Starting /dee2/code/volunteer_pipeline.sh SRR7180114 current disk space = 3056773013504 free memory = 1576679908 SRR7180114 SRAfilesize a83f6e9c41fe8faba36518bad961b4dc SRR7180114.sra SRR7180114.sra file validated SRR7180114 is paired end SRR7180114 is conventional basespace SRR7180114 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7180114_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 44 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 27.81925 33.0 25.0 33.0 18.0 34.0 2 30.20125 31.0 28.0 33.0 25.0 34.0 3 31.7705 33.0 31.0 33.0 28.0 34.0 4 32.08525 33.0 31.0 33.0 30.0 34.0 5 32.77675 33.0 33.0 33.0 32.0 34.0 6 37.117 38.0 37.0 38.0 36.0 38.0 7 37.238 38.0 38.0 38.0 36.0 38.0 8 37.48775 38.0 38.0 38.0 37.0 38.0 9 37.6085 38.0 38.0 38.0 38.0 38.0 10-14 37.662400000000005 38.0 38.0 38.0 38.0 38.0 15-19 37.614 38.0 38.0 38.0 38.0 38.0 20-24 37.59925 38.0 38.0 38.0 38.0 38.0 25-29 37.61944999999999 38.0 38.0 38.0 38.0 38.0 30-34 37.573 38.0 38.0 38.0 38.0 38.0 35-39 37.5675 38.0 38.0 38.0 38.0 38.0 40-44 37.5067 38.0 38.0 38.0 38.0 38.0 45-49 37.4791 38.0 38.0 38.0 37.8 38.0 50-54 37.43705 38.0 38.0 38.0 37.2 38.0 55-59 37.433099999999996 38.0 38.0 38.0 37.0 38.0 60-64 37.344049999999996 38.0 38.0 38.0 37.0 38.0 65-69 37.298899999999996 38.0 38.0 38.0 37.0 38.0 70-74 37.2859 38.0 38.0 38.0 37.0 38.0 75-79 37.27575 38.0 38.0 38.0 37.0 38.0 80-84 37.16035 38.0 38.0 38.0 36.8 38.0 85-89 37.126050000000006 38.0 38.0 38.0 36.0 38.0 90-94 37.052550000000004 38.0 38.0 38.0 36.0 38.0 95-99 36.972449999999995 38.0 38.0 38.0 36.0 38.0 100-104 36.82495 38.0 38.0 38.0 35.6 38.0 105-109 36.70865 38.0 38.0 38.0 34.8 38.0 110-114 36.6235 38.0 38.0 38.0 34.6 38.0 115-119 36.59345 38.0 38.0 38.0 34.4 38.0 120-124 36.454249999999995 38.0 38.0 38.0 34.0 38.0 125-129 36.2978 38.0 38.0 38.0 33.8 38.0 130-134 36.00405000000001 38.0 37.2 38.0 33.2 38.0 135-139 35.86274999999999 38.0 36.8 38.0 32.8 38.0 140-144 35.57395 38.0 36.0 38.0 31.8 38.0 145-149 35.2856 38.0 36.0 38.0 31.2 38.0 150-151 32.410624999999996 36.5 33.5 38.0 16.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 6 1.0 7 0.0 8 1.0 9 0.0 10 1.0 11 0.0 12 1.0 13 1.0 14 0.0 15 1.0 16 3.0 17 3.0 18 1.0 19 0.0 20 1.0 21 1.0 22 4.0 23 5.0 24 6.0 25 6.0 26 7.0 27 11.0 28 16.0 29 15.0 30 39.0 31 26.0 32 56.0 33 71.0 34 110.0 35 202.0 36 558.0 37 2853.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 31.88097768331562 14.133900106269925 12.991498405951116 40.99362380446333 2 19.06429822366775 18.864148111083313 37.0778083562672 24.993745308981737 3 19.3 22.275 28.65 29.775000000000002 4 21.099999999999998 28.675 24.425 25.8 5 21.875 32.4 25.35 20.375 6 18.2 34.725 27.250000000000004 19.825 7 13.950000000000001 22.925 43.575 19.55 8 17.75 23.9 31.85 26.5 9 17.5 23.625 33.925 24.95 10-14 19.32 28.785 27.67 24.224999999999998 15-19 19.74 28.194999999999997 28.02 24.044999999999998 20-24 19.105 28.73 28.189999999999998 23.974999999999998 25-29 18.93 28.915000000000003 