Starting /dee2/code/volunteer_pipeline.sh SRR7169819 current disk space = 3052901117952 free memory = 1457061372 SRR7169819 SRAfilesize 10340887afeec5d21ce9d897c9443025 SRR7169819.sra SRR7169819.sra file validated SRR7169819 is paired end SRR7169819 is conventional basespace SRR7169819 read1 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169819_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 23.936 18.0 18.0 32.0 18.0 32.0 2 23.9505 25.0 18.0 30.0 18.0 33.0 3 27.031 29.0 25.0 31.0 18.0 33.0 4 30.41775 31.0 29.0 33.0 27.0 33.0 5 31.902 33.0 32.0 33.0 31.0 33.0 6 36.30075 38.0 36.0 38.0 33.0 38.0 7 36.70725 38.0 37.0 38.0 34.0 38.0 8 37.19225 38.0 38.0 38.0 36.0 38.0 9 37.35175 38.0 38.0 38.0 37.0 38.0 10-14 37.47265 38.0 38.0 38.0 37.0 38.0 15-19 37.5321 38.0 38.0 38.0 37.4 38.0 20-24 37.51690000000001 38.0 38.0 38.0 37.6 38.0 25-29 37.529849999999996 38.0 38.0 38.0 37.8 38.0 30-34 37.47545 38.0 38.0 38.0 37.6 38.0 35-39 37.41825000000001 38.0 38.0 38.0 37.0 38.0 40-44 37.364999999999995 38.0 38.0 38.0 37.0 38.0 45-49 37.41735 38.0 38.0 38.0 37.0 38.0 50-54 37.3365 38.0 38.0 38.0 37.0 38.0 55-59 37.162600000000005 38.0 38.0 38.0 36.2 38.0 60-64 37.09695000000001 38.0 38.0 38.0 36.2 38.0 65-69 37.194649999999996 38.0 38.0 38.0 36.2 38.0 70-74 37.24195 38.0 38.0 38.0 36.6 38.0 75-79 37.111450000000005 38.0 38.0 38.0 36.0 38.0 80-84 37.0548 38.0 38.0 38.0 36.0 38.0 85-89 36.8236 38.0 38.0 38.0 35.4 38.0 90-94 36.79715 38.0 38.0 38.0 35.0 38.0 95-99 36.872550000000004 38.0 38.0 38.0 35.4 38.0 100-104 36.77990000000001 38.0 38.0 38.0 35.0 38.0 105-109 36.463300000000004 38.0 38.0 38.0 34.2 38.0 110-114 36.19 38.0 38.0 38.0 33.8 38.0 115-119 36.22365 38.0 37.6 38.0 33.6 38.0 120-124 36.201150000000005 38.0 37.6 38.0 33.6 38.0 125-129 36.16675 38.0 37.0 38.0 33.4 38.0 130-134 35.8834 38.0 36.6 38.0 32.2 38.0 135-139 35.50619999999999 38.0 36.0 38.0 31.0 38.0 140-144 35.06015 38.0 35.4 38.0 28.8 38.0 145-149 34.7762 38.0 35.4 38.0 28.8 38.0 150-151 31.19825 36.5 31.0 38.0 14.5 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 9 1.0 10 0.0 11 0.0 12 0.0 13 0.0 14 2.0 15 0.0 16 2.0 17 1.0 18 0.0 19 2.0 20 2.0 21 2.0 22 4.0 23 4.0 24 7.0 25 8.0 26 9.0 27 15.0 28 19.0 29 24.0 30 43.0 31 45.0 32 72.0 33 99.0 34 155.0 35 298.0 36 794.0 37 2392.0 >>END_MODULE >>Per base sequence content fail #Base G A T C 1 41.528822055137844 11.979949874686717 9.223057644110275 37.26817042606516 2 25.224999999999998 13.525 34.125 27.125 3 19.325 21.3 24.925 34.449999999999996 4 23.5 30.45 21.975 24.075 5 23.225 32.425 24.725 19.625 6 20.275000000000002 34.675 24.349999999999998 20.7 7 14.2 24.775 42.65 18.375 8 18.154538634658664 25.656414103525883 29.80745186296574 26.38159539884971 9 17.775 25.5 33.050000000000004 23.674999999999997 10-14 20.21 30.349999999999998 26.484999999999996 22.955000000000002 15-19 19.285 29.049999999999997 27.38 24.285 20-24 20.39 27.73 28.67 23.21 25-29 20.125 28.87 27.644999999999996 23.36 30-34 20.335 29.054999999999996 27.339999999999996 23.27 35-39 20.244999999999997 29.020000000000003 27.250000000000004 23.485 40-44 19.78 29.515 