MrX-NGS
commented
4 years ago I managed to solve this issue with using fastx_trimmer. But i have difficulty to choose the trimming option and Expected error value for dada2 based on the below figaro results:
{"trimPosition": [215, 259], "maxExpectedError": [2, 1], "readRetentionPercent": 87.76, "score": 86.76182339323117} {"trimPosition": [216, 258], "maxExpectedError": [2, 1], "readRetentionPercent": 87.7, "score": 86.69567853599382} {"trimPosition": [217, 257], "maxExpectedError": [2, 1], "readRetentionPercent": 87.66, "score": 86.65985007165693} {"trimPosition": [218, 256], "maxExpectedError": [2, 1], "readRetentionPercent": 87.58, "score": 86.58268107154669} {"trimPosition": [219, 255], "maxExpectedError": [2, 1], "readRetentionPercent": 87.51, "score": 86.50826810715468} {"trimPosition": [220, 254], "maxExpectedError": [2, 1], "readRetentionPercent": 87.43, "score": 86.43247712490354} {"trimPosition": [221, 253], "maxExpectedError": [2, 1], "readRetentionPercent": 87.31, "score": 86.31396758901995} {"trimPosition": [222, 252], "maxExpectedError": [2, 1], "readRetentionPercent": 87.17, "score": 86.16789769595414} {"trimPosition": [223, 251], "maxExpectedError": [2, 1], "readRetentionPercent": 86.97, "score": 85.96946312424208} {"trimPosition": [224, 250], "maxExpectedError": [2, 1], "readRetentionPercent": 86.73, "score": 85.72830999889759} {"trimPosition": [225, 249], "maxExpectedError": [2, 1], "readRetentionPercent": 86.51, "score": 85.50920515929886} {"trimPosition": [226, 248], "maxExpectedError": [2, 1], "readRetentionPercent": 86.25, "score": 85.24738176606769} {"trimPosition": [227, 247], "maxExpectedError": [2, 1], "readRetentionPercent": 86.04, "score": 85.0448131407783} {"trimPosition": [228, 246], "maxExpectedError": [2, 1], "readRetentionPercent": 85.79, "score": 84.79401389042002} {"trimPosition": [229, 245], "maxExpectedError": [2, 1], "readRetentionPercent": 85.52, "score": 84.51565428287951} {"trimPosition": [230, 244], "maxExpectedError": [2, 1], "readRetentionPercent": 85.12, "score": 84.11602910373719} {"trimPosition": [231, 243], "maxExpectedError": [2, 1], "readRetentionPercent": 84.81, "score": 83.80873112115533} {"trimPosition": [232, 242], "maxExpectedError": [2, 1], "readRetentionPercent": 84.55, "score": 83.54690772792416} {"trimPosition": [233, 241], "maxExpectedError": [2, 1], "readRetentionPercent": 84.22, "score": 83.22169551317386} {"trimPosition": [243, 231], "maxExpectedError": [3, 1], "readRetentionPercent": 87.13, "score": 83.1265571601808} {"trimPosition": [234, 240], "maxExpectedError": [2, 1], "readRetentionPercent": 84.01, "score": 83.0108587807298} {"trimPosition": [208, 266], "maxExpectedError": [1, 1], "readRetentionPercent": 82.91, "score": 82.91120052915886} {"trimPosition": [244, 230], "maxExpectedError": [3, 1], "readRetentionPercent": 86.86, "score": 82.85922169551318} {"trimPosition": [235, 239], "maxExpectedError": [2, 1], "readRetentionPercent": 83.81, "score": 82.8055341197222} {"trimPosition": [209, 265], "maxExpectedError": [1, 1], "readRetentionPercent": 82.71, "score": 82.70587586815125} {"trimPosition": [245, 229], "maxExpectedError": [3, 1], "readRetentionPercent": 86.62, "score": 82.61669055230956} {"trimPosition": [236, 238], "maxExpectedError": [2, 1], "readRetentionPercent": 83.57, "score": 82.5671370300959} {"trimPosition": [210, 264], "maxExpectedError": [1, 1], "readRetentionPercent": 82.44, "score": 82.43854040348363} {"trimPosition": [246, 228], "maxExpectedError": [3, 1], "readRetentionPercent": 86.33, "score": 82.3328188733326} {"trimPosition": [237, 237], "maxExpectedError": [2, 1], "readRetentionPercent": 83.28, "score": 82.2763752618234} {"trimPosition": [247, 227], "maxExpectedError": [3, 1], "readRetentionPercent": 86.08, "score": 82.08339764083343} {"trimPosition": [211, 263], "maxExpectedError": [1, 1], "readRetentionPercent": 82.08, "score": 82.08301179583287} {"trimPosition": [238, 236], "maxExpectedError": [2, 1], "readRetentionPercent": 82.96, "score": 81.95529710065043} {"trimPosition": [248, 226], "maxExpectedError": [3, 1], "readRetentionPercent": 85.81, "score": 81.80641605115203} {"trimPosition": [212, 262], "maxExpectedError": [1, 1], "readRetentionPercent": 81.77, "score": 81.77020174181457} {"trimPosition": [239, 235], "maxExpectedError": [2, 1], "readRetentionPercent": 82.61, "score": 81.60803660015434} {"trimPosition": [249, 225], "maxExpectedError": [3, 1], "readRetentionPercent": 85.54, "score": 81.54459265792084} {"trimPosition": [213, 261], "maxExpectedError": [1, 1], "readRetentionPercent": 81.5, "score": 81.50424429500606} {"trimPosition": [214, 260], "maxExpectedError": [1, 1], "readRetentionPercent": 81.26, "score": 81.26033513394334} {"trimPosition": [240, 234], "maxExpectedError": [2, 1], "readRetentionPercent": 82.24, "score": 81.24286186748981} {"trimPosition": [250, 224], "maxExpectedError": [3, 1], "readRetentionPercent": 85.24, "score": 81.23591665747988} {"trimPosition": [241, 233], "maxExpectedError": [2, 1], "readRetentionPercent": 81.98, "score": 80.97552640282218} {"trimPosition": [251, 223], "maxExpectedError": [3, 1], "readRetentionPercent": 84.9, "score": 80.89830228199757} {"trimPosition": [242, 232], "maxExpectedError": [2, 1], "readRetentionPercent": 81.69, "score": 