Starting /dee2/code/volunteer_pipeline.sh SRR6958154 current disk space = 1550597193728 free memory = 1349840704 SRR6958154 SRAfilesize bc2e1762ed9aa1b662b2c5cf079281c8 SRR6958154.sra SRR6958154.sra file validated SRR6958154 is paired end SRR6958154 is conventional basespace SRR6958154 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958154_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 25.12325 27.0 18.0 33.0 18.0 33.0 2 29.64425 31.0 27.0 33.0 25.0 33.0 3 29.71925 31.0 29.0 33.0 25.0 33.0 4 29.6145 31.0 29.0 33.0 25.0 33.0 5 31.62775 33.0 32.0 33.0 30.0 33.0 6 35.9575 37.0 36.0 38.0 33.0 38.0 7 36.76525 38.0 37.0 38.0 34.0 38.0 8 36.83175 38.0 37.0 38.0 34.0 38.0 9 37.24025 38.0 38.0 38.0 36.0 38.0 10-14 37.36035 38.0 38.0 38.0 36.6 38.0 15-19 37.4078 38.0 38.0 38.0 37.0 38.0 20-24 37.3217 38.0 38.0 38.0 36.6 38.0 25-29 37.4463 38.0 38.0 38.0 37.0 38.0 30-34 37.4162 38.0 38.0 38.0 37.4 38.0 35-39 37.528949999999995 38.0 38.0 38.0 37.6 38.0 40-44 37.490750000000006 38.0 38.0 38.0 37.8 38.0 45-49 37.43205 38.0 38.0 38.0 37.0 38.0 50-54 37.28535000000001 38.0 38.0 38.0 36.8 38.0 55-59 37.241550000000004 38.0 38.0 38.0 36.2 38.0 60-64 37.23245 38.0 38.0 38.0 36.0 38.0 65-69 37.16295 38.0 38.0 38.0 36.0 38.0 70-74 37.0186 38.0 38.0 38.0 36.0 38.0 75-79 36.6074 38.0 37.8 38.0 33.8 38.0 80-84 35.650999999999996 38.0 36.2 38.0 29.2 38.0 85-89 36.76205 38.0 38.0 38.0 34.6 38.0 90-94 36.672549999999994 38.0 38.0 38.0 34.4 38.0 95-99 36.50015 38.0 37.8 38.0 34.2 38.0 100-104 36.297000000000004 38.0 37.0 38.0 34.0 38.0 105-109 36.30345 38.0 37.4 38.0 33.8 38.0 110-114 36.16915 38.0 37.4 38.0 33.4 38.0 115-119 35.87265 38.0 36.6 38.0 32.4 38.0 120-124 35.664649999999995 38.0 36.2 38.0 31.4 38.0 125-129 35.43485 38.0 35.8 38.0 30.0 38.0 130-134 35.052550000000004 38.0 35.0 38.0 28.6 38.0 135-139 35.003699999999995 38.0 35.2 38.0 28.6 38.0 140-144 34.33485 38.0 33.8 38.0 26.0 38.0 145-149 33.7981 38.0 33.4 38.0 23.2 38.0 150-151 28.974249999999998 35.5 27.0 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 10 1.0 11 0.0 12 0.0 13 1.0 14 2.0 15 1.0 16 1.0 17 0.0 18 5.0 19 3.0 20 2.0 21 5.0 22 2.0 23 4.0 24 7.0 25 7.0 26 11.0 27 14.0 28 22.0 29 32.0 30 51.0 31 65.0 32 71.0 33 144.0 34 182.0 35 366.0 36 1011.0 37 1990.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 49.752925877763325 9.05071521456437 6.189856957087126 35.006501950585175 2 24.425 12.174999999999999 35.35 28.050000000000004 3 22.275 17.349999999999998 25.15 35.225 4 26.424999999999997 24.775 23.05 25.75 5 26.424999999999997 29.275000000000002 24.075 20.225 6 21.475 33.074999999999996 23.625 21.825 7 17.075000000000003 25.25 39.65 18.025 8 20.125 23.549999999999997 29.825000000000003 26.5 9 18.875 22.825 34.050000000000004 24.25 10-14 22.025 27.625 26.71 23.64 15-19 23.695 25.845000000000002 26.21 24.25 20-24 23.294999999999998 26.115 26.875 23.715 25-29 