27.255000000000003 23.45 45-49 20.535 28.875 27.21 23.380000000000003 50-54 19.950000000000003 28.655 27.485 23.91 55-59 20.31 29.035 27.084999999999997 23.57 60-64 19.415 29.054999999999996 27.675 23.855 65-69 20.24 29.12 27.155 23.485 70-74 20.69 29.035 27.255000000000003 23.02 75-79 20.064999999999998 29.535 26.76 23.64 80-84 20.645 28.754999999999995 26.700000000000003 23.9 85-89 20.22 29.455 26.955000000000002 23.369999999999997 90-94 20.155 29.455 27.375 23.015 95-99 20.29 28.92 27.455000000000002 23.335 100-104 21.055 28.970000000000002 27.07 22.905 105-109 20.241980019077264 29.203273256689595 26.823635724684973 23.731110999548168 110-114 20.477506911284244 28.62025634581553 27.07212867554662 23.830108067353606 115-119 20.525 29.220000000000002 26.979999999999997 23.275000000000002 120-124 20.105 29.375 26.634999999999998 23.885 125-129 20.7 29.005 25.77 24.525 130-134 20.925 28.749999999999996 26.755000000000003 23.57 135-139 20.341017050852543 28.57142857142857 26.851342567128356 24.23621181059053 140-144 21.291064553227663 28.88144407220361 26.55632781639082 23.27116355817791 145-149 21.224999999999998 28.84 26.345000000000002 23.59 150-151 20.96512064008001 28.803600450056255 25.778222277784725 24.453056632079008 >>END_MODULE >>Per sequence GC content pass #GC Content Count 0 0.0 1 0.0 2 0.0 3 0.5 4 0.5 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 1.0 19 1.0 20 0.0 21 0.0 22 1.0 23 1.0 24 2.5 25 4.5 26 5.0 27 7.5 28 10.5 29 19.5 30 24.5 31 23.5 32 31.0 33 43.5 34 48.0 35 63.5 36 87.5 37 106.5 38 126.0 39 159.0 40 191.0 41 218.5 42 239.5 43 252.0 44 275.5 45 283.0 46 268.0 47 260.0 48 241.5 49 210.0 50 171.5 51 136.5 52 119.0 53 99.5 54 78.0 55 51.0 56 34.0 57 24.5 58 17.5 59 15.5 60 10.5 61 7.5 62 10.0 63 6.5 64 1.5 65 1.0 66 0.5 67 1.0 68 2.5 69 2.0 70 1.5 71 1.0 72 0.0 73 0.5 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 0.25 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.025 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 0.40499999999999997 110-114 0.525 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.005 140-144 0.005 145-149 0.0 150-151 0.0125 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.125 #Duplication Level Percentage of deduplicated Percentage of total 1 99.11727616645649 98.25 2 0.8827238335435058 1.7500000000000002 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 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.037500000000000006 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.0625 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.16249999999999998 0.0 0.0 0.0 0.0 78-79 0.275 0.0 0.0 0.0 0.0 80-81 0.325 0.0 0.0 0.0 0.0 82-83 0.38749999999999996 0.0 0.0 0.0 0.0 84-85 0.4875 0.0 0.0 0.0 0.0 86-87 0.575 0.0 0.0 0.0 0.0 88-89 0.6625000000000001 0.0 0.0 0.0 0.0 90-91 0.725 0.0 0.0 0.0 0.0 92-93 0.95 0.0 0.0 0.0 0.0 94-95 1.1625 0.0 0.0 0.0 0.0 96-97 1.25 0.0 0.0 0.0 0.0 98-99 1.4 0.0 0.0 0.0 0.0 100-101 1.6375000000000002 0.0 0.0 0.0 0.0 102-103 1.9749999999999999 0.0 0.0 0.0 0.0 104-105 2.2249999999999996 0.0 0.0 0.0 0.0 106-107 2.525 0.0 0.0 0.0 0.0 108-109 2.8875 0.0 0.0 