Starting /dee2/code/volunteer_pipeline.sh ERR3959309 current disk space = 1516105830400 free memory = 1596738600 ERR3959309 SRAfilesize efed6b4540f24337e862f97ceaabad92 ERR3959309.sra ERR3959309.sra file validated ERR3959309 is paired end ERR3959309 is conventional basespace ERR3959309 read1 length is 20-140 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3959309_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 20-140 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5535 37.0 37.0 37.0 37.0 37.0 2 36.51 37.0 37.0 37.0 37.0 37.0 3 36.569 37.0 37.0 37.0 37.0 37.0 4 36.5095 37.0 37.0 37.0 37.0 37.0 5 36.559 37.0 37.0 37.0 37.0 37.0 6 36.5205 37.0 37.0 37.0 37.0 37.0 7 36.53 37.0 37.0 37.0 37.0 37.0 8 36.5255 37.0 37.0 37.0 37.0 37.0 9 36.55 37.0 37.0 37.0 37.0 37.0 10-14 36.53439999999999 37.0 37.0 37.0 37.0 37.0 15-19 36.50279999999999 37.0 37.0 37.0 37.0 37.0 20-24 36.45542882181646 37.0 37.0 37.0 37.0 37.0 25-29 36.4300862901683 37.0 37.0 37.0 37.0 37.0 30-34 36.43350788727554 37.0 37.0 37.0 37.0 37.0 35-39 36.41582105628541 37.0 37.0 37.0 37.0 37.0 40-44 36.45210386802893 37.0 37.0 37.0 37.0 37.0 45-49 36.40950872928306 37.0 37.0 37.0 37.0 37.0 50-54 36.423201174710286 37.0 37.0 37.0 37.0 37.0 55-59 36.439138592575844 37.0 37.0 37.0 37.0 37.0 60-64 36.37001874017129 37.0 37.0 37.0 37.0 37.0 65-69 36.40353474116803 37.0 37.0 37.0 37.0 37.0 70-74 36.37836320135615 37.0 37.0 37.0 37.0 37.0 75-79 36.43868973405656 37.0 37.0 37.0 37.0 37.0 80-84 36.358510877239084 37.0 37.0 37.0 37.0 37.0 85-89 36.41129677567937 37.0 37.0 37.0 37.0 37.0 90-94 36.34179278649129 37.0 37.0 37.0 37.0 37.0 95-99 36.306501732643525 37.0 37.0 37.0 37.0 37.0 100-104 36.38028985686218 37.0 37.0 37.0 37.0 37.0 105-109 36.27705045296929 37.0 37.0 37.0 37.0 37.0 110-114 36.29429522271117 37.0 37.0 37.0 37.0 37.0 115-119 36.32132753909165 37.0 37.0 37.0 37.0 37.0 120-124 36.33519439860479 37.0 37.0 37.0 37.0 37.0 125-129 36.24688435793959 37.0 37.0 37.0 37.0 37.0 130-134 36.10777287960806 37.0 37.0 37.0 37.0 37.0 135-139 36.09454551172938 37.0 37.0 37.0 37.0 37.0 140 36.619732113688336 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 26 1.0 27 0.0 28 2.0 29 8.0 30 13.0 31 42.0 32 48.0 33 101.0 34 146.0 35 288.0 36 2817.0 37 534.0 >>END_MODULE >>Per base sequence content pass #Base G A T C 1 26.575 24.925 20.075000000000003 28.425 2 25.8 21.425 23.075000000000003 29.7 3 24.15 22.7 26.05 27.1 4 24.349999999999998 23.45 24.5 27.700000000000003 5 23.225 23.35 26.174999999999997 27.250000000000004 6 24.575 24.55 23.825 27.05 7 25.35 23.375 23.35 27.925 8 25.074999999999996 23.599999999999998 22.900000000000002 28.425 9 25.874999999999996 22.95 24.525 26.650000000000002 10-14 24.935 24.255 23.71 27.1 15-19 24.385 24.435000000000002 23.84 27.339999999999996 20-24 25.34267133566783 23.781890945472735 23.936968484242122 26.93846923461731 25-29 25.502581841880982 23.602546748884546 23.848197723968518 27.046673685265954 30-34 25.489998994873858 23.922002211277515 23.952155995577446 26.63584279827118 35-39 25.02517623363545 23.856998992950654 23.595166163141997 27.522658610271904 40-44 25.210550204246307 23.75813202884664 23.974986131423673 27.05633163548338 45-49 25.24477642071263 23.377409912183307 24.2505299283335 27.12728373877057 50-54 25.478898155168057 