Starting /dee2/code/volunteer_pipeline.sh ERR3959285 current disk space = 1547753226240 free memory = 1603302772 ERR3959285 SRAfilesize ad3a3a627b0dd63d5bcb9f6b20ab5e2e ERR3959285.sra ERR3959285.sra file validated ERR3959285 is paired end ERR3959285 is conventional basespace ERR3959285 read1 length is 21-140 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3959285_1.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 21-140 %GC 52 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.574 37.0 37.0 37.0 37.0 37.0 2 36.4375 37.0 37.0 37.0 37.0 37.0 3 36.5435 37.0 37.0 37.0 37.0 37.0 4 36.47 37.0 37.0 37.0 37.0 37.0 5 36.6115 37.0 37.0 37.0 37.0 37.0 6 36.5075 37.0 37.0 37.0 37.0 37.0 7 36.547 37.0 37.0 37.0 37.0 37.0 8 36.4335 37.0 37.0 37.0 37.0 37.0 9 36.562 37.0 37.0 37.0 37.0 37.0 10-14 36.4906 37.0 37.0 37.0 37.0 37.0 15-19 36.4928 37.0 37.0 37.0 37.0 37.0 20-24 36.42368665219199 37.0 37.0 37.0 37.0 37.0 25-29 36.43207755018216 37.0 37.0 37.0 37.0 37.0 30-34 36.447386024310234 37.0 37.0 37.0 37.0 37.0 35-39 36.42893038812228 37.0 37.0 37.0 37.0 37.0 40-44 36.458170294926404 37.0 37.0 37.0 37.0 37.0 45-49 36.43495756416564 37.0 37.0 37.0 37.0 37.0 50-54 36.430998225037676 37.0 37.0 37.0 37.0 37.0 55-59 36.40678359841968 37.0 37.0 37.0 37.0 37.0 60-64 36.380906064908736 37.0 37.0 37.0 37.0 37.0 65-69 36.379544723800294 37.0 37.0 37.0 37.0 37.0 70-74 36.34978788454407 37.0 37.0 37.0 37.0 37.0 75-79 36.382858228404544 37.0 37.0 37.0 37.0 37.0 80-84 36.361098582460365 37.0 37.0 37.0 37.0 37.0 85-89 36.33452572759438 37.0 37.0 37.0 37.0 37.0 90-94 36.390888990712355 37.0 37.0 37.0 37.0 37.0 95-99 36.35038281155774 37.0 37.0 37.0 37.0 37.0 100-104 36.370317900146134 37.0 37.0 37.0 37.0 37.0 105-109 36.3160318323004 37.0 37.0 37.0 37.0 37.0 110-114 36.30821953187503 37.0 37.0 37.0 37.0 37.0 115-119 36.307723145999155 37.0 37.0 37.0 37.0 37.0 120-124 36.323850889482394 37.0 37.0 37.0 37.0 37.0 125-129 36.260940118202875 37.0 37.0 37.0 37.0 37.0 130-134 36.14312358141727 37.0 37.0 37.0 37.0 37.0 135-139 36.15642434763252 37.0 37.0 37.0 37.0 37.0 140 36.540350877192985 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 27 2.0 28 5.0 29 9.0 30 15.0 31 42.0 32 50.0 33 96.0 34 128.0 35 326.0 36 2844.0 37 483.0 >>END_MODULE >>Per base sequence content pass #Base G A T C 1 26.400000000000002 25.074999999999996 19.6 28.925 2 24.975 21.825 24.474999999999998 28.725 3 23.849999999999998 22.825 25.974999999999998 27.35 4 23.200000000000003 23.275000000000002 24.349999999999998 29.175 5 25.374999999999996 24.05 24.625 25.95 6 23.825 23.724999999999998 24.55 27.900000000000002 7 24.9 24.85 24.25 26.0 8 24.9 23.849999999999998 24.5 26.75 9 24.224999999999998 24.875 23.575 27.325 10-14 24.9 24.525 23.97 26.605 15-19 24.725 24.125 23.935000000000002 27.215 20-24 24.678573215268397 24.203311821501828 24.57851818500175 26.539596778228024 25-29 24.222512038523274 24.518459069020867 24.046950240770464 27.212078651685395 30-34 24.50364413169138 24.27243025885901 24.398089972354864 26.825835637094748 35-39 24.96476746527079 24.1393195087578 23.696396215019124 27.199516810952286 40-44 25.1159040516025 