80.69027670598611} {"trimPosition": [252, 222], "maxExpectedError": [3, 1], "readRetentionPercent": 84.61, "score": 80.61305258516151} {"trimPosition": [253, 221], "maxExpectedError": [3, 1], "readRetentionPercent": 84.3, "score": 80.29610847756587} {"trimPosition": [254, 220], "maxExpectedError": [3, 1], "readRetentionPercent": 83.84, "score": 79.83585051262264} {"trimPosition": [255, 219], "maxExpectedError": [3, 1], "readRetentionPercent": 83.46, "score": 79.45551758350788} {"trimPosition": [256, 218], "maxExpectedError": [3, 1], "readRetentionPercent": 83.14, "score": 79.13719545805314} {"trimPosition": [257, 217], "maxExpectedError": [3, 1], "readRetentionPercent": 82.78, "score": 78.78028883254326} {"trimPosition": [258, 216], "maxExpectedError": [3, 1], "readRetentionPercent": 82.43, "score": 78.42889427846984} {"trimPosition": [259, 215], "maxExpectedError": [3, 1], "readRetentionPercent": 82.04, "score": 78.04304927791864} {"trimPosition": [260, 214], "maxExpectedError": [4, 1], "readRetentionPercent": 86.65, "score": 77.65251901664645} {"trimPosition": [261, 213], "maxExpectedError": [4, 1], "readRetentionPercent": 86.4, "score": 77.39758571271084} {"trimPosition": [262, 212], "maxExpectedError": [4, 1], "readRetentionPercent": 86.12, "score": 77.12336015874766} {"trimPosition": [263, 211], "maxExpectedError": [4, 1], "readRetentionPercent": 85.87, "score": 76.87118289053026} {"trimPosition": [264, 210], "maxExpectedError": [4, 1], "readRetentionPercent": 85.61, "score": 76.60660346158086} {"trimPosition": [265, 209], "maxExpectedError": [4, 1], "readRetentionPercent": 85.27, "score": 76.26761106823945} {"trimPosition": [266, 208], "maxExpectedError": [4, 1], "readRetentionPercent": 85.01, "score": 76.0112997464447} {"trimPosition": [267, 207], "maxExpectedError": [4, 1], "readRetentionPercent": 82.88, "score": 73.87675008268107} {"trimPosition": [207, 267], "maxExpectedError": [1, 1], "readRetentionPercent": 49.44, "score": 49.436390695623416}
Any help is appreciated! I like to know the best trimposition [X,Y] and maxExpectedError[Z,1] based on the above result from fagero
Is it so that the highest score 86.76 best parameters ({"trimPosition": [215, 259], "maxExpectedError": [2, 1],})?
Best Regards, Bala
carolinebrunel
michael-weinstein
Hi,
I understand from your documentation that both R1 and R2 reads needs to be in same read length. However, my dataset (16S amplicon sequencing with 515FY-926Rjed primer) has below sequence length distribution when primerclipped is implemented! I like to know whether there is a possibility to apply fagero to this dataset? Any help is appreciated!
mothur > summary.seqs(fasta=all.primerclipped.R1.fasta)
Using 8 processors.
Minimum: 1 111 111 0 3 1 2.5%-tile: 1 267 267 0 3 428447 25%-tile: 1 268 268 0 4 4284468 Median: 1 269 269 0 4 8568936 75%-tile: 1 270 270 0 5 12853404 97.5%-tile: 1 271 271 0 6 16709425 Maximum: 1 277 277 122 163 17137871 Mean: 1 269 269 0 4
of Seqs: 17137871
It took 191 secs to summarize 17137871 sequences.
Output File Names: all.R1.summary
mothur > summary.seqs(fasta=all.primerclipped.R2.fasta)
Using 8 processors.
Minimum: 1 80 80 0 3 1 2.5%-tile: 1 267 267 0 3 428447 25%-tile: 1 268 268 0 4 4284468 Median: 1 269 269 0 4 8568936 75%-tile: 1 270 270 0 5 12853404 97.5%-tile: 1 271 271 0 6 16709425 Maximum: 1 277 277 119 275 17137871 Mean: 1 269 269 0 4
of Seqs: 17137871
It took 191 secs to summarize 17137871 sequences.
I am getting the below error:
python figaro/figaro.py -i input.files -o
output -a 413 -f 20 -r 20
Forward read files appear to be of different lengths or of varied lengths. {(271, 0.9195959595959596), (271, 0.2928282828282828), (270, 3.7046464646464647), (269, 0.6731313131313131), (269, 1.0723232323232323), (270, 0.41414141414141414), (268, 0.4682828282828283), (267, 0.24606060606060606), (269, 1.3692929292929292), (256, 555.1894949494949), (271, 0.3695959595959596), (259, 668.1155555555556), (270, 0.3066666666666667), (270, 0.2690909090909091), (270, 0.2726262626262626), (270, 0.37212121212121213), (270, 0.2718181818181818), (270, 0.31272727272727274), (270, 0.47434343434343434), (271, 0.3283838383838384), (270, 0.23272727272727273), (270, 0.2403030303030303), (270, 0.3712121212121212), (266, 255.0112121212121), (253, 651.5571717171717), (268, 0.2605050505050505), (271, 0.3903030303030303), (267, 34.545050505050504), (269, 0.5756565656565656), (271, 0.27111111111111114), (271, 0.38171717171717173), (271, 0.26626262626262626), (271, 0.3413131313131313), (271, 0.3106060606060606), (271, 0.40404040404040403), (270, 0.287979797979798), (271, 0.2726262626262626), (271, 0.23272727272727273), (271, 0.31303030303030305), (269, 0.24888888888888888), (271, 0.6076767676767677), (252, 1114.1874747474747), (269, 0.23545454545454544), (268, 3.5534343434343434), (268, 3.6641414141414144), (268, 3.534949494949495), (268, 3.071111111111111), (266, 104.25161616161616), (269, 2.64), (269, 1.2398989898989898), (269, 0.3914141414141414), (271, 0.25212121212121213), (269, 2.2622222222222224), (271, 3.5736363636363637), (271, 0.3211111111111111), (269, 0.6435353535353535), (271, 0.39141414141414144), (269, 1.4071717171717173), (267, 0.28929292929292927), (270, 0.5317171717171717), (268, 0.2727272727272727), (268, 0.8238383838383838), (268, 