28.305000000000003 23.849999999999998 30-34 19.93 28.365000000000002 27.994999999999997 23.71 35-39 19.39 28.575 28.105000000000004 23.93 40-44 19.905 28.235 27.944999999999997 23.915 45-49 19.78 28.444999999999997 27.455000000000002 24.32 50-54 19.715 28.435 27.779999999999998 24.07 55-59 19.814999999999998 28.355000000000004 27.694999999999997 24.135 60-64 19.615 27.975 27.985 24.425 65-69 19.735 28.134999999999998 27.955000000000002 24.175 70-74 19.415 28.18 28.689999999999998 23.715 75-79 18.990000000000002 27.935 28.9 24.175 80-84 20.23 27.560000000000002 28.000000000000004 24.21 85-89 20.155 27.6 28.84 23.405 90-94 20.44 27.42 28.175 23.965 95-99 20.39 28.125 27.944999999999997 23.54 100-104 20.43 28.125 27.455000000000002 23.990000000000002 105-109 20.055 28.08 28.449999999999996 23.415 110-114 20.84 28.12 27.925 23.115 115-119 20.4 28.28 27.905 23.415 120-124 20.3 28.310000000000002 27.339999999999996 24.05 125-129 20.585 27.935 27.400000000000002 24.08 130-134 20.465 28.449999999999996 27.534999999999997 23.549999999999997 135-139 21.060000000000002 28.050000000000004 27.029999999999998 23.86 140-144 20.65 28.494999999999997 27.775 23.080000000000002 145-149 21.805 27.544999999999998 26.83 23.82 150-151 21.69067000626174 27.977457733249842 26.29931120851597 24.032561051972447 >>END_MODULE >>Per sequence GC content pass #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 0.5 12 0.5 13 0.0 14 1.0 15 1.0 16 0.5 17 1.0 18 0.5 19 0.0 20 0.5 21 1.0 22 0.5 23 0.0 24 1.0 25 2.0 26 3.5 27 5.0 28 7.5 29 15.5 30 22.0 31 25.0 32 32.0 33 41.5 34 62.5 35 76.5 36 88.5 37 118.5 38 145.0 39 170.5 40 198.5 41 219.0 42 258.5 43 272.0 44 266.5 45 272.5 46 261.5 47 248.0 48 220.0 49 196.5 50 179.0 51 135.0 52 100.0 53 87.5 54 60.0 55 39.5 56 31.5 57 29.0 58 26.5 59 18.0 60 14.5 61 11.5 62 10.5 63 7.0 64 2.5 65 4.0 66 3.0 67 0.5 68 0.5 69 0.5 70 0.0 71 0.5 72 1.0 73 0.5 74 0.0 75 0.0 76 0.0 77 0.0 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 warn #Base N-Count 1 5.8999999999999995 2 0.075 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 0.1875 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.625 #Duplication Level Percentage of deduplicated Percentage of total 1 99.62358845671268 99.25 2 0.37641154328732745 0.75 3 0.0 0.0 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 0.025 0.0 0.0 0.0 0.0 60-61 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.025 0.0 0.0 0.0 0.0 66-67 0.025 0.0 0.0 0.0 0.0 68-69 0.025 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 0.05 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 0.075 0.0 0.0 0.0 0.0 86-87 0.075 0.0 0.0 0.0 0.0 88-89 0.1 0.0 0.0 0.0 0.0 90-91 0.1 0.0 0.0 0.0 0.0 92-93 0.1 0.0 0.0 0.0 0.0 94-95 0.1 0.0 0.0 0.0 0.0 96-97 0.1625 0.0 0.0 0.0 0.0 98-99 0.25 0.0 0.0 0.0 0.0 100-101 0.3375 0.0 0.0 0.0 0.0 102-103 0.3875 0.0 0.0 0.0 0.0 104-105 0.475 0.0 0.0 0.0 0.0 106-107 0.525 0.0 0.0 0.0 0.0 108-109 0.6 0.0 0.0 0.0 0.0 110-111 0.6875 0.0 0.0 0.0 0.0 