Representation and manipulation of short genomic alignments
Home Page: https://bioconductor.org/packages/GenomicAlignments
GenomicAlignments is an R/Bioconductor package for representing and manipulating short genomic alignments (typically aligned reads).
See https://bioconductor.org/packages/GenomicAlignments for more information including how to install the release version of the package (please refrain from installing directly from GitHub).
Hello,
I would like to point out, that when I use a BamViews object with the summarizeOverlaps method, the whole Bam file is loaded into Memory, if I do not explicitly provide the param argument.
Here is an example
library(GenomicAlignments)
library(microbenchmark)
tiny_bam <- system.file("extdata", "ex1.bam", package="Rsamtools", mustWork=TRUE)
fl <- c(tiny_bam,tiny_bam)
rngs <- GRanges(c("seq1", "seq2"), IRanges(1, c(15, 15)))
samp <- DataFrame(info=c("ex1","ex2"), row.names=c("ex1","ex2"))
# define the BamViews for multiple files using Rsamtools
view <- BamViews(bamPaths = fl, bamSamples=samp, bamRanges=rngs)
So these function calls will have different memory footprints because in one case we are loading the whole BAM file,
se <- summarizeOverlaps(view, mode=Union, ignore.strand=TRUE)
while in the other we only load the reads that are in the given ranges.
se <- summarizeOverlaps(view,
mode=Union,
ignore.strand=TRUE,
param=ScanBamParam(which = rngs))
Best,
Alex
In release and devel, summarizeOverlaps() produces the following spurious warning:
library(GenomicAlignments)
library(TxDb.Dmelanogaster.UCSC.dm3.ensGene)
exbygene <- exonsBy(TxDb.Dmelanogaster.UCSC.dm3.ensGene, "gene")
library(pasillaBamSubset)
reads <- readGAlignmentsList(untreated3_chr4())
se <- summarizeOverlaps(exbygene, reads)
# Warning message:
# In if (all(strand(reads) == "*")) ignore.strand <- TRUE :
# the condition has length > 1 and only the first element will be used
Looks like there was an attempt at getting rid of this warning back in 2014 (see 7cfab64) but this fix only addresses the case where reads is a GRangesList object. However reads can be a GAlignments, GAlignmentPairs, GAlignmentsList, GRanges, or GRangesList object, and the fix doesn't address the case where reads is a GAlignmentsList object.
Suggested fix: Replace the first 7 lines (if statement) of internal helper .summarizeOverlaps() with:
if (!isTRUEorFALSE(ignore.strand))
stop("'ignore.strand' must be TRUE or FALSE")
if (!ignore.strand) {
reads_strand <- strand(reads)
if (is(reads_strand, "List"))
reads_strand <- unlist(reads_strand, use.names=FALSE)
if (all(reads_strand == "*"))
ignore.strand <- TRUE
}
The idea is to unlist the strand only if it's a List derivative, which is more robust than unlisting based on the class of reads. The fix also checks ignore.strand which will avoid obscure warnings or errors if the user doesn't supply a TRUE or a FALSE.
Thanks,
H.
