Starting /dee2/code/volunteer_pipeline.sh SRR12666369 current disk space = 1543171444736 free memory = 1606498404 SRR12666369 SRAfilesize b73c886cfda867f978d30fb071ae90f5 SRR12666369.sra SRR12666369.sra file validated SRR12666369 is paired end SRR12666369 is conventional basespace SRR12666369 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666369_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 36.5055 37.0 37.0 37.0 37.0 37.0 2 36.3185 37.0 37.0 37.0 37.0 37.0 3 36.547 37.0 37.0 37.0 37.0 37.0 4 36.5795 37.0 37.0 37.0 37.0 37.0 5 36.5595 37.0 37.0 37.0 37.0 37.0 6 36.5605 37.0 37.0 37.0 37.0 37.0 7 36.5105 37.0 37.0 37.0 37.0 37.0 8 36.5735 37.0 37.0 37.0 37.0 37.0 9 36.577 37.0 37.0 37.0 37.0 37.0 10-14 36.5503 37.0 37.0 37.0 37.0 37.0 15-19 36.5391 37.0 37.0 37.0 37.0 37.0 20-24 36.4919 37.0 37.0 37.0 37.0 37.0 25-29 36.4682 37.0 37.0 37.0 37.0 37.0 30-34 36.4154 37.0 37.0 37.0 37.0 37.0 35-39 36.4096 37.0 37.0 37.0 37.0 37.0 40-44 36.3744 37.0 37.0 37.0 37.0 37.0 45-49 36.3512 37.0 37.0 37.0 37.0 37.0 50-54 36.3754 37.0 37.0 37.0 37.0 37.0 55-59 36.3067 37.0 37.0 37.0 37.0 37.0 60-64 36.2993 37.0 37.0 37.0 37.0 37.0 65-69 36.2668 37.0 37.0 37.0 37.0 37.0 70-74 36.2832 37.0 37.0 37.0 37.0 37.0 75-79 36.24209999999999 37.0 37.0 37.0 37.0 37.0 80-84 36.178000000000004 37.0 37.0 37.0 37.0 37.0 85-89 36.197199999999995 37.0 37.0 37.0 37.0 37.0 90-94 36.1639 37.0 37.0 37.0 37.0 37.0 95-99 36.083 37.0 37.0 37.0 37.0 37.0 100-104 36.110699999999994 37.0 37.0 37.0 37.0 37.0 105-109 36.199 37.0 37.0 37.0 37.0 37.0 110-114 36.0737 37.0 37.0 37.0 37.0 37.0 115-119 36.0133 37.0 37.0 37.0 37.0 37.0 120-124 36.0212 37.0 37.0 37.0 37.0 37.0 125-129 35.9794 37.0 37.0 37.0 37.0 37.0 130-134 35.95399999999999 37.0 37.0 37.0 37.0 37.0 135-139 35.9755 37.0 37.0 37.0 37.0 37.0 140-144 35.799 37.0 37.0 37.0 37.0 37.0 145-149 35.67 37.0 37.0 37.0 37.0 37.0 150-151 35.41075 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 20 2.0 21 1.0 22 3.0 23 0.0 24 6.0 25 5.0 26 4.0 27 8.0 28 10.0 29 18.0 30 28.0 31 35.0 32 54.0 33 97.0 34 120.0 35 293.0 36 2818.0 37 498.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.075 13.325000000000001 6.2 34.4 2 23.28664332166083 15.832916458229116 36.99349674837419 23.88694347173587 3 20.349999999999998 24.025 26.625 28.999999999999996 4 26.6 29.7 20.200000000000003 23.5 5 25.6 33.45 22.575 18.375 6 22.325 34.375 21.45 21.85 7 17.724999999999998 21.325 39.825 21.125 8 20.724999999999998 20.925 28.375 29.975 9 19.55 20.825 30.2 29.425 10-14 22.99 27.025 24.435000000000002 25.55 15-19 22.97 25.974999999999998 25.385 25.669999999999998 20-24 22.24 26.400000000000002 25.564999999999998 25.795 25-29 22.655 25.56 25.505 26.279999999999998 30-34 22.55 26.235000000000003 25.005 