Question: Issue with wavClusteR
0
gravatar for btharada
5 weeks ago by
btharada0
btharada0 wrote:

I am having an issue with the getAllSub function in the wavClusteR package. I have read my bam file using the readSortedBam function,

library(wavClusteR)
bam <- readSortedBam("~/parclip/bam/replicate_1.bam")
countTable <- getAllSub(bam, minCov=10)

but when I attempt to run the getAllSub function on the data, I get the following error:

Loading required package: doMC
Loading required package: foreach
Loading required package: iterators
Considering substitutions, n = 28204, processing in 29 chunks
   chunk #: 1
   chunk #: 2
   chunk #: 3
   chunk #: 4
   chunk #: 5
   chunk #: 6
   chunk #: 7
   chunk #: 8
   chunk #: 9
   chunk #: 10
   chunk #: 11
   chunk #: 12
   chunk #: 13
   chunk #: 14
   chunk #: 15
   chunk #: 16
   chunk #: 17
   chunk #: 18
   chunk #: 19
   chunk #: 20
   chunk #: 21
   chunk #: 22
   chunk #: 23
   chunk #: 24
   chunk #: 25
   chunk #: 26
   chunk #: 27
   chunk #: 28
   chunk #: 29
Error in { : 
  task 1 failed - "solving row 7017: range cannot be determined from the supplied arguments (too many NAs)"

My bam file has been sorted and indexed via samtools as directed in the instructions. The error seems to occur during the "at <- IRanges(unlist(offset), width = 1)" call within the processChunk function within the processMD function called by getAllSub:

>   at <- IRanges(unlist(offset), width = 1)
Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") : 
  solving row 7017: range cannot be determined from the supplied arguments (too many NAs)

Please advise as to how to get around this error message.

Here is the my session info for reference

R version 3.6.0 (2019-04-26)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 18.04.2 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/openblas/libblas.so.3
LAPACK: /usr/lib/x86_64-linux-gnu/libopenblasp-r0.2.20.so

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

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

other attached packages:
 [1] doMC_1.3.6           iterators_1.0.12     foreach_1.4.7        wavClusteR_2.18.0   
 [5] Rsamtools_2.0.0      Biostrings_2.52.0    XVector_0.24.0       GenomicRanges_1.36.0
 [9] GenomeInfoDb_1.20.0  IRanges_2.18.2       S4Vectors_0.22.0     BiocGenerics_0.30.0 

loaded via a namespace (and not attached):
 [1] Biobase_2.44.0              httr_1.4.1                  bit64_0.9-7                
 [4] splines_3.6.0               Formula_1.2-3               assertthat_0.2.1           
 [7] latticeExtra_0.6-28         blob_1.2.0                  GenomeInfoDbData_1.2.1     
[10] progress_1.2.2              pillar_1.4.2                RSQLite_2.1.2              
[13] backports_1.1.4             lattice_0.20-38             glue_1.3.1                 
[16] digest_0.6.20               checkmate_1.9.4             RColorBrewer_1.1-2         
[19] colorspace_1.4-1            htmltools_0.4.0             Matrix_1.2-17              
[22] XML_3.98-1.20               pkgconfig_2.0.2             biomaRt_2.40.4             
[25] zlibbioc_1.30.0             purrr_0.3.2                 scales_1.0.0               
[28] ifultools_2.0-5             BiocParallel_1.18.1         htmlTable_1.13.1           
[31] tibble_2.1.3                ggplot2_3.2.1               SummarizedExperiment_1.14.1
[34] GenomicFeatures_1.36.4      nnet_7.3-12                 lazyeval_0.2.2             
[37] survival_2.44-1.1           magrittr_1.5                crayon_1.3.4               
[40] mclust_5.4.5                memoise_1.1.0               MASS_7.3-51.4              
[43] foreign_0.8-72              data.table_1.12.2           tools_3.6.0                
[46] prettyunits_1.0.2           hms_0.5.1                   matrixStats_0.54.0         
[49] stringr_1.4.0               munsell_0.5.0               cluster_2.1.0              
[52] DelayedArray_0.10.0         AnnotationDbi_1.46.1        wmtsa_2.0-3                
[55] ade4_1.7-13                 compiler_3.6.0              rlang_0.4.0                
[58] grid_3.6.0                  RCurl_1.95-4.12             rstudioapi_0.10            
[61] htmlwidgets_1.5.1           bitops_1.0-6                base64enc_0.1-3            
[64] gtable_0.3.0                codetools_0.2-16            DBI_1.0.0                  
[67] R6_2.4.0                    gridExtra_2.3               GenomicAlignments_1.20.1   
[70] knitr_1.24                  dplyr_0.8.3                 rtracklayer_1.44.3         
[73] seqinr_3.6-1                bit_1.1-14                  zeallot_0.1.0              
[76] Hmisc_4.2-0                 stringi_1.4.3               Rcpp_1.0.2                 
[79] rpart_4.1-15                vctrs_0.2.0                 acepack_1.4.1              
[82] splus2R_1.2-2               xfun_0.9                    tidyselect_0.2.5
wavcluster • 36 views
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