0.2516161616161616), (268, 0.25), (268, 0.31272727272727274), (271, 0.24686868686868688), (271, 0.24606060606060606), (270, 3.496868686868687), (268, 0.6596969696969697), (268, 0.24242424242424243), (270, 3.442020202020202), (261, 417.500101010101), (269, 1.1388888888888888), (269, 0.3672727272727273), (269, 0.5086868686868687), (269, 0.28929292929292927), (269, 0.5142424242424243), (269, 0.2702020202020202), (269, 0.2677777777777778), (269, 0.2925252525252525), (270, 0.31313131313131315), (269, 0.6327272727272727), (269, 0.6096969696969697), (270, 0.47464646464646465), (271, 0.33171717171717174), (270, 0.49808080808080807), (269, 1.0378787878787878), (268, 1.521111111111111), (267, 0.2475757575757576), (271, 0.43272727272727274), (270, 0.25242424242424244), (270, 0.24242424242424243), (270, 0.2723232323232323), (270, 0.41373737373737374), (270, 0.2727272727272727), (270, 0.25), (270, 0.2516161616161616), (270, 0.3115151515151515), (270, 0.8293939393939394), (270, 0.49404040404040406), (271, 0.28474747474747475), (267, 85.84030303030302), (271, 0.2677777777777778), (271, 0.9761616161616161), (268, 0.24606060606060606), (270, 0.3329292929292929), (268, 44.591010101010106), (271, 0.743030303030303), (271, 0.26262626262626265), (271, 0.30494949494949497), (271, 0.4382828282828283), (271, 0.2913131313131313), (271, 0.5959595959595959), (271, 0.3081818181818182), (271, 0.28929292929292927), (266, 146.64888888888888), (271, 0.6798989898989899), (270, 0.28474747474747475), (267, 1.782929292929293), (265, 215.1478787878788), (270, 0.3485858585858586), (269, 0.32686868686868686), (269, 1.2197979797979799), (269, 0.2475757575757576), (270, 0.6766666666666667), (269, 1.0246464646464646), (269, 0.24434343434343433), (271, 0.9147474747474748), (269, 0.2690909090909091), (269, 0.2605050505050505), (269, 0.33080808080808083), (261, 492.5546464646465), (269, 0.2913131313131313), (263, 327.8354545454546), (267, 0.24888888888888888), (267, 0.25212121212121213), (271, 0.4415151515151515), (267, 0.2509090909090909), (267, 0.292020202020202), (270, 0.22666666666666666), (243, 769.2945454545455), (267, 16.684747474747475), (266, 169.4920202020202), (268, 0.8099999999999999), (269, 1.218080808080808), (269, 1.3756565656565656), (269, 1.2342424242424241), (257, 534.3248484848484), (269, 1.425858585858586), (269, 0.2828282828282828), (268, 0.2403030303030303), (268, 0.2726262626262626), (268, 0.2718181818181818), (268, 0.27111111111111114), (268, 0.3701010101010101), (271, 2.2152525252525255), (271, 0.24434343434343433), (268, 0.26626262626262626), (269, 1.1009090909090908), (270, 0.30818181818181817), (271, 0.2475757575757576), (270, 1.2222222222222223), (271, 0.25565656565656564), (271, 0.31555555555555553), (256, 836.310606060606), (269, 0.2726262626262626), (269, 0.2403030303030303), (269, 0.27111111111111114), (269, 0.37333333333333335), (269, 0.2718181818181818), (269, 0.30818181818181817), (269, 0.24353535353535355), (268, 1.6218181818181818), (269, 0.41404040404040404), (269, 0.26626262626262626), (268, 1.4064646464646464), (268, 1.8524242424242425), (269, 4.214545454545455), (268, 1.8933333333333333), (269, 4.536969696969697), (269, 4.201616161616162), (271, 1.9288888888888889), (271, 1.4605050505050505), (271, 1.2738383838383838), (270, 0.2509090909090909), (270, 0.25212121212121213), (270, 0.3938383838383838), (270, 0.25252525252525254), (270, 0.2928282828282828), (270, 0.2904040404040404), (270, 0.24888888888888888), (270, 0.292020202020202), (270, 0.2864646464646465), (271, 0.2828282828282828), (270, 0.4584848484848485), (271, 0), (265, 219.42414141414142), (269, 0.3938383838383838), (268, 0.24434343434343433), (269, 0.3009090909090909), (269, 0.3712121212121212), (271, 0.2509090909090909), (271, 0.39232323232323235), (271, 0.24888888888888888), (271, 0.4302020202020202), (267, 22.343434343434343), (271, 0.2605050505050505), (270, 1.7107070707070706), (270, 1.799090909090909), (270, 1.646060606060606), (270, 1.3182828282828283), (270, 1.4314141414141415), (270, 1.4682828282828282), (269, 7.777777777777778), (270, 1.3708080808080807), (270, 1.3216161616161617), (270, 1.6852525252525252), (271, 0.33080808080808083), (271, 4.5473737373737375), (269, 0.24606060606060606), (270, 0.30494949494949497), (237, 747.6035353535353), (268, 0.25646464646464645), (270, 1.145858585858586), (270, 0.4091919191919192), (268, 0.25242424242424244), (269, 2.3838383838383836), (269, 0.2581818181818182), (267, 0.25242424242424244), (267, 0.2516161616161616), (267, 0.3115151515151515), (270, 0.39232323232323235), (267, 0.2723232323232323), (270, 0.24434343434343433), (269, 0.292020202020202), (271, 0.5923232323232324), (270, 2.554646464646465), (270, 2.9753535353535354), (270, 2.6475757575757575), (268, 0.23545454545454544), (269, 0.2509090909090909), (268, 0.26454545454545453), (268, 0.2925252525252525), (268, 0.26262626262626265), (268, 0.28929292929292927), (268, 0.29292929292929293), (268, 0.5288888888888889), (243, 763.4685858585859), (268, 0.2677777777777778), (268, 0.2702020202020202), (269, 1.4387878787878787), (266, 148.60717171717172), (270, 0.26626262626262626), (269, 0.38383838383838387), (269, 0.7575757575757576), (269, 0.2723232323232323), (269, 0.6278787878787879), (269, 0.2516161616161616), (269, 0.25242424242424244), (269, 