112-113 0.8875 0.0 0.0 0.0 0.0 114-115 1.025 0.0 0.0 0.0 0.0 116-117 1.1 0.0 0.0 0.0 0.0 118-119 1.2374999999999998 0.0 0.0 0.0 0.0 120-121 1.5 0.0 0.0 0.0 0.0 122-123 2.05 0.0 0.0 0.0 0.0 124-125 2.4625 0.0 0.0 0.0 0.0 126-127 2.7249999999999996 0.0 0.0 0.0 0.0 128-129 2.9625 0.0 0.0 0.0 0.0 130-131 3.3625 0.0 0.0 0.0 0.0 132-133 3.75 0.0 0.0 0.0 0.0 134-135 4.15 0.0 0.0 0.0 0.0 136-137 4.550000000000001 0.0 0.0 0.0 0.0 138-139 5.0625 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position GGCAGCT 10 0.0056249425 154.6 1 CACGAGA 10 0.0068396386 144.9375 145 >>END_MODULE SRR7180114 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7180114_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 33.00275 33.0 33.0 34.0 32.0 34.0 2 33.146 34.0 33.0 34.0 32.0 34.0 3 33.203 34.0 33.0 34.0 33.0 34.0 4 33.14875 34.0 33.0 34.0 33.0 34.0 5 33.0985 34.0 33.0 34.0 33.0 34.0 6 37.2585 38.0 38.0 38.0 37.0 38.0 7 37.36675 38.0 38.0 38.0 37.0 38.0 8 37.296 38.0 38.0 38.0 37.0 38.0 9 37.217 38.0 38.0 38.0 37.0 38.0 10-14 37.24935000000001 38.0 38.0 38.0 37.0 38.0 15-19 37.1683 38.0 38.0 38.0 37.0 38.0 20-24 37.2204 38.0 38.0 38.0 37.0 38.0 25-29 37.181599999999996 38.0 38.0 38.0 37.0 38.0 30-34 37.12865 38.0 38.0 38.0 37.0 38.0 35-39 37.02275000000001 38.0 38.0 38.0 37.0 38.0 40-44 36.9681 38.0 38.0 38.0 36.8 38.0 45-49 37.05555 38.0 38.0 38.0 37.0 38.0 50-54 37.1134 38.0 38.0 38.0 37.0 38.0 55-59 37.07085 38.0 38.0 38.0 37.0 38.0 60-64 37.07185 38.0 38.0 38.0 36.6 38.0 65-69 36.921049999999994 38.0 38.0 38.0 36.0 38.0 70-74 36.920449999999995 38.0 38.0 38.0 36.0 38.0 75-79 36.83040000000001 38.0 38.0 38.0 36.0 38.0 80-84 36.86055 38.0 38.0 38.0 36.0 38.0 85-89 36.67094999999999 38.0 38.0 38.0 35.2 38.0 90-94 36.59785 38.0 38.0 38.0 35.0 38.0 95-99 36.57215 38.0 38.0 38.0 34.6 38.0 100-104 36.34945 38.0 38.0 38.0 34.0 38.0 105-109 36.24485 38.0 38.0 38.0 34.0 38.0 110-114 36.183 38.0 38.0 38.0 34.0 38.0 115-119 35.86395 38.0 37.2 38.0 33.0 38.0 120-124 35.674400000000006 38.0 37.2 38.0 31.6 38.0 125-129 35.513400000000004 38.0 37.0 38.0 31.0 38.0 130-134 35.38935 38.0 36.0 38.0 31.0 38.0 135-139 34.8421 38.0 35.8 38.0 28.0 38.0 140-144 34.590500000000006 38.0 35.0 38.0 27.4 38.0 145-149 33.947500000000005 38.0 34.6 38.0 24.0 38.0 150-151 30.39125 36.5 29.0 38.0 8.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 6.0 3 5.0 4 2.0 5 2.0 6 3.0 7 1.0 8 0.0 9 0.0 10 2.0 11 1.0 12 3.0 13 1.0 14 3.0 15 3.0 16 2.0 17 7.0 18 1.0 19 1.0 20 1.0 21 7.0 22 9.0 23 7.0 24 12.0 25 17.0 26 15.0 27 20.0 28 19.0 29 21.0 30 38.0 31 49.0 32 56.0 33 98.0 34 114.0 35 225.0 36 559.0 37 2690.