23.896391856480548 24.097964120137068 26.889739971779886 45-49 24.92553137779573 24.28434391881658 23.769374463573484 27.020750239814205 50-54 25.345132743362832 23.342604298356513 23.640960809102403 27.671302149178256 55-59 24.788532644481588 24.226308058552398 23.85149166793294 27.133667629033077 60-64 25.11158449989856 23.808074660174476 23.645769933049298 27.434570906877664 65-69 25.13472292831723 23.87391967463142 24.112862226741232 26.878495170310117 70-74 25.281672189650777 23.767524853428498 23.767524853428498 27.183278103492224 75-79 25.150833418549958 23.913488086716434 23.376623376623375 27.559055118110237 80-84 25.1821446895844 23.853258081067214 24.135454079014877 26.829143150333508 85-89 26.01898668868022 23.253534206996182 23.635331751109277 27.092147353214322 90-94 24.94418194091074 23.43839243989823 23.993976841995952 27.623448777195076 95-99 25.607974115436804 24.02150088717253 23.22826427304039 27.142260724350276 100-104 25.23689197725837 23.483891345546432 23.694461991998317 27.584754685196884 105-109 25.095765056394974 23.72845286231113 23.536922749521175 27.638859331772718 110-114 25.83063646170442 23.166127292340885 23.31715210355987 27.686084142394822 115-119 25.942156003505694 23.729184925503944 23.477212971078 26.85144609991236 120-124 25.923867741039174 23.495415393164766 23.23978883023062 27.340928035565437 125-129 26.044018058690742 23.50451467268623 23.05869074492099 27.392776523702032 130-134 26.319981793354575 23.298816568047336 23.577605826126536 26.803595812471553 135-139 26.377571371588125 23.39164624764944 23.04974642429768 27.181035956464754 140 25.526315789473685 24.47368421052632 22.982456140350877 27.017543859649123 >>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 0.5 21 0.5 22 0.5 23 1.0 24 1.0 25 1.5 26 1.5 27 1.0 28 2.0 29 8.5 30 15.0 31 13.5 32 13.0 33 16.5 34 20.0 35 30.0 36 48.5 37 58.0 38 68.0 39 89.5 40 111.5 41 135.5 42 153.5 43 163.5 44 166.0 45 177.5 46 176.5 47 166.0 48 161.5 49 156.5 50 145.5 51 117.5 52 117.5 53 124.0 54 117.5 55 110.5 56 92.5 57 84.0 58 80.0 59 72.0 60 66.5 61 66.5 62 67.0 63 70.0 64 74.0 65 63.0 66 64.5 67 72.0 68 66.0 69 69.0 70 65.0 71 54.5 72 53.0 73 52.5 74 41.0 75 34.0 76 31.0 77 25.0 78 22.5 79 12.0 80 9.5 81 9.5 82 5.0 83 3.5 84 4.0 85 5.5 86 3.5 87 1.0 88 0.5 89 0.5 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 0.0 >>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 0.0 140 0.0 >>END_MODULE >>Sequence Length Distribution warn #Length Count 20-24 10.0 25-29 8.0 30-34 6.0 35-39 5.0 40-44 8.0 45-49 5.0 50-54 7.0 55-59 6.0 60-64 4.0 65-69 13.0 70-74 11.0 75-79 14.0 80-84 19.0 85-89 26.0 90-94 13.0 95-99 27.0 100-104 37.0 105-109 48.0 110-114 59.0 115-119 53.0 120-124 57.0 125-129 46.0 130-134 5.0 135-139 93.0 140-141 3420.