Starting /dee2/code/volunteer_pipeline.sh SRR22215357 current disk space = 3053484224512 free memory = 1462087068 SRR22215357 SRAfilesize 83022a1f4177fc1059bb3d846e81d9d5 SRR22215357.sra SRR22215357.sra file validated SRR22215357 is paired end SRR22215357 is conventional basespace SRR22215357 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR22215357_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 43 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.898 37.0 37.0 37.0 37.0 37.0 2 36.035 37.0 37.0 37.0 37.0 37.0 3 36.2145 37.0 37.0 37.0 37.0 37.0 4 36.3225 37.0 37.0 37.0 37.0 37.0 5 36.331 37.0 37.0 37.0 37.0 37.0 6 36.3415 37.0 37.0 37.0 37.0 37.0 7 36.257 37.0 37.0 37.0 37.0 37.0 8 36.303 37.0 37.0 37.0 37.0 37.0 9 36.1625 37.0 37.0 37.0 37.0 37.0 10-14 36.3326 37.0 37.0 37.0 37.0 37.0 15-19 36.2316 37.0 37.0 37.0 37.0 37.0 20-24 36.2187 37.0 37.0 37.0 37.0 37.0 25-29 36.17809999999999 37.0 37.0 37.0 37.0 37.0 30-34 36.0952 37.0 37.0 37.0 37.0 37.0 35-39 36.062400000000004 37.0 37.0 37.0 37.0 37.0 40-44 36.0347 37.0 37.0 37.0 37.0 37.0 45-49 35.98459999999999 37.0 37.0 37.0 37.0 37.0 50-54 35.9525 37.0 37.0 37.0 37.0 37.0 55-59 35.908899999999996 37.0 37.0 37.0 37.0 37.0 60-64 35.903 37.0 37.0 37.0 37.0 37.0 65-69 35.8189 37.0 37.0 37.0 37.0 37.0 70-74 35.7531 37.0 37.0 37.0 37.0 37.0 75-79 35.8213 37.0 37.0 37.0 37.0 37.0 80-84 35.7664 37.0 37.0 37.0 37.0 37.0 85-89 35.702 37.0 37.0 37.0 37.0 37.0 90-94 35.6648 37.0 37.0 37.0 37.0 37.0 95-99 35.6272 37.0 37.0 37.0 37.0 37.0 100-104 35.652699999999996 37.0 37.0 37.0 37.0 37.0 105-109 35.548700000000004 37.0 37.0 37.0 37.0 37.0 110-114 35.5992 37.0 37.0 37.0 37.0 37.0 115-119 35.5945 37.0 37.0 37.0 37.0 37.0 120-124 35.5286 37.0 37.0 37.0 37.0 37.0 125-129 35.481700000000004 37.0 37.0 37.0 37.0 37.0 130-134 35.4349 37.0 37.0 37.0 34.6 37.0 135-139 35.412499999999994 37.0 37.0 37.0 37.0 37.0 140-144 35.2472 37.0 37.0 37.0 29.8 37.0 145-149 35.2739 37.0 37.0 37.0 32.2 37.0 150-151 35.08 37.0 37.0 37.0 25.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 22 3.0 23 2.0 24 4.0 25 11.0 26 10.0 27 18.0 28 21.0 29 38.0 30 56.0 31 77.0 32 91.0 33 129.0 34 201.0 35 453.0 36 2695.0 37 191.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 35.36523929471033 11.083123425692696 15.3904282115869 38.16120906801007 2 30.852130325814535 12.205513784461154 34.9874686716792 21.954887218045112 3 26.0 21.2 23.599999999999998 29.2 4 29.125 26.875 20.549999999999997 23.45 5 26.650000000000002 31.75 22.825 18.775 6 20.05 33.900000000000006 25.275 20.775 7 13.05 29.849999999999998 39.75 17.349999999999998 8 17.849999999999998 26.424999999999997 33.15 22.575 9 20.075000000000003 22.900000000000002 31.900000000000002 25.124999999999996 10-14 19.535 31.085 27.38 22.0 15-19 19.675 29.544999999999998 28.09 22.689999999999998 20-24 19.945 30.314999999999998 27.42 22.32 