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 34.4672336168084 16.18309154577289 18.78439219609805 30.565282641320664 2 25.1 23.0 35.175 16.725 3 22.625 24.975 31.1 21.3 4 23.674999999999997 34.725 22.3 19.3 5 24.25 36.05 23.0 16.7 6 19.6 36.325 24.474999999999998 19.6 7 19.979994998749685 18.254563640910227 42.11052763190798 19.654913728432106 8 22.18609304652326 23.686843421710854 27.48874437218609 26.638319159579787 9 22.125 25.900000000000002 29.099999999999998 22.875 10-14 23.27 28.965000000000003 25.805 21.959999999999997 15-19 24.141035258814703 27.826956739184794 27.631907976994246 20.400100025006253 20-24 23.621810905452726 27.528764382191095 27.70885442721361 21.14057028514257 25-29 23.76351621946336 28.699439327192632 26.70204245094113 20.835002002402884 30-34 23.04609218436874 28.476953907815634 27.139278557114228 21.337675350701403 35-39 23.207660683846385 29.068484909254988 27.00792138774692 20.71593301915171 40-44 23.621415680770003 28.233406857830357 27.416282334068576 20.72889512733106 45-49 23.738233526937712 28.244542359303026 27.448427798918484 20.568796314840775 50-54 24.054621848739497 28.396358543417367 26.790716286514606 20.75830332132853 55-59 23.87335567448607 28.08482969039164 27.44460561196419 20.597209023158104 60-64 24.19862979446917 27.69415412311847 27.78916837525629 20.318047707156072 65-69 23.85977195439088 27.835567113422684 27.980596119223843 20.324064812962593 70-74 23.317331733173315 28.552855285528555 26.957695769576954 21.172117211721172 75-79 23.485 28.1 27.495000000000005 20.919999999999998 80-84 23.622362236223623 28.272827282728276 27.177717771777175 20.927092709270926 85-89 23.79 27.705000000000002 27.97 20.535 90-94 23.724999999999998 28.015 27.779999999999998 20.48 95-99 24.335 27.950000000000003 27.500000000000004 20.215 100-104 23.65 28.860000000000003 27.49 20.0 105-109 23.990000000000002 28.315 27.284999999999997 20.41 110-114 23.935000000000002 28.134999999999998 27.650000000000002 20.28 115-119 24.43 28.42 27.71 19.439999999999998 120-124 23.825 28.335 27.46 20.380000000000003 125-129 25.045 28.384999999999998 27.22 19.35 130-134 25.040000000000003 28.139999999999997 27.439999999999998 19.38 135-139 24.73 28.325 27.51 19.435 140-144 25.39 28.38 27.245 18.985 145-149 25.525 28.455000000000002 27.089999999999996 18.93 150-151 25.592773805043283 29.00514364571572 26.408229833145153 18.993852716095848 >>END_MODULE >>Per sequence GC content pass #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 0.5 13 0.5 14 0.0 15 0.0 16 0.0 17 0.0 18 1.0 19 1.0 20 0.5 21 1.0 22 0.5 23 0.5 24 1.0 25 3.5 26 5.0 27 4.0 28 3.5 29 5.0 30 7.0 31 13.5 32 21.0 33 26.5 34 34.5 35 50.5 36 75.5 37 101.0 38 134.5 39 158.5 40 195.0 41 242.5 42 261.0 43 271.0 44 284.0 45 296.5 46 279.5 47 249.5 48 239.5 49 215.0 50 166.0 51 132.5 52 111.0 53 86.5 54 75.0 55 58.0 56 42.0 57 34.0 58 28.5 59 21.5 60 12.5 61 11.5 62 10.5 63 9.0 64 7.0 65 4.5 66 2.0 67 1.5 68 1.5 69 0.5 70 0.0 71 0.0 72 0.0 73 0.0 74 0.0 75 0.0 76 0.5 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 0.05 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.025 8 0.05 9 0.0 10-14 0.0 15-19 0.025 20-24 0.05 25-29 0.12 30-34 0.2 35-39 0.27 40-44 0.26 45-49 0.13999999999999999 50-54 0.04 55-59 0.034999999999999996 60-64 0.015 65-69 0.02 70-74 0.01 75-79 0.0 80-84 0.01 