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.39999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 94.4385593220339 89.14999999999999 2 5.217161016949152 9.85 3 0.31779661016949157 0.8999999999999999 4 0.026483050847457626 0.1 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 0.0 0.0 0.0 0.0 0.0 118-119 0.0 0.0 0.0 0.0 0.0 120-121 0.0 0.0 0.0 0.0 0.0 122-123 0.0 0.0 0.0 0.0 0.0 124-125 0.0125 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 warn #Sequence Count PValue Obs/Exp Max Max Obs/Exp Position ACACCGT 10 0.0098477 128.3 1 >>END_MODULE ERR3959285 read2 length is 21-140 nt ##FastQC 0.11.5 >>Basic Statistics pass #Measure Value Filename ERR3959285_2.fastq File type Conventional base calls Encoding Sanger / Illumina 1.9 Total Sequences 4000 Sequences flagged as poor quality 0 Sequence length 21-140 %GC 53 >>END_MODULE >>Per base sequence quality pass #Base Mean Median Lower Quartile Upper Quartile 10th Percentile 90th Percentile 1 36.5305 37.0 37.0 37.0 37.0 37.0 2 36.5185 37.0 37.0 37.0 37.0 37.0 3 36.5075 37.0 37.0 37.0 37.0 37.0 4 36.4565 37.0 37.0 37.0 37.0 37.0 5 36.444 37.0 37.0 37.0 37.0 37.0 6 36.476 37.0 37.0 37.0 37.0 37.0 7 36.461 37.0 37.0 37.0 37.0 37.0 8 36.5115 37.0 37.0 37.0 37.0 37.0 9 36.541 37.0 37.0 37.0 37.0 37.0 10-14 36.4514 37.0 37.0 37.0 37.0 37.0 15-19 36.445800000000006 37.0 37.0 37.0 37.0 37.0 20-24 36.374819603761615 37.0 37.0 37.0 37.0 37.0 25-29 36.3625564417956 37.0 37.0 37.0 37.0 37.0 30-34 36.367811806152744 37.0 37.0 37.0 37.0 37.0 35-39 36.384981058247185 37.0 37.0 37.0 37.0 37.0 40-44 36.34205341276191 37.0 37.0 37.0 37.0 37.0 45-49 36.33012982784386 37.0 37.0 37.0 37.0 37.0 50-54 36.29265404421808 37.0 37.0 37.0 37.0 37.0 55-59 36.32693091738891 37.0 37.0 37.0 37.0 37.0 60-64 36.33052681968628 37.0 37.0 37.0 37.0 37.0 65-69 36.26251468743904 37.0 37.0 37.0 37.0 37.0 70-74 36.285482846456624 37.0 37.0 37.0 37.0 37.0 75-79 36.28064139625563 37.0 37.0 37.0 37.0 37.0 80-84 36.23173641066135 37.0 37.0 37.0 37.0 37.0 85-89 36.30857416252934 37.0 37.0 37.0 37.0 37.0 90-94 36.30381631290463 37.0 37.0 37.0 37.0 37.0 95-99 36.27614670303525 37.0 37.0 37.0 37.0 37.0 100-104 36.1877167356374 37.0 37.0 37.0 37.0 37.0 105-109 36.222530164145645 37.0 37.0 37.0 37.0 37.0 110-114 36.17817051875686 37.0 37.0 37.0 37.0 37.0 115-119 36.088000911927224 37.0 37.0 37.0 37.0 37.0 120-124 36.09219161200397 37.0 37.0 37.0 37.0 37.0 125-129 35.96382848524039 37.0 37.0 37.0 37.0 37.0 130-134 36.07442590879342 37.0 37.0 37.0 37.0 37.0 135-139 35.984233388078465 37.0 37.0 37.0 37.0 37.0 140 36.4026402640264 37.0 37.0 37.0 37.0 37.0 >>END_MODULE >>Per sequence quality scores pass #Quality Count 27 1.0 28 1.0 29 1.0 30 13.0 31 45.0 32 53.0 33 87.0 34 162.0 35 536.0 36 2736.0 37 365.0 >>END_MODULE >>Per base sequence content pass #Base G A T C 1 29.325000000000003 21.975 19.650000000000002 29.049999999999997 2 29.5 19.1 22.7 28.7 3 25.6 23.025000000000002 23.875 27.500000000000004 4 24.525 24.75 24.8 25.924999999999997 5 27.075 23.75 24.425 24.75 6 28.199999999999996 22.225 23.3 26.275 7 27.6 24.05 21.525 26.825 8 27.1 24.525 23.150000000000002 25.224999999999998 9 27.224999999999998 23.575 22.95 26.25 10-14 27.345000000000002 23.630000000000003 22.64 26.384999999999998 15-19 26.784999999999997 23.815 22.73 26.669999999999998 20-24 27.132209494272423 23.66564954229403 22.84027812515632 26.361862838277222 25-29 27.012127894156563 23.65941665831412 22.89265310213491 26.435802345394404 30-34 27.384599929680043 23.31608820131599 