0.2807070707070707), (269, 0.25), (269, 0.5135353535353535), (269, 0.49242424242424243), (270, 1.6657575757575758), (267, 16.687272727272727), (268, 0.2723232323232323), (269, 1.1903030303030302), (271, 0.37333333333333335), (270, 0.3914141414141414), (246, 745.7627272727273), (268, 0.292020202020202), (270, 0.2581818181818182), (270, 0.2702020202020202), (270, 0.2677777777777778), (270, 0.2602020202020202), (270, 0.26454545454545453), (270, 0.8172727272727273), (270, 0.3939393939393939), (270, 0.3009090909090909), (270, 0.534949494949495), (270, 0.29292929292929293), (268, 0.3106060606060606), (268, 2.0883838383838382), (260, 615.4887878787879), (268, 0.3914141414141414), (269, 3.23989898989899), (269, 3.227878787878788), (269, 3.9127272727272726), (249, 709.310707070707), (269, 3.932929292929293), (271, 0.24242424242424243), (271, 0.3434343434343434), (271, 0.351010101010101), (271, 0.4261616161616162), (271, 0.25242424242424244), (271, 0.2723232323232323), (271, 0.5571717171717172), (271, 0.388989898989899), (271, 0.25), (271, 0.2516161616161616), (269, 0.25212121212121213), (270, 0.7834343434343435), (270, 0.26262626262626265), (270, 0.5126262626262627), (269, 1.1534343434343435), (269, 0.2297979797979798), (265, 218.89888888888888), (238, 753.5227272727273), (268, 0.30303030303030304), (269, 0.4116161616161616), (267, 0.2718181818181818), (267, 0.27111111111111114), (267, 0.2726262626262626), (267, 0.2690909090909091), (269, 0.41373737373737374), (270, 0.24606060606060606), (269, 0.24242424242424243), (269, 0.31272727272727274), (270, 1.1337373737373737), (271, 0.2864646464646465), (268, 0.2509090909090909), (268, 0.24888888888888888), (268, 0.25212121212121213), (268, 0.25252525252525254), (268, 0.25292929292929295), (248, 741.1186868686868), (268, 0.32515151515151514), (268, 0.2904040404040404), (270, 0.45444444444444443), (268, 0.25565656565656564), (271, 0.582929292929293), (271, 0.5741414141414142), (240, 765.6035353535353), (269, 0.2928282828282828), (269, 0.43343434343434345), (270, 3.0925252525252525), (270, 0.3333333333333333), (265, 38.87030303030303), (269, 0.2904040404040404)} Reverse read files appear to be of different lengths or of varied lengths. {(271, 0.2581818181818182), (269, 0.39232323232323235), (268, 0.41404040404040404), (269, 0.25), (270, 0.33080808080808083), (270, 0.2718181818181818), (270, 0.2726262626262626), (270, 0.3066666666666667), (270, 0.2690909090909091), (270, 0.44636363636363635), (270, 0.4495959595959596), (270, 0.39959595959595956), (270, 0.2403030303030303), (270, 0.3106060606060606), (270, 0.26626262626262626), (271, 0.2718181818181818), (271, 0.4084848484848485), (271, 0.2726262626262626), (271, 0.27111111111111114), (271, 0.38171717171717173), (271, 0.34535353535353536), (271, 0.31303030303030305), (271, 0.26626262626262626), (270, 0.595050505050505), (271, 0.4763636363636364), (269, 0.24888888888888888), (270, 0.287979797979798), (270, 0.27111111111111114), (268, 0.4504040404040404), (268, 3.9324242424242426), (268, 3.993838383838384), (268, 3.331717171717172), (269, 2.43020202020202), (269, 2.525252525252525), (270, 0.8844444444444445), (267, 0.2677777777777778), (267, 0.2913131313131313), (267, 0.5006060606060606), (269, 0.4019191919191919), (270, 1.7632323232323233), (268, 0.25242424242424244), (268, 0.25), (268, 0.49), (268, 0.2723232323232323), (268, 0.2727272727272727), (268, 0.2516161616161616), (269, 5.502525252525253), (270, 0.31303030303030305), (268, 0.9761616161616162), (268, 0.24242424242424243), (270, 1.3506060606060606), (270, 0.6060606060606061), (269, 0.40595959595959596), (269, 0.6112121212121212), (269, 0.2702020202020202), (269, 0.26454545454545453), (269, 0.2581818181818182), (269, 0.3672727272727273), (269, 0.2677777777777778), (269, 0.26262626262626265), (269, 0.3935353535353535), (269, 0.30414141414141416), (269, 99.38222222222223), (270, 0.6327272727272727), (268, 0.6160606060606061), (267, 0.2475757575757576), (267, 0.24434343434343433), (270, 0.2516161616161616), (270, 0.2727272727272727), (270, 0.85010101010101), (270, 0.25242424242424244), (270, 0), (270, 0.3526262626262626), (270, 0.2723232323232323), (270, 0.31272727272727274), (270, 0.6509090909090909), (268, 99.18090909090908), (271, 0.28474747474747475), (268, 0.24606060606060606), (271, 0.38575757575757574), (271, 0.2677777777777778), (271, 0.3559595959595959), (271, 0.2925252525252525), (271, 0.3081818181818182), (271, 0.7377777777777778), (271, 0.30494949494949497), (271, 0.40595959595959596), (271, 0.3324242424242424), (271, 0.2913131313131313), (271, 0.2702020202020202), (269, 0.2475757575757576), (269, 0.24434343434343433), (269, 0.2605050505050505), (269, 0.2913131313131313), (267, 0.25212121212121213), (267, 0.22333333333333333), (267, 0.2605050505050505), (267, 0.2904040404040404), (267, 0.2509090909090909), (267, 0.4697979797979798), (267, 0.39232323232323235), (271, 0.4415151515151515), (271, 0.3009090909090909), (267, 0.2928282828282828), (269, 1.4004040404040403), (269, 1.9566666666666668), (269, 1.673838383838384), (271, 2.0743434343434344), (268, 0.2690909090909091), (268, 0.2726262626262626), (268, 0.2403030303030303), (268, 0.31303030303030305), (268, 0.2718181818181818), (271, 0.2475757575757576), (268, 0.31222222222222223), (271, 