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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