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 0.36250000000000004 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.375 #Duplication Level Percentage of deduplicated Percentage of total 1 99.44654088050314 98.825 2 0.4779874213836478 0.95 3 0.07547169811320754 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 0.0125 0.0 28-29 0.0 0.0 0.0 0.025 0.0 30-31 0.0 0.0 0.0 0.025 0.0 32-33 0.0 0.0 0.0 0.025 0.0 34-35 0.0 0.0 0.0 0.025 0.0 36-37 0.0 0.0 0.0 0.025 0.0 38-39 0.0 0.0 0.0 0.025 0.0 40-41 0.0 0.0 0.0 0.025 0.0 42-43 0.0 0.0 0.0 0.025 0.0 44-45 0.0 0.0 0.0 0.025 0.0 46-47 0.0 0.0 0.0 0.025 0.0 48-49 0.0 0.0 0.0 0.025 0.0 50-51 0.0 0.0 0.0 0.025 0.0 52-53 0.0 0.0 0.0 0.025 0.0 54-55 0.0 0.0 0.0 0.025 0.0 56-57 0.0 0.0 0.0 0.025 0.0 58-59 0.025 0.0 0.0 0.025 0.0 60-61 0.025 0.0 0.0 0.025 0.0 62-63 0.025 0.0 0.0 0.025 0.0 64-65 0.025 0.0 0.0 0.025 0.0 66-67 0.025 0.0 0.0 0.025 0.0 68-69 0.025 0.0 0.0 0.025 0.0 70-71 0.025 0.0 0.0 0.025 0.0 72-73 0.025 0.0 0.0 0.025 0.0 74-75 0.025 0.0 0.0 0.025 0.0 76-77 0.05 0.0 0.0 0.025 0.0 78-79 0.05 0.0 0.0 0.025 0.0 80-81 0.05 0.0 0.0 0.025 0.0 82-83 0.0625 0.0 0.0 0.025 0.0 84-85 0.075 0.0 0.0 0.025 0.0 86-87 0.075 0.0 0.0 0.025 0.0 88-89 0.1 0.0 0.0 0.025 0.0 90-91 0.1 0.0 0.0 0.025 0.0 92-93 0.125 0.0 0.0 0.025 0.0 94-95 0.125 0.0 0.0 0.025 0.0 96-97 0.1875 0.0 0.0 0.025 0.0 98-99 0.275 0.0 0.0 0.025 0.0 100-101 0.3625 0.0 0.0 0.025 0.0 102-103 0.4125 0.0 0.0 0.025 0.0 104-105 0.5 0.0 0.0 0.025 0.0 106-107 0.55 0.0 0.0 0.025 0.0 108-109 0.625 0.0 0.0 0.025 0.0 110-111 0.7125 0.0 0.0 0.025 0.0 112-113 0.9125 0.0 0.0 0.025 0.0 114-115 1.025 0.0 0.0 0.025 0.0 116-117 1.1 0.0 0.0 0.025 0.0 118-119 1.25 0.0 0.0 0.025 0.0 120-121 1.5499999999999998 0.0 0.0 0.025 0.0 122-123 2.1125 0.0 0.0 0.025 0.0 124-125 2.5375 0.0 0.0 0.025 0.0 126-127 2.8 0.0 0.0 0.025 0.0 128-129 3.0125 0.0 0.0 0.025 0.0 130-131 3.4124999999999996 0.0 0.0 0.025 0.0 132-133 3.8 0.0 0.0 0.025 0.0 134-135 4.1875 0.0 0.0 0.025 0.0 136-137 4.6 0.0 0.0 0.025 0.0 138-139 5.125 0.0 0.0 0.025 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CTGGAAT 10 0.006830828 145.0 1 GGAAGAG 40 0.005621335 54.375 145 TCGGAAG 35 0.0035366106 20.714287 140-144 GAGAGAG 40 0.0076550315 18.125 90-94 >>END_MODULE Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra Read 858007 spots for SRR7180114.sra Written 858007 spots for SRR7180114.sra Read 858002 spots for SRR7180114.sra Written 858002 spots for SRR7180114.sra SRR ids: ['SRR7180114.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_ceo7v_ax SRR7180114.sra spots: 17160045 blocks: [[1, 858002], [858003, 1716004], [1716005, 2574006], [2574007, 3432008], [3432009, 4290010], [4290011, 5148012], [5148013, 6006014], [6006015, 6864016], [6864017, 7722018], [7722019, 8580020], [8580021, 9438022], [9438023, 10296024], [10296025, 11154026], [11154027, 12012028], [12012029, 12870030], [12870031, 13728032], [13728033, 14586034], [14586035, 15444036], [15444037, 16302038], [16302039, 