22.853985634637603 26.445326234366366 35-39 26.805108608205952 23.783185840707965 22.837892196299276 26.573813354786807 40-44 27.883211678832115 23.699974830103194 22.889504153032973 25.527309338031714 45-49 27.23969111189623 23.72179881895725 22.868823499722403 26.169686569424115 50-54 27.252502780867633 23.784002426939026 22.4239053493781 26.53958944281525 55-59 27.27272727272727 23.975690048113446 22.891871359837936 25.85971131932135 60-64 27.499112441040722 23.705431860830757 22.828016432520158 25.967439265608363 65-69 27.570093457943923 23.664160910199104 22.526412027631043 26.239333604225923 70-74 27.450282284726107 23.986572402217586 22.85234728650628 25.710798026550023 75-79 27.1740791685771 23.78114014977839 22.81827907687605 26.226501604768455 80-84 27.485708452429563 23.433033891384238 23.116578195181706 25.964679461004494 85-89 28.163327882256745 23.436222403924774 22.879190515126737 25.52125919869174 90-94 28.059319867041676 23.676809000255687 23.088724111480442 25.175147021222195 95-99 27.820473409160773 23.49113638692489 23.445025105031252 25.243365098883082 100-104 27.136477955140382 24.128727608684493 22.95334394087153 25.7814504953036 105-109 27.839449069791343 24.37043889402816 22.124576009867404 25.665536026313085 110-114 28.010700138896034 23.643191522197643 22.56288903750193 25.783219301404394 115-119 28.703274039700954 23.79994844031967 22.763598865687033 24.73317865429234 120-124 27.785533322992606 24.223152887648002 23.04948037847061 24.941833410888787 125-129 28.158168574401664 23.76690946930281 22.679500520291363 25.395421436004163 130-134 28.548166824246245 24.19371782750289 22.68620653429982 24.571908813951048 135-139 28.078505856283638 24.02659069325736 23.52537722908093 24.369526221378074 140 29.510451045104514 23.789878987898792 22.717271727172715 23.982398239823983 >>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 0.5 20 1.0 21 0.5 22 0.0 23 0.0 24 0.0 25 0.0 26 2.0 27 2.0 28 2.0 29 3.5 30 4.5 31 7.5 32 11.0 33 14.5 34 15.0 35 20.0 36 40.0 37 51.0 38 61.5 39 75.5 40 93.5 41 111.5 42 127.5 43 148.0 44 149.5 45 147.5 46 166.5 47 165.5 48 148.0 49 137.0 50 136.0 51 140.0 52 127.0 53 115.0 54 102.0 55 96.5 56 92.5 57 83.0 58 83.5 59 85.5 60 80.5 61 82.5 62 87.5 63 87.5 64 94.5 65 94.5 66 83.5 67 79.0 68 82.0 69 71.5 70 68.5 71 74.0 72 59.5 73 51.0 74 49.0 75 40.5 76 35.5 77 32.0 78 22.0 79 18.0 80 13.0 81 9.5 82 8.5 83 4.0 84 2.0 85 1.5 86 3.0 87 3.0 88 1.0 89 0.0 90 0.5 91 1.0 92 1.0 93 0.5 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 6.0 25-29 10.0 30-34 4.0 35-39 5.0 40-44 10.0 45-49 6.0 50-54 7.0 55-59 6.0 60-64 6.0 65-69 6.0 70-74 6.0 75-79 7.0 80-84 5.0 85-89 4.0 90-94 6.0 95-99 6.0 100-104 7.0 105-109 3.0 110-114 8.0 115-119 9.0 120-124 14.0 125-129 44.0 130-134 17.0 135-139 162.0 140-141 3636.0 >>END_MODULE >>Sequence Duplication Levels pass #Total Deduplicated Percentage 94.69999999999999 #Duplication Level Percentage of deduplicated Percentage of total 1 94.74656810982049 89.725 2 4.936642027455122 9.35 3 0.29039070749736007 0.8250000000000001 4 0.026399155227032733 0.1 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 0.05 0.0 0.0 0.0 0.0 