25-29 19.81 30.014999999999997 27.0 23.175 30-34 19.53 29.04 27.889999999999997 23.54 35-39 20.07 29.715000000000003 27.175 23.04 40-44 19.835 29.535 27.455000000000002 23.175 45-49 19.865 28.299999999999997 27.67 24.165 50-54 19.93 29.235 27.265 23.57 55-59 19.744999999999997 29.68 27.279999999999998 23.294999999999998 60-64 19.84 28.95 27.500000000000004 23.71 65-69 19.82 29.75 26.619999999999997 23.810000000000002 70-74 20.78 29.74 25.874999999999996 23.605 75-79 20.06 29.04 27.534999999999997 23.365 80-84 19.98 28.49 27.76 23.77 85-89 20.095 29.080000000000002 27.345000000000002 23.48 90-94 19.865 29.43 27.12 23.585 95-99 19.55 29.225 27.415 23.810000000000002 100-104 20.4 28.22 27.845 23.535 105-109 19.835 29.235 27.089999999999996 23.84 110-114 19.86 28.625 27.860000000000003 23.655 115-119 20.549999999999997 28.349999999999998 27.38 23.72 120-124 20.465 28.470000000000002 27.43 23.635 125-129 20.544999999999998 28.87 27.315 23.27 130-134 20.369999999999997 28.499999999999996 26.855 24.275 135-139 20.68 28.999999999999996 26.745 23.575 140-144 21.04 28.084999999999997 27.48 23.395 145-149 20.655 29.244999999999997 26.484999999999996 23.615 150-151 20.6875 29.262500000000003 26.375 23.674999999999997 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 1.0 1 0.5 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 0.5 16 1.0 17 0.5 18 0.5 19 1.5 20 2.0 21 1.0 22 3.0 23 3.5 24 3.0 25 7.5 26 9.5 27 11.5 28 18.5 29 29.5 30 33.0 31 33.0 32 48.0 33 65.5 34 81.5 35 100.0 36 106.0 37 123.0 38 161.0 39 178.0 40 178.5 41 206.0 42 215.5 43 228.5 44 247.0 45 233.5 46 233.5 47 223.5 48 190.5 49 165.5 50 146.0 51 118.0 52 94.0 53 92.0 54 83.0 55 62.0 56 50.5 57 52.0 58 43.5 59 19.5 60 12.5 61 12.5 62 10.0 63 7.5 64 10.0 65 8.0 66 5.5 67 6.0 68 5.0 69 5.0 70 4.5 71 2.0 72 0.5 73 1.0 74 1.5 75 1.5 76 1.0 77 0.5 78 0.0 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.0 85 0.0 86 0.0 87 0.0 88 0.0 89 0.0 90 0.0 91 0.0 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.0 98 0.0 99 0.0 100 0.0 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.75 2 0.25 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 92.025 #Duplication Level Percentage of deduplicated Percentage of total 1 92.09453952730236 84.75 2 7.199130671013311 13.25 3 0.6519967400162999 1.7999999999999998 4 0.05433306166802499 0.2 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 pass #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 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.037500000000000006 0.0 0.0 0.0 0.0 100-101 0.075 0.0 0.0 0.0 0.0 102-103 0.0875 0.0 0.0 0.0 0.0 104-105 0.125 0.0 0.0 0.0 0.0 106-107 0.125 0.0 0.0 0.0 0.0 108-109 0.125 0.0 0.0 0.0 0.0 110-111 0.15 0.0 0.0 0.0 0.0 112-113 0.15 0.0 0.0 0.0 0.0 114-115 0.1875 0.0 0.0 0.0 0.0 116-117 0.225 0.0 0.0 0.0 0.0 118-119 0.2875 0.0 0.0 0.0 0.0 120-121 0.35 0.0 0.0 0.0 