26.21 35-39 22.845 25.66 25.424999999999997 26.07 40-44 22.32 26.16 25.515 26.005 45-49 23.06 25.785000000000004 25.115 26.040000000000003 50-54 22.945 26.150000000000002 25.335 25.569999999999997 55-59 22.85 25.88 24.935 26.334999999999997 60-64 23.615 25.515 24.935 25.935000000000002 65-69 22.785 25.615 25.205 26.395000000000003 70-74 23.005 26.165 25.290000000000003 25.540000000000003 75-79 23.345 25.71 24.67 26.275 80-84 23.044999999999998 25.685000000000002 25.0 26.27 85-89 23.435 25.66 25.115 25.790000000000003 90-94 23.145 26.119999999999997 24.63 26.105 95-99 23.32 25.990000000000002 24.915000000000003 25.775 100-104 23.485 25.55 25.485000000000003 25.480000000000004 105-109 23.169999999999998 25.419999999999998 24.985 26.424999999999997 110-114 23.555 25.679999999999996 24.560000000000002 26.205000000000002 115-119 23.895 25.779999999999998 24.29 26.035000000000004 120-124 24.255 25.585 24.45 25.71 125-129 23.87 25.575 24.8 25.755 130-134 24.22 25.935000000000002 24.715 25.130000000000003 135-139 23.799999999999997 25.705 24.404999999999998 26.090000000000003 140-144 23.965 25.66 24.605 25.77 145-149 23.84 25.28 24.995 25.885 150-151 22.975 26.237500000000004 24.349999999999998 26.437500000000004 >>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 0.0 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 0.5 26 1.0 27 1.0 28 2.5 29 4.0 30 5.5 31 10.5 32 15.5 33 19.0 34 24.5 35 34.5 36 47.0 37 56.5 38 80.0 39 102.5 40 118.0 41 135.5 42 167.5 43 199.0 44 210.5 45 205.5 46 210.5 47 198.5 48 182.0 49 182.0 50 182.0 51 177.0 52 153.5 53 138.5 54 122.0 55 104.0 56 91.0 57 87.5 58 74.5 59 68.0 60 66.0 61 57.0 62 57.0 63 52.5 64 48.5 65 57.5 66 59.5 67 46.5 68 30.5 69 25.0 70 25.0 71 19.0 72 14.0 73 11.0 74 7.5 75 5.5 76 4.0 77 2.0 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 0.05 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 90.77499999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 90.91159460203801 82.525 2 8.234646103001927 14.95 3 0.6609749380335995 1.7999999999999998 4 0.16524373450839988 0.6 5 0.02754062241806665 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 CCGGCGCCGAAGGGGATGAACTCGAAGTCCCCGCCCTTAAAGTCCACCTT 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 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 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 0.0625 0.0 0.0 0.0 0.0 84-85 0.15 0.0 0.0 0.0 0.0 86-87 0.175 0.0 0.0 0.0 0.0 88-89 0.25 0.0 0.0 0.0 0.0 90-91 0.3125 0.0 0.0 0.0 0.0 92-93 0.44999999999999996 0.0 0.0 0.0 0.0 94-95 0.55 0.0 0.0 0.0 0.0 96-97 0.6625000000000001 0.0 0.0 0.0 0.0 98-99 0.7625 0.0 0.0 0.0 0.0 100-101 0.8875 0.0 0.0 0.0 0.0 102-103 1.0625 0.0 0.0 0.0 0.0 104-105 1.2625 0.0 0.0 0.0 0.0 106-107 1.45 0.0 0.0 0.0 