0.0 0.0 110-111 3.175 0.0 0.0 0.0 0.0 112-113 3.4625 0.0 0.0 0.0 0.0 114-115 3.8625 0.0 0.0 0.0 0.0 116-117 4.4 0.0 0.0 0.0 0.0 118-119 4.8 0.0 0.0 0.0 0.0 120-121 5.2 0.0 0.0 0.0 0.0 122-123 5.6875 0.0 0.0 0.0 0.0 124-125 6.0875 0.0 0.0 0.0 0.0 126-127 6.574999999999999 0.0 0.0 0.0 0.0 128-129 7.15 0.0 0.0 0.0 0.0 130-131 7.8125 0.0 0.0 0.0 0.0 132-133 8.2875 0.0 0.0 0.0 0.0 134-135 8.825 0.0 0.0 0.0 0.0 136-137 9.287500000000001 0.0 0.0 0.0 0.0 138-139 9.850000000000001 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position CCCACAC 10 0.006830828 145.0 1 >>END_MODULE SRR7169819 read2 length is 151 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename SRR7169819_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 32.805 33.0 33.0 34.0 32.0 34.0 2 32.95225 34.0 33.0 34.0 32.0 34.0 3 33.0515 34.0 33.0 34.0 32.0 34.0 4 33.068 34.0 33.0 34.0 32.0 34.0 5 32.95775 34.0 33.0 34.0 32.0 34.0 6 37.18575 38.0 38.0 38.0 37.0 38.0 7 37.14375 38.0 38.0 38.0 37.0 38.0 8 37.11125 38.0 38.0 38.0 37.0 38.0 9 37.14725 38.0 38.0 38.0 37.0 38.0 10-14 37.08565 38.0 38.0 38.0 36.8 38.0 15-19 37.04214999999999 38.0 38.0 38.0 36.6 38.0 20-24 37.092 38.0 38.0 38.0 37.0 38.0 25-29 37.06145 38.0 38.0 38.0 36.4 38.0 30-34 36.8323 38.0 38.0 38.0 35.6 38.0 35-39 36.7684 38.0 38.0 38.0 35.6 38.0 40-44 36.77075 38.0 38.0 38.0 35.4 38.0 45-49 36.83425 38.0 38.0 38.0 35.8 38.0 50-54 36.463350000000005 38.0 38.0 38.0 34.6 38.0 55-59 36.274899999999995 38.0 37.6 38.0 33.0 38.0 60-64 36.5944 38.0 38.0 38.0 34.8 38.0 65-69 36.8621 38.0 38.0 38.0 35.8 38.0 70-74 36.51025 38.0 38.0 38.0 35.2 38.0 75-79 35.56785 38.0 38.0 38.0 33.0 38.0 80-84 36.18705 38.0 38.0 38.0 33.4 38.0 85-89 36.497949999999996 38.0 38.0 38.0 34.6 38.0 90-94 36.4902 38.0 38.0 38.0 34.2 38.0 95-99 36.304550000000006 38.0 38.0 38.0 34.0 38.0 100-104 35.94285 38.0 37.6 38.0 32.8 38.0 105-109 34.9935 38.0 37.0 38.0 28.6 38.0 110-114 33.263850000000005 38.0 35.2 38.0 15.0 38.0 115-119 33.23525 38.0 36.0 38.0 14.8 38.0 120-124 33.311400000000006 38.0 35.0 38.0 17.2 38.0 125-129 33.6848 38.0 35.4 38.0 18.2 38.0 130-134 34.362199999999994 38.0 35.0 38.0 24.6 38.0 135-139 33.836400000000005 38.0 34.2 38.0 21.8 38.0 140-144 33.201299999999996 38.0 33.0 38.0 20.8 38.0 145-149 33.08555 38.0 33.0 38.0 16.6 38.0 150-151 28.518749999999997 35.5 17.5 38.0 2.0 38.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 2 2.0 3 3.0 4 1.0 5 4.0 6 1.0 7 0.0 8 0.0 9 2.0 10 0.0 11 1.0 12 2.0 13 2.0 14 3.0 15 5.0 16 0.0 17 8.0 18 7.0 19 7.0 20 7.0 21 16.0 22 12.0 23 32.0 24 21.0 25 17.0 26 25.0 27 35.0 28 42.0 29 69.0 30 67.0 31 81.0 32 134.0 33 151.0 34 198.0 35 263.0 36 602.0 37 2180.0 >>END_MODULE >>Per base sequence content warn #Base G A T C 1 36.475 19.275000000000002 15.85 28.4 2 27.025 25.674999999999997 30.75 16.55 3 20.9 28.325 30.599999999999998 20.175 4 24.2 34.275 22.3 19.225 5 24.61230615307654 35.74287143571786 21.660830415207606 17.983991995998 6 21.205301325331334 37.80945236309077 22.980745186296573 18.00450112528132 7 19.05 21.825 40.150000000000006 18.975 8 23.05 24.525 27.525 24.9 9 23.125 25.55 28.449999999999996 