58-59 0.05 0.0 0.0 0.0 0.0 60-61 0.05 0.0 0.0 0.0 0.0 62-63 0.05 0.0 0.0 0.0 0.0 64-65 0.0625 0.0 0.0 0.0 0.0 66-67 0.15 0.0 0.0 0.0 0.0 68-69 0.175 0.0 0.0 0.0 0.0 70-71 0.175 0.0 0.0 0.0 0.0 72-73 0.2375 0.0 0.0 0.0 0.0 74-75 0.2875 0.0 0.0 0.0 0.0 76-77 0.375 0.0 0.0 0.0 0.0 78-79 0.3875 0.0 0.0 0.0 0.0 80-81 0.4125 0.0 0.0 0.0 0.0 82-83 0.4625 0.0 0.0 0.0 0.0 84-85 0.5874999999999999 0.0 0.0 0.0 0.0 86-87 0.6875 0.0 0.0 0.0 0.0 88-89 0.8999999999999999 0.0 0.0 0.0 0.0 90-91 1.0125 0.0 0.0 0.0 0.0 92-93 1.15 0.0 0.0 0.0 0.0 94-95 1.275 0.0 0.0 0.0 0.0 96-97 1.625 0.0 0.0 0.0 0.0 98-99 1.9 0.0 0.0 0.0 0.0 100-101 2.2375 0.0 0.0 0.0 0.0 102-103 2.5250000000000004 0.0 0.0 0.0 0.0 104-105 2.8125 0.0 0.0 0.0 0.0 106-107 3.3375 0.0 0.0 0.0 0.0 108-109 3.7625 0.0 0.0 0.0 0.0 110-111 4.25 0.0 0.0 0.0 0.0 112-113 4.75 0.0 0.0 0.0 0.0 114-115 5.1875 0.0 0.0 0.0 0.0 116-117 5.775 0.0 0.0 0.0 0.0 118-119 6.125 0.0 0.0 0.0 0.0 120-121 6.4875 0.0 0.0 0.0 0.0 122-123 7.050000000000001 0.0 0.0 0.0 0.0 124-125 7.4875 0.0 0.0 0.0 0.0 126-127 7.625 0.0 0.0 0.0 0.0 128 7.65 0.0 0.0 0.0 0.0 >>END_MODULE >>Kmer Content pass >>END_MODULE Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707832 spots for ERR3959285.sra Written 2707832 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra Read 2707816 spots for ERR3959285.sra Written 2707816 spots for ERR3959285.sra SRR ids: ['ERR3959285.sra'] extra args: ['--split-files', '--defline-qual', '+'] tempdir: /tmp/pfd_keudeek4 ERR3959285.sra spots: 54156336 blocks: [[1, 2707816], [2707817, 5415632], [5415633, 8123448], [8123449, 10831264], [10831265, 13539080], [13539081, 16246896], [16246897, 18954712], [18954713, 21662528], [21662529, 24370344], [24370345, 27078160], [27078161, 29785976], [29785977, 32493792], [32493793, 35201608], [35201609, 37909424], [37909425, 40617240], [40617241, 43325056], [43325057, 46032872], [46032873, 48740688], [48740689, 51448504], [51448505, 54156336]] ERR3959285 file size 16662904 ERR3959285 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 ERR3959285 ERR3959285_1.fastq ERR3959285_2.fastq Input file: ERR3959285_1.fastq Paired file: ERR3959285_2.fastq trimmed: ERR3959285-trimmed-pair1.fastq, ERR3959285-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 Sat Dec 7 02:31:27 2024 >> started Sat Dec 7 02:32:48 2024 >> done (81.089s) 54156336 read pairs processed; of these: 0 ( 0.00%) short read pairs filtered out after trimming by size control 1 ( 0.00%) empty read pairs filtered out after trimming by size control 54156335 (100.00%) read pairs available; of these: 116844 ( 0.22%) trimmed read pairs available after processing 54039491 (99.78%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 19 2 0.00% 20 433 0.00% 21 1004 0.00% 22 1402 0.00% 23 1884 0.00% 24 2154 0.00% 25 2574 0.00% 26 2789 0.01% 27 3147 0.01% 28 3473 0.01% 29 3599 0.01% 30 3788 0.01% 31 4045 0.01% 32 4247 0.01% 33 4406 0.01% 34 4531 0.01% 35 4683 0.01% 36 4777 0.01% 37 4902 0.01% 38 5178 0.01% 39 4991 0.01% 40 5185 0.01% 41 5306 0.01% 42 5570 0.01% 43 5625 0.01% 44 5525 0.01% 45 5717 0.01% 46 5730 0.01% 47 6164 0.01% 48 6068 0.01% 49 6002 0.01% 50 6112 