Error: BiocParallel errors
Entering edit mode
Last seen 6 months ago

Hi , I am trying to create a metagene plot using R. i mapped using star and files were indexed. But when i try to plot i'm getting error which i'm not sure. Can you please help me with this.

> bam_files <-c(system.file("extdata/ Aligned.sortedByCoord.out.bam", package="metagene"))
> regions <- c(system.file("extdata/list2.bed", package="metagene"))
> mg <- metagene$new(regions = regions, bam_files = bam_files, assay = 'rnaseq', paired_end = TRUE)

Error: BiocParallel errors
  1 remote errors, element index: 1
  0 unevaluated and other errors
  first remote error: scan() expected 'an integer', got '3337105133371051'

> sessionInfo()
R version 4.1.2 (2021-11-01)
Platform: x86_64-apple-darwin17.0 (64-bit)
Running under: macOS Monterey 12.1

Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.1/Resources/lib/libRlapack.dylib

[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8

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

other attached packages:
 [1] metagene_2.24.0                        BiocParallel_1.28.3                    R6_2.5.1                              
 [4] GenomicAlignments_1.30.0               Rsamtools_2.10.0                       pasillaBamSubset_0.30.0               
 [7] BSgenome.Hsapiens.NCBI.GRCh38_1.3.1000 BSgenome_1.60.0                        rtracklayer_1.54.0                    
[10] Biostrings_2.62.0                      XVector_0.34.0                         GenomicFeatures_1.46.3                
[13] AnnotationDbi_1.56.2                   gread_0.99.2                           SummarizedExperiment_1.24.0           
[16] Biobase_2.54.0                         GenomicRanges_1.46.1                   GenomeInfoDb_1.30.0                   
[19] IRanges_2.28.0                         S4Vectors_0.32.3                       BiocGenerics_0.40.0                   
[22] MatrixGenerics_1.6.0                   matrixStats_0.61.0                    

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.24.0       bitops_1.0-7              bit64_4.0.5               filelock_1.0.2            progress_1.2.2           
 [6] httr_1.4.2                tools_4.1.2               utf8_1.2.2                KernSmooth_2.23-20        DBI_1.1.2                
[11] lazyeval_0.2.2            colorspace_2.0-2          withr_2.4.3               tidyselect_1.1.1          prettyunits_1.1.1        
[16] bit_4.0.4                 curl_4.3.2                compiler_4.1.2            EnsDb.Hsapiens.v86_2.99.0 xml2_1.3.3               
[21] DelayedArray_0.20.0       caTools_1.18.2            scales_1.1.1              rappdirs_0.3.3            stringr_1.4.0            
[26] digest_0.6.29             pkgconfig_2.0.3           dbplyr_2.1.1              fastmap_1.1.0             ensembldb_2.16.4         
[31] rlang_0.4.12              rstudioapi_0.13           RSQLite_2.2.9             BiocIO_1.4.0              generics_0.1.1           
[36] gtools_3.9.2              dplyr_1.0.7               RCurl_1.98-1.5            magrittr_2.0.1            GenomeInfoDbData_1.2.7   
[41] muStat_1.7.0              Matrix_1.4-0              Rcpp_1.0.8                munsell_0.5.0             fansi_1.0.2              
[46] lifecycle_1.0.1           stringi_1.7.6             yaml_2.2.1                zlibbioc_1.40.0           gplots_3.1.1             
[51] BiocFileCache_2.2.0       grid_4.1.2                blob_1.2.2                parallel_4.1.2            crayon_1.4.2             
[56] lattice_0.20-45           hms_1.1.1                 KEGGREST_1.34.0           pillar_1.6.4              rjson_0.2.21             
[61] biomaRt_2.50.2            XML_3.99-0.8              glue_1.6.0                data.table_1.14.2         BiocManager_1.30.16      
[66] png_0.1-7                 vctrs_0.3.8               gtable_0.3.0              purrr_0.3.4               assertthat_0.2.1         
[71] cachem_1.0.6              ggplot2_3.3.5             restfulr_0.0.13           AnnotationFilter_1.16.0   snow_0.4-4               
[76] tibble_3.1.6              memoise_2.0.1             ellipsis_0.3.2
Bioconductor metagene GenomicAlignments • 736 views
Entering edit mode

I came across the same problem, have you solved it?


Login before adding your answer.

Traffic: 207 users visited in the last hour
Help About
Access RSS

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6