I wrote a script which creates interaction maps using HiTC

Running the script on windows everything works perfectly.

Running the same script with the same data in my VM with Debian installed i get following error:

Loading Genomic intervals ...

Error in .Call2("solve_user_SEW0", start, end, width, PACKAGE = "IRanges") :

solving row 1: negative widths are not allowed

Calls: lapply ... GenomicData -> IRanges -> solveUserSEW0 -> .Call2 -> .Call

I checked the data which is fine otherwise it would not be able to run on windows.

The line causing the error, where 'path_matrix' is the path to a matrix file generated by HiC-Pro :

interaction_matrix_full <- HiTC::importC(path_matrix, xgi.bed = path_bed, rm.trans = T)

Here is the output of sessionInfo("HiTC") for both systems:

R version 3.4.3 (2017-11-30)

Platform: x86_64-pc-linux-gnu (64-bit)

Running under: Debian GNU/Linux 9 (stretch)

Matrix products: default

BLAS: /mnt/software/x86_64/packages/r/3.4.3-stretch-local/lib/R/lib/libRblas.so

LAPACK: /mnt/software/x86_64/packages/r/3.4.3-stretch-local/lib/R/lib/libRlapack.so

locale:

 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               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    LC_PAPER=en_US.UTF-8       LC_NAME=C                 

 [9] LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C       

attached base packages:

character(0)

other attached packages:

[1] HiTC_1.22.0

loaded via a namespace (and not attached):

 [1] XVector_0.18.0             GenomicRanges_1.30.3       BiocGenerics_0.24.0        zlibbioc_1.24.0           

 [5] GenomicAlignments_1.14.1   IRanges_2.12.0             grDevices_3.4.3            BiocParallel_1.12.0       

 [9] lattice_0.20-35            GenomeInfoDb_1.14.0        tools_3.4.3                utils_3.4.3               

[13] SummarizedExperiment_1.8.1 parallel_3.4.3             grid_3.4.3                 Biobase_2.38.0            

[17] matrixStats_0.53.1         stats_3.4.3                datasets_3.4.3             yaml_2.1.17               

[21] base_3.4.3                 Matrix_1.2-12              GenomeInfoDbData_1.0.0     rtracklayer_1.38.3        

[25] RColorBrewer_1.1-2         graphics_3.4.3             S4Vectors_0.16.0           bitops_1.0-6              

[29] RCurl_1.95-4.10            DelayedArray_0.4.1         compiler_3.4.3             methods_3.4.3             

[33] Biostrings_2.46.0          Rsamtools_1.30.0           stats4_3.4.3               XML_3.98-1.10

R version 3.4.2 (2017-09-28)

Platform: x86_64-w64-mingw32/x64 (64-bit)

Running under: Windows 7 x64 (build 7601) Service Pack 1

Matrix products: default

locale:

[1] LC_COLLATE=German_Germany.1252  LC_CTYPE=German_Germany.1252    LC_MONETARY=German_Germany.1252 LC_NUMERIC=C                   

[5] LC_TIME=German_Germany.1252    

attached base packages:

character(0)

other attached packages:

[1] HiTC_1.22.0

loaded via a namespace (and not attached):

 [1] XVector_0.18.0             HiTC_1.22.0                GenomicRanges_1.30.0       BiocGenerics_0.24.0        zlibbioc_1.24.0           

 [6] GenomicAlignments_1.14.1   IRanges_2.12.0             grDevices_3.4.2            BiocParallel_1.12.0        lattice_0.20-35           

[11] GenomeInfoDb_1.14.0        tools_3.4.2                utils_3.4.2                SummarizedExperiment_1.8.1 parallel_3.4.2            

[16] grid_3.4.2                 Biobase_2.38.0             matrixStats_0.53.1         stats_3.4.2                datasets_3.4.2            

[21] base_3.4.2                 Matrix_1.2-12              GenomeInfoDbData_1.0.0     rtracklayer_1.38.3         RColorBrewer_1.1-2        

[26] graphics_3.4.2             S4Vectors_0.16.0           bitops_1.0-6               RCurl_1.95-4.10            DelayedArray_0.4.1        

[31] compiler_3.4.2             methods_3.4.2              Biostrings_2.46.0          Rsamtools_1.30.0           stats4_3.4.2              

[36] XML_3.98-1.10

Hi,

Indeed, it looks like the file was read, but that the parsing failed when it tries to create the GenomicRanges object (negatives widths).

I'm wondering if the file could be corrupted by Windows character for instance ?

Could you try ;

xgi <- rtracklayer::import(xgi.bed, format = "bed")
xgi
cdata <- read.table(con, comment.char = "#", colClasses = c("character",
        "character", "numeric"), check.names = FALSE)
head(cdata)

Thanks

Thanks. It looks good. I think the error occur on the xgi object. Did you check if your have intervals with negative widths ?

The importC function is a small function. Could you try to excecute it line by line to see where exactly it crashed ...

or at least ;

 xgi <- rtracklayer::import(xgi.bed, format = "bed")
 xgi <- sortSeqlevels(xgi)
 names(xgi) <- id(xgi)

Thanks

Great ! Thanks. Nicolas