22.875 10-14 23.0 28.54 26.995 21.465 15-19 22.8607151787947 27.701925481370342 28.617154288572145 20.820205051262818 20-24 23.0803861737782 27.43234455504977 27.817517883047373 21.669751388124656 25-29 23.214642928585715 27.70554110822164 28.335667133426686 20.744148829765955 30-34 23.310489720374168 27.7574908708919 28.777950077534893 20.15406933119904 35-39 22.8225524038221 28.05042773525439 28.735804692580917 20.391215168342587 40-44 23.490872718179546 27.6419104776194 28.33708427106777 20.530132533133283 45-49 23.386693346673336 27.938969484742373 27.85892946473237 20.815407703851925 50-54 23.34834834834835 27.442442442442445 28.428428428428425 20.78078078078078 55-59 23.634816557385253 28.14955703488663 28.054457180039037 20.161169227689076 60-64 23.484393757503 27.290916366546618 28.921568627450984 20.3031212484994 65-69 23.705926481620406 27.60190047511878 27.831957989497376 20.86021505376344 70-74 22.75476262473541 27.890333635722204 28.197762322346538 21.157141417195845 75-79 22.0854154860646 28.25202204935346 28.870228221111745 20.792334243470197 80-84 23.61237030321346 27.818071925052884 28.14042510325375 20.429132668479905 85-89 23.254766551568835 27.64850122604214 28.834509332932996 20.262222889456037 90-94 23.39137396177324 27.704393075152606 29.035324727309114 19.868908235765034 95-99 23.914565826330534 27.62104841936775 28.281312525010005 20.18307322929172 100-104 23.56624092161282 27.978963185574756 28.2694715752567 20.18532431755572 105-109 23.628995023854717 27.266198122402912 28.322987739188427 20.781819114553944 110-114 24.350735567475702 27.840033990121622 27.717881990546502 20.091348451856177 115-119 24.743159943765548 27.814426300421758 27.700875959770737 19.74153779604196 120-124 25.160741803496467 27.073702109570114 28.125830277910623 19.639725809022796 125-129 24.512271869100065 27.601216698132998 27.76903713027061 20.11747430249633 130-134 25.02263353787345 28.080675988331155 27.487174328538376 19.409516145257015 135-139 25.403891361976694 27.744710648727057 27.31956184664633 19.53183614264993 140-144 25.10631910741982 27.422824836143494 27.57292239955971 19.89793365687697 145-149 24.904942965779465 27.116269761857115 28.16690014008405 19.811887132279367 150-151 26.189879759519037 27.89328657314629 26.891282565130258 19.025551102204407 >>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 0.5 18 1.5 19 1.5 20 0.5 21 0.0 22 0.0 23 0.0 24 2.0 25 3.0 26 4.0 27 5.5 28 5.0 29 9.0 30 16.0 31 20.5 32 28.0 33 40.5 34 48.5 35 68.0 36 91.0 37 114.0 38 144.0 39 172.5 40 194.5 41 223.0 42 245.0 43 260.0 44 293.5 45 298.5 46 297.5 47 279.0 48 235.0 49 204.5 50 163.5 51 130.5 52 112.5 53 84.5 54 58.5 55 37.0 56 21.5 57 20.5 58 19.5 59 13.5 60 7.0 61 6.0 62 5.0 63 3.5 64 3.5 65 1.5 66 1.5 67 1.5 68 1.0 69 1.0 70 0.5 71 0.5 72 0.0 73 0.0 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 0.0 2 0.0 3 0.0 4 0.0 5 0.05 6 0.025 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.025 20-24 0.045 25-29 0.02 30-34 0.045 35-39 0.055 40-44 0.025 45-49 0.05 50-54 0.1 55-59 0.105 60-64 0.04 65-69 0.025 70-74 0.79 75-79 2.945 80-84 0.73 85-89 0.08499999999999999 90-94 0.06999999999999999 95-99 0.04 100-104 0.17500000000000002 105-109 2.535 110-114 5.8549999999999995 115-119 7.53 120-124 5.905 125-129 4.66 130-134 0.59 135-139 0.034999999999999996 140-144 0.065 145-149 0.06 150-151 0.2 >>END_MODULE >>Sequence Length Distribution pass #Length Count 151 4000.