0.0 108-109 1.75 0.0 0.0 0.0 0.0 110-111 2.0875 0.0 0.0 0.0 0.0 112-113 2.3 0.0 0.0 0.0 0.0 114-115 2.5375 0.0 0.0 0.0 0.0 116-117 2.8625 0.0 0.0 0.0 0.0 118-119 3.0375 0.0 0.0 0.0 0.0 120-121 3.4375 0.0 0.0 0.0 0.0 122-123 3.7249999999999996 0.0 0.0 0.0 0.0 124-125 4.225 0.0 0.0 0.0 0.0 126-127 4.625 0.0 0.0 0.0 0.0 128-129 5.0875 0.0 0.0 0.0 0.0 130-131 5.737500000000001 0.0 0.0 0.0 0.0 132-133 6.3375 0.0 0.0 0.0 0.0 134-135 6.8375 0.0 0.0 0.0 0.0 136-137 7.4125 0.0 0.0 0.0 0.0 138-139 8.0 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position AATCTCC 10 0.006830828 145.0 5 CAATCTC 10 0.006830828 145.0 4 >>END_MODULE SRR12666369 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR12666369_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 36.113 37.0 37.0 37.0 37.0 37.0 2 36.101 37.0 37.0 37.0 37.0 37.0 3 36.133 37.0 37.0 37.0 37.0 37.0 4 36.242 37.0 37.0 37.0 37.0 37.0 5 36.263 37.0 37.0 37.0 37.0 37.0 6 36.117 37.0 37.0 37.0 37.0 37.0 7 36.1555 37.0 37.0 37.0 37.0 37.0 8 36.194 37.0 37.0 37.0 37.0 37.0 9 36.2105 37.0 37.0 37.0 37.0 37.0 10-14 36.2466 37.0 37.0 37.0 37.0 37.0 15-19 36.1926 37.0 37.0 37.0 37.0 37.0 20-24 36.2249 37.0 37.0 37.0 37.0 37.0 25-29 36.1605 37.0 37.0 37.0 37.0 37.0 30-34 36.1136 37.0 37.0 37.0 37.0 37.0 35-39 36.1151 37.0 37.0 37.0 37.0 37.0 40-44 36.04109999999999 37.0 37.0 37.0 37.0 37.0 45-49 36.042899999999996 37.0 37.0 37.0 37.0 37.0 50-54 36.05919999999999 37.0 37.0 37.0 37.0 37.0 55-59 35.9937 37.0 37.0 37.0 37.0 37.0 60-64 35.9351 37.0 37.0 37.0 37.0 37.0 65-69 36.021100000000004 37.0 37.0 37.0 37.0 37.0 70-74 35.9249 37.0 37.0 37.0 37.0 37.0 75-79 35.9418 37.0 37.0 37.0 37.0 37.0 80-84 35.927499999999995 37.0 37.0 37.0 37.0 37.0 85-89 35.9274 37.0 37.0 37.0 37.0 37.0 90-94 35.851299999999995 37.0 37.0 37.0 37.0 37.0 95-99 35.8001 37.0 37.0 37.0 37.0 37.0 100-104 35.876 37.0 37.0 37.0 37.0 37.0 105-109 35.8296 37.0 37.0 37.0 37.0 37.0 110-114 35.7857 37.0 37.0 37.0 37.0 37.0 115-119 35.778099999999995 37.0 37.0 37.0 37.0 37.0 120-124 35.759899999999995 37.0 37.0 37.0 37.0 37.0 125-129 35.728300000000004 37.0 37.0 37.0 37.0 37.0 130-134 35.664300000000004 37.0 37.0 37.0 37.0 37.0 135-139 35.5098 37.0 37.0 37.0 37.0 37.0 140-144 35.3892 37.0 37.0 37.0 37.0 37.0 145-149 35.2426 37.0 37.0 37.0 32.2 37.0 150-151 35.034499999999994 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 12 1.0 13 6.0 14 7.0 15 4.0 16 6.0 17 4.0 18 1.0 19 3.0 20 5.0 21 3.0 22 3.0 23 17.0 24 7.0 25 9.0 26 6.0 27 9.0 28 9.0 29 8.0 30 24.0 31 41.0 32 43.0 33 104.0 34 162.0 35 398.0 36 2654.0 37 466.