23.70988122314885 23.174121809451606 27.637098812231486 55-59 25.839453026082555 23.31729551785262 23.83388199544188 27.009369460622946 60-64 25.55307489344429 24.010554089709764 23.447331033083014 26.989039983762943 65-69 25.405625349677024 23.95605513453029 23.406744316158893 27.231575199633795 70-74 25.22117105599591 24.30580414216313 23.32907184863206 27.1439529532089 75-79 26.46696125783578 23.57928270475799 23.014078717500773 26.93967731990546 80-84 25.807952841408554 23.703397280107556 23.703397280107556 26.785252598376335 85-89 26.26941924721093 23.798352622250025 23.4230007298509 26.509227400688147 90-94 25.85281111813013 23.41019161928827 23.383870288481788 27.353126974099812 95-99 26.32028621776045 23.986757088695466 23.057617343941903 26.635339349602177 100-104 26.16332987834815 23.57209099339916 23.501172876547923 26.76340625170476 105-109 26.10122358175751 23.620689655172413 23.120133481646274 27.1579532814238 110-114 25.679603351000168 22.938394027469084 23.54248589502479 27.839516726505952 115-119 26.021694517736734 22.931691586045147 23.465259454705365 27.58135444151275 120-124 26.25823213098906 23.019757114373753 23.09226028638753 27.629750468249654 125-129 25.992870098192505 22.972043279754832 23.747576458815438 27.28751016323723 130-134 26.465555485138477 23.068635528233727 23.911527980226886 26.554281006400913 135-139 26.99148773980434 23.777156650997334 22.90052089950451 26.33083470969381 140 28.16073178699771 22.7703364913427 23.4890558640967 25.57987585756289 >>END_MODULE >>Per sequence GC content fail #GC Content Count 0 1.0 1 1.0 2 0.5 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 0.0 24 0.5 25 1.0 26 1.0 27 2.0 28 5.0 29 4.0 30 5.5 31 12.0 32 17.0 33 22.5 34 29.5 35 39.5 36 49.5 37 54.0 38 59.5 39 77.0 40 85.0 41 106.0 42 135.5 43 143.5 44 167.5 45 185.5 46 178.0 47 172.0 48 162.5 49 164.5 50 165.0 51 134.5 52 125.5 53 116.0 54 103.5 55 107.0 56 96.0 57 86.0 58 88.0 59 84.5 60 71.5 61 70.0 62 70.5 63 68.0 64 72.0 65 76.5 66 75.5 67 71.0 68 66.0 69 63.5 70 58.5 71 56.5 72 57.0 73 54.5 74 47.0 75 37.5 76 36.0 77 31.0 78 20.5 79 15.0 80 14.0 81 9.0 82 4.0 83 4.5 84 4.5 85 4.0 86 2.0 87 0.5 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 0.0 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 0.006352029473416756 140 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 20-24 6.0 25-29 12.0 30-34 8.0 35-39 5.0 40-44 5.0 45-49 4.0 50-54 8.0 55-59 7.0 60-64 7.0 65-69 21.0 70-74 18.0 75-79 23.0 80-84 26.0 85-89 35.0 90-94 42.0 95-99 79.0 100-104 69.0 105-109 84.0 110-114 92.0 115-119 98.0 120-124 106.0 125-129 87.0 130-134 6.0 135-139 91.0 140-141 3061.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 96.2 #Duplication Level Percentage of deduplicated Percentage of total 1 96.17983367983368 92.525 2 3.6902286902286905 7.1 3 0.12993762993762994 0.375 4 0.0 0.0 5 0.0 0.0 6 0.0 0.0 7 0.0 0.0 8 0.0 0.0 9 0.0 0.0 >10 0.0 0.0 >50 0.0 0.0 >100 0.0 0.0 >500 0.0 0.0 >1k 0.0 0.0 >5k 0.0 0.0 >10k+ 0.0 0.0 >>END_MODULE >>Overrepresented sequences pass >>END_MODULE >>Adapter Content pass #Position Illumina Universal Adapter Illumina Small RNA 3' Adapter Illumina Small RNA 5' Adapter Nextera Transposase Sequence SOLID Small RNA Adapter 1 0.0 0.0 0.0 0.0 0.0 2 0.0 0.0 0.0 0.0 0.0 3 0.0 0.0 0.0 0.0 0.0 4 0.0 