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 99.15 #Duplication Level Percentage of deduplicated Percentage of total 1 99.14271306101867 98.3 2 0.8572869389813415 1.7000000000000002 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 0.025 0.0 0.0 0.0 0.0 62-63 0.025 0.0 0.0 0.0 0.0 64-65 0.037500000000000006 0.0 0.0 0.0 0.0 66-67 0.05 0.0 0.0 0.0 0.0 68-69 0.0625 0.0 0.0 0.0 0.0 70-71 0.075 0.0 0.0 0.0 0.0 72-73 0.1 0.0 0.0 0.0 0.0 74-75 0.125 0.0 0.0 0.0 0.0 76-77 0.16249999999999998 0.0 0.0 0.0 0.0 78-79 0.275 0.0 0.0 0.0 0.0 80-81 0.325 0.0 0.0 0.0 0.0 82-83 0.38749999999999996 0.0 0.0 0.0 0.0 84-85 0.4625 0.0 0.0 0.0 0.0 86-87 0.55 0.0 0.0 0.0 0.0 88-89 0.6375 0.0 0.0 0.0 0.0 90-91 0.7 0.0 0.0 0.0 0.0 92-93 0.95 0.0 0.0 0.0 0.0 94-95 1.15 0.0 0.0 0.0 0.0 96-97 1.25 0.0 0.0 0.0 0.0 98-99 1.4 0.0 0.0 0.0 0.0 100-101 1.65 0.0 0.0 0.0 0.0 102-103 2.0 0.0 0.0 0.0 0.0 104-105 2.2750000000000004 0.0 0.0 0.0 0.0 106-107 2.5625 0.0 0.0 0.0 0.0 108-109 2.875 0.0 0.0 0.0 0.0 110-111 3.0999999999999996 0.0 0.0 0.0 0.0 112-113 3.3875 0.0 0.0 0.0 0.0 114-115 3.775 0.0 0.0 0.0 0.0 116-117 4.225 0.0 0.0 0.0 0.0 118-119 4.5875 0.0 0.0 0.0 0.0 120-121 4.925000000000001 0.0 0.0 0.0 0.0 122-123 5.3625 0.0 0.0 0.0 0.0 124-125 5.725 0.0 0.0 0.0 0.0 126-127 6.2 0.0 0.0 0.0 0.0 128-129 6.725 0.0 0.0 0.0 0.0 130-131 7.3375 0.0 0.0 0.0 0.0 132-133 7.7875 0.0 0.0 0.0 0.0 134-135 8.2625 0.0 0.0 0.0 0.0 136-137 8.7375 0.0 0.0 0.0 0.0 138-139 9.2875 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TATGTGG 10 0.007096334 143.1625 4 GGACAAA 10 0.007096334 143.1625 4 >>END_MODULE Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625466 spots for SRR7169819.sra Written 625466 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra Read 625452 spots for SRR7169819.sra Written 625452 spots for SRR7169819.sra SRR ids: ['SRR7169819.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_1snlyvbu SRR7169819.sra spots: 12509054 blocks: [[1, 625452], [625453, 1250904], [1250905, 1876356], [1876357, 2501808], [2501809, 3127260], [3127261, 3752712], [3752713, 4378164], [4378165, 5003616], [5003617, 5629068], [5629069, 6254520], [6254521, 6879972], [6879973, 7505424], [7505425, 8130876], [8130877, 8756328], [8756329, 9381780], [9381781, 10007232], [10007233, 10632684], [10632685, 11258136], [11258137, 11883588], [11883589, 12509054]] SRR7169819 file size 4217207 SRR7169819 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 SRR7169819 SRR7169819_1.fastq SRR7169819_2.fastq Input file: SRR7169819_1.fastq Paired file: SRR7169819_2.fastq trimmed: SRR7169819-trimmed-pair1.fastq, SRR7169819-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 20:43:33 2025 >> started Tue Feb 11 20:43:52 2025 >> done (19.090s) 12509054 read pairs processed; of these: 11860 ( 0.09%) short