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 46.575 17.1 7.925 28.4 2 28.749999999999996 20.424999999999997 29.825000000000003 21.0 3 24.05 22.900000000000002 29.125 23.925 4 27.450000000000003 30.975 18.75 22.825 5 28.050000000000004 32.75 18.55 20.65 6 22.7 34.725 20.325 22.25 7 21.325 15.575 37.325 25.775 8 20.95 20.875 25.15 33.025 9 24.175 19.650000000000002 27.150000000000002 29.025000000000002 10-14 25.405 25.295 23.76 25.540000000000003 15-19 26.83 24.23 23.830000000000002 25.11 20-24 25.775 25.105 24.63 24.490000000000002 25-29 25.985000000000003 24.825 24.255 24.935 30-34 25.77 25.045 24.25 24.935 35-39 25.840000000000003 24.779999999999998 24.65 24.73 40-44 25.64 24.97 24.97 24.42 45-49 25.75 25.35 24.435000000000002 24.465 50-54 25.990000000000002 25.345000000000002 24.535 24.13 55-59 26.005 25.180000000000003 24.73 24.085 60-64 26.61 25.025 24.385 23.98 65-69 26.25 24.505 24.84 24.404999999999998 70-74 26.529999999999998 25.22 24.545 23.705000000000002 75-79 26.13 25.995 24.445 23.43 80-84 26.56 25.285000000000004 24.765 23.39 85-89 26.405 25.46 24.474999999999998 23.66 90-94 25.979999999999997 25.96 24.740000000000002 23.32 95-99 27.025 25.21 25.005 22.759999999999998 100-104 26.44 25.900000000000002 24.375 23.285 105-109 26.515 24.795 25.145 23.544999999999998 110-114 26.045 25.729999999999997 24.610000000000003 23.615 115-119 26.495 25.5 24.77 23.235 120-124 26.540000000000003 25.825 24.455 23.18 125-129 26.125 25.635 25.1 23.14 130-134 27.04 25.785000000000004 24.645 22.53 135-139 27.22 25.685000000000002 24.65 22.445 140-144 27.515 25.745 24.67 22.07 145-149 27.855 25.900000000000002 24.16 22.085 150-151 28.549999999999997 25.2375 24.45 21.762500000000003 >>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 1.0 6 0.5 7 1.0 8 1.0 9 0.5 10 0.5 11 0.0 12 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.5 18 1.5 19 1.0 20 0.5 21 1.0 22 0.5 23 0.5 24 0.5 25 0.5 26 1.0 27 2.5 28 4.5 29 5.0 30 4.5 31 8.5 32 9.5 33 12.5 34 22.5 35 26.0 36 39.5 37 53.5 38 66.0 39 90.5 40 115.0 41 120.0 42 131.0 43 165.5 44 184.0 45 192.5 46 190.5 47 173.0 48 175.0 49 175.0 50 163.5 51 162.0 52 150.0 53 145.5 54 139.0 55 114.0 56 87.5 57 77.0 58 80.0 59 86.0 60 88.5 61 81.5 62 81.5 63 74.5 64 60.5 65 61.5 66 63.0 67 53.5 68 47.5 69 42.5 70 35.0 71 28.5 72 18.0 73 18.5 74 18.0 75 10.0 76 7.5 77 3.5 78 2.0 79 1.0 80 0.5 81 0.5 82 0.0 83 0.5 84 1.5 85 1.5 86 1.0 87 1.0 88 1.0 89 1.0 90 1.0 91 0.5 92 0.5 93 1.5 94 1.5 95 0.5 96 0.5 97 1.0 98 1.0 99 0.5 100 1.0 >>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 90.5 #Duplication Level Percentage of deduplicated Percentage of total 1 90.77348066298343 82.15 2 8.342541436464089 15.1 3 0.6353591160220995 1.725 4 0.13812154696132595 0.5 5 0.08287292817679558 0.375 6 0.027624309392265196 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 GTTGGCTTCTCCTCCCCCTCACTAGTCCTCGGTTCCGGTTCCGGTTCGTT 5 0.125 No Hit