0.24434343434343433), (271, 0.9465656565656566), (268, 0.27111111111111114), (268, 0.2928282828282828), (269, 0.35666666666666663), (270, 0.37363636363636366), (270, 0.29292929292929293), (269, 0.2726262626262626), (269, 0.26626262626262626), (269, 0.27111111111111114), (269, 0.2718181818181818), (269, 0.2690909090909091), (269, 0.31303030303030305), (268, 1.1590909090909092), (268, 1.5256565656565657), (268, 1.2480808080808081), (270, 0.25), (268, 1.951919191919192), (268, 1.572828282828283), (268, 1.723131313131313), (268, 1.083939393939394), (271, 1.2382828282828282), (271, 1.0766666666666667), (271, 1.7086868686868688), (271, 1.4928282828282828), (271, 1.7247474747474747), (271, 1.0505050505050506), (270, 0.2904040404040404), (270, 0.2928282828282828), (270, 0.25212121212121213), (270, 0.292020202020202), (270, 0.45494949494949494), (270, 0.25252525252525254), (270, 0.2509090909090909), (270, 0.2864646464646465), (269, 0.2904040404040404), (270, 0.24888888888888888), (271, 0.3478787878787879), (271, 0.5288888888888889), (271, 0.28929292929292927), (269, 0.3938383838383838), (268, 0.24434343434343433), (268, 0.2475757575757576), (271, 0.388989898989899), (271, 0.35747474747474745), (271, 0.2509090909090909), (271, 0.33080808080808083), (271, 0.24888888888888888), (271, 0.25212121212121213), (271, 0.292020202020202), (270, 1.205959595959596), (271, 0.2904040404040404), (270, 0.24242424242424243), (271, 0.32515151515151514), (270, 1.4685858585858584), (270, 1.0378787878787878), (270, 1.223838383838384), (270, 1.6180808080808082), (270, 1.6641414141414141), (270, 0.3283838383838384), (270, 0.30494949494949497), (269, 0.24606060606060606), (271, 0.2690909090909091), (270, 3.742525252525253), (267, 0.25), (267, 0.25242424242424244), (267, 0.2516161616161616), (267, 0.2723232323232323), (267, 0.4884848484848485), (270, 0.2475757575757576), (269, 0.292020202020202), (270, 0.24434343434343433), (267, 0.23797979797979796), (270, 2.9894949494949494), (270, 2.8307070707070707), (270, 2.4746464646464648), (269, 8.130404040404041), (269, 0.2509090909090909), (268, 0.6751515151515152), (268, 0.3712121212121212), (268, 0.2677777777777778), (268, 0.2702020202020202), (268, 0.5029292929292929), (268, 0.3672727272727273), (268, 0.2581818181818182), (268, 0.26454545454545453), (268, 0.3332323232323232), (268, 0.2925252525252525), (271, 0.6125252525252526), (269, 0.2723232323232323), (269, 0.5963636363636364), (269, 0.9352525252525252), (269, 0.25242424242424244), (269, 0.2516161616161616), (269, 0.24242424242424243), (269, 0.5903030303030303), (269, 0.6281818181818182), (270, 0.6685858585858586), (269, 0.23797979797979796), (270, 3.5332323232323235), (269, 0.6338383838383839), (270, 1.4314141414141415), (270, 0.3591919191919192), (270, 0.26454545454545453), (270, 0.6160606060606061), (270, 0.2581818181818182), (270, 0.9627272727272728), (270, 0.6711111111111111), (270, 0.2702020202020202), (270, 0.2677777777777778), (270, 0.8213131313131313), (270, 0.2925252525252525), (268, 2.1586868686868685), (271, 0.4722222222222222), (269, 3.7271717171717174), (269, 3.318787878787879), (268, 0.22666666666666666), (269, 0.7377777777777778), (271, 0.2516161616161616), (271, 0.8358585858585859), (271, 0.35343434343434343), (271, 0.31626262626262625), (271, 0.3526262626262626), (271, 0.25), (271, 0.2723232323232323), (271, 0.25242424242424244), (271, 0.287979797979798), (270, 0.3094949494949495), (269, 0.25212121212121213), (270, 0.26262626262626265), (271, 1.0925252525252525), (270, 0.2913131313131313), (269, 0.2297979797979798), (270, 0.31222222222222223), (267, 0.2726262626262626), (267, 0.2690909090909091), (267, 0.23272727272727273), (267, 0.26626262626262626), (270, 0.24606060606060606), (270, 0.46464646464646464), (269, 0.3283838383838384), (268, 0.292020202020202), (268, 0.2509090909090909), (268, 0.24888888888888888), (268, 0.2864646464646465), (268, 0.25252525252525254), (268, 0.25212121212121213), (268, 0.494949494949495), (268, 0.2904040404040404), (270, 0.45444444444444443), (268, 0.2605050505050505), (267, 20.098888888888887), (269, 0.2928282828282828), (270, 3.151111111111111), (271, 0.4509090909090909), (269, 0.25565656565656564)} Forward reads appear to not be of consistent length. {(271, 0.9195959595959596), (271, 0.2928282828282828), (270, 3.7046464646464647), (269, 0.6731313131313131), (269, 1.0723232323232323), (270, 0.41414141414141414), (268, 0.4682828282828283), (267, 0.24606060606060606), (269, 1.3692929292929292), (256, 555.1894949494949), (271, 0.3695959595959596), (259, 668.1155555555556), (270, 0.3066666666666667), (270, 0.2690909090909091), (270, 0.2726262626262626), (270, 0.37212121212121213), (270, 0.2718181818181818), (270, 0.31272727272727274), (270, 0.47434343434343434), (271, 0.3283838383838384), (270, 0.23272727272727273), (270, 0.2403030303030303), (270, 0.3712121212121212), (266, 255.0112121212121), (253, 651.5571717171717), (268, 0.2605050505050505), (271, 0.3903030303030303), (267, 34.545050505050504), (269, 0.5756565656565656), (271, 0.27111111111111114), (271, 0.38171717171717173), (271, 0.26626262626262626), (271, 0.3413131313131313), (271, 0.3106060606060606), (271, 0.40404040404040403), (270, 0.287979797979798), (271, 0.2726262626262626), (271, 0.23272727272727273), (271, 