read pairs filtered out after trimming by size control 11122 ( 0.09%) empty read pairs filtered out after trimming by size control 12486072 (99.82%) read pairs available; of these: 5919186 (47.41%) trimmed read pairs available after processing 6566886 (52.59%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 2 0.00% 19 3 0.00% 20 3 0.00% 21 3 0.00% 22 2 0.00% 23 1 0.00% 24 4 0.00% 25 0 0.00% 26 2 0.00% 27 4 0.00% 28 1 0.00% 29 2 0.00% 30 1 0.00% 31 8 0.00% 32 3 0.00% 33 7 0.00% 34 15 0.00% 35 7 0.00% 36 7 0.00% 37 18 0.00% 38 16 0.00% 39 18 0.00% 40 27 0.00% 41 28 0.00% 42 31 0.00% 43 42 0.00% 44 41 0.00% 45 36 0.00% 46 66 0.00% 47 56 0.00% 48 56 0.00% 49 78 0.00% 50 115 0.00% 51 129 0.00% 52 127 0.00% 53 140 0.00% 54 158 0.00% 55 190 0.00% 56 182 0.00% 57 218 0.00% 58 232 0.00% 59 315 0.00% 60 335 0.00% 61 385 0.00% 62 453 0.00% 63 551 0.00% 64 537 0.00% 65 601 0.00% 66 686 0.01% 67 771 0.01% 68 851 0.01% 69 984 0.01% 70 1205 0.01% 71 1382 0.01% 72 1574 0.01% 73 1764 0.01% 74 1959 0.02% 75 2223 0.02% 76 2432 0.02% 77 2622 0.02% 78 2877 0.02% 79 3231 0.03% 80 3658 0.03% 81 4127 0.03% 82 4550 0.04% 83 5333 0.04% 84 6255 0.05% 85 6943 0.06% 86 7289 0.06% 87 7854 0.06% 88 8169 0.07% 89 8722 0.07% 90 9657 0.08% 91 10252 0.08% 92 11115 0.09% 93 12161 0.10% 94 13305 0.11% 95 14235 0.11% 96 15081 0.12% 97 15365 0.12% 98 16118 0.13% 99 16515 0.13% 100 17172 0.14% 101 18525 0.15% 102 19709 0.16% 103 20580 0.16% 104 22191 0.18% 105 23026 0.18% 106 23586 0.19% 107 24352 0.20% 108 24833 0.20% 109 25688 0.21% 110 26257 0.21% 111 27711 0.22% 112 28878 0.23% 113 29765 0.24% 114 31488 0.25% 115 32324 0.26% 116 33300 0.27% 117 34040 0.27% 118 34739 0.28% 119 34564 0.28% 120 35191 0.28% 121 36253 0.29% 122 37289 0.30% 123 39146 0.31% 124 40871 0.33% 125 42334 0.34% 126 44337 0.36% 127 45455 0.36% 128 45726 0.37% 129 46132 0.37% 130 46949 0.38% 131 47665 0.38% 132 49233 0.39% 133 51390 0.41% 134 52664 0.42% 135 55374 0.44% 136 58147 0.47% 137 59942 0.48% 138 62075 0.50% 139 64882 0.52% 140 69075 0.55% 141 73677 0.59% 142 77699 0.62% 143 86226 0.69% 144 96645 0.77% 145 112627 0.90% 146 134590 1.08% 147 176627 1.41% 148 258170 2.07% 149 490932 3.93% 150 2622614 21.00% 151 6566886 52.59% 12486072 reads passed initial QC criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=2.59 fanout-score-rank=30 prefix-density=0.23 prefix-fanout=2.4 sequence=CTGGCCATTCAAT criterion=fanout-score sequence-density=0.02 sequence-density-rank=41 fanout-score=86.78 fanout-score-rank=1 prefix-density=0.27 prefix-fanout=6.5 sequence=TCTCCTTCCTCTAAATGATAAGGTTCAGTGGACTTCTCGCGACGTCGCCGGCGGCGAACCGCCCACGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGAATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCAAAGATTACCCGGGCCTGTCGGCCAAGGCTATAGACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCTTGGCCTGGAAGGCCATAGTCCCTCTAAGAAGCTGGCCGCGGAGGGTCACCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCAC criterion=sequence-density sequence-density=0.21 sequence-density-rank=1 fanout-score=3.53 fanout-score-rank=26 prefix-density=0.23 prefix-fanout=3.2 sequence=TGCTTTGAGAGA criterion=fanout-score