IRanges: solving row 5: range cannot be determined from the supplied arguments (too many NAs)
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jovel_juan ▴ 10
@jovel_juan-7129
Last seen 3 months ago
Canada

I am trying to implement DMDeepm6A1.0 to call methlyation peaks on RNAseq data.

I installed the package taking care of Rpackages version, as recommended in https://github.com/NWPU-903PR/DMDeepm6A1.0.

The program works wonderfully with the toy data provided by the authors, but fails with real data, which is way larger, with the error message described below. I have tried to troubleshoot with the programmer of DMDeep6A1.0 but we believe that the problem is generated either by IRanges of rtracklayer. I am posting the error message hereafter, and at the end of the message my sessionInfo(). Any help highly appreciated. Thanks!

Error message:

[1] "The bam files used:"
[1] "2 IP replicate(s)"
[1] "2 Input replicate(s)"
[1] "---------------------------------"
[1] "Peak calling result: "
[1] "2895 peaks detected on merged data."
[1] "Please check 'peak.bed/xls' under /home/juan/juan/UofA/projects_analysis/brunoSaleme/2019/IP_190711s1/FunDMDeep-m6A/DMDeepm6A_out/exomepeak_untreated"
[1] "1849 consistent peaks detected on every replicates. (Recommended list)"
[1] "Please check 'con_peak.bed/xls' under /home/juan/juan/UofA/projects_analysis/brunoSaleme/2019/IP_190711s1/FunDMDeep-m6A/DMDeepm6A_out/exomepeak_untreated"
[1] "Detecting sites for IP/Input paire 1 ----------------------------"
[1] "Converting BED12 to GRangesList"
[1] "It may take a few minutes"
[1] "Cutting peak to Single Base..."
Time difference of 28.77714 secs
[1] "Searching peak for motifs..."
Time difference of 33.51559 secs
[1] "Making input from peak region..."
[1] "Counting reads for single base..."
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 5: range cannot be determined from the supplied arguments (too many NAs)

Session Info

R version 3.5.1 (2018-07-02)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.10

Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

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

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

other attached packages:
 [1] devtools_2.2.0                         
 [2] usethis_1.5.1                          
 [3] DMDeepm6A_1.0.3                        
 [4] org.Hs.eg.db_3.7.0                     
 [5] BSgenome.Hsapiens.UCSC.hg19_1.4.0      
 [6] BSgenome_1.50.0                        
 [7] TxDb.Hsapiens.UCSC.hg19.knownGene_3.2.2
 [8] DESeq_1.34.1                           
 [9] lattice_0.20-35                        
[10] QNB_0.99.2                             
[11] locfit_1.5-9.1                         
[12] keras_2.2.5.0                          
[13] exomePeak_2.16.0                       
[14] Guitar_1.20.1                          
[15] ggplot2_3.2.1                          
[16] GenomicAlignments_1.18.1               
[17] SummarizedExperiment_1.12.0            
[18] DelayedArray_0.8.0                     
[19] BiocParallel_1.16.6                    
[20] matrixStats_0.55.0                     
[21] rtracklayer_1.42.2                     
[22] GenomicFeatures_1.34.8                 
[23] AnnotationDbi_1.44.0                   
[24] Biobase_2.42.0                         
[25] Rsamtools_1.34.1                       
[26] Biostrings_2.50.2                      
[27] XVector_0.22.0                         
[28] GenomicRanges_1.34.0                   
[29] GenomeInfoDb_1.18.2                    
[30] IRanges_2.16.0                         
[31] S4Vectors_0.20.1                       
[32] BiocGenerics_0.28.0                    

loaded via a namespace (and not attached):
 [1] bitops_1.0-6           fs_1.3.1               bit64_0.9-7           
 [4] RColorBrewer_1.1-2     progress_1.2.2         httr_1.4.1            
 [7] rprojroot_1.3-2        tools_3.5.1            backports_1.1.4       
[10] R6_2.4.0               DT_0.8                 DBI_1.0.0             
[13] lazyeval_0.2.2         colorspace_1.4-1       withr_2.1.2           
[16] processx_3.4.1         tidyselect_0.2.5       prettyunits_1.0.2     
[19] curl_4.0               bit_1.1-14             compiler_3.5.1        
[22] cli_1.1.0              desc_1.2.0             scales_1.0.0          
[25] genefilter_1.64.0      callr_3.3.1            tfruns_1.4            
[28] stringr_1.4.0          digest_0.6.20          base64enc_0.1-3       
[31] pkgconfig_2.0.2        htmltools_0.3.6        sessioninfo_1.1.1     
[34] htmlwidgets_1.3        rlang_0.4.1            RSQLite_2.1.2         
[37] generics_0.0.2         jsonlite_1.6           tensorflow_2.0.0      
[40] dplyr_0.8.3            RCurl_1.95-4.12        magrittr_1.5          
[43] GenomeInfoDbData_1.2.0 Matrix_1.2-14          Rcpp_1.0.2            
[46] munsell_0.5.0          reticulate_1.13        stringi_1.4.3         
[49] whisker_0.4            zlibbioc_1.28.0        pkgbuild_1.0.5        
[52] blob_1.2.0             crayon_1.3.4           splines_3.5.1         
[55] annotate_1.60.1        hms_0.5.1              ps_1.3.0              
[58] zeallot_0.1.0          pillar_1.4.2           pkgload_1.0.2         
[61] geneplotter_1.60.0     biomaRt_2.38.0         XML_3.98-1.20         
[64] glue_1.3.1             remotes_2.1.0          BiocManager_1.30.4    
[67] vctrs_0.2.0            testthat_2.2.1         gtable_0.3.0          
[70] purrr_0.3.3            assertthat_0.2.1       xtable_1.8-4          
[73] survival_2.42-6        tibble_2.1.3           memoise_1.1.0         
[76] ellipsis_0.2.0.1 

IRanges rtracklayer • 871 views
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Entering edit mode
@james-w-macdonald-5106
Last seen 5 hours ago
United States

Well, it's an error that comes from IRanges but it's doubtful that it's caused by IRanges, as I can easily reproduce.

> IRanges(c(1,2,3,4,NA), c(2,3,4,5,NA))
 Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
   solving row 5: range cannot be determined from the supplied arguments (too many NAs)

So it looks like you are getting some NA positions somewhere, which IRanges doesn't like, which is coming up right after the function tells you

[1] "Counting reads for single base..."

Which should be relatively easy for you or the maintainer to track down. You should probably update though, as you are using > 1 year old packages. The current version of IRanges has a different error for that situation.

> IRanges(c(1,2,3,4,NA), c(2,3,4,5,NA))
 Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :
   In range 5: at least two out of 'start', 'end', and 'width', must
   be supplied.
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Entering edit mode

Thank you James. So the problems, you think, it in the BED files being processed?

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Entering edit mode

Thank you James. So the problems, you think, it in the BED files being processed?

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Entering edit mode

I have no idea. All I can tell you is that somewhere IRanges is getting called, and there are NA values, for at least the fifth position.

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