22.79 26.090000000000003 26.99 24.13 30-34 22.66 25.96 26.575 24.805 35-39 22.67 26.26 27.04 24.03 40-44 22.86 26.21 26.669999999999998 24.26 45-49 22.470000000000002 26.44 26.479999999999997 24.610000000000003 50-54 22.115000000000002 26.66 26.46 24.765 55-59 22.575 25.724999999999998 26.810000000000002 24.89 60-64 22.48 26.905 26.26 24.355 65-69 22.58 25.535000000000004 27.27 24.615000000000002 70-74 22.575 26.490000000000002 26.435 24.5 75-79 22.89 26.02 26.345000000000002 24.745 80-84 22.665 25.91 26.834999999999997 24.59 85-89 22.7 25.965 26.665 24.67 90-94 22.875 26.27 26.424999999999997 24.43 95-99 22.86 25.705 26.85 24.585 100-104 23.22232223222322 26.002600260026004 26.262626262626267 24.51245124512451 105-109 23.3 26.035000000000004 25.840000000000003 24.825 110-114 23.125 26.605 25.985000000000003 24.285 115-119 23.165 27.075 25.330000000000002 24.43 120-124 23.195 26.22 26.085 24.5 125-129 22.67 26.68 26.075 24.575 130-134 22.925 26.840000000000003 25.555 24.68 135-139 22.17 26.38 26.369999999999997 25.080000000000002 140-144 22.74 26.205000000000002 26.075 24.98 145-149 22.470000000000002 26.47 25.52 25.540000000000003 150-151 21.7875 26.875 25.575 25.7625 >>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 0.5 20 0.5 21 0.0 22 1.0 23 1.0 24 0.0 25 0.0 26 0.5 27 3.5 28 4.5 29 4.0 30 8.0 31 11.0 32 15.0 33 24.0 34 32.5 35 43.0 36 58.5 37 78.0 38 98.0 39 131.0 40 164.0 41 175.0 42 191.0 43 212.5 44 217.5 45 219.0 46 217.5 47 201.0 48 196.5 49 201.5 50 185.5 51 159.0 52 130.5 53 117.0 54 109.5 55 90.5 56 87.0 57 87.0 58 73.0 59 61.5 60 54.5 61 51.5 62 41.0 63 32.5 64 34.0 65 30.5 66 27.0 67 29.0 68 25.5 69 20.0 70 17.0 71 7.0 72 3.5 73 5.5 74 4.5 75 2.5 76 1.0 77 0.5 78 1.5 79 1.0 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 3.875 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 0.01 105-109 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 99.47500000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 99.54762503141494 99.02499999999999 2 0.3769791404875597 0.75 3 0.07539582809751194 0.22499999999999998 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 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 0.0125 0.0 0.0 0.0 0.0 78-79 0.037500000000000006 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.0875 0.0 0.0 0.0 0.0 86-87 0.21250000000000002 0.0 0.0 0.0 0.0 88-89 0.2375 0.0 0.0 0.0 0.0 90-91 0.30000000000000004 0.0 0.0 0.0 0.0 92-93 0.375 0.0 0.0 0.0 0.0 94-95 0.44999999999999996 0.0 0.0 0.0 0.0 96-97 0.5 0.0 0.0 0.0 0.0 98-99 0.5375000000000001 0.0 0.0 0.0 0.0 100-101 0.6499999999999999 0.0 0.0 0.0 0.0 102-103 0.7875 0.0 0.0 0.0 0.0 104-105 0.9625 0.0 0.0 0.0 0.0 106-107 1.1749999999999998 0.0 0.0 0.0 0.0 108-109 1.35 0.0 0.0 0.0 0.0 110-111 1.625 0.0 0.0 0.0 0.0 112-113 1.975 0.0 0.0 0.0 0.0 114-115 2.2375 0.0 0.0 0.0 0.0 116-117 2.5625 0.0 0.0 0.0 0.0 118-119 2.9625000000000004 