Starting /dee2/code/volunteer_pipeline.sh SRR7171428 current disk space = 3088668827648 free memory = 1413046008 SRR7171428 SRAfilesize 4a8a9414a687f9c4109245f0fcbbbeb4 SRR7171428.sra SRR7171428.sra file validated SRR7171428 is paired end SRR7171428 is conventional basespace SRR7171428 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171428_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 fail #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 24.25 18.0 18.0 33.0 18.0 33.0 2 26.93925 27.0 25.0 31.0 18.0 33.0 3 30.54375 32.0 30.0 33.0 27.0 33.0 4 31.82775 33.0 32.0 33.0 30.0 33.0 5 32.22525 33.0 33.0 33.0 32.0 33.0 6 36.50025 38.0 37.0 38.0 34.0 38.0 7 36.902 38.0 37.0 38.0 35.0 38.0 8 37.2885 38.0 38.0 38.0 36.0 38.0 9 37.45375 38.0 38.0 38.0 37.0 38.0 10-14 37.479400000000005 38.0 38.0 38.0 37.0 38.0 15-19 37.5313 38.0 38.0 38.0 37.6 38.0 20-24 37.5244 38.0 38.0 38.0 37.8 38.0 25-29 37.486650000000004 38.0 38.0 38.0 38.0 38.0 30-34 37.47089999999999 38.0 38.0 38.0 37.6 38.0 35-39 37.4787 38.0 38.0 38.0 38.0 38.0 40-44 37.419650000000004 38.0 38.0 38.0 37.2 38.0 45-49 37.467349999999996 38.0 38.0 38.0 37.6 38.0 50-54 37.390049999999995 38.0 38.0 38.0 37.0 38.0 55-59 37.342949999999995 38.0 38.0 38.0 37.0 38.0 60-64 37.257999999999996 38.0 38.0 38.0 37.0 38.0 65-69 37.214800000000004 38.0 38.0 38.0 36.4 38.0 70-74 37.117149999999995 38.0 38.0 38.0 36.0 38.0 75-79 37.10225 38.0 38.0 38.0 36.0 38.0 80-84 37.08624999999999 38.0 38.0 38.0 36.0 38.0 85-89 37.16065 38.0 38.0 38.0 36.0 38.0 90-94 37.06949999999999 38.0 38.0 38.0 36.0 38.0 95-99 36.919 38.0 38.0 38.0 35.6 38.0 100-104 36.68385 38.0 38.0 38.0 34.6 38.0 105-109 36.66340000000001 38.0 38.0 38.0 34.6 38.0 110-114 36.7644 38.0 38.0 38.0 35.0 38.0 115-119 36.6279 38.0 38.0 38.0 34.2 38.0 120-124 36.535849999999996 38.0 38.0 38.0 34.0 38.0 125-129 36.44545 38.0 38.0 38.0 34.0 38.0 130-134 36.3168 38.0 38.0 38.0 33.6 38.0 135-139 36.2593 38.0 37.6 38.0 33.2 38.0 140-144 36.04565000000001 38.0 36.6 38.0 33.0 38.0 145-149 35.7922 38.0 36.0 38.0 31.4 38.0 150-151 34.051249999999996 37.0 33.5 38.0 22.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 15 1.0 16 0.0 17 0.0 18 0.0 19 0.0 20 0.0 21 0.0 22 2.0 23 4.0 24 8.0 25 6.0 26 11.0 27 10.0 28 16.0 29 19.0 30 30.0 31 49.0 32 66.0 33 79.0 34 145.0 35 224.0 36 550.0 37 2780.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 43.970736629667 10.797174571140262 8.955600403632694 36.276488395560044 2 23.799999999999997 14.45 32.95 28.799999999999997 3 20.175 20.3 25.35 34.175 4 23.25 27.925 22.725 26.1 5 22.55 30.925000000000004 24.15 22.375 6 19.475 34.65 25.674999999999997 20.200000000000003 7 14.799999999999999 25.45 40.375 19.375 8 18.95 25.825 29.849999999999998 25.374999999999996 9 17.349999999999998 24.325 32.5 25.825 10-14 20.015 29.095 26.945000000000004 23.945 15-19 19.875 28.294999999999998 27.560000000000002 24.27 20-24 20.035 28.37 27.944999999999997 23.65 25-29 19.99 28.435 