17160045]] SRR7180114 file size 5793275 SRR7180114 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 SRR7180114 SRR7180114_1.fastq SRR7180114_2.fastq Input file: SRR7180114_1.fastq Paired file: SRR7180114_2.fastq trimmed: SRR7180114-trimmed-pair1.fastq, SRR7180114-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 Mon Feb 10 21:13:07 2025 >> started Mon Feb 10 21:13:26 2025 >> done (19.221s) 17160045 read pairs processed; of these: 26318 ( 0.15%) short read pairs filtered out after trimming by size control 15553 ( 0.09%) empty read pairs filtered out after trimming by size control 17118174 (99.76%) read pairs available; of these: 6274169 (36.65%) trimmed read pairs available after processing 10844005 (63.35%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 3 0.00% 20 6 0.00% 21 2 0.00% 22 4 0.00% 23 6 0.00% 24 7 0.00% 25 8 0.00% 26 10 0.00% 27 8 0.00% 28 8 0.00% 29 5 0.00% 30 9 0.00% 31 4 0.00% 32 6 0.00% 33 4 0.00% 34 4 0.00% 35 10 0.00% 36 10 0.00% 37 8 0.00% 38 4 0.00% 39 7 0.00% 40 10 0.00% 41 7 0.00% 42 8 0.00% 43 15 0.00% 44 14 0.00% 45 14 0.00% 46 22 0.00% 47 17 0.00% 48 20 0.00% 49 29 0.00% 50 22 0.00% 51 20 0.00% 52 23 0.00% 53 46 0.00% 54 39 0.00% 55 40 0.00% 56 55 0.00% 57 73 0.00% 58 70 0.00% 59 101 0.00% 60 78 0.00% 61 102 0.00% 62 119 0.00% 63 129 0.00% 64 151 0.00% 65 168 0.00% 66 205 0.00% 67 200 0.00% 68 241 0.00% 69 267 0.00% 70 297 0.00% 71 372 0.00% 72 412 0.00% 73 442 0.00% 74 530 0.00% 75 650 0.00% 76 788 0.00% 77 896 0.01% 78 971 0.01% 79 1158 0.01% 80 1268 0.01% 81 1393 0.01% 82 1652 0.01% 83 1853 0.01% 84 3092 0.02% 85 4173 0.02% 86 4594 0.03% 87 5132 0.03% 88 5388 0.03% 89 5661 0.03% 90 5934 0.03% 91 6297 0.04% 92 6687 0.04% 93 6828 0.04% 94 7322 0.04% 95 7749 0.05% 96 8332 0.05% 97 8949 0.05% 98 9659 0.06% 99 10104 0.06% 100 10767 0.06% 101 11249 0.07% 102 11709 0.07% 103 12805 0.07% 104 13743 0.08% 105 14526 0.08% 106 15516 0.09% 107 16761 0.10% 108 17230 0.10% 109 18395 0.11% 110 19313 0.11% 111 20290 0.12% 112 21180 0.12% 113 22623 0.13% 114 23923 0.14% 115 25227 0.15% 116 26484 0.15% 117 27836 0.16% 118 29341 0.17% 119 30440 0.18% 120 32549 0.19% 121 33718 0.20% 122 34829 0.20% 123 35588 0.21% 124 37137 0.22% 125 38149 0.22% 126 39530 0.23% 127 41687 0.24% 128 42917 0.25% 129 44587 0.26% 130 46788 0.27% 131 49314 0.29% 132 50755 0.30% 133 53874 0.31% 134 55928 0.33% 135 58696 0.34% 136 60985 0.36% 137 64381 0.38% 138 67398 0.39% 139 71111 0.42% 140 75309 0.44% 141 81001 0.47% 142 87699 0.51% 143 95302 0.56% 144 105788 0.62% 145 120418 0.70% 146 141732 0.83% 147 182023 1.06% 148 263872 1.54% 149 517694 3.02% 150 3133029 18.30% 151 10844005 63.35% 17118174 reads passed initial QC criterion=sequence-density sequence-density=0.37 sequence-density-rank=1 fanout-score=3.25 fanout-score-rank=19 prefix-density=0.41 prefix-fanout=2.9 sequence=CCACATTTGCAGCCACTGCC criterion=fanout-score sequence-density=0.02 sequence-density-rank=32 fanout-score=106.34 fanout-score-rank=1 prefix-density=0.17 