0.0 0.0 0.0 0.0 5 0.0 0.0 0.0 0.0 0.0 6 0.0 0.0 0.0 0.0 0.0 7 0.0 0.0 0.0 0.0 0.0 8 0.0 0.0 0.0 0.0 0.0 9 0.0 0.0 0.0 0.0 0.0 10-11 0.0 0.0 0.0 0.0 0.0 12-13 0.0 0.0 0.0 0.0 0.0 14-15 0.0 0.0 0.0 0.0 0.0 16-17 0.0 0.0 0.0 0.0 0.0 18-19 0.0 0.0 0.0 0.0 0.0 20-21 0.0 0.0 0.0 0.0 0.0 22-23 0.0 0.0 0.0 0.0 0.0 24-25 0.0 0.0 0.0 0.0 0.0 26-27 0.0 0.0 0.0 0.0 0.0 28-29 0.0 0.0 0.0 0.0 0.0 30-31 0.0 0.0 0.0 0.0 0.0 32-33 0.0 0.0 0.0 0.0 0.0 34-35 0.0 0.0 0.0 0.0 0.0 36-37 0.0 0.0 0.0 0.0 0.0 38-39 0.0 0.0 0.0 0.0 0.0 40-41 0.0 0.0 0.0 0.0 0.0 42-43 0.0 0.0 0.0 0.0 0.0 44-45 0.0 0.0 0.0 0.0 0.0 46-47 0.0 0.0 0.0 0.0 0.0 48-49 0.0 0.0 0.0 0.0 0.0 50-51 0.0 0.0 0.0 0.0 0.0 52-53 0.0 0.0 0.0 0.0 0.0 54-55 0.0 0.0 0.0 0.0 0.0 56-57 0.0 0.0 0.0 0.0 0.0 58-59 0.0 0.0 0.0 0.0 0.0 60-61 0.0 0.0 0.0 0.0 0.0 62-63 0.0 0.0 0.0 0.0 0.0 64-65 0.0 0.0 0.0 0.0 0.0 66-67 0.0 0.0 0.0 0.0 0.0 68-69 0.0 0.0 0.0 0.0 0.0 70-71 0.0 0.0 0.0 0.0 0.0 72-73 0.0 0.0 0.0 0.0 0.0 74-75 0.0 0.0 0.0 0.0 0.0 76-77 0.0 0.0 0.0 0.0 0.0 78-79 0.0 0.0 0.0 0.0 0.0 80-81 0.0 0.0 0.0 0.0 0.0 82-83 0.0 0.0 0.0 0.0 0.0 84-85 0.0 0.0 0.0 0.0 0.0 86-87 0.0 0.0 0.0 0.0 0.0 88-89 0.0 0.0 0.0 0.0 0.0 90-91 0.0 0.0 0.0 0.0 0.0 92-93 0.0 0.0 0.0 0.0 0.0 94-95 0.0 0.0 0.0 0.0 0.0 96-97 0.0 0.0 0.0 0.0 0.0 98-99 0.0 0.0 0.0 0.0 0.0 100-101 0.0 0.0 0.0 0.0 0.0 102-103 0.0 0.0 0.0 0.0 0.0 104-105 0.0 0.0 0.0 0.0 0.0 106-107 0.0 0.0 0.0 0.0 0.0 108-109 0.0 0.0 0.0 0.0 0.0 110-111 0.0 0.0 0.0 0.0 0.0 112-113 0.0 0.0 0.0 0.0 0.0 114-115 0.0 0.0 0.0 0.0 0.0 116-117 0.0125 0.0 0.0 0.0 0.0 118-119 0.025 0.0 0.0 0.0 0.0 120-121 0.025 0.0 0.0 0.0 0.0 122-123 0.025 0.0 0.0 0.0 0.0 124-125 0.025 0.0 0.0 0.0 0.0 126-127 0.025 0.0 0.0 0.0 0.0 128 0.025 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE ERR3959309 read2 length is 20-140 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3959309_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 20-140 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.564 37.0 37.0 37.0 37.0 37.0 2 36.5645 37.0 37.0 37.0 37.0 37.0 3 36.522 37.0 37.0 37.0 37.0 37.0 4 36.514 37.0 37.0 37.0 37.0 37.0 5 36.507 37.0 37.0 37.0 37.0 37.0 6 36.512 37.0 37.0 37.0 37.0 37.0 7 36.4895 37.0 37.0 37.0 37.0 37.0 8 36.5295 37.0 37.0 37.0 37.0 37.0 9 36.4825 37.0 37.0 37.0 37.0 37.0 10-14 36.4548 37.0 37.0 37.0 37.0 37.0 15-19 36.4491 37.0 37.0 37.0 37.0 37.0 20-24 36.413497817048054 37.0 37.0 37.0 37.0 37.0 25-29 36.4084066263522 37.0 37.0 37.0 37.0 37.0 30-34 36.42463846111137 37.0 37.0 37.0 37.0 37.0 35-39 36.4250960747555 37.0 37.0 37.0 37.0 37.0 40-44 36.38874292218999 37.0 37.0 37.0 37.0 37.0 45-49 36.38673463043808 37.0 37.0 37.0 37.0 37.0 50-54 36.358132559966364 37.0 37.0 37.0 37.0 37.0 55-59 36.35532101997166 37.0 37.0 37.0 37.0 37.0 60-64 36.3974079925235 37.0 37.0 37.0 37.0 37.0 65-69 36.335582302038816 37.0 37.0 37.0 37.0 37.0 70-74 36.34149622262559 37.0 37.0 37.0 37.0 37.0 75-79 36.3677206998755 37.0 37.0 37.0 37.0 37.0 80-84 36.34791550520935 37.0 37.0 37.0 37.0 37.0 85-89 36.38167708640789 37.0 37.0 37.0 37.0 37.0 90-94 36.301720579819275 37.0 37.0 37.0 37.0 37.0 95-99 36.301371618873844 37.0 37.0 37.0 37.0 37.0 100-104 36.21839104599293 37.0 37.0 37.0 37.0 37.0 105-109 36.175120593997335 37.0 37.0 37.0 37.0 37.0 110-114 36.15397759636316 37.0 37.0 37.0 37.0 