DECIPHER - AlignSeqs error is.leaf(dend) node stack overflow
1
0
Entering edit mode
@emmaberdan-14191
Last seen 4.0 years ago

Hello,

I have 16,500 OTUs and am trying to do a sequence alignment using DECIPHER.  If I run the code with a smaller number of OTUs (approx 11K) everything works fine but if I run with all my data I get the error:

"error is.leaf(dend) node stack overflow"

 

Traceback gets me the following:

 

44: .collapse(dend[[2]], collapse)
43: .collapse(dend[[2]], collapse)
42: .collapse(dend[[2]], collapse)
41: .collapse(dend[[2]], collapse)
40: .collapse(dend[[2]], collapse)
39: .collapse(dend[[2]], collapse)
38: .collapse(dend[[2]], collapse)
37: .collapse(dend[[2]], collapse)
36: .collapse(dend[[2]], collapse)
35: .collapse(dend[[2]], collapse)
34: .collapse(dend[[2]], collapse)
33: .collapse(dend[[2]], collapse)
32: .collapse(dend[[2]], collapse)
31: .collapse(dend[[2]], collapse)
30: .collapse(dend[[2]], collapse)
29: .collapse(dend[[2]], collapse)
28: .collapse(dend[[2]], collapse)
27: .collapse(dend[[2]], collapse)
26: .collapse(dend[[2]], collapse)
25: .collapse(dend[[2]], collapse)
24: .collapse(dend[[2]], collapse)
23: .collapse(dend[[2]], collapse)
22: .collapse(dend[[2]], collapse)
21: .collapse(dend[[2]], collapse)
20: .collapse(dend[[2]], collapse)
19: .collapse(dend[[2]], collapse)
18: .collapse(dend[[2]], collapse)
17: .collapse(dend[[2]], collapse)
16: .collapse(dend[[2]], collapse)
15: .collapse(dend[[2]], collapse)
14: .collapse(dend[[2]], collapse)
13: .collapse(dend[[2]], collapse)
12: .collapse(dend[[2]], collapse)
11: .collapse(dend[[2]], collapse)
10: .collapse(dend[[2]], collapse)
9: .collapse(dend[[2]], collapse)
8: .collapse(dend[[2]], collapse)
7: .collapse(dend[[2]], collapse)
6: .collapse(dend[[2]], collapse)
5: .collapse(d, collapse)
4: IdClusters(d, method = "single", type = "dendrogram", verbose = verbose,
       processors = processors)
3: withCallingHandlers(expr, warning = function(w) invokeRestart("muffleWarning"))
2: suppressWarnings(guideTree <- IdClusters(d, method = "single",
       type = "dendrogram", verbose = verbose, processors = processors))
1: AlignSeqs(DNAStringSet(seqs), anchor = NA, processors = 10)

 

My original command is:  alignment <- AlignSeqs(DNAStringSet(seqs), anchor=NA, processors=10)

Session info is as follows:

R version 3.4.1 (2017-06-30)
Platform: x86_64-redhat-linux-gnu (64-bit)
Running under: Scientific Linux release 6.9 (Carbon)

Matrix products: default
BLAS: /usr/lib64/R/lib/libRblas.so
LAPACK: /usr/lib64/R/lib/libRlapack.so

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C              
 [3] LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8    
 [5] LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8   
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                 
 [9] LC_ADDRESS=C               LC_TELEPHONE=C            
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:
[1] stats4    parallel  stats     graphics  grDevices utils     datasets 
[8] methods   base     

other attached packages:
 [1] phyloseq_1.20.0     dada2_1.4.0         Rcpp_0.12.13       
 [4] DECIPHER_2.4.0      RSQLite_2.0         Biostrings_2.44.2  
 [7] XVector_0.16.0      IRanges_2.10.5      S4Vectors_0.14.7   
[10] BiocGenerics_0.22.1

loaded via a namespace (and not attached):
 [1] ape_4.1                    lattice_0.20-35           
 [3] Rsamtools_1.28.0           digest_0.6.12             
 [5] foreach_1.4.3              GenomeInfoDb_1.12.3       
 [7] plyr_1.8.4                 ShortRead_1.34.2          
 [9] ggplot2_2.2.1              zlibbioc_1.22.0           
[11] rlang_0.1.2                lazyeval_0.2.0            
[13] data.table_1.10.4-2        vegan_2.4-4               
[15] blob_1.1.0                 Matrix_1.2-10             
[17] splines_3.4.1              BiocParallel_1.10.1       
[19] stringr_1.2.0              igraph_1.1.2              
[21] RCurl_1.95-4.8             bit_1.1-12                
[23] munsell_0.4.3              DelayedArray_0.2.7        
[25] compiler_3.4.1             pkgconfig_2.0.1           
[27] multtest_2.32.0            mgcv_1.8-17               
[29] biomformat_1.4.0           SummarizedExperiment_1.6.5
[31] tibble_1.3.4               GenomeInfoDbData_0.99.0   
[33] codetools_0.2-15           matrixStats_0.52.2        
[35] permute_0.9-4              GenomicAlignments_1.12.2  
[37] MASS_7.3-47                bitops_1.0-6              
[39] grid_3.4.1                 nlme_3.1-131              
[41] jsonlite_1.5               gtable_0.2.0              
[43] DBI_0.7                    magrittr_1.5              
[45] scales_0.5.0               RcppParallel_4.3.20       
[47] stringi_1.1.5              hwriter_1.3.2             
[49] reshape2_1.4.2             latticeExtra_0.6-28       
[51] RColorBrewer_1.1-2         iterators_1.0.8           
[53] tools_3.4.1                ade4_1.7-8                
[55] bit64_0.9-7                Biobase_2.36.2            
[57] survival_2.41-3            colorspace_1.3-2          
[59] rhdf5_2.20.0               cluster_2.0.6             
[61] GenomicRanges_1.28.6       memoise_1.1.0             

 

I have removed all chimeras and there are no duplicate sequences.  I tried increasing the expression number in R but that did not help. Any advice is much appreciated!!!

 

 

 

 

 

decipher alignment • 636 views
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0
Entering edit mode
Erik Wright ▴ 10
@erik-wright-7838
Last seen 4.0 years ago
United States

Hi Emma,

Sorry for the difficulties that you are having with DECIPHER.  This is a known issue when aligning tens-of-thousands of sequences in versions < 2.5.  It will be fixed in the next release of DECIPHER, available on November 1st, 2017.

Erik

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