27.555000000000003 24.02 30-34 20.376018800940045 28.331416570828544 27.226361318065905 24.066203310165506 35-39 20.346103831149346 28.093428028408525 27.65329598879664 23.907172151645494 40-44 20.185 28.275 27.615000000000002 23.925 45-49 20.080000000000002 27.810000000000002 28.04 24.07 50-54 20.4 27.865000000000002 27.73 24.005000000000003 55-59 20.025000000000002 28.63 27.029999999999998 24.315 60-64 20.9 27.82 27.51 23.77 65-69 20.119999999999997 28.439999999999998 27.224999999999998 24.215 70-74 20.53 28.92 26.875 23.674999999999997 75-79 20.064999999999998 28.084999999999997 26.865 24.985 80-84 20.61 27.950000000000003 27.48 23.96 85-89 20.595 28.144999999999996 27.205000000000002 24.055 90-94 20.73 27.16 28.02 24.09 95-99 20.73 27.35 27.650000000000002 24.27 100-104 20.61 27.685 28.065 23.64 105-109 20.44 28.265 27.415 23.880000000000003 110-114 20.24 28.244999999999997 27.325 24.19 115-119 20.64 27.744999999999997 27.485 24.13 120-124 20.585 28.22 26.650000000000002 24.545 125-129 21.26 28.21 26.365 24.165 130-134 21.529999999999998 27.465 26.51 24.495 135-139 20.955 27.855 27.155 24.035 140-144 21.18 26.979999999999997 26.900000000000002 24.94 145-149 20.395 28.29 26.515 24.8 150-151 20.875 28.475 26.4625 24.1875 >>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 0.5 10 0.5 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 0.5 21 1.0 22 0.5 23 0.0 24 1.5 25 2.0 26 3.0 27 5.0 28 6.0 29 7.0 30 10.0 31 17.0 32 23.0 33 29.5 34 33.0 35 39.0 36 73.0 37 96.5 38 122.0 39 151.5 40 170.5 41 221.0 42 244.5 43 261.0 44 290.0 45 285.5 46 269.0 47 264.0 48 245.0 49 215.5 50 198.5 51 159.5 52 123.0 53 105.0 54 82.5 55 63.0 56 46.0 57 33.0 58 23.5 59 15.5 60 11.5 61 11.0 62 10.5 63 7.5 64 5.0 65 3.5 66 3.0 67 2.5 68 1.0 69 1.0 70 1.5 71 1.0 72 1.5 73 1.5 74 0.5 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 pass #Base N-Count 1 0.8999999999999999 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 0.005 35-39 0.03 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 99.775 #Duplication Level Percentage of deduplicated Percentage of total 1 99.77449260836883 99.55000000000001 2 0.22550739163117012 0.44999999999999996 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 0.0 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 0.025 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.0875 0.0 0.0 0.0 0.0 84-85 0.16249999999999998 0.0 0.0 0.0 0.0 86-87 0.1875 0.0 0.0 0.0 0.0 88-89 0.225 0.0 0.0 0.0 0.0 90-91 0.25 0.0 0.0 0.0 0.0 92-93 0.2625 0.0 0.0 0.0 0.0 94-95 0.32499999999999996 0.0 0.0 0.0 0.0 96-97 0.4875 0.0 0.0 0.0 0.0 98-99 0.6375 0.0 0.0 0.0 0.0 100-101 0.8625 0.0 0.0 0.0 0.0 102-103 1.0 0.0 0.0 0.0 0.0 104-105 1.275 0.0 0.0 0.0 0.0 106-107 1.5875 0.0 0.0 0.0 0.0 108-109 1.775 0.0 0.0 0.0 0.0 110-111 1.9249999999999998 0.0 0.0 0.0 0.0 112-113 2.3875 0.0 0.0 0.0 0.0 114-115 2.9124999999999996 0.0 0.0 0.0 0.0 116-117 3.375 0.0 0.0 0.0 0.0 118-119 3.7125000000000004 0.0 0.0 0.0 0.0 120-121 