37.0 115-119 36.03792351122786 37.0 37.0 37.0 37.0 37.0 120-124 36.03252787775321 37.0 37.0 37.0 37.0 37.0 125-129 35.90403541869492 37.0 37.0 37.0 37.0 37.0 130-134 35.928847833623465 37.0 37.0 37.0 37.0 37.0 135-139 35.74944748149144 37.0 37.0 37.0 37.0 37.0 140 36.395044146966676 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 26 2.0 27 2.0 28 1.0 29 7.0 30 8.0 31 30.0 32 42.0 33 77.0 34 192.0 35 492.0 36 2787.0 37 360.0 >>END_MODULE >>Per base sequence content pass #Base G A T C 1 28.050000000000004 22.775000000000002 18.5 30.675 2 27.85 19.650000000000002 23.95 28.549999999999997 3 27.1 20.599999999999998 23.325000000000003 28.975 4 25.2 24.25 24.474999999999998 26.075 5 27.275 23.125 24.0 25.6 6 27.150000000000002 21.224999999999998 23.325000000000003 28.299999999999997 7 27.55 24.3 21.375 26.775 8 26.924999999999997 24.25 22.95 25.874999999999996 9 26.974999999999998 22.675 23.375 26.974999999999998 10-14 26.66 23.645 22.795 26.900000000000002 15-19 26.99 23.43 23.05 26.529999999999998 20-24 27.117117117117118 23.61861861861862 22.46746746746747 26.796796796796794 25-29 27.103600441279713 23.503159161568547 22.409988968007223 26.983251429144516 30-34 27.239819004524886 23.172448466566113 23.122171945701357 26.465560583207644 35-39 26.887030132016527 24.024992441801874 22.73505996170513 26.352917464476466 40-44 27.637684083114788 23.885414565261247 22.46318337704257 26.0137179745814 45-49 27.38522147583211 23.30925804333552 22.6880145461892 26.617505934643166 50-54 27.43967218090757 23.66064653209895 22.51732685789447 26.382354429099003 55-59 27.176446741664133 23.522853957636567 22.757677105503195 26.54302219519611 60-64 27.62837426425817 23.244367769433733 22.90947838441242 26.217779581895677 65-69 27.726441917140537 23.146831844029244 22.710194963444355 26.416531275385864 70-74 27.298602287166457 23.70520965692503 22.891994917407878 26.104193138500637 75-79 27.96092796092796 23.38217338217338 22.924297924297925 25.73260073260073 80-84 27.52176791078976 23.443148836498803 23.178369570752075 25.856713681959363 85-89 27.80157030692363 23.167125522585906 22.606301621290914 26.42500254919955 90-94 28.268082282680822 23.628196620897352 22.648154764943087 25.455566331478742 95-99 27.82746460878009 24.025144375734655 22.34885266009097 25.798538355394285 100-104 27.86105284698419 23.942292934977235 22.867959277638512 25.32869494040006 105-109 28.24235583829263 23.69690129283809 22.74779396675559 25.312948902113686 110-114 28.82507333642118 23.49338685605476 22.901549071071997 24.779990736452064 115-119 29.26274428704374 24.268431392823906 22.526108985627133 23.94271533450522 120-124 29.467394128345028 24.084177708495712 22.23434658352819 24.21408157963107 125-129 29.527517626012838 23.902978006945176 22.787540776596867 23.781963590445123 130-134 30.07551009478927 23.954372623574145 22.840464842285655 23.129652439350934 135-139 31.25611213734652 23.302184070411823 22.4872324242095 22.954471368032163 140 31.928225576758756 24.52292794075762 21.219025918541725 22.329820563941897 >>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 0.5 22 1.0 23 1.0 24 1.5 25 3.0 26 2.0 27 0.0 28 1.5 29 3.0 30 3.5 31 7.0 32 10.0 33 13.5 34 20.0 35 27.5 36 36.0 37 41.5 38 58.5 39 79.0 40 83.0 41 96.5 42 113.5 43 119.0 44 134.0 45 153.5 46 170.5 