Error importing UCSC phastCons annotation in BigWig format
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Delta._.43 ▴ 20
@a6fd600c
Last seen 10 days ago
Poland

I'm trying to import the UCSC phastCons.30way BigWig file using rtracklayer as an Rle Object using

rtracklayer::import("hg38.phyloP30way.bw", format = "BigWig", as = "RleList")

But it throws this error -

Error in .local(con, format, text, ...) : negative length vectors are not allowed

I can load other BigWig files without any issues but it seems the negative values in the phastCons BigWig is causing this error. I would be grateful if someone could advise me on how to solve this issue.

This issue is similar to - rtracklayer import bigwig error

sessionInfo( )
R version 4.2.2 Patched (2022-11-10 r83330)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.5 LTS

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.9.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.9.0

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

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

other attached packages:
 [1] doParallel_1.0.17           iterators_1.0.14            foreach_1.5.2               ggpubr_0.5.0                VennDiagram_1.7.3          
 [6] futile.logger_1.4.3         kableExtra_1.3.4            ggrepel_0.9.2               Rsubread_2.10.5             DESeq2_1.36.0              
[11] SummarizedExperiment_1.26.1 Biobase_2.56.0              MatrixGenerics_1.8.1        matrixStats_0.63.0          rtracklayer_1.56.1         
[16] data.table_1.14.6           forcats_0.5.2               stringr_1.4.1               dplyr_1.0.10                purrr_0.3.5                
[21] readr_2.1.3                 tidyr_1.2.1                 tibble_3.1.8                ggplot2_3.4.0               tidyverse_1.3.2            
[26] GenomicRanges_1.50.1        GenomeInfoDb_1.34.3         IRanges_2.32.0              S4Vectors_0.36.0            BiocGenerics_0.44.0
GenomicRanges rtracklayer • 34 views
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