0.01% 51 6358 0.01% 52 6457 0.01% 53 6534 0.01% 54 6617 0.01% 55 6594 0.01% 56 6826 0.01% 57 7001 0.01% 58 6851 0.01% 59 7060 0.01% 60 7363 0.01% 61 7321 0.01% 62 7555 0.01% 63 7600 0.01% 64 7665 0.01% 65 7873 0.01% 66 8132 0.02% 67 8133 0.02% 68 8332 0.02% 69 8467 0.02% 70 8781 0.02% 71 8864 0.02% 72 9089 0.02% 73 9387 0.02% 74 9747 0.02% 75 9854 0.02% 76 10294 0.02% 77 10434 0.02% 78 10566 0.02% 79 13721 0.03% 80 51214 0.09% 81 51448 0.09% 82 50180 0.09% 83 49585 0.09% 84 49113 0.09% 85 49955 0.09% 86 49929 0.09% 87 50439 0.09% 88 50706 0.09% 89 50960 0.09% 90 50561 0.09% 91 50425 0.09% 92 51639 0.10% 93 52341 0.10% 94 53123 0.10% 95 53029 0.10% 96 53056 0.10% 97 55170 0.10% 98 55691 0.10% 99 56285 0.10% 100 57638 0.11% 101 58804 0.11% 102 60933 0.11% 103 64168 0.12% 104 65947 0.12% 105 68403 0.13% 106 69731 0.13% 107 73427 0.14% 108 75305 0.14% 109 81480 0.15% 110 87646 0.16% 111 87712 0.16% 112 103093 0.19% 113 99764 0.18% 114 109757 0.20% 115 118883 0.22% 116 136411 0.25% 117 154943 0.29% 118 175234 0.32% 119 185487 0.34% 120 200704 0.37% 121 202001 0.37% 122 222861 0.41% 123 235607 0.44% 124 251545 0.46% 125 261353 0.48% 126 401112 0.74% 127 414764 0.77% 128 420464 0.78% 129 296835 0.55% 130 302084 0.56% 131 308770 0.57% 132 310445 0.57% 133 74158 0.14% 134 58077 0.11% 135 41345 0.08% 136 42774 0.08% 137 51650 0.10% 138 87222 0.16% 139 1724315 3.18% 140 44908145 82.92% 54156335 reads passed initial QC criterion=sequence-density sequence-density=0.13 sequence-density-rank=1 fanout-score=4.29 fanout-score-rank=19 prefix-density=0.15 prefix-fanout=3.9 sequence=TGCCGCACTTGCAGGATGACCCGCAGTTGCAGTTTCCTCCGCAGCAAGACATCT criterion=fanout-score sequence-density=0.05 sequence-density-rank=36 fanout-score=360.41 fanout-score-rank=1 prefix-density=0.82 prefix-fanout=20.1 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=6.93 sequence-density-rank=1 fanout-score=46.23 fanout-score-rank=1 prefix-density=7.92 prefix-fanout=40.5 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTCGCATTGGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA criterion=fanout-score sequence-density=6.93 sequence-density-rank=1 fanout-score=46.23 fanout-score-rank=1 prefix-density=7.92 prefix-fanout=40.5 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTCGCATTGGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA 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 TGCCGCACTTGCAGGATGACCCGCAGTTGCAGTTTCCTCCGCAGCAAGACATCT -y AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTCGCATTGGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA -o ERR3959285 ERR3959285_1.fastq ERR3959285_2.fastq Input file: ERR3959285_1.fastq Paired file: ERR3959285_2.fastq trimmed: ERR3959285-trimmed-pair1.fastq, ERR3959285-trimmed-pair2.fastq Parameters used: -- 3' end adapter sequence (-x): TGCCGCACTTGCAGGATGACCCGCAGTTGCAGTTTCCTCCGCAGCAAGACATCT -- paired 3' end adapter sequence (-y): AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTCGCATTGGTGTAGATCTCGGTGGTCGCCGT -- 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 Sat Dec 7 02:37:12 2024 >> started Sat Dec 7 02:37:46 2024 >> done (33.444s) 27078168 read pairs processed; of