0.0 0.0 0.0 0.0 120-121 3.425 0.0 0.0 0.0 0.0 122-123 3.8625 0.0 0.0 0.0 0.0 124-125 4.2875 0.0 0.0 0.0 0.0 126-127 4.7875 0.0 0.0 0.0 0.0 128-129 5.1875 0.0 0.0 0.0 0.0 130-131 5.5875 0.0 0.0 0.0 0.0 132-133 6.0 0.0 0.0 0.0 0.0 134-135 6.6 0.0 0.0 0.0 0.0 136-137 7.1 0.0 0.0 0.0 0.0 138-139 7.6875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ATTAGAT 10 0.0068343505 144.975 6 >>END_MODULE SRR6958154 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR6958154_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 47 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 33.17675 33.0 33.0 34.0 33.0 34.0 2 33.272 34.0 33.0 34.0 33.0 34.0 3 33.29 34.0 33.0 34.0 33.0 34.0 4 33.266 34.0 33.0 34.0 33.0 34.0 5 33.28 34.0 33.0 34.0 33.0 34.0 6 37.52275 38.0 38.0 38.0 38.0 38.0 7 37.53525 38.0 38.0 38.0 38.0 38.0 8 37.411 38.0 38.0 38.0 38.0 38.0 9 37.53175 38.0 38.0 38.0 38.0 38.0 10-14 37.46155 38.0 38.0 38.0 38.0 38.0 15-19 36.1711 38.0 36.6 38.0 31.4 38.0 20-24 36.00605 38.0 36.2 38.0 30.2 38.0 25-29 37.31645 38.0 38.0 38.0 37.2 38.0 30-34 37.4953 38.0 38.0 38.0 38.0 38.0 35-39 37.34760000000001 38.0 38.0 38.0 37.4 38.0 40-44 37.35340000000001 38.0 38.0 38.0 37.6 38.0 45-49 37.35955 38.0 38.0 38.0 37.4 38.0 50-54 37.18045 38.0 38.0 38.0 37.0 38.0 55-59 37.241249999999994 38.0 38.0 38.0 37.0 38.0 60-64 37.22465 38.0 38.0 38.0 37.0 38.0 65-69 37.195150000000005 38.0 38.0 38.0 37.0 38.0 70-74 37.1374 38.0 38.0 38.0 37.0 38.0 75-79 37.04615 38.0 38.0 38.0 36.6 38.0 80-84 36.920449999999995 38.0 38.0 38.0 36.2 38.0 85-89 36.896550000000005 38.0 38.0 38.0 36.0 38.0 90-94 35.293 38.0 35.4 38.0 29.0 38.0 95-99 33.7208 37.4 31.8 38.0 23.0 38.0 100-104 34.3226 37.8 33.4 38.0 25.8 38.0 105-109 36.32645 38.0 37.8 38.0 34.0 38.0 110-114 36.19025 38.0 37.8 38.0 32.8 38.0 115-119 35.3129 38.0 36.4 38.0 28.0 38.0 120-124 35.40024999999999 38.0 36.4 38.0 29.6 38.0 125-129 35.554050000000004 38.0 36.4 38.0 31.2 38.0 130-134 33.6814 37.6 32.4 38.0 25.0 38.0 135-139 33.407250000000005 37.6 31.8 38.0 24.0 38.0 140-144 33.6644 38.0 34.0 38.0 21.2 38.0 145-149 33.76585 38.0 33.8 38.0 21.8 38.0 150-151 29.29875 35.5 24.0 38.0 7.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 5.0 3 2.0 4 2.0 5 0.0 6 1.0 7 0.0 8 0.0 9 1.0 10 0.0 11 2.0 12 0.0 13 7.0 14 2.0 15 3.0 16 1.0 17 3.0 18 3.0 19 2.0 20 2.0 21 2.0 22 10.0 23 8.0 24 9.0 25 10.0 26 13.0 27 12.0 28 14.0 29 29.0 30 49.0 31 53.0 32 80.0 33 133.0 34 180.0 35 410.0 36 1195.0 37 1757.