47 166.5 48 157.5 49 157.0 50 148.0 51 139.5 52 129.5 53 118.5 54 117.0 55 111.0 56 94.5 57 84.5 58 84.5 59 91.5 60 89.0 61 85.5 62 92.5 63 93.5 64 89.5 65 86.5 66 75.0 67 76.0 68 76.0 69 72.5 70 72.0 71 67.0 72 64.5 73 54.5 74 47.0 75 42.5 76 42.5 77 33.5 78 22.5 79 19.5 80 13.0 81 11.0 82 9.5 83 4.5 84 1.0 85 0.5 86 1.0 87 0.5 88 0.5 89 1.0 90 0.5 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 0.5 >>END_MODULE >>Per base N content pass #Base N-Count 1 0.0 2 0.0 3 0.0 4 0.0 5 0.0 6 0.0 7 0.0 8 0.0 9 0.0 10-14 0.0 15-19 0.0 20-24 0.0 25-29 0.0 30-34 0.0 35-39 0.0 40-44 0.0 45-49 0.0 50-54 0.0 55-59 0.0 60-64 0.0 65-69 0.0 70-74 0.0 75-79 0.0 80-84 0.0 85-89 0.0 90-94 0.0 95-99 0.0 100-104 0.0 105-109 0.0 110-114 0.0 115-119 0.0 120-124 0.0 125-129 0.0 130-134 0.0 135-139 0.0 140 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 20-24 9.0 25-29 9.0 30-34 9.0 35-39 6.0 40-44 4.0 45-49 8.0 50-54 6.0 55-59 6.0 60-64 3.0 65-69 3.0 70-74 5.0 75-79 2.0 80-84 6.0 85-89 4.0 90-94 4.0 95-99 5.0 100-104 7.0 105-109 11.0 110-114 17.0 115-119 21.0 120-124 22.0 125-129 78.0 130-134 52.0 135-139 192.0 140-141 3511.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 95.85000000000001 #Duplication Level Percentage of deduplicated Percentage of total 1 95.93114241001565 91.95 2 3.808033385498174 7.3 3 0.2608242044861763 0.75 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 fail #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 0.05 0.0 0.0 0.0 0.0 66-67 0.0875 0.0 0.0 0.0 0.0 68-69 0.1625 0.0 0.0 0.0 0.0 70-71 0.3 0.0 0.0 0.0 0.0 72-73 0.4125 0.0 0.0 0.0 0.0 74-75 0.5874999999999999 0.0 0.0 0.0 0.0 76-77 0.675 0.0 0.0 0.0 0.0 78-79 0.875 0.0 0.0 0.0 0.0 80-81 1.0375 0.0 0.0 0.0 0.0 82-83 1.225 0.0 0.0 0.0 0.0 84-85 1.4625 0.0 0.0 0.0 0.0 86-87 1.6625 0.0 0.0 0.0 0.0 88-89 2.0 0.0 0.0 0.0 0.0 90-91 2.35 0.0 0.0 0.0 0.0 92-93 2.725 0.0 0.0 0.0 0.0 94-95 3.1875 0.0 0.0 0.0 0.0 96-97 3.75 0.0 0.0 0.0 0.0 98-99 4.5375 0.0 0.0 0.0 0.0 100-101 5.199999999999999 0.0 0.0 0.0 0.0 102-103 5.775 0.0 0.0 0.0 0.0 104-105 6.3125 0.0 0.0 0.0 0.0 106-107 7.0625 0.0 0.0 0.0 0.0 108-109 7.8625 0.0 0.0 0.0 0.0 110-111 8.5625 0.0 0.0 0.0 0.0 112-113 9.5125 0.0 0.0 0.0 0.0 114-115 10.4375 0.0 0.0 0.0 0.0 116-117 11.212499999999999 0.0 0.0 0.0 0.0 118-119 12.1875 0.0 0.0 0.0 0.0 120-121 13.087499999999999 0.0 0.0 0.0 0.0 122-123 14.1375 0.0 0.0 0.0 0.0 124-125 15.2375 0.0 0.0 0.0 0.0 126-127 15.575 0.0 0.0 0.0 0.0 128 15.575 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position TCCTTGT 10 0.009341046 130.5875 2 >>END_MODULE Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626093 spots for ERR3959309.sra Written 2626093 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra Read 2626087 spots for ERR3959309.sra Written 2626087 spots for ERR3959309.sra SRR ids: ['ERR3959309.