prefix-fanout=13.7 sequence=CTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAA criterion=sequence-density sequence-density=0.62 sequence-density-rank=1 fanout-score=2.50 fanout-score-rank=27 prefix-density=0.63 prefix-fanout=2.4 sequence=ATGTACCCTGACTTAGGTTTCTCAGA criterion=fanout-score sequence-density=0.08 sequence-density-rank=25 fanout-score=35.95 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=10.5 sequence=AAGGCCAAGATCCAGGACAAGGA SRR7180114 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 10 21:14:17 Started mapping on | Feb 10 21:14:17 Finished on | Feb 10 21:17:10 Mapping speed, Million of reads per hour | 356.22 Number of input reads | 17118174 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 15425222 Uniquely mapped reads % | 90.11% Average mapped length | 295.26 Number of splices: Total | 15131110 Number of splices: Annotated (sjdb) | 14845908 Number of splices: GT/AG | 14886483 Number of splices: GC/AG | 191742 Number of splices: AT/AC | 10871 Number of splices: Non-canonical | 42014 Mismatch rate per base, % | 0.33% Deletion rate per base | 0.03% Deletion average length | 2.64 Insertion rate per base | 0.02% Insertion average length | 2.58 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 382144 % of reads mapped to multiple loci | 2.23% Number of reads mapped to too many loci | 236909 % of reads mapped to too many loci | 1.38% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 6.02% % of reads unmapped: other | 0.25% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 1333551 1333551 1333551 N_multimapping 382144 382144 382144 N_noFeature 404028 15276281 468110 N_ambiguous 158484 947 73064 UnstrandedReadsAssigned:14862710 PositiveStrandReadsAssigned:147994 NegativeStrandReadsAssigned:14884048 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=150 echo kmer=145 SRR7180114 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: SRR7180114-trimmed-pair1.fastq SRR7180114-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 17,118,174 reads, 14,956,486 reads pseudoaligned [quant] estimated average fragment length: 232.682 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,181 rounds 52401 SRR7180114.ke.tsv 34699 SRR7180114.se.tsv 87100 total ==> SRR7180114.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1786.32 1505 54.5187 Potri.005G024800.1.v4.1 1035 803.318 284 22.877 Potri.004G059700.1.v4.1 961 729.349 7 0.621055 Potri.007G009000.2.v4.1 1416 1184.32 0 0 Potri.003G141000.2.v4.1 2943 2711.32 749 17.8759 Potri.016G087400.1.v4.1 270 79.5518 967 786.582 Potri.015G069301.1.v4.1 564 334.897 0 0 Potri.010G195200.1.v4.1 1773 1541.32 474.626 19.9263 Potri.012G127500.1.v4.1 977 745.329 6940 602.531 ==> SRR7180114.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 37 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 514 Potri.001G212900.v4.1 1 Potri.001G182400.v4.1 0 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 433 SRR7180114 completed mapping pipeline successfully