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 42.3 19.875 9.525 28.299999999999997 2 29.25 24.25 29.125 17.375 3 20.9 26.075 29.925 23.1 4 25.4 32.975 20.45 21.175 5 27.05 34.4 19.5 19.05 6 22.400000000000002 36.8 20.9 19.900000000000002 7 22.725 20.1 36.525 20.65 8 22.75 23.75 27.1 26.400000000000002 9 23.65 23.849999999999998 28.825 23.674999999999997 10-14 25.505 27.265 24.32 22.91 15-19 24.72 26.395000000000003 26.11 22.775000000000002 20-24 24.855 26.490000000000002 25.36 23.294999999999998 25-29 24.905 26.82 25.069999999999997 23.205000000000002 30-34 24.66 26.51 25.865 22.965 35-39 25.1 26.529999999999998 25.28 23.09 40-44 24.685000000000002 26.465 25.419999999999998 23.43 45-49 24.63 26.11 25.555 23.705000000000002 50-54 24.8873761137251 26.60927019721694 25.903493843227547 22.599859845830412 55-59 24.844751602564102 26.872996794871796 25.220352564102566 23.06189903846154 60-64 24.743403594853053 26.620938266659994 25.619586441696292 23.016071696790668 65-69 24.648345597437054 26.45041798067778 25.96986534514692 22.931371076738248 70-74 24.514222756410255 26.432291666666668 26.056690705128204 22.996794871794872 75-79 24.722083124687032 26.57486229344016 25.658487731597397 23.044566850275412 80-84 23.974937343358395 26.421052631578945 26.235588972431078 23.36842105263158 85-89 24.436316264154726 26.245114740956012 25.904399238400643 23.414169756488626 90-94 24.744744744744747 26.366366366366368 26.076076076076077 22.812812812812812 95-99 24.732259033129818 26.934240816735063 25.86828145330798 22.465218696827144 100-104 25.310310310310307 26.51151151151151 25.68068068068068 22.4974974974975 105-109 25.11136693528205 26.567896291105658 25.73201861955053 22.588718154061766 110-114 24.83735361825643 26.774096687018318 25.873285957361624 22.51526373736363 115-119 25.409220603694248 26.976022425789658 25.569404815537865 22.045352154978225 120-124 25.616650823034977 26.54225246410167 25.446540251163256 22.394556461700105 125-129 25.354015511633726 27.545659244433324 25.088816612459347 22.011508631473607 130-134 25.593957885259837 27.17951282949032 25.148802080728256 22.077727204521583 135-139 25.837128985434703 26.938285199459433 25.57685569848341 21.647730116622455 140-144 25.75749987479341 27.315069865277707 25.021285120448738 21.90614513948014 145-149 25.792398978518854 27.059235892043464 24.946171949326523 22.20219318011116 150-151 26.152304609218437 26.352705410821642 25.35070140280561 22.14428857715431 >>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 0.5 24 2.0 25 3.0 26 2.0 27 3.0 28 4.0 29 5.5 30 9.0 31 13.0 32 20.5 33 32.0 34 37.5 35 37.5 36 46.5 37 69.5 38 86.0 39 108.0 40 147.0 41 176.0 42 203.5 43 214.0 44 219.0 45 230.5 46 204.5 47 194.0 48 213.0 49 191.5 50 159.5 51 149.0 52 135.5 53 122.0 54 95.5 55 74.0 56 78.0 57 81.5 58 85.5 59 84.0 60 70.0 61 60.0 62 55.5 63 48.0 64 40.0 65 34.0 66 27.5 67 23.5 68 22.5 69 16.5 70 14.5 71 15.5 72 15.0 73 9.5 74 3.5 75 3.5 76 2.5 77 0.5 78 0.0 79 0.5 80 0.5 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 0.11 55-59 0.16 60-64 0.135 65-69 0.11499999999999999 70-74 0.16 75-79 0.15 80-84 0.25 85-89 0.21 90-94 0.1 95-99 0.09 100-104 0.1 105-109 0.105 110-114 0.09 115-119 0.11499999999999999 120-124 0.065 125-129 0.075 130-134 0.034999999999999996 135-139 0.105 