0.31303030303030305), (269, 0.24888888888888888), (271, 0.6076767676767677), (252, 1114.1874747474747), (269, 0.23545454545454544), (268, 3.5534343434343434), (268, 3.6641414141414144), (268, 3.534949494949495), (268, 3.071111111111111), (266, 104.25161616161616), (269, 2.64), (269, 1.2398989898989898), (269, 0.3914141414141414), (271, 0.25212121212121213), (269, 2.2622222222222224), (271, 3.5736363636363637), (271, 0.3211111111111111), (269, 0.6435353535353535), (271, 0.39141414141414144), (269, 1.4071717171717173), (267, 0.28929292929292927), (270, 0.5317171717171717), (268, 0.2727272727272727), (268, 0.8238383838383838), (268, 0.2516161616161616), (268, 0.25), (268, 0.31272727272727274), (271, 0.24686868686868688), (271, 0.24606060606060606), (270, 3.496868686868687), (268, 0.6596969696969697), (268, 0.24242424242424243), (270, 3.442020202020202), (261, 417.500101010101), (269, 1.1388888888888888), (269, 0.3672727272727273), (269, 0.5086868686868687), (269, 0.28929292929292927), (269, 0.5142424242424243), (269, 0.2702020202020202), (269, 0.2677777777777778), (269, 0.2925252525252525), (270, 0.31313131313131315), (269, 0.6327272727272727), (269, 0.6096969696969697), (270, 0.47464646464646465), (271, 0.33171717171717174), (270, 0.49808080808080807), (269, 1.0378787878787878), (268, 1.521111111111111), (267, 0.2475757575757576), (271, 0.43272727272727274), (270, 0.25242424242424244), (270, 0.24242424242424243), (270, 0.2723232323232323), (270, 0.41373737373737374), (270, 0.2727272727272727), (270, 0.25), (270, 0.2516161616161616), (270, 0.3115151515151515), (270, 0.8293939393939394), (270, 0.49404040404040406), (271, 0.28474747474747475), (267, 85.84030303030302), (271, 0.2677777777777778), (271, 0.9761616161616161), (268, 0.24606060606060606), (270, 0.3329292929292929), (268, 44.591010101010106), (271, 0.743030303030303), (271, 0.26262626262626265), (271, 0.30494949494949497), (271, 0.4382828282828283), (271, 0.2913131313131313), (271, 0.5959595959595959), (271, 0.3081818181818182), (271, 0.28929292929292927), (266, 146.64888888888888), (271, 0.6798989898989899), (270, 0.28474747474747475), (267, 1.782929292929293), (265, 215.1478787878788), (270, 0.3485858585858586), (269, 0.32686868686868686), (269, 1.2197979797979799), (269, 0.2475757575757576), (270, 0.6766666666666667), (269, 1.0246464646464646), (269, 0.24434343434343433), (271, 0.9147474747474748), (269, 0.2690909090909091), (269, 0.2605050505050505), (269, 0.33080808080808083), (261, 492.5546464646465), (269, 0.2913131313131313), (263, 327.8354545454546), (267, 0.24888888888888888), (267, 0.25212121212121213), (271, 0.4415151515151515), (267, 0.2509090909090909), (267, 0.292020202020202), (270, 0.22666666666666666), (243, 769.2945454545455), (267, 16.684747474747475), (266, 169.4920202020202), (268, 0.8099999999999999), (269, 1.218080808080808), (269, 1.3756565656565656), (269, 1.2342424242424241), (257, 534.3248484848484), (269, 1.425858585858586), (269, 0.2828282828282828), (268, 0.2403030303030303), (268, 0.2726262626262626), (268, 0.2718181818181818), (268, 0.27111111111111114), (268, 0.3701010101010101), (271, 2.2152525252525255), (271, 0.24434343434343433), (268, 0.26626262626262626), (269, 1.1009090909090908), (270, 0.30818181818181817), (271, 0.2475757575757576), (270, 1.2222222222222223), (271, 0.25565656565656564), (271, 0.31555555555555553), (256, 836.310606060606), (269, 0.2726262626262626), (269, 0.2403030303030303), (269, 0.27111111111111114), (269, 0.37333333333333335), (269, 0.2718181818181818), (269, 0.30818181818181817), (269, 0.24353535353535355), (268, 1.6218181818181818), (269, 0.41404040404040404), (269, 0.26626262626262626), (268, 1.4064646464646464), (268, 1.8524242424242425), (269, 4.214545454545455), (268, 1.8933333333333333), (269, 4.536969696969697), (269, 4.201616161616162), (271, 1.9288888888888889), (271, 1.4605050505050505), (271, 1.2738383838383838), (270, 0.2509090909090909), (270, 0.25212121212121213), (270, 0.3938383838383838), (270, 0.25252525252525254), (270, 0.2928282828282828), (270, 0.2904040404040404), (270, 0.24888888888888888), (270, 0.292020202020202), (270, 0.2864646464646465), (271, 0.2828282828282828), (270, 0.4584848484848485), (271, 0), (265, 219.42414141414142), (269, 0.3938383838383838), (268, 0.24434343434343433), (269, 0.3009090909090909), (269, 0.3712121212121212), (271, 0.2509090909090909), (271, 0.39232323232323235), (271, 0.24888888888888888), (271, 0.4302020202020202), (267, 22.343434343434343), (271, 0.2605050505050505), (270, 1.7107070707070706), (270, 1.799090909090909), (270, 1.646060606060606), (270, 1.3182828282828283), (270, 1.4314141414141415), (270, 1.4682828282828282), (269, 7.777777777777778), (270, 1.3708080808080807), (270, 1.3216161616161617), (270, 1.6852525252525252), (271, 0.33080808080808083), (271, 4.5473737373737375), (269, 0.24606060606060606), (270, 0.30494949494949497), (237, 747.6035353535353), (268, 0.25646464646464645), (270, 1.145858585858586), (270, 0.4091919191919192), (268, 0.25242424242424244), (269, 2.3838383838383836), (269, 0.2581818181818182), (267, 0.25242424242424244), (267, 0.2516161616161616), (267, 0.3115151515151515), (270, 0.39232323232323235), (267, 0.2723232323232323), (270, 0.24434343434343433), (269, 0.292020202020202), (271, 