mm10 reference genome about descan2

[CN3ves]

library("RUVSeq")
library("edgeR")
BiocParallel::register(BiocParallel::SerialParam())
bam.files <- list.files("alignment",pattern="bam$", full.names=TRUE)

peaksGRL <- DEScan2::findPeaks(files=bam.files[1], filetype="bam", genomeName="mm10",
    binSize=50, minWin=50, maxWin=1000, zthresh=10, minCount=0.1, sigwin=10,
    minCompWinWidth=5000, maxCompWinWidth=10000, save=FALSE, 
    outputFolder="peaks", force=TRUE, onlyStdChrs=TRUE, chr=NULL, verbose=TRUE)

Save is false, not saving results!
processing alignment/001.co.bam
Get seqlengths from genome mm10
Error in value[3L] :
Unable to retrieve the genome mm10 returned: Error in .order_seqlevels(chrom_sizes[, "chrom"]): !anyNA(m31) is not TRUE

[CN3ves]

sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux 8.2 (Ootpa)

Matrix products: default
BLAS/LAPACK: /dcsrsoft/spack/hetre/v1.2/spack/opt/spack/linux-rhel8-zen2/gcc-9.3.0/openblas-0.3.15-ut6l356qhn3isvdrp46r4mndx75bwxji/lib/libopenblas_zenp-r0.3.15.so

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

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

other attached packages:
[1] RUVSeq_1.24.0 edgeR_3.32.1
[3] limma_3.46.0 EDASeq_2.24.0
[5] ShortRead_1.48.0 GenomicAlignments_1.26.0
[7] SummarizedExperiment_1.20.0 MatrixGenerics_1.2.1
[9] matrixStats_0.58.0 Rsamtools_2.6.0
[11] Biostrings_2.58.0 XVector_0.30.0
[13] BiocParallel_1.24.1 Biobase_2.50.0
[15] DEScan2_1.10.0 GenomicRanges_1.42.0
[17] GenomeInfoDb_1.26.2 IRanges_2.24.1
[19] S4Vectors_0.28.1 BiocGenerics_0.36.0

loaded via a namespace (and not attached):
[1] ProtGenerics_1.22.0 bitops_1.0-6 bit64_4.0.5
[4] RColorBrewer_1.1-2 progress_1.2.2 httr_1.4.2
[7] tools_4.0.5 R6_2.5.0 DBI_1.1.0
[10] lazyeval_0.2.2 colorspace_2.0-0 tidyselect_1.1.0
[13] prettyunits_1.1.1 bit_4.0.4 curl_4.3
[16] compiler_4.0.5 VennDiagram_1.7.0 graph_1.68.0
[19] formatR_1.7 xml2_1.3.2 DelayedArray_0.16.1
[22] rtracklayer_1.50.0 scales_1.1.1 RBGL_1.66.0
[25] askpass_1.1 rappdirs_0.3.1 stringr_1.4.0
[28] digest_0.6.27 R.utils_2.11.0 jpeg_0.1-8.1
[31] pkgconfig_2.0.3 dbplyr_2.0.0 ensembldb_2.14.1
[34] BSgenome_1.58.0 regioneR_1.22.0 rlang_0.4.10
[37] RSQLite_2.2.2 generics_0.1.0 hwriter_1.3.2
[40] R.oo_1.24.0 dplyr_1.0.3 RCurl_1.98-1.2
[43] magrittr_2.0.1 GenomeInfoDbData_1.2.1 futile.logger_1.4.3
[46] Matrix_1.3-3 Rcpp_1.0.7 munsell_0.5.0
[49] R.methodsS3_1.8.1 lifecycle_0.2.0 stringi_1.5.3
[52] MASS_7.3-54 zlibbioc_1.36.0 plyr_1.8.6
[55] BiocFileCache_1.14.0 grid_4.0.5 blob_1.2.1
[58] crayon_1.3.4 lattice_0.20-44 splines_4.0.5
[61] multtest_2.46.0 GenomicFeatures_1.42.1 hms_1.0.0
[64] KEGGREST_1.30.1 locfit_1.5-9.4 pillar_1.4.7
[67] biomaRt_2.46.2 futile.options_1.0.1 XML_3.99-0.5
[70] glue_1.4.2 latticeExtra_0.6-29 lambda.r_1.2.4
[73] data.table_1.14.2 png_0.1-7 vctrs_0.3.6
[76] gtable_0.3.0 openssl_1.4.3 purrr_0.3.4
[79] assertthat_0.2.1 ggplot2_3.3.3 aroma.light_3.20.0
[82] AnnotationFilter_1.14.0 survival_3.2-7 ChIPpeakAnno_3.24.2
[85] tibble_3.0.5 AnnotationDbi_1.52.0 memoise_1.1.0
[88] ellipsis_0.3.1

[drighelli]

Dear Carlos (@CN3ves),

could you please try to update the GenomeInfoDb package and try to execute the findPeaks function again?

I'm trying it with my example bam files and mm10 genome and it's working.

Also, once working, you'd prefer to use bigger binSize and the minWin/maxWin to speed up the peak calling process... Just in case you're not interested in very small peaks...

[CN3ves]

Hi @drighelli, I updated GenomeInfoDb from v1.26.2 to v1.26.7 and it still has the same issue. Though I just noticed the R version on the cluster I'm using is not >4.1. I tested it on my personal computer with R-v4.1.2 (which updates GenomeInfoDb to v1.28.4) and it seems to run without any problem.

I guess it was an R version issue then :) Thanks for looking into this

[drighelli]

Thanks @CN3ves :)

let me know if you have any other issues...