these: 13 ( 0.00%) short read pairs filtered out after trimming by size control 38 ( 0.00%) empty read pairs filtered out after trimming by size control 27078117 (100.00%) read pairs available; of these: 38785 ( 0.14%) trimmed read pairs available after processing 27039332 (99.86%) untrimmed read pairs available after processing Length distribution of reads after trimming: length count percentage 18 1 0.00% 19 0 0.00% 20 214 0.00% 21 479 0.00% 22 674 0.00% 23 931 0.00% 24 1095 0.00% 25 1256 0.00% 26 1434 0.01% 27 1571 0.01% 28 1700 0.01% 29 1795 0.01% 30 1913 0.01% 31 2011 0.01% 32 2112 0.01% 33 2252 0.01% 34 2280 0.01% 35 2335 0.01% 36 2350 0.01% 37 2474 0.01% 38 2611 0.01% 39 2481 0.01% 40 2628 0.01% 41 2680 0.01% 42 2704 0.01% 43 2759 0.01% 44 2770 0.01% 45 2808 0.01% 46 2865 0.01% 47 3026 0.01% 48 3050 0.01% 49 3000 0.01% 50 3046 0.01% 51 3219 0.01% 52 3225 0.01% 53 3320 0.01% 54 3360 0.01% 55 3334 0.01% 56 3374 0.01% 57 3552 0.01% 58 3404 0.01% 59 3533 0.01% 60 3700 0.01% 61 3697 0.01% 62 3840 0.01% 63 3811 0.01% 64 3782 0.01% 65 3909 0.01% 66 4137 0.02% 67 4081 0.02% 68 4186 0.02% 69 4243 0.02% 70 4484 0.02% 71 4530 0.02% 72 4524 0.02% 73 4679 0.02% 74 4963 0.02% 75 4904 0.02% 76 5138 0.02% 77 5244 0.02% 78 5248 0.02% 79 6916 0.03% 80 25537 0.09% 81 25805 0.10% 82 25211 0.09% 83 24640 0.09% 84 24584 0.09% 85 24969 0.09% 86 25093 0.09% 87 25123 0.09% 88 25318 0.09% 89 25581 0.09% 90 25220 0.09% 91 25358 0.09% 92 25903 0.10% 93 26150 0.10% 94 26817 0.10% 95 26424 0.10% 96 26536 0.10% 97 27757 0.10% 98 27845 0.10% 99 27994 0.10% 100 28825 0.11% 101 29291 0.11% 102 30321 0.11% 103 31986 0.12% 104 32890 0.12% 105 34108 0.13% 106 34836 0.13% 107 36817 0.14% 108 37648 0.14% 109 40798 0.15% 110 43606 0.16% 111 43882 0.16% 112 51488 0.19% 113 49900 0.18% 114 54483 0.20% 115 59306 0.22% 116 68382 0.25% 117 77343 0.29% 118 87702 0.32% 119 92872 0.34% 120 100700 0.37% 121 101410 0.37% 122 111703 0.41% 123 117687 0.43% 124 125721 0.46% 125 130526 0.48% 126 200707 0.74% 127 207231 0.77% 128 210654 0.78% 129 148901 0.55% 130 150266 0.55% 131 154099 0.57% 132 155675 0.57% 133 37131 0.14% 134 29036 0.11% 135 20696 0.08% 136 21995 0.08% 137 28288 0.10% 138 53648 0.20% 139 885698 3.27% 140 22416354 82.78% criterion=sequence-density sequence-density=0.13 sequence-density-rank=1 fanout-score=4.67 fanout-score-rank=17 prefix-density=0.14 prefix-fanout=4.1 sequence=TGCCGCACTTGCAGGATGACCCGCAGTTGCAGTTTCCTCCGCAGCAAGACATCT criterion=fanout-score sequence-density=0.05 sequence-density-rank=36 fanout-score=319.35 fanout-score-rank=1 prefix-density=0.83 prefix-fanout=19.8 sequence=GGCGGCGGCGAACCGCCCCCGTCGCCGCGATCCGAACACTTCACCGGACCATTCAATCGGTAGGAGCGACGGGCGGTGTGTACAAAGGGCAGGGACGTAGTCAACGCGAGCTGATGACTCGCGCTTACTAGGCATTCCTCGTTGAAGACCAACAATTGCAATGATCTATCCCCATCACGATGAAATTTCCCAAGATTACCCGGGCCTGTCGGCCAAGGCTATATACTCGTTGAATACATCAGTGTAGCGCGCGTGCGGCCCAGAACATCTAAGGGCATCACAGACCTGTTATTGCCTCAAACTTCCGTCGCCTAAACGGCGATAGTCCCTCTAAGAAGCTAGCTGCGGAGGGATGGCTCCGCATAGCTAGTTAGCAGGCTGAGGTCTCGTTCGTTAACGGAATTAACCAGACAAATCGCTCCACCAACTAAGAACGGCCATGCACCACCACCCATAGAATCAAGAAAGAGCTCTCAGTCTGTCAATCCTTGCTATGTCTGGACCTGGTAAG criterion=sequence-density