0.5923232323232324), (270, 2.554646464646465), (270, 2.9753535353535354), (270, 2.6475757575757575), (268, 0.23545454545454544), (269, 0.2509090909090909), (268, 0.26454545454545453), (268, 0.2925252525252525), (268, 0.26262626262626265), (268, 0.28929292929292927), (268, 0.29292929292929293), (268, 0.5288888888888889), (243, 763.4685858585859), (268, 0.2677777777777778), (268, 0.2702020202020202), (269, 1.4387878787878787), (266, 148.60717171717172), (270, 0.26626262626262626), (269, 0.38383838383838387), (269, 0.7575757575757576), (269, 0.2723232323232323), (269, 0.6278787878787879), (269, 0.2516161616161616), (269, 0.25242424242424244), (269, 0.2807070707070707), (269, 0.25), (269, 0.5135353535353535), (269, 0.49242424242424243), (270, 1.6657575757575758), (267, 16.687272727272727), (268, 0.2723232323232323), (269, 1.1903030303030302), (271, 0.37333333333333335), (270, 0.3914141414141414), (246, 745.7627272727273), (268, 0.292020202020202), (270, 0.2581818181818182), (270, 0.2702020202020202), (270, 0.2677777777777778), (270, 0.2602020202020202), (270, 0.26454545454545453), (270, 0.8172727272727273), (270, 0.3939393939393939), (270, 0.3009090909090909), (270, 0.534949494949495), (270, 0.29292929292929293), (268, 0.3106060606060606), (268, 2.0883838383838382), (260, 615.4887878787879), (268, 0.3914141414141414), (269, 3.23989898989899), (269, 3.227878787878788), (269, 3.9127272727272726), (249, 709.310707070707), (269, 3.932929292929293), (271, 0.24242424242424243), (271, 0.3434343434343434), (271, 0.351010101010101), (271, 0.4261616161616162), (271, 0.25242424242424244), (271, 0.2723232323232323), (271, 0.5571717171717172), (271, 0.388989898989899), (271, 0.25), (271, 0.2516161616161616), (269, 0.25212121212121213), (270, 0.7834343434343435), (270, 0.26262626262626265), (270, 0.5126262626262627), (269, 1.1534343434343435), (269, 0.2297979797979798), (265, 218.89888888888888), (238, 753.5227272727273), (268, 0.30303030303030304), (269, 0.4116161616161616), (267, 0.2718181818181818), (267, 0.27111111111111114), (267, 0.2726262626262626), (267, 0.2690909090909091), (269, 0.41373737373737374), (270, 0.24606060606060606), (269, 0.24242424242424243), (269, 0.31272727272727274), (270, 1.1337373737373737), (271, 0.2864646464646465), (268, 0.2509090909090909), (268, 0.24888888888888888), (268, 0.25212121212121213), (268, 0.25252525252525254), (268, 0.25292929292929295), (248, 741.1186868686868), (268, 0.32515151515151514), (268, 0.2904040404040404), (270, 0.45444444444444443), (268, 0.25565656565656564), (271, 0.582929292929293), (271, 0.5741414141414142), (240, 765.6035353535353), (269, 0.2928282828282828), (269, 0.43343434343434345), (270, 3.0925252525252525), (270, 0.3333333333333333), (265, 38.87030303030303), (269, 0.2904040404040404)} Reverse reads appear to not be of consistent length. {(271, 0.2581818181818182), (269, 0.39232323232323235), (268, 0.41404040404040404), (269, 0.25), (270, 0.33080808080808083), (270, 0.2718181818181818), (270, 0.2726262626262626), (270, 0.3066666666666667), (270, 0.2690909090909091), (270, 0.44636363636363635), (270, 0.4495959595959596), (270, 0.39959595959595956), (270, 0.2403030303030303), (270, 0.3106060606060606), (270, 0.26626262626262626), (271, 0.2718181818181818), (271, 0.4084848484848485), (271, 0.2726262626262626), (271, 0.27111111111111114), (271, 0.38171717171717173), (271, 0.34535353535353536), (271, 0.31303030303030305), (271, 0.26626262626262626), (270, 0.595050505050505), (271, 0.4763636363636364), (269, 0.24888888888888888), (270, 0.287979797979798), (270, 0.27111111111111114), (268, 0.4504040404040404), (268, 3.9324242424242426), (268, 3.993838383838384), (268, 3.331717171717172), (269, 2.43020202020202), (269, 2.525252525252525), (270, 0.8844444444444445), (267, 0.2677777777777778), (267, 0.2913131313131313), (267, 0.5006060606060606), (269, 0.4019191919191919), (270, 1.7632323232323233), (268, 0.25242424242424244), (268, 0.25), (268, 0.49), (268, 0.2723232323232323), (268, 0.2727272727272727), (268, 0.2516161616161616), (269, 5.502525252525253), (270, 0.31303030303030305), (268, 0.9761616161616162), (268, 0.24242424242424243), (270, 1.3506060606060606), (270, 0.6060606060606061), (269, 0.40595959595959596), (269, 0.6112121212121212), (269, 0.2702020202020202), (269, 0.26454545454545453), (269, 0.2581818181818182), (269, 0.3672727272727273), (269, 0.2677777777777778), (269, 0.26262626262626265), (269, 0.3935353535353535), (269, 0.30414141414141416), (269, 99.38222222222223), (270, 0.6327272727272727), (268, 0.6160606060606061), (267, 0.2475757575757576), (267, 0.24434343434343433), (270, 0.2516161616161616), (270, 0.2727272727272727), (270, 0.85010101010101), (270, 0.25242424242424244), (270, 0), (270, 0.3526262626262626), (270, 0.2723232323232323), (270, 0.31272727272727274), (270, 0.6509090909090909), (268, 99.18090909090908), (271, 0.28474747474747475), (268, 0.24606060606060606), (271, 0.38575757575757574), (271, 0.2677777777777778), (271, 0.3559595959595959), (271, 0.2925252525252525), (271, 0.3081818181818182), (271, 0.7377777777777778), (271, 0.30494949494949497), (271, 0.40595959595959596), (271, 0.3324242424242424), (271, 0.2913131313131313), (271, 0.2702020202020202), (269, 0.2475757575757576), (269, 0.24434343434343433), (269, 0.2605050505050505), (269, 