140-144 0.165 145-149 0.145 150-151 0.2 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.3 #Duplication Level Percentage of deduplicated Percentage of total 1 99.52165156092649 98.825 2 0.3272910372608258 0.65 3 0.12588116817724068 0.375 4 0.0 0.0 5 0.0 0.0 6 0.025176233635448138 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 CTGCAATTGCAAGCTTGTGTCAAAGAAGAGGGTAGCACCTGATCCTCTTG 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 0.0 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 0.0125 0.0 0.0 0.0 0.0 78-79 0.037500000000000006 0.0 0.0 0.0 0.0 80-81 0.05 0.0 0.0 0.0 0.0 82-83 0.075 0.0 0.0 0.0 0.0 84-85 0.0875 0.0 0.0 0.0 0.0 86-87 0.1875 0.0 0.0 0.0 0.0 88-89 0.21250000000000002 0.0 0.0 0.0 0.0 90-91 0.2375 0.0 0.0 0.0 0.0 92-93 0.2875 0.0 0.0 0.0 0.0 94-95 0.32499999999999996 0.0 0.0 0.0 0.0 96-97 0.375 0.0 0.0 0.0 0.0 98-99 0.4125 0.0 0.0 0.0 0.0 100-101 0.5249999999999999 0.0 0.0 0.0 0.0 102-103 0.6625 0.0 0.0 0.0 0.0 104-105 0.8375 0.0 0.0 0.0 0.0 106-107 1.0499999999999998 0.0 0.0 0.0 0.0 108-109 1.225 0.0 0.0 0.0 0.0 110-111 1.4375 0.0 0.0 0.0 0.0 112-113 1.7625000000000002 0.0 0.0 0.0 0.0 114-115 1.9375 0.0 0.0 0.0 0.0 116-117 2.2125 0.0 0.0 0.0 0.0 118-119 2.525 0.0 0.0 0.0 0.0 120-121 2.8625 0.0 0.0 0.0 0.0 122-123 3.2 0.0 0.0 0.0 0.0 124-125 3.4000000000000004 0.0 0.0 0.0 0.0 126-127 3.7249999999999996 0.0 0.0 0.0 0.0 128-129 4.075 0.0 0.0 0.0 0.0 130-131 4.4 0.0 0.0 0.0 0.0 132-133 4.775 0.0 0.0 0.0 0.0 134-135 5.3375 0.0 0.0 0.0 0.0 136-137 5.7875 0.0 0.0 0.0 0.0 138-139 6.2875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623569 spots for SRR6958154.sra Written 623569 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra Read 623565 spots for SRR6958154.sra Written 623565 spots for SRR6958154.sra SRR ids: ['SRR6958154.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_99rv4aaj SRR6958154.sra spots: 12471304 blocks: [[1, 623565], [623566, 1247130], [1247131, 1870695], [1870696, 2494260], [2494261, 3117825], [3117826, 3741390], [3741391, 4364955], [4364956, 4988520], [4988521, 5612085], [5612086, 6235650], [6235651, 6859215], [6859216, 7482780], [7482781, 8106345], [8106346, 8729910], [8729911, 9353475], [9353476, 9977040], [9977041, 10600605], [10600606, 11224170], [11224171, 11847735], [11847736, 12471304]] SRR6958154 file size 4204415 SRR6958154 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 SRR6958154 SRR6958154_1.fastq SRR6958154_2.fastq Input file: SRR6958154_1.fastq Paired file: SRR6958154_2.fastq trimmed: SRR6958154-trimmed-pair1.fastq, SRR6958154-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 Fri Dec 6 14:22:49 2024 >> started Fri Dec 6 14:23:04 2024 >> done (15.583s) 12471304 read pairs processed; of these: 4414 ( 0.04%) short read pairs filtered out after trimming by size control 7180 ( 0.06%) empty read pairs filtered out after trimming by size control 12459710 (99.91%) read pairs available; of these: 7335182 (58.87%) trimmed read pairs available after processing 5124528 (41.13%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 7 0.00% 19 5 0.00% 20 5 0.00% 21 7 0.00% 22 6 0.00% 23 5 0.00% 24 6 0.00% 25 4 0.00% 26 5 0.00% 27 7 0.00% 28 13 0.00% 29 6 0.00% 30 3 0.00% 31 9 0.00% 32 8 0.00% 33 13 0.00% 34 11 0.00% 35 13 0.00% 36 10 0.00% 37 20 0.00% 38 16 0.00% 39 23 0.00% 40 18 0.00% 41 20 0.00% 42 25 0.00% 43 22 0.00% 44 23 0.00% 45 34 0.00% 46 33 0.00% 47 44 0.00% 48 46 0.00% 49 50 0.00% 50 57 0.00% 51 57 0.00% 52 65 0.00% 53 82 0.00% 54 71 0.00% 55 76 0.00% 56 96 0.00% 57 117 0.00% 58 121 0.00% 59 152 0.00% 60 164 0.00% 61 177 0.00% 62 186 0.00% 63 220 0.00% 64 275 0.00% 65 272 0.00% 66 317 0.00% 67 332 0.00% 68 362 0.00% 69 446 0.00% 70 527 0.00% 71 602 0.00% 72 680 0.01% 73 808 0.01% 74 883 0.01% 75 1074 0.01% 76 1182 0.01% 77 1215 0.01% 78 1333 0.01% 79 1644 0.01% 80 1911 0.02% 81 1844 0.01% 82 2201 0.02% 83 2391 0.02% 84 2883 0.02% 85 3274 0.03% 86 3709 0.03% 87 3831 0.03% 88 4353 0.03% 89 4523 0.04% 90 4942 0.04% 91 5324 0.04% 92 5948 0.05% 93 6487 0.05% 94 7122 0.06% 95 7607 0.06% 96 8409 0.07% 97 8772 0.07% 98 9810 0.08% 99 10833 0.09% 100 13681 0.11% 101 14405 0.12% 102 11593 0.09% 103 12112 0.10% 104 13120 0.11% 105 13575 0.11% 106 14599 0.12% 107 15152 0.12% 108 16203 0.13% 109 16707 0.13% 110 17838 0.14% 111 18701 0.15% 112 19781 0.16% 113 20426 0.16% 114 21946 0.18% 115 23195 0.19% 116 24336 0.20% 117 24775 0.20% 118 26131 0.21% 119 27075 0.22% 120 28541 0.23% 121 29662 0.24% 122 30944 0.25% 123 32476 0.26% 124 34297 0.28% 125 35828 0.29% 126 37598 0.30% 127 39357 0.32% 128 40871 0.33% 129 43167 0.35% 130 45205 0.36% 131 46880 0.38% 132 49388 0.40% 133 52294 0.42% 134 55645 0.45% 135 59584 0.48% 136 63205 0.51% 137 67511 0.54% 138 71699 0.58% 139 77092 0.62% 140 84684 0.68% 141 93384 0.75% 142 103737 0.83% 143 116374 0.93% 144 135947 1.09% 145 168556 1.35% 146 211944 1.70% 147 288752 2.32% 148 425811 3.42% 149 810217 6.50% 150 3468897 27.84% 151 5124528 41.13% 12459710 reads passed initial QC criterion=sequence-density sequence-density=0.48 sequence-density-rank=1 fanout-score=4.13 fanout-score-rank=22 prefix-density=0.62 prefix-fanout=3.2 sequence=GCAGGTGCAGCTGGTGC criterion=fanout-score sequence-density=0.02 sequence-density-rank=36 fanout-score=159.08 fanout-score-rank=1 prefix-density=0.38 prefix-fanout=8.1 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=0.26 sequence-density-rank=1 fanout-score=4.33 fanout-score-rank=22 prefix-density=0.35 prefix-fanout=3.3 sequence=CTTCGACAACACCATGGGAGGCTTTTACATCGCCCCGGCCTTCATGGACAAGCTCGTCGTCCACCTCTCCAAGAACTTCATGACCCTGCCCAACATCAAGGTGCCACTCATCTTGGGTATCTGGGGAGGCAAGGGTCAAGGAAAATCCTTCCAATGTGAGCTTGTCTTCGCCAAGATGGGCATCAACCCAATCATGATGAGCGCCGGAGAGCTGGAGAGCGGAAACGCCGGAGAGCCAGCCAAGCTGATCAGGCAGCGGTACCGTGAGGCCGCAGACTTGATCAAGAAGGGTAAGATGTGCTGCCTCTTCATCAACGATCTCGACGCTGGTGCGGGTCGGATGGGCGGGACCACCCAGTACACCGTCAACAACCAGATGGTTAACGCCACCCTGATGAACATCGCGGATGCCCCCACCAACGTGCAGCTCCCTGGGATGTACAACAAGGAGGAGAACCCCCGTGTGCCCATCATCGTCACTGGTAACGATTTCTCCACGCTCTACGCGCCA criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=207.95 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=9.5 sequence=AAGAAGCACACACAAGCCTAGAAGCCTTCAGCTTAATCTTCTTCCTAAGCAAGTTCGAGCACTCGACCGAAGATGTCTTGCTGCGGAGGAAACTGCAACTGCGGGTCATCCTGCAAGTGCGGCA SRR6958154 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 06 14:24:02 Started mapping on | Dec 06 14:24:02 Finished on | Dec 06 14:25:11 Mapping speed, Million of reads per hour | 650.07 Number of input reads | 12459710 Average input read length | 293 UNIQUE READS: Uniquely mapped reads number | 12091065 Uniquely mapped reads % | 97.04% Average mapped length | 292.91 Number of splices: Total | 13623515 Number of splices: Annotated (sjdb) | 12772018 Number of splices: GT/AG | 13437568 Number of splices: GC/AG | 159475 Number of splices: AT/AC | 5945 Number of splices: Non-canonical | 20527 Mismatch rate per base, % | 0.22% Deletion rate per base | 0.01% Deletion average length | 2.38 Insertion rate per base | 0.01% Insertion average length | 2.38 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 132713 % of reads mapped to multiple loci | 1.07% Number of reads mapped to too many loci | 14752 % of reads mapped to too many loci | 0.12% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.20% % of reads unmapped: other | 0.58% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 239456 239456 239456 N_multimapping 132713 132713 132713 N_noFeature 533227 11753000 645518 N_ambiguous 271880 1682 46262 UnstrandedReadsAssigned:11285958 PositiveStrandReadsAssigned:336383 NegativeStrandReadsAssigned:11399285 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR6958154 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: SRR6958154-trimmed-pair1.fastq SRR6958154-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,459,710 reads, 11,431,349 reads pseudoaligned [quant] estimated average fragment length: 237.048 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,264 rounds 52973 SRR6958154.ke.tsv 35125 SRR6958154.se.tsv 88098 total ==> SRR6958154.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 700.401 0 0 PNS24247 1044 807.952 43.4625 7.4767 PNS24249 1928 1691.95 13.1438 1.07973 PNS24246 1044 807.952 43.4625 7.4767 PNS24248 1044 807.952 43.4625 7.4767 PNS24244 1471 1234.95 26.4686 2.97894 PNS24243 293 93.4658 0 0 KQK14069 1603 1366.95 3406.04 346.32 KQK14071 474 244.281 67.383 38.3391 ==> SRR6958154.se.tsv <== BRADI_1g14170v3 3978 BRADI_1g53295v3 112 BRADI_1g59795v3 492 BRADI_1g07683v3 0 BRADI_1g00485v3 5 BRADI_1g20270v3 154 BRADI_1g74790v3 33 BRADI_1g09890v3 0 BRADI_1g77505v3 207 BRADI_1g48960v3 0 SRR6958154 completed mapping pipeline successfully