sequence-density=0.01 sequence-density-rank=40 fanout-score=47.42 fanout-score-rank=1 prefix-density=0.16 prefix-fanout=1.9 sequence=AAGGAGTCTGACATGTGTGCGAGTCAACGGGCGAGTAAACCCGTAAGGCGCAAGGAAGCTGACTGGCGGGATCCCCTCGAGGGTTGCACCGCCGACCGACCTTGATCTTCTGAGAAGGGTTCGAGTGAGAGCATGCCTGTCGGGACCCGAAAGATGGTGAACTATGCCTGAGCGGGGCGAAGCCAGAGGAAACTCTGGTGGAGGCCCGCAGCGATACTGACGTGCAAATCGTTCGTCTGACTTGGGTATAGGGGCGAAAGACTAATCGAACCGTCTAGTAGCTGGTTCCCTCCGAAGTTTCCCTCAGGATAGCTGGAGCTC SRR7169819 testing PE reads STAR mapping to Ensembl genome Started job on | Feb 11 20:44:34 Started mapping on | Feb 11 20:44:34 Finished on | Feb 11 20:46:21 Mapping speed, Million of reads per hour | 420.09 Number of input reads | 12486072 Average input read length | 291 UNIQUE READS: Uniquely mapped reads number | 11864280 Uniquely mapped reads % | 95.02% Average mapped length | 291.07 Number of splices: Total | 10936675 Number of splices: Annotated (sjdb) | 10754550 Number of splices: GT/AG | 10783475 Number of splices: GC/AG | 121799 Number of splices: AT/AC | 9232 Number of splices: Non-canonical | 22169 Mismatch rate per base, % | 0.35% Deletion rate per base | 0.03% Deletion average length | 2.76 Insertion rate per base | 0.02% Insertion average length | 2.36 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 218583 % of reads mapped to multiple loci | 1.75% Number of reads mapped to too many loci | 141444 % of reads mapped to too many loci | 1.13% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 1.91% % of reads unmapped: other | 0.19% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 412351 412351 412351 N_multimapping 218583 218583 218583 N_noFeature 297952 11722898 362023 N_ambiguous 123784 952 45733 UnstrandedReadsAssigned:11442544 PositiveStrandReadsAssigned:140430 NegativeStrandReadsAssigned:11456524 Dataset is classified negative stranded MeadianReadLen=151 20thPercentileLength=149 echo kmer=145 SRR7169819 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: SRR7169819-trimmed-pair1.fastq SRR7169819-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 12,486,072 reads, 11,480,995 reads pseudoaligned [quant] estimated average fragment length: 217.995 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,046 rounds 52401 SRR7169819.ke.tsv 34699 SRR7169819.se.tsv 87100 total ==> SRR7169819.ke.tsv <== target_id length eff_length est_counts tpm Potri.005G200100.1.v4.1 2018 1801.01 253 14.0635 Potri.005G024800.1.v4.1 1035 818.005 24 2.93727 Potri.004G059700.1.v4.1 961 744.03 5 0.672774 Potri.007G009000.2.v4.1 1416 1199.01 0 0 Potri.003G141000.2.v4.1 2943 2726.01 243.036 8.9255 Potri.016G087400.1.v4.1 270 90.7093 874.573 965.236 Potri.015G069301.1.v4.1 564 349.395 0 0 Potri.010G195200.1.v4.1 1773 1556.01 21 1.35113 Potri.012G127500.1.v4.1 977 760.024 2560 337.211 ==> SRR7169819.se.tsv <== Potri.001G166300.v4.1 0 Potri.001G448400.v4.1 1380 Potri.001G233950.v4.1 0 Potri.001G122700.v4.1 200 Potri.001G212900.v4.1 0 Potri.001G182400.v4.1 5 Potri.001G256600.v4.1 0 Potri.001G040500.v4.1 0 Potri.001G416900.v4.1 0 Potri.001G452600.v4.1 0 SRR7169819 completed mapping pipeline successfully