0.0 122-123 0.375 0.0 0.0 0.0 0.0 124-125 0.475 0.0 0.0 0.0 0.0 126-127 0.6375 0.0 0.0 0.0 0.0 128-129 1.0 0.0 0.0 0.0 0.0 130-131 1.2 0.0 0.0 0.0 0.0 132-133 1.55 0.0 0.0 0.0 0.0 134-135 1.7374999999999998 0.0 0.0 0.0 0.0 136-137 2.1 0.0 0.0 0.0 0.0 138-139 2.6 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CAATATC 10 0.0068343505 144.975 9 >>END_MODULE SRR22215357 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR22215357_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 151 %GC 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 35.871 37.0 37.0 37.0 37.0 37.0 2 36.291 37.0 37.0 37.0 37.0 37.0 3 36.2505 37.0 37.0 37.0 37.0 37.0 4 36.215 37.0 37.0 37.0 37.0 37.0 5 36.13 37.0 37.0 37.0 37.0 37.0 6 36.1265 37.0 37.0 37.0 37.0 37.0 7 36.167 37.0 37.0 37.0 37.0 37.0 8 36.219 37.0 37.0 37.0 37.0 37.0 9 36.303 37.0 37.0 37.0 37.0 37.0 10-14 36.2154 37.0 37.0 37.0 37.0 37.0 15-19 36.1837 37.0 37.0 37.0 37.0 37.0 20-24 36.2005 37.0 37.0 37.0 37.0 37.0 25-29 36.082499999999996 37.0 37.0 37.0 37.0 37.0 30-34 36.0039 37.0 37.0 37.0 37.0 37.0 35-39 36.0315 37.0 37.0 37.0 37.0 37.0 40-44 36.0166 37.0 37.0 37.0 37.0 37.0 45-49 36.00600000000001 37.0 37.0 37.0 37.0 37.0 50-54 35.91270000000001 37.0 37.0 37.0 37.0 37.0 55-59 35.940599999999996 37.0 37.0 37.0 37.0 37.0 60-64 35.9212 37.0 37.0 37.0 37.0 37.0 65-69 35.8267 37.0 37.0 37.0 37.0 37.0 70-74 35.89229999999999 37.0 37.0 37.0 37.0 37.0 75-79 35.7607 37.0 37.0 37.0 37.0 37.0 80-84 35.710300000000004 37.0 37.0 37.0 37.0 37.0 85-89 35.7627 37.0 37.0 37.0 37.0 37.0 90-94 35.7019 37.0 37.0 37.0 37.0 37.0 95-99 35.756099999999996 37.0 37.0 37.0 37.0 37.0 100-104 35.638 37.0 37.0 37.0 37.0 37.0 105-109 35.6461 37.0 37.0 37.0 37.0 37.0 110-114 35.670399999999994 37.0 37.0 37.0 37.0 37.0 115-119 35.5858 37.0 37.0 37.0 37.0 37.0 120-124 35.44259999999999 37.0 37.0 37.0 37.0 37.0 125-129 35.465 37.0 37.0 37.0 37.0 37.0 130-134 35.394600000000004 37.0 37.0 37.0 34.6 37.0 135-139 35.4055 37.0 37.0 37.0 34.6 37.0 140-144 35.299099999999996 37.0 37.0 37.0 34.6 37.0 145-149 35.1243 37.0 37.0 37.0 27.4 37.0 150-151 35.198 37.0 37.0 37.0 31.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 13 2.0 14 0.0 15 1.0 16 1.0 17 0.0 18 1.0 19 1.0 20 4.0 21 2.0 22 1.0 23 6.0 24 8.0 25 12.0 26 13.0 27 13.0 28 20.0 29 29.0 30 36.0 31 41.0 32 63.0 33 94.0 34 229.0 35 649.0 36 2542.0 37 232.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 30.225 21.85 16.375 31.55 2 28.7 26.924999999999997 29.975 14.399999999999999 3 22.45 31.15 28.849999999999998 17.549999999999997 4 24.775 35.6 21.975 17.65 5 28.125 34.875 21.9 15.1 6 20.3 39.300000000000004 24.474999999999998 15.925 7 20.275000000000002 17.724999999999998 41.699999999999996 20.3 8 22.325 22.95 29.9 24.825 9 24.45 24.175 28.625 22.75 10-14 23.86 28.46 27.384999999999998 20.294999999999998 15-19 24.26 27.675 27.495000000000005 