problem with phangorn
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vhertzb • 0
@vhertzb-13331
Last seen 5.1 years ago

I am trying to run phangorn and I am running into a problem with the NJ command.

 

The R “chunk” that terminates in the NJ call is as follows:

 

  1. # First align the sequences
  2. library(DECIPHER)
  3. seqs <- getSequences(st)
  4.  
  5. # This next command will allow propagation of sequence names to the tip labels of the tree
  6. names(seqs) <- seqs
  7. alignment <- AlignSeqs(DNAStringSet(seqs), anchor=NA)
  8.  
  9. # Now create the tree
  10.  
  11. library(phangorn)
  12.  
  13. # Construct the tree
  14. phang.align <- phyDat(as(alignment, "matrix"), type="DNA")
  15. dm <- dist.ml(phang.align)
  16. treeNJ <- NJ(dm) # Tip order will not equal sequence order

 

The result of this chunk, terminating in the error is as follows:

 

  1. 3.
  1. nj(x)
  1. 2.
  1. reorder(nj(x), "postorder")
  1. Loading required package: Biostrings
  2. Loading required package: BiocGenerics
  3. Loading required package: parallel
  4.  
  5. Attaching package: ‘BiocGenerics’
  6.  
  7. The following objects are masked from ‘package:parallel’:
  8.  
  9.     clusterApply, clusterApplyLB, clusterCall, clusterEvalQ,
  10.     clusterExport, clusterMap, parApply, parCapply, parLapply,
  11.     parLapplyLB, parRapply, parSapply, parSapplyLB
  12.  
  13. The following object is masked from ‘package:gridExtra’:
  14.  
  15.     combine
  16.  
  17. The following objects are masked from ‘package:stats’:
  18.  
  19.     IQR, mad, sd, var, xtabs
  20.  
  21. The following objects are masked from ‘package:base’:
  22.  
  23.     anyDuplicated, append, as.data.frame, cbind, colMeans,
  24.     colnames, colSums, do.call, duplicated, eval, evalq, Filter,
  25.     Find, get, grep, grepl, intersect, is.unsorted, lapply,
  26.     lengths, Map, mapply, match, mget, order, paste, pmax,
  27.     pmax.int, pmin, pmin.int, Position, rank, rbind, Reduce,
  28.     rowMeans, rownames, rowSums, sapply, setdiff, sort, table,
  29.     tapply, union, unique, unsplit, which, which.max, which.min
  30.  
  31. Loading required package: S4Vectors
  32. Loading required package: stats4
  33.  
  34. Attaching package: ‘S4Vectors’
  35.  
  36. The following object is masked from ‘package:base’:
  37.  
  38.     expand.grid
  39.  
  40. Loading required package: IRanges
  41.  
  42. Attaching package: ‘IRanges’
  43.  
  44. The following object is masked from ‘package:phyloseq’:
  45.  
  46.     distance
  47.  
  48. Loading required package: XVector
  49.  
  50. Attaching package: ‘Biostrings’
  51.  
  52. The following object is masked from ‘package:base’:
  53.  
  54.     strsplit
  55.  
  56. Loading required package: RSQLite
  57. Determining distance matrix based on shared 7-mers:
  58.   |================================================================| 100%
  59.  
  60. Time difference of 3.85 secs
  61.  
  62. Clustering into groups by similarity:
  63.   |================================================================| 100%
  64.  
  65. Time difference of 1.62 secs
  66.  
  67. Aligning Sequences:
  68.   |================================================================| 100%
  69.  
  70. Time difference of 5.07 secs
  71.  
  72. Determining distance matrix based on alignment:
  73.   |================================================================| 100%
  74.  
  75. Time difference of 1.93 secs
  76.  
  77. Reclustering into groups by similarity:
  78.   |================================================================| 100%
  79.  
  80. Time difference of 2.3 secs
  81.  
  82. Realigning Sequences:
  83.   |================================================================| 100%
  84.  
  85. Time difference of 4.21 secs
  86.  
  87. Loading required package: ape
  88.  
  89. Attaching package: ‘ape’
  90.  
  91. The following object is masked from ‘package:Biostrings’:
  92.  
  93.     complement
  94.  
  95. data:image/png;base64,iVBORw0KGgoAAAANSUhEUgAAAAkAAAAJCAYAAADgkQYQAAAAKUlEQVR42mNgQAKi65/9Z8AHQApgmKACrAqxKcBpIkHryFJEstsYiAUAKIxac8kmY3AAAAAASUVORK5CYII= Hide Traceback
  96. Error in nj(x) : object 'C_nj' not found
  97.  
  98.  
  1. 1.
  1. NJ(dm)