4.075 0.0 0.0 0.0 0.0 122-123 4.5875 0.0 0.0 0.0 0.0 124-125 5.0 0.0 0.0 0.0 0.0 126-127 5.55 0.0 0.0 0.0 0.0 128-129 6.125 0.0 0.0 0.0 0.0 130-131 6.8 0.0 0.0 0.0 0.0 132-133 7.237500000000001 0.0 0.0 0.0 0.0 134-135 7.7625 0.0 0.0 0.0 0.0 136-137 8.4375 0.0 0.0 0.0 0.0 138-139 9.3375 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE SRR7171428 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7171428_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 32.97075 33.0 33.0 34.0 32.0 34.0 2 33.07625 34.0 33.0 34.0 32.0 34.0 3 33.10175 34.0 33.0 34.0 32.0 34.0 4 32.99925 34.0 33.0 34.0 32.0 34.0 5 33.0715 34.0 33.0 34.0 32.0 34.0 6 37.13925 38.0 38.0 38.0 37.0 38.0 7 37.223 38.0 38.0 38.0 37.0 38.0 8 37.17725 38.0 38.0 38.0 37.0 38.0 9 37.14425 38.0 38.0 38.0 37.0 38.0 10-14 37.127449999999996 38.0 38.0 38.0 37.0 38.0 15-19 37.0927 38.0 38.0 38.0 36.8 38.0 20-24 37.1142 38.0 38.0 38.0 37.0 38.0 25-29 37.11479999999999 38.0 38.0 38.0 37.0 38.0 30-34 37.10355 38.0 38.0 38.0 37.0 38.0 35-39 37.10675 38.0 38.0 38.0 37.0 38.0 40-44 36.5723 37.8 37.4 38.0 34.2 38.0 45-49 36.99805 38.0 38.0 38.0 36.2 38.0 50-54 37.03035 38.0 38.0 38.0 36.2 38.0 55-59 36.95915000000001 38.0 38.0 38.0 36.0 38.0 60-64 36.9005 38.0 38.0 38.0 36.0 38.0 65-69 36.8767 38.0 38.0 38.0 36.0 38.0 70-74 36.8378 38.0 38.0 38.0 36.0 38.0 75-79 36.88365 38.0 38.0 38.0 36.0 38.0 80-84 36.84654999999999 38.0 38.0 38.0 36.0 38.0 85-89 36.7425 38.0 38.0 38.0 35.0 38.0 90-94 36.6324 38.0 38.0 38.0 35.0 38.0 95-99 36.529700000000005 38.0 38.0 38.0 34.2 38.0 100-104 36.45625 38.0 38.0 38.0 34.2 38.0 105-109 36.39805 38.0 38.0 38.0 34.0 38.0 110-114 36.342549999999996 38.0 38.0 38.0 34.0 38.0 115-119 36.2726 38.0 38.0 38.0 34.0 38.0 120-124 36.08024999999999 38.0 37.8 38.0 33.2 38.0 125-129 36.0395 38.0 38.0 38.0 33.0 38.0 130-134 35.8451 38.0 37.0 38.0 31.6 38.0 135-139 35.80695 38.0 36.4 38.0 31.4 38.0 140-144 35.39110000000001 38.0 36.0 38.0 29.2 38.0 145-149 35.192049999999995 38.0 35.8 38.0 28.0 38.0 150-151 32.663000000000004 35.5 30.5 38.0 20.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 3 1.0 4 1.0 5 1.0 6 0.0 7 0.0 8 1.0 9 0.0 10 0.0 11 0.0 12 0.0 13 0.0 14 0.0 15 1.0 16 8.0 17 2.0 18 4.0 19 5.0 20 4.0 21 3.0 22 13.0 23 12.0 24 11.0 25 12.0 26 15.0 27 26.0 28 36.0 29 26.0 30 33.0 31 60.0 32 68.0 33 79.0 34 110.0 35 208.0 36 424.0 37 2836.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 37.025000000000006 20.0 16.625 26.35 2 27.002002002002 27.152152152152155 28.02802802802803 17.81781781781782 3 20.995995995995994 28.603603603603606 29.754754754754753 20.645645645645647 4 23.973973973973976 34.15915915915916 22.32232232232232 19.544544544544546 5 24.974974974974977 35.23523523523524 22.64764764764765 17.14214214214214 6 21.28192288432649 36.65498247371057 24.41161742613921 17.651477215823736 7 21.312296518908088 21.111945905334334 37.08990733784122 20.485850237916353 8 23.209814722083124 26.089133700550825 25.838758137205808 