20.57 20-24 23.715 27.97 27.91 20.405 25-29 24.345 27.42 27.750000000000004 20.485 30-34 23.825 28.005000000000003 27.955000000000002 20.215 35-39 24.23 27.49 27.994999999999997 20.285 40-44 23.31 27.644999999999996 28.38 20.665 45-49 23.97 27.505000000000003 28.09 20.435 50-54 23.73 27.384999999999998 28.294999999999998 20.59 55-59 24.23 27.54 28.065 20.165 60-64 23.595 27.77 28.63 20.005 65-69 23.535 27.26 28.255000000000003 20.95 70-74 24.285 27.85 27.544999999999998 20.32 75-79 24.035 27.584999999999997 28.055000000000003 20.325 80-84 24.82 26.665 28.415000000000003 20.1 85-89 24.015 28.08 28.255000000000003 19.650000000000002 90-94 23.96 27.529999999999998 28.49 20.02 95-99 23.79 27.455000000000002 28.470000000000002 20.285 100-104 23.205000000000002 27.865000000000002 28.79 20.14 105-109 23.825 27.639999999999997 28.794999999999998 19.74 110-114 23.965 27.794999999999998 28.17 20.07 115-119 23.775 27.055 29.38 19.79 120-124 23.905 27.115000000000002 28.605000000000004 20.375 125-129 23.69 28.189999999999998 28.565 19.555 130-134 23.755000000000003 27.975 28.470000000000002 19.8 135-139 24.09 27.315 28.985 19.61 140-144 23.82 28.415000000000003 28.1 19.665 145-149 24.355 28.395 27.555000000000003 19.695 150-151 25.2 28.1625 27.187499999999996 19.45 >>END_MODULE >>Per sequence GC content warn #GC Content Count 0 0.0 1 0.5 2 0.5 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 0.0 12 0.0 13 0.0 14 0.0 15 0.0 16 1.0 17 1.0 18 0.5 19 1.0 20 1.0 21 0.5 22 0.5 23 3.0 24 3.5 25 5.5 26 8.0 27 7.5 28 10.5 29 15.5 30 20.0 31 25.5 32 33.0 33 38.5 34 53.5 35 65.0 36 85.0 37 110.5 38 135.5 39 166.5 40 192.0 41 219.5 42 240.5 43 263.5 44 280.0 45 272.5 46 265.5 47 240.0 48 202.5 49 185.0 50 160.5 51 132.0 52 106.0 53 85.5 54 68.5 55 51.0 56 40.5 57 36.5 58 31.5 59 19.0 60 16.0 61 16.5 62 12.0 63 9.0 64 5.0 65 4.5 66 2.0 67 4.5 68 8.5 69 5.5 70 3.5 71 3.5 72 2.0 73 4.0 74 4.5 75 2.0 76 1.5 77 1.0 78 0.5 79 0.0 80 0.0 81 0.0 82 0.0 83 0.0 84 0.5 85 0.5 86 0.0 87 0.0 88 0.5 89 1.0 90 1.0 91 0.5 92 0.0 93 0.0 94 0.0 95 0.0 96 0.0 97 0.5 98 0.5 99 0.0 100 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 92.525 #Duplication Level Percentage of deduplicated Percentage of total 1 92.51553634152931 85.6 2 6.8900297216968385 12.75 3 0.5944339367738449 1.6500000000000001 4 0.0 0.0 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 pass #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 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.037500000000000006 0.0 0.0 0.0 0.0 100-101 0.075 0.0 0.0 0.0 0.0 102-103 0.0875 0.0 0.0 0.0 0.0 104-105 0.125 0.0 0.0 0.0 0.0 106-107 0.125 0.0 0.0 0.0 0.0 108-109 0.125 0.0 0.0 0.0 0.0 110-111 0.15 0.0 0.0 0.0 0.0 112-113 0.15 0.0 0.0 0.0 0.0 114-115 0.1875 0.0 0.0 0.0 0.0 116-117 0.225 0.0 0.0 0.0 0.0 118-119 0.2625 0.0 0.0 0.0 0.0 120-121 0.325 0.0 0.0 0.0 0.0 122-123 0.35 