0.2913131313131313), (267, 0.25212121212121213), (267, 0.22333333333333333), (267, 0.2605050505050505), (267, 0.2904040404040404), (267, 0.2509090909090909), (267, 0.4697979797979798), (267, 0.39232323232323235), (271, 0.4415151515151515), (271, 0.3009090909090909), (267, 0.2928282828282828), (269, 1.4004040404040403), (269, 1.9566666666666668), (269, 1.673838383838384), (271, 2.0743434343434344), (268, 0.2690909090909091), (268, 0.2726262626262626), (268, 0.2403030303030303), (268, 0.31303030303030305), (268, 0.2718181818181818), (271, 0.2475757575757576), (268, 0.31222222222222223), (271, 0.24434343434343433), (271, 0.9465656565656566), (268, 0.27111111111111114), (268, 0.2928282828282828), (269, 0.35666666666666663), (270, 0.37363636363636366), (270, 0.29292929292929293), (269, 0.2726262626262626), (269, 0.26626262626262626), (269, 0.27111111111111114), (269, 0.2718181818181818), (269, 0.2690909090909091), (269, 0.31303030303030305), (268, 1.1590909090909092), (268, 1.5256565656565657), (268, 1.2480808080808081), (270, 0.25), (268, 1.951919191919192), (268, 1.572828282828283), (268, 1.723131313131313), (268, 1.083939393939394), (271, 1.2382828282828282), (271, 1.0766666666666667), (271, 1.7086868686868688), (271, 1.4928282828282828), (271, 1.7247474747474747), (271, 1.0505050505050506), (270, 0.2904040404040404), (270, 0.2928282828282828), (270, 0.25212121212121213), (270, 0.292020202020202), (270, 0.45494949494949494), (270, 0.25252525252525254), (270, 0.2509090909090909), (270, 0.2864646464646465), (269, 0.2904040404040404), (270, 0.24888888888888888), (271, 0.3478787878787879), (271, 0.5288888888888889), (271, 0.28929292929292927), (269, 0.3938383838383838), (268, 0.24434343434343433), (268, 0.2475757575757576), (271, 0.388989898989899), (271, 0.35747474747474745), (271, 0.2509090909090909), (271, 0.33080808080808083), (271, 0.24888888888888888), (271, 0.25212121212121213), (271, 0.292020202020202), (270, 1.205959595959596), (271, 0.2904040404040404), (270, 0.24242424242424243), (271, 0.32515151515151514), (270, 1.4685858585858584), (270, 1.0378787878787878), (270, 1.223838383838384), (270, 1.6180808080808082), (270, 1.6641414141414141), (270, 0.3283838383838384), (270, 0.30494949494949497), (269, 0.24606060606060606), (271, 0.2690909090909091), (270, 3.742525252525253), (267, 0.25), (267, 0.25242424242424244), (267, 0.2516161616161616), (267, 0.2723232323232323), (267, 0.4884848484848485), (270, 0.2475757575757576), (269, 0.292020202020202), (270, 0.24434343434343433), (267, 0.23797979797979796), (270, 2.9894949494949494), (270, 2.8307070707070707), (270, 2.4746464646464648), (269, 8.130404040404041), (269, 0.2509090909090909), (268, 0.6751515151515152), (268, 0.3712121212121212), (268, 0.2677777777777778), (268, 0.2702020202020202), (268, 0.5029292929292929), (268, 0.3672727272727273), (268, 0.2581818181818182), (268, 0.26454545454545453), (268, 0.3332323232323232), (268, 0.2925252525252525), (271, 0.6125252525252526), (269, 0.2723232323232323), (269, 0.5963636363636364), (269, 0.9352525252525252), (269, 0.25242424242424244), (269, 0.2516161616161616), (269, 0.24242424242424243), (269, 0.5903030303030303), (269, 0.6281818181818182), (270, 0.6685858585858586), (269, 0.23797979797979796), (270, 3.5332323232323235), (269, 0.6338383838383839), (270, 1.4314141414141415), (270, 0.3591919191919192), (270, 0.26454545454545453), (270, 0.6160606060606061), (270, 0.2581818181818182), (270, 0.9627272727272728), (270, 0.6711111111111111), (270, 0.2702020202020202), (270, 0.2677777777777778), (270, 0.8213131313131313), (270, 0.2925252525252525), (268, 2.1586868686868685), (271, 0.4722222222222222), (269, 3.7271717171717174), (269, 3.318787878787879), (268, 0.22666666666666666), (269, 0.7377777777777778), (271, 0.2516161616161616), (271, 0.8358585858585859), (271, 0.35343434343434343), (271, 0.31626262626262625), (271, 0.3526262626262626), (271, 0.25), (271, 0.2723232323232323), (271, 0.25242424242424244), (271, 0.287979797979798), (270, 0.3094949494949495), (269, 0.25212121212121213), (270, 0.26262626262626265), (271, 1.0925252525252525), (270, 0.2913131313131313), (269, 0.2297979797979798), (270, 0.31222222222222223), (267, 0.2726262626262626), (267, 0.2690909090909091), (267, 0.23272727272727273), (267, 0.26626262626262626), (270, 0.24606060606060606), (270, 0.46464646464646464), (269, 0.3283838383838384), (268, 0.292020202020202), (268, 0.2509090909090909), (268, 0.24888888888888888), (268, 0.2864646464646465), (268, 0.25252525252525254), (268, 0.25212121212121213), (268, 0.494949494949495), (268, 0.2904040404040404), (270, 0.45444444444444443), (268, 0.2605050505050505), (267, 20.098888888888887), (269, 0.2928282828282828), (270, 3.151111111111111), (271, 0.4509090909090909), (269, 0.25565656565656564)} Traceback (most recent call last): File "figaro/figaro.py", line 213, in
resultTable, forwardCurve, reverseCurve = figaroSupport.trimParameterPrediction.performAnalysisLite(parameters.inputDirectory.value, parameters.minimumCombinedReadLength.value, subsample = parameters.subsample.value, percentile = parameters.percentile.value, forwardPrimerLength=parameters.forwardPrimerLength.value, reversePrimerLength=parameters.reversePrimerLength.value, namingStandardAlias=fileNamingStandard)