 

The session.info is as follows:

 

  1. R version 3.4.0 (2017-04-21)
  2. Platform: x86_64-apple-darwin15.6.0 (64-bit)
  3. Running under: macOS Sierra 10.12.5
  4.  
  5. Matrix products: default
  6. BLAS: /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
  7. LAPACK: /Library/Frameworks/R.framework/Versions/3.4/Resources/lib/libRlapack.dylib
  8.  
  9. locale:
  10. [1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
  11.  
  12. attached base packages:
  13. [1] stats4    parallel  stats     graphics  grDevices utils     datasets  methods 
  14. [9] base    
  15.  
  16. other attached packages:
  17. [1] phangorn_2.2.0       ape_4.1              DECIPHER_2.4.0     
  18.  [4] RSQLite_2.0          Biostrings_2.44.1    XVector_0.16.0      
  19.  [7] IRanges_2.10.2       S4Vectors_0.14.3     BiocGenerics_0.22.0
  20. [10] gridExtra_2.2.1      RColorBrewer_1.1-2   ggplot2_2.2.1      
  21. [13] phyloseq_1.20.0      dada2_1.4.0          Rcpp_0.12.11       
  22. [16] BiocInstaller_1.26.0
  23.  
  24. loaded via a namespace (and not attached):
  25. [1] lattice_0.20-35            Rsamtools_1.28.0         
  26.  [3] digest_0.6.12              foreach_1.4.3            
  27.  [5] GenomeInfoDb_1.12.2        plyr_1.8.4               
  28.  [7] ShortRead_1.34.0           zlibbioc_1.22.0           
  29.  [9] rlang_0.1.1                lazyeval_0.2.0           
  30. [11] data.table_1.10.4          vegan_2.4-3              
  31. [13] blob_1.1.0                 Matrix_1.2-10            
  32. [15] labeling_0.3               splines_3.4.0            
  33. [17] BiocParallel_1.10.1        stringr_1.2.0            
  34. [19] igraph_1.0.1               RCurl_1.95-4.8           
  35. [21] bit_1.1-12                 munsell_0.4.3            
  36. [23] DelayedArray_0.2.7         compiler_3.4.0           
  37. [25] multtest_2.32.0            mgcv_1.8-17              
  38. [27] biomformat_1.4.0           SummarizedExperiment_1.6.3
  39. [29] tibble_1.3.3               GenomeInfoDbData_0.99.0  
  40. [31] quadprog_1.5-5             codetools_0.2-15         
  41. [33] matrixStats_0.52.2         permute_0.9-4            
  42. [35] GenomicAlignments_1.12.1   MASS_7.3-47              
  43. [37] bitops_1.0-6               grid_3.4.0               
  44. [39] nlme_3.1-131               jsonlite_1.5             
  45. [41] gtable_0.2.0               DBI_0.7                   
  46. [43] magrittr_1.5               scales_0.4.1             
  47. [45] RcppParallel_4.3.20        stringi_1.1.5            
  48. [47] hwriter_1.3.2              reshape2_1.4.2           
  49. [49] latticeExtra_0.6-28        fastmatch_1.1-0          
  50. [51] iterators_1.0.8            tools_3.4.0              
  51. [53] ade4_1.7-6                 bit64_0.9-7              
  52. [55] Biobase_2.36.2             survival_2.41-3          
  53. [57] colorspace_1.3-2           rhdf5_2.20.0             
  54. [59] cluster_2.0.6              GenomicRanges_1.28.3     
  55. [61] memoise_1.1.0              knitr_1.16

 

Can you please advise – what am I doing wrong, how can I fix this?

software error phangorn • 1.4k views
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