0.0 0.0 0.0 0.0 124-125 0.4625 0.0 0.0 0.0 0.0 126-127 0.6375 0.0 0.0 0.0 0.0 128-129 1.0 0.0 0.0 0.0 0.0 130-131 1.2 0.0 0.0 0.0 0.0 132-133 1.575 0.0 0.0 0.0 0.0 134-135 1.8125 0.0 0.0 0.0 0.0 136-137 2.1624999999999996 0.0 0.0 0.0 0.0 138-139 2.65 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATGTGTG 10 0.006830828 145.0 8 AAAAGCT 10 0.006830828 145.0 1 GTTAAAA 10 0.006830828 145.0 6 >>END_MODULE Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062522 spots for SRR22215357.sra Written 2062522 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra Read 2062510 spots for SRR22215357.sra Written 2062510 spots for SRR22215357.sra SRR ids: ['SRR22215357.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_t1biab__ SRR22215357.sra spots: 41250212 blocks: [[1, 2062510], [2062511, 4125020], [4125021, 6187530], [6187531, 8250040], [8250041, 10312550], [10312551, 12375060], [12375061, 14437570], [14437571, 16500080], [16500081, 18562590], [18562591, 20625100], [20625101, 22687610], [22687611, 24750120], [24750121, 26812630], [26812631, 28875140], [28875141, 30937650], [30937651, 33000160], [33000161, 35062670], [35062671, 37125180], [37125181, 39187690], [39187691, 41250212]] SRR22215357 file size 13996926 SRR22215357 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 SRR22215357 SRR22215357_1.fastq SRR22215357_2.fastq Input file: SRR22215357_1.fastq Paired file: SRR22215357_2.fastq trimmed: SRR22215357-trimmed-pair1.fastq, SRR22215357-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): AGATCGGAAGAGCACACGTCTGAACTCCAGTCAC -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTA -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- end quality threshold (-q): 10 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Tue Feb 11 10:19:34 2025 >> started Tue Feb 11 10:20:21 2025 >> done (47.293s) 41250212 read pairs processed; of these: 90 ( 0.00%) short read pairs filtered out after trimming by size control 21145 ( 0.05%) empty read pairs filtered out after trimming by size control 41228977 (99.95%) read pairs available; of these: 3139097 ( 7.61%) trimmed read pairs available after processing 38089880 (92.39%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 4 0.00% 20 1 0.00% 21 5 0.00% 22 4 0.00% 23 4 0.00% 24 5 0.00% 25 9 0.00% 26 2 0.00% 27 5 0.00% 28 4 0.00% 29 9 0.00% 30 5 0.00% 31 4 0.00% 32 8 0.00% 33 8 0.00% 34 5 0.00% 35 11 0.00% 36 4 0.00% 37 8 0.00% 38 11 0.00% 39 8 0.00% 40 16 0.00% 41 10 0.00% 42 9 0.00% 43 12 0.00% 44 10 0.00% 45 9 0.00% 46 21 0.00% 47 14 0.00% 48 11 0.00% 49 23 0.00% 50 15 0.00% 51 12 0.00% 52 9 0.00% 53 21 0.00% 54 24 0.00% 55 11 0.00% 56 18 0.00% 57 26 0.00% 58 28 0.00% 59 22 0.00% 60 31 0.00% 61 29 0.00% 62 43 0.00% 63 45 0.00% 64 49 0.00% 65 45 0.00% 66 45 0.00% 67 71 0.00% 68 62 0.00% 69 87 0.00% 70 87 0.00% 71 79 0.00% 72 97 0.00% 73 105 0.00% 74 127 0.00% 75 