24.86229344016024 9 22.664663160530928 25.97044828449787 29.201101928374655 22.163786626596544 10-14 24.305103420644063 28.196524265037308 25.807582511143384 21.69078980317524 15-19 23.48374818450443 27.91606150147744 27.705714428807532 20.894475885210596 20-24 24.11478940251415 27.630590474282567 27.104722792607806 21.149897330595483 25-29 23.513215859030836 27.99359231077293 27.08249899879856 21.410692831397675 30-34 23.481133019717745 28.065258732859572 27.06435792212992 21.389250325292764 35-39 23.520288187321757 28.013208585580628 27.693000450292693 20.77350277680492 40-44 23.73873873873874 28.03803803803804 27.197197197197198 21.026026026026027 45-49 23.61187603264407 27.99279026686026 27.28683723026085 21.108496470234815 50-54 23.55415352260778 28.230934855540536 27.299584397376197 20.91532722447549 55-59 23.680520781171758 27.43114672008012 27.95192789183776 20.936404606910365 60-64 23.885828743114672 27.591387080620933 27.526289434151224 20.99649474211317 65-69 24.067677829503932 27.121189367772942 28.057265855734094 20.75386694698904 70-74 24.14569470155601 27.80807524891179 27.09761344874168 20.948616600790515 75-79 23.647364736473648 27.61276127612761 28.092809280928094 20.647064706470648 80-84 24.145 27.694999999999997 27.245 20.915 85-89 23.298979387632578 27.691614968981387 28.206924154492697 20.80248148889334 90-94 23.98898898898899 28.033033033033032 27.44744744744745 20.53053053053053 95-99 24.564302884615387 27.809495192307693 26.837940705128204 20.788261217948715 100-104 24.532932632106185 27.998998246932132 27.007262709742047 20.460806411219636 105-109 24.33258201853243 27.92887553218132 27.122464312546956 20.616078136739294 110-114 24.21616748472403 27.77221276169488 27.31643794450566 20.69518180907543 115-119 24.48284497871275 27.853744052091162 27.683446030553473 19.979964938642624 120-124 24.412957492615032 28.193060631853 27.61728333249887 19.776698543033095 125-129 24.64964964964965 27.902902902902905 27.37737737737738 20.07007007007007 130-134 25.305305305305303 27.61761761761762 26.896896896896898 20.18018018018018 135-139 26.471766119343208 27.172607128554265 26.576892270724873 19.77873448137765 140-144 25.674931129476587 28.20936639118457 26.20085149010769 19.91485098923115 145-149 25.740045078888052 27.578261958427248 26.79188580015026 19.889807162534435 150-151 25.532181317305287 27.798647633358375 27.210117705985475 19.459053343350863 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.0 4 0.5 5 0.5 6 0.5 7 1.0 8 0.5 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 0.5 18 0.5 19 0.0 20 0.0 21 0.0 22 0.0 23 0.0 24 0.0 25 1.5 26 5.5 27 5.0 28 2.0 29 2.5 30 9.0 31 10.0 32 9.0 33 18.5 34 30.5 35 43.5 36 66.5 37 95.5 38 124.5 39 150.5 40 191.0 41 219.5 42 252.5 43 297.0 44 294.0 45 277.0 46 278.0 47 282.0 48 252.5 49 211.5 50 179.5 51 147.5 52 129.5 53 101.0 54 72.0 55 53.5 56 36.0 57 32.0 58 27.0 59 18.0 60 15.0 61 16.0 62 13.5 63 9.5 64 6.5 65 3.5 66 1.5 67 