sequence-density=7.13 sequence-density-rank=1 fanout-score=46.16 fanout-score-rank=1 prefix-density=8.14 prefix-fanout=40.5 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTCGCATTGGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA criterion=fanout-score sequence-density=7.13 sequence-density-rank=1 fanout-score=46.16 fanout-score-rank=1 prefix-density=8.14 prefix-fanout=40.5 sequence=AGATCGGAAGAGCGTCGTGTAGGGAAAGAGTGTTCGCATTGGTGTAGATCTCGGTGGTCGCCGTATCATTAAAAA ERR3959285 testing PE reads STAR mapping to Ensembl genome Started job on | Dec 07 02:38:46 Started mapping on | Dec 07 02:38:46 Finished on | Dec 07 02:41:21 Mapping speed, Million of reads per hour | 1257.82 Number of input reads | 54156284 Average input read length | 272 UNIQUE READS: Uniquely mapped reads number | 44556749 Uniquely mapped reads % | 82.27% Average mapped length | 274.45 Number of splices: Total | 40905133 Number of splices: Annotated (sjdb) | 38667353 Number of splices: GT/AG | 40332543 Number of splices: GC/AG | 511857 Number of splices: AT/AC | 24642 Number of splices: Non-canonical | 36091 Mismatch rate per base, % | 0.07% Deletion rate per base | 0.00% Deletion average length | 1.49 Insertion rate per base | 0.00% Insertion average length | 1.15 MULTI-MAPPING READS: Number of reads mapped to multiple loci | 560612 % of reads mapped to multiple loci | 1.04% Number of reads mapped to too many loci | 239366 % of reads mapped to too many loci | 0.44% UNMAPPED READS: % of reads unmapped: too many mismatches | 0.00% % of reads unmapped: too short | 14.67% % of reads unmapped: other | 1.58% CHIMERIC READS: Number of chimeric reads | 0 % of chimeric reads | 0.00% N_unmapped 9149833 9149833 9149833 N_multimapping 560612 560612 560612 N_noFeature 1392528 43423874 1782847 N_ambiguous 1014617 7365 275628 UnstrandedReadsAssigned:42149604 PositiveStrandReadsAssigned:1125510 NegativeStrandReadsAssigned:42498274 Dataset is classified negative stranded MeadianReadLen=140 20thPercentileLength=140 echo kmer=135 ERR3959285 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: ERR3959285-trimmed-pair1.fastq ERR3959285-trimmed-pair2.fastq [quant] finding pseudoalignments for the reads ... done [quant] processed 54,156,284 reads, 50,209,665 reads pseudoaligned [quant] estimated average fragment length: 229.854 [ em] quantifying the abundances ... done [ em] the Expectation-Maximization algorithm ran for 1,244 rounds 52973 ERR3959285.ke.tsv 35125 ERR3959285.se.tsv 88098 total ==> ERR3959285.ke.tsv <== target_id length eff_length est_counts tpm PNS24245 936 707.456 0 0 PNS24247 1044 815.146 104.942 3.71676 PNS24249 1928 1699.15 730.011 12.4036 PNS24246 1044 815.146 104.942 3.71676 PNS24248 1044 815.146 104.942 3.71676 PNS24244 1471 1242.15 81.1623 1.88639 PNS24243 293 109.011 0 0 KQK14069 1603 1374.15 32936.2 691.975 KQK14071 474 256.958 1696.7 190.631 ==> ERR3959285.se.tsv <== BRADI_1g14170v3 30885 BRADI_1g53295v3 392 BRADI_1g59795v3 673 BRADI_1g07683v3 0 BRADI_1g00485v3 49 BRADI_1g20270v3 3219 BRADI_1g74790v3 1587 BRADI_1g09890v3 8 BRADI_1g77505v3 519 BRADI_1g48960v3 0 ERR3959285 completed mapping pipeline successfully