GTTTGAGGCAATAACAGGTCTGTGATGCCCTTAGATGTTCTGGGCCGCAC 5 0.125 No Hit TGATGGGCCGCGAGATCCCCGAGGGCACCAAGGTGCTCGTCAACACCTGG 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 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 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 0.0625 0.0 0.0 0.0 0.0 84-85 0.15 0.0 0.0 0.0 0.0 86-87 0.175 0.0 0.0 0.0 0.0 88-89 0.25 0.0 0.0 0.0 0.0 90-91 0.3125 0.0 0.0 0.0 0.0 92-93 0.44999999999999996 0.0 0.0 0.0 0.0 94-95 0.55 0.0 0.0 0.0 0.0 96-97 0.6625000000000001 0.0 0.0 0.0 0.0 98-99 0.7625 0.0 0.0 0.0 0.0 100-101 0.8875 0.0 0.0 0.0 0.0 102-103 1.0625 0.0 0.0 0.0 0.0 104-105 1.2625 0.0 0.0 0.0 0.0 106-107 1.45 0.0 0.0 0.0 0.0 108-109 1.75 0.0 0.0 0.0 0.0 110-111 2.0875 0.0 0.0 0.0 0.0 112-113 2.325 0.0 0.0 0.0 0.0 114-115 2.5625 0.0 0.0 0.0 0.0 116-117 2.9000000000000004 0.0 0.0 0.0 0.0 118-119 3.075 0.0 0.0 0.0 0.0 120-121 3.4375 0.0 0.0 0.0 0.0 122-123 3.75 0.0 0.0 0.0 0.0 124-125 4.25 0.0 0.0 0.0 0.0 126-127 4.6875 0.0 0.0 0.0 0.0 128-129 5.1625 0.0 0.0 0.0 0.0 130-131 5.8125 0.0 0.0 0.0 0.0 132-133 6.45 0.0 0.0 0.0 0.0 134-135 6.975 0.0 0.0 0.0 0.0 136-137 7.55 0.0 0.0 0.0 0.0 138-139 8.125 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATTCAAT 10 0.006830828 145.0 6 >>END_MODULE Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra Read 1591397 spots for SRR12666369.sra Written 1591397 spots for SRR12666369.sra SRR ids: ['SRR12666369.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_sw9k7z0l SRR12666369.sra spots: 31827940 blocks: [[1, 1591397], [1591398, 3182794], [3182795, 4774191], [4774192, 6365588], [6365589, 7956985], [7956986, 9548382], [9548383, 11139779], [11139780, 12731176], [12731177, 14322573], [14322574, 15913970], [15913971, 17505367], [17505368, 19096764], [19096765, 20688161], [20688162, 22279558], [22279559, 23870955], [23870956, 25462352], [25462353, 27053749], [27053750, 28645146], [28645147, 30236543], [30236544, 31827940]] SRR12666369 file size 10794826 SRR12666369 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 SRR12666369 SRR12666369_1.fastq SRR12666369_2.fastq Input file: SRR12666369_1.fastq Paired file: SRR12666369_2.fastq trimmed: SRR12666369-trimmed-pair1.fastq, SRR12666369-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 13:29:29 2024 >> started Sat Dec 7 13:30:01 2024 >> done (32.250s) 31827940 read pairs processed; of these: 70 ( 0.00%) short read pairs filtered out after trimming by size control 4457 ( 0.01%) empty read pairs filtered out after trimming by size control 31823413 (99.99%) read pairs available; of these: 3729869 (11.72%) trimmed read pairs available after processing 28093544 (88.28%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 3 0.00% 19 11 0.00% 20 11 0.00% 21 11 0.00% 22 13 0.00% 23 18 0.00% 