> sessionInfo()
R version 3.4.3 (2017-11-30)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.4 LTS
Matrix products: default
BLAS: /home/hpages/R/R-3.4.3/lib/libRblas.so
LAPACK: /home/hpages/R/R-3.4.3/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] pasillaBamSubset_0.16.0
[2] TxDb.Dmelanogaster.UCSC.dm3.ensGene_3.2.2
[3] GenomicFeatures_1.30.3
[4] AnnotationDbi_1.40.0
[5] GenomicAlignments_1.14.1
[6] Rsamtools_1.30.0
[7] Biostrings_2.46.0
[8] XVector_0.18.0
[9] SummarizedExperiment_1.8.1
[10] DelayedArray_0.4.1
[11] matrixStats_0.53.1
[12] Biobase_2.38.0
[13] GenomicRanges_1.30.3
[14] GenomeInfoDb_1.14.0
[15] IRanges_2.12.0
[16] S4Vectors_0.16.0
[17] BiocGenerics_0.24.0
loaded via a namespace (and not attached):
[1] Rcpp_0.12.16 compiler_3.4.3 prettyunits_1.0.2
[4] bitops_1.0-6 tools_3.4.3 zlibbioc_1.24.0
[7] progress_1.1.2 biomaRt_2.34.2 digest_0.6.15
[10] bit_1.1-12 RSQLite_2.0 memoise_1.1.0
[13] lattice_0.20-35 pkgconfig_2.0.1 Matrix_1.2-12
[16] DBI_0.8 GenomeInfoDbData_1.0.0 rtracklayer_1.38.3
[19] httr_1.3.1 stringr_1.3.0 bit64_0.9-7
[22] grid_3.4.3 R6_2.2.2 XML_3.98-1.10
[25] RMySQL_0.10.14 BiocParallel_1.12.0 magrittr_1.5
[28] blob_1.1.1 assertthat_0.2.0 stringi_1.1.7
[31] RCurl_1.95-4.10
This looks wrong:
library(GenomicAlignments)
mypos <- IRanges(1:7, width=1, names=rep("read1", 7))
alignment <- GAlignments("chr1", pos=1L, cigar="2S3M2D7M", strand("+"), names="read1")
mapFromAlignments(mypos, alignment)
# IRanges object with 7 ranges and 0 metadata columns:
# start end width
# <integer> <integer> <integer>
# read1 1 1 1
# read1 2 2 1
# read1 3 3 1
# read1 4 4 1
# read1 5 5 1
# read1 8 8 1
# read1 9 9 1
The reported deletion (ref pos 6 & 7) seems wrong. Should be ref pos 4 & 5.
sessionInfo():
> sessionInfo()
R Under development (unstable) (2019-10-30 r77336)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 16.04.6 LTS
Matrix products: default
BLAS: /home/hpages/R/R-4.0.r77336/lib/libRblas.so
LAPACK: /home/hpages/R/R-4.0.r77336/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicAlignments_1.23.1 Rsamtools_2.3.4
[3] Biostrings_2.55.4 XVector_0.27.0
[5] SummarizedExperiment_1.17.2 DelayedArray_0.13.4
[7] BiocParallel_1.21.2 matrixStats_0.55.0
[9] Biobase_2.47.2 GenomicRanges_1.39.2
[11] GenomeInfoDb_1.23.13 IRanges_2.21.3
[13] S4Vectors_0.25.12 BiocGenerics_0.33.0
loaded via a namespace (and not attached):
[1] lattice_0.20-38 crayon_1.3.4 bitops_1.0-6
[4] grid_4.0.0 zlibbioc_1.33.1 Matrix_1.2-18
[7] tools_4.0.0 RCurl_1.98-1.1 compiler_4.0.0
[10] GenomeInfoDbData_1.2.2
Hi,
I'm volunteering with Sweave2Rmd and we're trying to replace all Bioconductor Sweave vignettes R Markdown
vignettes. Would you be willing to accept a pull request with the R Markdown
version of GenomicAlignments? I also wanted to ask if you can assign this to me on the board?
Thanks for your time.