1.0 68 0.5 69 1.0 70 1.0 71 0.0 72 0.5 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 pass #Base N-Count 1 0.0 2 0.1 3 0.1 4 0.1 5 0.1 6 0.15 7 0.17500000000000002 8 0.15 9 0.17500000000000002 10-14 0.165 15-19 0.165 20-24 0.165 25-29 0.12 30-34 0.09 35-39 0.065 40-44 0.1 45-49 0.135 50-54 0.145 55-59 0.15 60-64 0.15 65-69 0.11499999999999999 70-74 0.065 75-79 0.01 80-84 0.0 85-89 0.06 90-94 0.1 95-99 0.16 100-104 0.17500000000000002 105-109 0.17500000000000002 110-114 0.16999999999999998 115-119 0.17500000000000002 120-124 0.135 125-129 0.1 130-134 0.1 135-139 0.12 140-144 0.17500000000000002 145-149 0.17500000000000002 150-151 0.17500000000000002 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.575 #Duplication Level Percentage of deduplicated Percentage of total 1 99.59829274416269 99.175 2 0.37660055234747675 0.75 3 0.025106703489831784 0.075 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 0.0 0.0 0.0 0.0 0.0 78-79 0.025 0.0 0.0 0.0 0.0 80-81 0.075 0.0 0.0 0.0 0.0 82-83 0.0875 0.0 0.0 0.0 0.0 84-85 0.16249999999999998 0.0 0.0 0.0 0.0 86-87 0.1875 0.0 0.0 0.0 0.0 88-89 0.225 0.0 0.0 0.0 0.0 90-91 0.2625 0.0 0.0 0.0 0.0 92-93 0.2875 0.0 0.0 0.0 0.0 94-95 0.35 0.0 0.0 0.0 0.0 96-97 0.5125 0.0 0.0 0.0 0.0 98-99 0.6625 0.0 0.0 0.0 0.0 100-101 0.8875 0.0 0.0 0.0 0.0 102-103 1.025 0.0 0.0 0.0 0.0 104-105 1.2875 0.0 0.0 0.0 0.0 106-107 1.5875 0.0 0.0 0.0 0.0 108-109 1.775 0.0 0.0 0.0 0.0 110-111 1.9249999999999998 0.0 0.0 0.0 0.0 112-113 2.35 0.0 0.0 0.0 0.0 114-115 2.8625 0.0 0.0 0.0 0.0 116-117 3.3 0.0 0.0 0.0 0.0 118-119 3.6375 0.0 0.0 0.0 0.0 120-121 4.012499999999999 0.0 0.0 0.0 0.0 122-123 4.45 0.0 0.0 0.0 0.0 124-125 4.8375 0.0 0.0 0.0 0.0 126-127 5.3625 0.0 0.0 0.0 0.0 128-129 5.9 0.0 0.0 0.0 0.0 130-131 6.5875 0.0 0.0 0.0 0.0 132-133 7.0375 0.0 0.0 0.0 0.0 134-135 7.5875 0.0 0.0 0.0 0.0 136-137 8.3625 0.0 0.0 0.0 0.0 138-139 9.225000000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACTGTGG 10 0.006830828 145.0 5 GGCTGGG 10 0.006830828 145.0 1 TGTGGCA 10 0.006830828 145.0 7 CATGTTG 10 0.006830828 145.0 7 CCGAAAG 10 0.006830828 145.0 145 >>END_MODULE Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937935 spots for SRR7171428.sra Written 937935 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra Read 937918 spots for SRR7171428.sra Written 937918 spots for SRR7171428.sra SRR ids: ['SRR7171428.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_pxl73ono SRR7171428.sra spots: 18758377 blocks: [[1, 937918], [937919, 1875836], [1875837, 2813754], [2813755, 3751672], [3751673, 4689590], [4689591, 5627508], [5627509, 6565426], [6565427, 7503344], [7503345, 8441262], [8441263, 9379180], [9379181, 10317098], [10317099, 11255016], [11255017, 12192934], [12192935, 13130852], [13130853, 14068770], [14068771, 15006688], [15006689, 15944606], [15944607, 16882524], [16882525, 17820442], [17820443, 18758377]] SRR7171428 file size 6334898 SRR7171428 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 