139 0.00% 76 153 0.00% 77 194 0.00% 78 198 0.00% 79 227 0.00% 80 234 0.00% 81 281 0.00% 82 297 0.00% 83 331 0.00% 84 397 0.00% 85 458 0.00% 86 510 0.00% 87 564 0.00% 88 596 0.00% 89 620 0.00% 90 765 0.00% 91 799 0.00% 92 909 0.00% 93 947 0.00% 94 1113 0.00% 95 1240 0.00% 96 1393 0.00% 97 1455 0.00% 98 1671 0.00% 99 1773 0.00% 100 1908 0.00% 101 2060 0.00% 102 2285 0.01% 103 2553 0.01% 104 2781 0.01% 105 3084 0.01% 106 3402 0.01% 107 3720 0.01% 108 4184 0.01% 109 4583 0.01% 110 5165 0.01% 111 5772 0.01% 112 6466 0.02% 113 7211 0.02% 114 7978 0.02% 115 9086 0.02% 116 10331 0.03% 117 11524 0.03% 118 13512 0.03% 119 15152 0.04% 120 17297 0.04% 121 19149 0.05% 122 22047 0.05% 123 24137 0.06% 124 27413 0.07% 125 30566 0.07% 126 34806 0.08% 127 39390 0.10% 128 43916 0.11% 129 48864 0.12% 130 54045 0.13% 131 60366 0.15% 132 65338 0.16% 133 71215 0.17% 134 77422 0.19% 135 84554 0.21% 136 92561 0.22% 137 100037 0.24% 138 108199 0.26% 139 117680 0.29% 140 126273 0.31% 141 133637 0.32% 142 142447 0.35% 143 150442 0.36% 144 159793 0.39% 145 167843 0.41% 146 176285 0.43% 147 185152 0.45% 148 195410 0.47% 149 204290 0.50% 150 217053 0.53% 151 38089880 92.39% 41228977 reads passed initial QC criterion=sequence-density sequence-density=0.29 sequence-density-rank=1 fanout-score=2.02 fanout-score-rank=29 prefix-density=0.30 prefix-fanout=2.0 sequence=GGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTACTATGTCTGGACCTGGTAAGTTTCCCCGTGTTGAGTCAAATTAAGCCGCAGGCTCCACTCCTGGTGGTGCCCTTCCGTCAATTCCTTTAAGTTTCAGCCTTGCGACCATACTCCCCCCAGAACCCAAAAACTTTGATTTCTCATAAGGTGCTGGCGGAGTCCTAAAAGCAACATCCGCC criterion=fanout-score sequence-density=0.09 sequence-density-rank=21 fanout-score=91.53 fanout-score-rank=1 prefix-density=0.52 prefix-fanout=16.7 sequence=CCACCACCATGGGCTCCCCAGCCACCATAGGTGTCAATAATGATCTTGCGTCCAGTGAGACCTGCATCACCATGAGGACCACCAATAACAAAACGGCCAGATGGGTTGAGGTGAAAGATAGTTTTCTCATCAAG criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=2.08 fanout-score-rank=30 prefix-density=0.25 prefix-fanout=2.1 sequence=GGGTAATCTTTGAAATTTCATCGTGATGGGGATAGATCATTGCAATTGTTGGTCTTCAACGAGGAATTCCTAGTAAGCGCGAGTCATCAGCTCGCGTTGACTACGTCCCTGCCCTTTGTACACACCGCCCGTCGCTCCTACCGATTGAATGGTCCGGTGAAGTGTTCGGATCGCGGCGACGTGGGCGGTTCGCCGCCGGCGACGTCGCGAGAAGTCCACTGAACCTTATCATTTAGAGGAAGGAGA criterion=fanout-score sequence-density=0.02 sequence-density-rank=37 fanout-score=82.92 fanout-score-rank=1 prefix-density=0.21 prefix-fanout=6.5 sequence=TCTTCTCTCTGTCTTCTTGATTCCTTGTTTTTCGTTCTGTTTATTACAGCAGCAATACCATAATCATGTCTCAGACTGTTGTCCTCAAGGTTGGTATGTCATGCGAAGGCTGTGTTGGGGCTGTGAAAAGGGTTTTGGGAAAAATGGAAGGTGTGGAATCATATGACATTGATTTGAAGGAGCAAAAAGTCACAGTGAAAGGAAATGTGCAGCCAGATGCTGTTCTTCAGACCGTCTCTAAGACCGGGAAGAAGACTGCCTTCTGGGAAGCAGAGGCACCAGCTGAACCCGCAAAGCCTGCAGAAACCGTGGCTGCTGCATAATGTTTATAATACCAATATTTACTATGTGAAACTGTGTTCTACTGGGTTATAGTTAGTTGGGCTTTCTATGATCATGATGTGGATTCTGGATATCCAGCATGCTTTTACTGGGATGTAAGCTATAATAATTTCTCTGGTACATTCATATGGTTATC