Hi, single-end read alignments with more than 3 junctions in the cigar string cause the following error:
suppressPackageStartupMessages(library(GenomicAlignments))
suppressPackageStartupMessages(library(TxDb.Hsapiens.UCSC.hg38.knownGene))
txdb <- TxDb.Hsapiens.UCSC.hg38.knownGene
tx <- exonsBy(txdb, by="tx")
aln <- GAlignments("chr1", pos=42837180L, cigar="5S11M1710N21M1111N21M98N27M91N16M",
strand("+"), names="read1")
ovtx <- findOverlaps(GRanges(aln), tx, ignore.strand=FALSE)
ovtxenc <- encodeOverlaps(grglist(aln), tx, hits=ovtx,
flip.query.if.wrong.strand=FALSE)
maskskpovtx <- isCompatibleWithSkippedExons(ovtxenc) # error
Error in paste0(build_compatible_encoding_subpatterns(njunc), collapse = skipped_exons_subpatterns[njunc + :
invalid 'collapse' argument
Here is my session information:
sessionInfo()
R version 4.3.2 (2023-10-31)
Platform: x86_64-apple-darwin20 (64-bit)
Running under: macOS Ventura 13.6.1
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/4.3-x86_64/Resources/lib/libRlapack.dylib; LAPACK version 3.11.0
locale:
[1] en_US.UTF-8/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
time zone: Europe/Madrid
tzcode source: internal
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] TxDb.Hsapiens.UCSC.hg38.knownGene_3.18.0 GenomicFeatures_1.54.1
[3] AnnotationDbi_1.64.1 GenomicAlignments_1.38.0
[5] Rsamtools_2.18.0 Biostrings_2.70.1
[7] XVector_0.42.0 SummarizedExperiment_1.32.0
[9] Biobase_2.62.0 MatrixGenerics_1.14.0
[11] matrixStats_1.1.0 GenomicRanges_1.54.1
[13] GenomeInfoDb_1.38.1 IRanges_2.36.0
[15] S4Vectors_0.40.2 BiocGenerics_0.48.1
[17] colorout_1.3-0
loaded via a namespace (and not attached):
[1] KEGGREST_1.42.0 rjson_0.2.21 lattice_0.22-5 vctrs_0.6.5
[5] tools_4.3.2 bitops_1.0-7 generics_0.1.3 curl_5.2.0
[9] parallel_4.3.2 tibble_3.2.1 fansi_1.0.6 RSQLite_2.3.4
[13] blob_1.2.4 pkgconfig_2.0.3 Matrix_1.6-4 dbplyr_2.4.0
[17] lifecycle_1.0.4 GenomeInfoDbData_1.2.11 compiler_4.3.2 stringr_1.5.1
[21] progress_1.2.3 codetools_0.2-19 yaml_2.3.7 RCurl_1.98-1.13
[25] pillar_1.9.0 crayon_1.5.2 BiocParallel_1.36.0 DelayedArray_0.28.0
[29] cachem_1.0.8 abind_1.4-5 tidyselect_1.2.0 digest_0.6.33
[33] stringi_1.8.2 restfulr_0.0.15 dplyr_1.1.4 biomaRt_2.58.0
[37] fastmap_1.1.1 grid_4.3.2 cli_3.6.2 SparseArray_1.2.2
[41] magrittr_2.0.3 S4Arrays_1.2.0 XML_3.99-0.16 utf8_1.2.4
[45] rappdirs_0.3.3 filelock_1.0.3 prettyunits_1.2.0 bit64_4.0.5
[49] httr_1.4.7 bit_4.0.5 png_0.1-8 hms_1.1.3
[53] memoise_2.0.1 BiocIO_1.12.0 BiocFileCache_2.10.1 rtracklayer_1.62.0
[57] rlang_1.1.2 glue_1.6.2 DBI_1.1.3 xml2_1.3.6
[61] R6_2.5.1 zlibbioc_1.48.0
I've submitted a PR that fixes it.
cheers,
robert.
Hey there and thanks for the amazing package, it's been really helpful!
I stumbled upon an issue which I would like to share with you.
So I have generated a synthetic bam file using NEAT that contains reads in the TP53 region (it's located in the 17th chromosome and spans for about 19k bases).
My interest is to benchmark the somatic variants which are produced by GATK-Mutect2 and to do that I need to know exactly the Allele Frequencies (AF) of the variants and hence the number of all bases in each chromosomal position.
To my great surprise I found that at certain chromosomal positions, although the coverage is correct, the reported bases do differ!
Below I present the lines of code that I am using in R with the help of "GenomicAlignments" library.
library(GenomicAlignments)
bam = scanBam("1/1_golden.bam")
#Read genomic alignments
olaps <- readGAlignments("1/1_golden.bam")
#chromosomal position
p=474
# reads in chromosomal position
index = which(start(olaps) <= p & end(olaps) >= p)
#extract reads from bam
my_seqs = bam[[1]]$seq[index]
#distance from position p
ret = p - start(olaps[index, ]) + 1
out = mapply(function(x, y) {
str_sub(x, y, y)
}, as.character(my_seqs), ret)
out = data.table(
"base" = out
)
out = out[, by = base, .N]
I am also attaching a print screen.