SRR7171428 SRR7171428_1.fastq SRR7171428_2.fastq Input file: SRR7171428_1.fastq Paired file: SRR7171428_2.fastq trimmed: SRR7171428-trimmed-pair1.fastq, SRR7171428-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 Thu Feb 13 17:23:32 2025 >> started Thu Feb 13 17:24:07 2025 >> done (34.802s) 18758377 read pairs processed; of these: 13 ( 0.00%) short read pairs filtered out after trimming by size control 1381 ( 0.01%) empty read pairs filtered out after trimming by size control 18756983 (99.99%) read pairs available; of these: 2807627 (14.97%) trimmed read pairs available after processing 15949356 (85.03%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 0 0.00% 20 1 0.00% 21 2 0.00% 22 0 0.00% 23 2 0.00% 24 2 0.00% 25 1 0.00% 26 2 0.00% 27 1 0.00% 28 2 0.00% 29 1 0.00% 30 0 0.00% 31 3 0.00% 32 7 0.00% 33 3 0.00% 34 2 0.00% 35 3 0.00% 36 0 0.00% 37 3 0.00% 38 6 0.00% 39 2 0.00% 40 5 0.00% 41 11 0.00% 42 4 0.00% 43 12 0.00% 44 10 0.00% 45 9 0.00% 46 15 0.00% 47 11 0.00% 48 24 0.00% 49 25 0.00% 50 29 0.00% 51 29 0.00% 52 38 0.00% 53 46 0.00% 54 51 0.00% 55 51 0.00% 56 48 0.00% 57 58 0.00% 58 80 0.00% 59 124 0.00% 60 137 0.00% 61 139 0.00% 62 197 0.00% 63 186 0.00% 64 220 0.00% 65 240 0.00% 66 285 0.00% 67 334 0.00% 68 424 0.00% 69 446 0.00% 70 594 0.00% 71 645 0.00% 72 768 0.00% 73 944 0.01% 74 1147 0.01% 75 1267 0.01% 76 1406 0.01% 77 1566 0.01% 78 1729 0.01% 79 1942 0.01% 80 2394 0.01% 81 2771 0.01% 82 3119 0.02% 83 3606 0.02% 84 4133 0.02% 85 4599 0.02% 86 5082 0.03% 87 5516 0.03% 88 6231 0.03% 89 6557 0.03% 90 7257 0.04% 91 8297 0.04% 92 9026 0.05% 93 10178 0.05% 94 11088 0.06% 95 12156 0.06% 96 13134 0.07% 97 13792 0.07% 98 14334 0.08% 99 15651 0.08% 100 16654 0.09% 101 18100 0.10% 102 19403 0.10% 103 20908 0.11% 104 21920 0.12% 105 23483 0.13% 106 24897 0.13% 107 25718 0.14% 108 26580 0.14% 109 27483 0.15% 110 28876 0.15% 111 30665 0.16% 112 32256 0.17% 113 33845 0.18% 114 35651 0.19% 115 37983 0.20% 116 39210 0.21% 117 41365 0.22% 118 43032 0.23% 119 42930 0.23% 120 43045 0.23% 121 44392 0.24% 122 46421 0.25% 123 48025 0.26% 124 50929 0.27% 125 52326 0.28% 126 53925 0.29% 127 54798 0.29% 128 56170 0.30% 129 57311 0.31% 130 57466 0.31% 131 58744 0.31% 132 61418 0.33% 133 62994 0.34% 134 64528 0.34% 135 66681 0.36% 136 68780 0.37% 137 69165 0.37% 138 70637 0.38% 139 71446 0.38% 140 72148 0.38% 141 74891 0.40% 142 76825 0.41% 143 76724 0.41% 144 82460 0.44% 145 82017 0.44% 146 80495 0.43% 147 83497 0.45% 148 84030 0.45% 149 82697 0.44% 150 87421 0.47% 151 15949356 85.03% 18756983 reads passed initial QC criterion=sequence-density sequence-density=0.25 sequence-density-rank=1 fanout-score=2.96 fanout-score-rank=25 prefix-density=0.37 prefix-fanout=2.0 sequence=CACTTGCAGCCATTCTCAGCACCAGAGTTCATCTCAGACC criterion=fanout-score sequence-density=0.03 sequence-density-rank=34 fanout-score=107.03 fanout-score-rank=1 prefix-density=0.22 prefix-fanout=14.1 