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_2shtbs7g ERR3959309.sra spots: 52521746 blocks: [[1, 2626087], [2626088, 5252174], [5252175, 7878261], [7878262, 10504348], [10504349, 13130435], [13130436, 15756522], [15756523, 18382609], [18382610, 21008696], [21008697, 23634783], [23634784, 26260870], [26260871, 28886957], [28886958, 31513044], [31513045, 34139131], [34139132, 36765218], [36765219, 39391305], [39391306, 42017392], [42017393, 44643479], [44643480, 47269566], [47269567, 49895653], [49895654, 52521746]] ERR3959309 file size 15877211 ERR3959309 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 ERR3959309 ERR3959309_1.fastq ERR3959309_2.fastq Input file: ERR3959309_1.fastq Paired file: ERR3959309_2.fastq trimmed: ERR3959309-trimmed-pair1.fastq, ERR3959309-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 Dec 12 02:28:22 2024 >> started Thu Dec 12 02:35:39 2024 >> done (437.222s) 52521746 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 0 ( 0.00%) empty read pairs filtered out after trimming by size control 52521746 (100.00%) read pairs available; of these: 157599 ( 0.30%) trimmed read pairs available after processing 52364147 (99.70%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 19 1 0.00% 20 371 0.00% 21 896 0.00% 22 1380 0.00% 23 1796 0.00% 24 2029 0.00% 25 2304 0.00% 26 2681 0.01% 27 3095 0.01% 28 3258 0.01% 29 3421 0.01% 30 3600 0.01% 31 3872 0.01% 32 4014 0.01% 33 4129 0.01% 34 4281 0.01% 35 4450 0.01% 36 4553 0.01% 37 4772 0.01% 38 4843 0.01% 39 4858 0.01% 40 4828 0.01% 41 5134 0.01% 42 5111 0.01% 43 5405 0.01% 44 5348 0.01% 45 5461 0.01% 46 5531 0.01% 47 5628 0.01% 48 5878 0.01% 49 6032 0.01% 50 6076 0.01% 51 6208 0.01% 52 6186 0.01% 53 6330 0.01% 54 6590 0.01% 55 6664 0.01% 56 6949 0.01% 57 7037 0.01% 58 7126 0.01% 59 7571 0.01% 60 7560 0.01% 61 7883 0.02% 62 8038 0.02% 63 8179 0.02% 64 8338 0.02% 65 8655 0.02% 66 9059 0.02% 67 9422 0.02% 68 9525 0.02% 69 9819 0.02% 70 10369 0.02% 71 10681 0.02% 72 11177 0.02% 73 11836 0.02% 74 12274 0.02% 75 13005 0.02% 76 13570 0.03% 77 13939 0.03% 78 14716 0.03% 79 17971 0.03% 80 50816 0.10% 81 50103 0.10% 82 51182 0.10% 83 50488 0.10% 84 50822 0.10% 85 51919 0.10% 86 52600 0.10% 87 53766 0.10% 88 55376 0.11% 89 56080 0.11% 90 56437 0.11% 91 58628 0.11% 92 60396 0.11% 93 61458 0.12% 94 63561 0.12% 95 65091 0.12% 96 68069 0.13% 97 71594 0.14% 98 74140 0.14% 99 77298 0.15% 100 81113 0.15% 101 85500 0.16% 102 90393 0.17% 103 93868 0.18% 104 102313 0.19% 105 104199 0.20% 106 108183 0.21% 107 113026 0.22% 108 122145 0.23% 109 127843 0.24% 110 135386 0.26% 111 140101 0.27% 112 149358 0.28% 113 157046 0.30% 114 162023 0.31% 115 173654 0.33% 116 202201 0.38% 117 211308 0.40% 118 246521 0.47% 119 311957 0.59% 120 284778 0.54% 121 341814 0.65% 122 400859 0.76% 123 429899 0.82% 124 453834 0.86% 125 468859 0.89% 126 726397 1.38% 127 739519 1.41% 128 744846 1.42% 129 522743 1.00% 130 522291 0.99% 131 531566 1.01% 132 536184 1.02% 133 66679 0.13% 134 51097 0.10% 135 35123 0.07% 136 37451 0.07% 137 48166 0.09% 138 88996 0.17% 139 1481194 2.82% 140 39509776 75.23% 52521746 reads passed initial QC criterion=sequence-density sequence-density=0.18 sequence-density-rank=1 fanout-score=197.36 fanout-score-rank=5 prefix-density=0.72 prefix-fanout=49.4 sequence=GAGATCGGAAGA criterion=fanout-score sequence-density=0.07 sequence-density-rank=23 fanout-score=244.91 fanout-score-rank=1 prefix-density=0.90 prefix-fanout=20.1 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGC criterion=sequence-density sequence-density=13.93 sequence-density-rank=1 fanout-score=45.27 fanout-score-rank=1 prefix-density=15.60 prefix-fanout=40.4 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGGTG criterion=fanout-score sequence-density=13.93 