24 26 0.00% 25 13 0.00% 26 21 0.00% 27 29 0.00% 28 30 0.00% 29 22 0.00% 30 42 0.00% 31 33 0.00% 32 35 0.00% 33 32 0.00% 34 21 0.00% 35 40 0.00% 36 39 0.00% 37 47 0.00% 38 60 0.00% 39 40 0.00% 40 51 0.00% 41 48 0.00% 42 55 0.00% 43 70 0.00% 44 62 0.00% 45 62 0.00% 46 72 0.00% 47 71 0.00% 48 74 0.00% 49 89 0.00% 50 77 0.00% 51 88 0.00% 52 123 0.00% 53 105 0.00% 54 147 0.00% 55 154 0.00% 56 136 0.00% 57 169 0.00% 58 205 0.00% 59 221 0.00% 60 215 0.00% 61 286 0.00% 62 288 0.00% 63 339 0.00% 64 355 0.00% 65 388 0.00% 66 484 0.00% 67 519 0.00% 68 575 0.00% 69 685 0.00% 70 805 0.00% 71 922 0.00% 72 1005 0.00% 73 1366 0.00% 74 1426 0.00% 75 1606 0.01% 76 1840 0.01% 77 2072 0.01% 78 2232 0.01% 79 2642 0.01% 80 3110 0.01% 81 3395 0.01% 82 4249 0.01% 83 4647 0.01% 84 5161 0.02% 85 5861 0.02% 86 6311 0.02% 87 7048 0.02% 88 7771 0.02% 89 8498 0.03% 90 9560 0.03% 91 10872 0.03% 92 11992 0.04% 93 13474 0.04% 94 14772 0.05% 95 16145 0.05% 96 17629 0.06% 97 18367 0.06% 98 19261 0.06% 99 21062 0.07% 100 22578 0.07% 101 24452 0.08% 102 26861 0.08% 103 28997 0.09% 104 30494 0.10% 105 32584 0.10% 106 33757 0.11% 107 35395 0.11% 108 36918 0.12% 109 38606 0.12% 110 40119 0.13% 111 42687 0.13% 112 44971 0.14% 113 47233 0.15% 114 50090 0.16% 115 52126 0.16% 116 53031 0.17% 117 55091 0.17% 118 56012 0.18% 119 57516 0.18% 120 58970 0.19% 121 61034 0.19% 122 63699 0.20% 123 66080 0.21% 124 69370 0.22% 125 71091 0.22% 126 72885 0.23% 127 74129 0.23% 128 74903 0.24% 129 76106 0.24% 130 77450 0.24% 131 79675 0.25% 132 82003 0.26% 133 84627 0.27% 134 86207 0.27% 135 89623 0.28% 136 91186 0.29% 137 91313 0.29% 138 93045 0.29% 139 93979 0.30% 140 93984 0.30% 141 95837 0.30% 142 97389 0.31% 143 99084 0.31% 144 102371 0.32% 145 104564 0.33% 146 106213 0.33% 147 108030 0.34% 148 107121 0.34% 149 107303 0.34% 150 109169 0.34% 151 28093544 88.28% 31823413 reads passed initial QC criterion=sequence-density sequence-density=0.17 sequence-density-rank=1 fanout-score=5.31 fanout-score-rank=24 prefix-density=0.21 prefix-fanout=4.1 sequence=GTGATGGTCTTGCC criterion=fanout-score sequence-density=0.05 sequence-density-rank=23 fanout-score=338.62 fanout-score-rank=1 prefix-density=0.63 prefix-fanout=28.6 sequence=TCTTCTTCTTGTC criterion=sequence-density sequence-density=0.50 sequence-density-rank=1 fanout-score=2.25 fanout-score-rank=30 prefix-density=0.52 prefix-fanout=2.2 sequence=CGGTTCCGGTTC criterion=fanout-score sequence-density=0.04 sequence-density-rank=30 fanout-score=463.60 fanout-score-rank=1 prefix-density=0.99 prefix-fanout=18.8 