sequence=TCTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAA criterion=sequence-density sequence-density=0.30 sequence-density-rank=1 fanout-score=3.20 fanout-score-rank=26 prefix-density=0.32 prefix-fanout=3.1 sequence=ATGTACCCTGACTT criterion=fanout-score sequence-density=0.08 sequence-density-rank=28 fanout-score=37.15 fanout-score-rank=1 prefix-density=0.31 prefix-fanout=9.4 sequence=AAGGCCAAGATCCAGGACAAGGA SRR7171428 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 13 17:25:04 Started mapping on | Feb 13 17:25:05 Finished on | Feb 13 17:27:58 Mapping speed, Million of reads per hour | 390.32 Number of input reads | 18756983 Average input read length | 295 UNIQUE READS: Uniquely mapped reads number | 17460951 Uniquely mapped reads % | 93.09% Average mapped length | 293.99 Number of splices: Total | 17654255 Number of splices: Annotated (sjdb) | 17363866 Number of splices: GT/AG | 17387776 Number of splices: GC/AG | 213974 Number of splices: AT/AC | 12280 Number of splices: Non-canonical | 40225 Mismatch rate per base, % | 0.39% Deletion rate per base | 0.03% Deletion average length | 2.44 Insertion rate per base | 0.02% Insertion average length | 2.50 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 425159 % of reads mapped to multiple loci | 2.27% Number of reads mapped to too many loci | 222108 % of reads mapped to too many loci | 1.18% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 3.19% % of reads unmapped: other | 0.27% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 870874 870874 870874 N_multimapping 425159 425159 425159 N_noFeature 372082 17320507 426014 N_ambiguous 165380 1089 78104 UnstrandedReadsAssigned:16923489 PositiveStrandReadsAssigned:139355 NegativeStrandReadsAssigned:16956833 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=151 echo kmer=147 SRR7171428 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: SRR7171428-trimmed-pair1.fastq SRR7171428-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 18,756,983 reads, 17,141,145 reads pseudoaligned [quant] estimated average fragment length: 217.005 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,134 rounds 52401 SRR7171428.ke.tsv 34699 SRR7171428.se.tsv 87100 total ==> SRR7171428.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1802 1180 36.87 Potri.005G024800.1.v4.1 1035 818.995 703 48.3302 Potri.004G059700.1.v4.1 961 744.995 12 0.906927 Potri.007G009000.2.v4.1 1416 1200 0 0 Potri.003G141000.2.v4.1 2943 2727 951.218 19.64 Potri.016G087400.1.v4.1 270 88.5511 1223 777.638 Potri.015G069301.1.v4.1 564 350.304 0 0 Potri.010G195200.1.v4.1 1773 1557 247 8.93212 Potri.012G127500.1.v4.1 977 760.995 4709 348.411 ==> SRR7171428.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 44 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 447 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 4 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 1 Potri.001G452600.v4.1 154 SRR7171428 completed mapping pipeline successfully