sequence-density-rank=1 fanout-score=45.27 fanout-score-rank=1 prefix-density=15.60 prefix-fanout=40.4 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGGTG Potential 3prime adapter identified. Now checking if in reference sequence /dee2/code/volunteer_pipeline.sh: line 905: -f: command not found /dee2/code/volunteer_pipeline.sh: line 906: -f: command not found Adapter seq not found in reference. Now shuffling file before clipping skewer v0.2.2 [April 4, 2016] COMMAND LINE: skewer -f sanger -l 18 -t 20 -x GAGATCGGAAGA -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGGTG -o ERR3959309 ERR3959309_1.fastq ERR3959309_2.fastq Input file: ERR3959309_1.fastq Paired file: ERR3959309_2.fastq trimmed: ERR3959309-trimmed-pair1.fastq, ERR3959309-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): GAGATCGGAAGA -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGGTG -- maximum error ratio allowed (-r): 0.100 -- maximum indel error ratio allowed (-d): 0.030 -- minimum read length allowed after trimming (-l): 18 -- file format (-f): Sanger/Illumina 1.8+ FASTQ -- number of concurrent threads (-t): 20 Thu Dec 12 03:00:34 2024 >> started Thu Dec 12 03:04:58 2024 >> done (264.251s) 39391310 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 3 ( 0.00%) empty read pairs filtered out after trimming by size control 39391307 (100.00%) read pairs available; of these: 55907 ( 0.14%) trimmed read pairs available after processing 39335400 (99.86%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 1 0.00% 20 279 0.00% 21 690 0.00% 22 1025 0.00% 23 1325 0.00% 24 1523 0.00% 25 1729 0.00% 26 2046 0.01% 27 2321 0.01% 28 2469 0.01% 29 2602 0.01% 30 2699 0.01% 31 2858 0.01% 32 2982 0.01% 33 3067 0.01% 34 3220 0.01% 35 3395 0.01% 36 3367 0.01% 37 3598 0.01% 38 3593 0.01% 39 3606 0.01% 40 3631 0.01% 41 3896 0.01% 42 3849 0.01% 43 4118 0.01% 44 4000 0.01% 45 4052 0.01% 46 4203 0.01% 47 4214 0.01% 48 4418 0.01% 49 4536 0.01% 50 4592 0.01% 51 4682 0.01% 52 4625 0.01% 53 4739 0.01% 54 4923 0.01% 55 4939 0.01% 56 5274 0.01% 57 5282 0.01% 58 5393 0.01% 59 5666 0.01% 60 5630 0.01% 61 5947 0.02% 62 6025 0.02% 63 6076 0.02% 64 6221 0.02% 65 6430 0.02% 66 6818 0.02% 67 7072 0.02% 68 7156 0.02% 69 7345 0.02% 70 7834 0.02% 71 7972 0.02% 72 8402 0.02% 73 8959 0.02% 74 9272 0.02% 75 9762 0.02% 76 10103 0.03% 77 10468 0.03% 78 10967 0.03% 79 13568 0.03% 80 38224 0.10% 81 37679 0.10% 82 38479 0.10% 83 37902 0.10% 84 38326 0.10% 85 39017 0.10% 86 39248 0.10% 87 40417 0.10% 88 41751 0.11% 89 41951 0.11% 90 42543 0.11% 91 43933 0.11% 92 45307 0.12% 93 46100 0.12% 94 47764 0.12% 95 48906 0.12% 96 50833 0.13% 97 53748 0.14% 98 55746 0.14% 99 57940 0.15% 100 60671 0.15% 101 64225 0.16% 102 67888 0.17% 103 70465 0.18% 104 76888 0.20% 105 77969 0.20% 106 80914 0.21% 107 84906 0.22% 108 91558 0.23% 109 95859 0.24% 110 101598 0.26% 111 104861 0.27% 112 111829 0.28% 113 117548 0.30% 114 121705 0.31% 115 130050 0.33% 116 151610 0.38% 117 158477 0.40% 118 184855 0.47% 119 233626 0.59% 120 213566 0.54% 121 256320 0.65% 122 300840 0.76% 123 322491 0.82% 124 340852 0.87% 125 351903 0.89% 126 544390 1.38% 127 554746 1.41% 128 558486 1.42% 129 391928 0.99% 130 391384 0.99% 131 398764 1.01% 132 402338 1.02% 133 50147 0.13% 134 38547 0.10% 135 26863 0.07% 136 30071 0.08% 137 41285 0.10% 138 