to multiple loci | 1.23% Number of reads mapped to too many loci | 58148 % of reads mapped to too many loci | 0.20% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.98% % of reads unmapped: other | 1.02% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 925884 925884 925884 N_multimapping 356153 356153 356153 N_noFeature 930477 26964919 1148897 N_ambiguous 524490 3685 69866 UnstrandedReadsAssigned:26184229 PositiveStrandReadsAssigned:670592 NegativeStrandReadsAssigned:26420433 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12666601 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: SRR12666601-trimmed-pair1.fastq SRR12666601-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 28,921,233 reads, 26,851,938 reads pseudoaligned [quant] estimated average fragment length: 271.176 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,211 rounds 52973 SRR12666601.ke.tsv 35125 SRR12666601.se.tsv 88098 total ==> SRR12666601.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 666.677 0 0 PNS24247 1044 773.824 146.145 10.886 PNS24249 1928 1657.82 139.439 4.84807 PNS24246 1044 773.824 146.145 10.886 PNS24248 1044 773.824 146.145 10.886 PNS24244 1471 1200.82 225.125 10.8061 PNS24243 293 94.7253 0 0 KQK14069 1603 1332.82 6103.31 263.947 KQK14071 474 234.134 94.9532 23.3759 ==> SRR12666601.se.tsv <== BRADI_1g14170v3 6827 BRADI_1g53295v3 258 BRADI_1g59795v3 625 BRADI_1g07683v3 0 BRADI_1g00485v3 78 BRADI_1g20270v3 2041 BRADI_1g74790v3 87 BRADI_1g09890v3 0 BRADI_1g77505v3 211 BRADI_1g48960v3 0 SRR12666601 completed mapping pipeline successfully