sequence=CGCCGCCGCCCCTCGTCCTCTGTGTTCCTTCTCCGAGTTTCAGCCATGGGTAAGGAGAAGACTCACATCAACATCGTGGTCATTGGCCATGTCGACTCTGGCAAGTCGACCACCACTGGCCACCTGATCTACAAGCTTGGAGGTATTGACAAGCGTGTGATCGAGAGGTTCGAGAAGGAGGCTGCTGAGATGAACAAGAGGTCATTCAAGTACGCGTGGGTGCTTGACAAGCTGAAGGCTGAGCGTGAGAGAGGTATCACCATCGATATTGCCTTGTGGAAGTTCGAGACCACCAAGTACTACTGCACCGTCATTGATGCCCCTGGACACCGTGACTTCATCAAGAACATGATTACCGGTACCTCCCAGGCTGACTGTGCCGTGCTTATCATTGACTCCACGACTGGAGGTTTTGAGGCTGGTATCTCCAAGGATGGCCAGACCCGTGAGCATGCCCTCCTTGCTTTCACTCTTGGAGTGAAGCAGATGATCTGCTGCTGCAACAAGATGG SRR12666369 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 13:30:42 Started mapping on | Dec 07 13:30:42 Finished on | Dec 07 13:33:34 Mapping speed, Million of reads per hour | 666.07 Number of input reads | 31823413 Average input read length | 296 UNIQUE READS: Uniquely mapped reads number | 30063811 Uniquely mapped reads % | 94.47% Average mapped length | 295.68 Number of splices: Total | 32622273 Number of splices: Annotated (sjdb) | 30606619 Number of splices: GT/AG | 32162766 Number of splices: GC/AG | 380554 Number of splices: AT/AC | 22779 Number of splices: Non-canonical | 56174 Mismatch rate per base, % | 0.21% Deletion rate per base | 0.01% Deletion average length | 2.48 Insertion rate per base | 0.01% Insertion average length | 1.96 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 416551 % of reads mapped to multiple loci | 1.31% Number of reads mapped to too many loci | 53604 % of reads mapped to too many loci | 0.17% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.17% % of reads unmapped: other | 0.88% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1343051 1343051 1343051 N_multimapping 416551 416551 416551 N_noFeature 1028051 29330711 1267021 N_ambiguous 582736 3965 92034 UnstrandedReadsAssigned:28453024 PositiveStrandReadsAssigned:729135 NegativeStrandReadsAssigned:28704756 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR12666369 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: SRR12666369-trimmed-pair1.fastq SRR12666369-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 31,823,413 reads, 29,159,619 reads pseudoaligned [quant] estimated average fragment length: 268.533 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,194 rounds 52973 SRR12666369.ke.tsv 35125 SRR12666369.se.tsv 88098 total ==> SRR12666369.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 669.609 0 0 PNS24247 1044 776.467 131.727 8.84452 PNS24249 1928 1660.47 123.67 3.88291 PNS24246 1044 776.467 131.727 8.84452 PNS24248 1044 776.467 131.727 8.84452 PNS24244 1471 1203.47 274.149 11.8762 PNS24243 293 97.2811 2 1.07183 KQK14069 1603 1335.47 9123.68 356.172 KQK14071 474 237.144 179.755 39.5177 ==> SRR12666369.se.tsv <== BRADI_1g14170v3 10181 BRADI_1g53295v3 180 BRADI_1g59795v3 747 BRADI_1g07683v3 0 BRADI_1g00485v3 97 BRADI_1g20270v3 2461 BRADI_1g74790v3 40 BRADI_1g09890v3 0 BRADI_1g77505v3 250 BRADI_1g48960v3 0 SRR12666369 completed mapping pipeline successfully