80792 0.21% 139 1141778 2.90% 140 29579045 75.09% criterion=sequence-density sequence-density=0.19 sequence-density-rank=1 fanout-score=193.67 fanout-score-rank=5 prefix-density=0.74 prefix-fanout=48.8 sequence=GAGATCGGAAGA criterion=fanout-score sequence-density=0.08 sequence-density-rank=19 fanout-score=270.60 fanout-score-rank=1 prefix-density=0.84 prefix-fanout=27.2 sequence=CGCCGCCGCCGC criterion=sequence-density sequence-density=14.19 sequence-density-rank=1 fanout-score=45.15 fanout-score-rank=1 prefix-density=15.90 prefix-fanout=40.3 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGGTG criterion=fanout-score sequence-density=14.19 sequence-density-rank=1 fanout-score=45.15 fanout-score-rank=1 prefix-density=15.90 prefix-fanout=40.3 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTGGTG ERR3959309 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 12 03:07:08 Started mapping on | Dec 12 03:07:09 Finished on | Dec 12 03:30:05 Mapping speed, Million of reads per hour | 137.41 Number of input reads | 52521743 Average input read length | 269 UNIQUE READS: Uniquely mapped reads number | 36619069 Uniquely mapped reads % | 69.72% Average mapped length | 273.31 Number of splices: Total | 32637275 Number of splices: Annotated (sjdb) | 30734446 Number of splices: GT/AG | 32189134 Number of splices: GC/AG | 396104 Number of splices: AT/AC | 19911 Number of splices: Non-canonical | 32126 Mismatch rate per base, % | 0.07% Deletion rate per base | 0.00% Deletion average length | 1.51 Insertion rate per base | 0.00% Insertion average length | 1.14 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 450657 % of reads mapped to multiple loci | 0.86% Number of reads mapped to too many loci | 404039 % of reads mapped to too many loci | 0.77% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 25.85% % of reads unmapped: other | 2.80% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 15600673 15600673 15600673 N_multimapping 450657 450657 450657 N_noFeature 1256051 35663926 1627434 N_ambiguous 875787 7664 294286 UnstrandedReadsAssigned:34487231 PositiveStrandReadsAssigned:947479 NegativeStrandReadsAssigned:34697349 Dataset is classified negative stranded MeadianReadLen=140 20thPercentileLength=136 echo kmer=131 ERR3959309 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: ERR3959309-trimmed-pair1.fastq ERR3959309-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 52,521,743 reads, 47,568,036 reads pseudoaligned [quant] estimated average fragment length: 201.608 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,244 rounds 52973 ERR3959309.ke.tsv 35125 ERR3959309.se.tsv 88098 total ==> ERR3959309.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 735.769 0 0 PNS24247 1044 843.392 98.5625 3.66036 PNS24249 1928 1727.39 748.429 13.5706 PNS24246 1044 843.392 98.5625 3.66036 PNS24248 1044 843.392 98.5625 3.66036 PNS24244 1471 1270.39 121.884 3.00503 PNS24243 293 128.39 2 0.487908 KQK14069 1603 1402.39 20473.2 457.253 KQK14071 474 283.701 965.398 106.582 ==> ERR3959309.se.tsv <== BRADI_1g14170v3 16198 BRADI_1g53295v3 736 BRADI_1g59795v3 551 BRADI_1g07683v3 0 BRADI_1g00485v3 36 BRADI_1g20270v3 2372 BRADI_1g74790v3 1218 BRADI_1g09890v3 5 BRADI_1g77505v3 366 BRADI_1g48960v3 0 ERR3959309 completed mapping pipeline successfully