SRR22215357 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 10:21:07 Started mapping on | Feb 11 10:21:07 Finished on | Feb 11 10:24:52 Mapping speed, Million of reads per hour | 659.66 Number of input reads | 41228977 Average input read length | 300 UNIQUE READS: Uniquely mapped reads number | 37900830 Uniquely mapped reads % | 91.93% Average mapped length | 299.03 Number of splices: Total | 30336671 Number of splices: Annotated (sjdb) | 29654695 Number of splices: GT/AG | 29861699 Number of splices: GC/AG | 369868 Number of splices: AT/AC | 38828 Number of splices: Non-canonical | 66276 Mismatch rate per base, % | 0.31% Deletion rate per base | 0.02% Deletion average length | 2.26 Insertion rate per base | 0.02% Insertion average length | 1.85 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 826132 % of reads mapped to multiple loci | 2.00% Number of reads mapped to too many loci | 701401 % of reads mapped to too many loci | 1.70% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.83% % of reads unmapped: other | 2.54% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 2502015 2502015 2502015 N_multimapping 826132 826132 826132 N_noFeature 1565082 37387049 1761377 N_ambiguous 495977 2587 176960 UnstrandedReadsAssigned:35839771 PositiveStrandReadsAssigned:511194 NegativeStrandReadsAssigned:35962493 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR22215357 Starting Kallisto paired end mapping to ensembl reference transcriptome [quant] fragment length distribution will be estimated from the data [index] k-mer length: 31 [index] number of targets: 52,400 [index] number of k-mers: 62,057,036 [index] number of equivalence classes: 130,681 [quant] running in paired-end mode [quant] will process pair 1: SRR22215357-trimmed-pair1.fastq SRR22215357-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 41,228,977 reads, 37,355,167 reads pseudoaligned [quant] estimated average fragment length: 199.01 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,203 rounds 52401 SRR22215357.ke.tsv 34699 SRR22215357.se.tsv 87100 total ==> SRR22215357.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1819.99 3979 54.9419 Potri.005G024800.1.v4.1 1035 836.99 1228.04 36.8714 Potri.004G059700.1.v4.1 961 762.997 93 3.06308 Potri.007G009000.2.v4.1 1416 1217.99 0 0 Potri.003G141000.2.v4.1 2943 2744.99 879.357 8.05051 Potri.016G087400.1.v4.1 270 77.5215 1938 628.247 Potri.015G069301.1.v4.1 564 366.055 0 0 Potri.010G195200.1.v4.1 1773 1574.99 124 1.97853 Potri.012G127500.1.v4.1 977 778.997 6313 203.657 ==> SRR22215357.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 2867 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 940 Potri.001G212900.v4.1 20 Potri.001G182400.v4.1 72 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 3 SRR22215357 completed mapping pipeline successfully