Comments (5)
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
from descan2.
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
from descan2.
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...
from descan2.
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
from descan2.
Thanks @CN3ves :)
let me know if you have any other issues...
from descan2.
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