On the left you see the out parameter which contains the bases from the chromosomal position p (in this case p=474) and on the right you see the info as produced by IGV for the same position p. The coverage is the same (478 in both cases), the difference is found in the base content of the reads.
I am very curious to see what causes this systematic deviation between IGV and my code. If anyone has faced this problem before or has any clue, I would really appreciate it!
Thanks in advance,
Stella
sorry, I have a question,
when I installed the package in R 4.0.2, it was wrong with the S4Vectors 0.26.1 but need to >=0.27.12, how to solve this question?
Thanks
Does the opposite function exist to queryLocs2refLocs ?
i.e. given a reference location, finding the position in the query that corresponds to it. This would be a basic useful function.
Thanks.
Hey there,
It seems to me that due to how most RNAseq libraries are now constructed, most people who want to count reads per feature with summarizeOverlaps will actually want to use ignore.strand = FALSE and preprocess.reads = invertStrand. However, I only stumbled across this after realizing that my output was wildly different from what htseq-count with -s reverse gave me when I only used ignore.strand = FALSE.
That you need to use preprocess.reads = invertStrand with most modern stranded RNAseq libraries is not mentioned in the documentation for summarizeOverlaps or in the example RNAseq workflow (which is not this package, but it's still confusing). The only information that I could find to lead me to this was in the bioconductor support forums.
Could the documentation be clarified in some way? I could see this tripping up new users.
This is the example code to reproduce the error:
library(GenomicAlignments)
library(BSgenome.Hsapiens.UCSC.hg19)
aln1_file <- system.file("extdata", "ex1.bam", package="Rsamtools")
aln1 <- readGAlignments(aln1_file)
summarizeJunctions(aln1, genome="BSgenome.Hsapiens.UCSC.hg19")
This will produces the following error message:
Error in .get_xscat_ans_cardinality(...) :
xscat() cannot mix arguments made of 0 sequence with arguments made of 1 or more sequences
In addition: Warning message:
In .Seqinfo.mergexy(x, y) :
The 2 combined objects have no sequence levels in common. (Use
suppressWarnings() to suppress this warning.)
Dear Sir,
I have used granges function in this package for a long time. However, I got an error after updating GenomicAlignments (version 1.16.0) through bioconductor.
I used granges like below
t.record.range <- granges(temp, on.discordant.seqnames="drop");
Error in .local(x, use.names, use.mcols, ...) :
unused argument (on.discordant.seqnames = "drop")
the argument on.discordant.seqnames seemed to be removed.
I have search the solution using google, but I got nothing.
Now my question are:
Hi,
by accident I tried to access the metadata column from GAlignment object directly via $. This ended up in a bit ungraceful exit.
library(GenomicAlignments)
ga <- readGAlignments(file, param = ScanBamParam(what = "qual"))
ga$qual # this crashes
#> Error: evaluation nested too deeply: infinite recursion / options(expressions=)?
mcols(ga)$qual # this works
#> A PhredQuality instance of length x
#> width seqI don't know, if that is expected behavior or it is just the way it needs to be (please close the issue if that is the case).
However, a more graceful exit might benefit understanding the GAlignment class. I stumbled onto this by assuming it might work like a GRanges/DataFrame object.
Felix
sessionInfo()
#> R version 3.6.0 (2019-04-26)
#> Platform: x86_64-w64-mingw32/x64 (64-bit)
#> Running under: Windows 10 x64 (build 18362)
#>
#> Matrix products: default
#>
#> locale:
#> [1] LC_COLLATE=German_Germany.1252 LC_CTYPE=German_Germany.1252
#> [3] LC_MONETARY=German_Germany.1252 LC_NUMERIC=C
#> [5] LC_TIME=German_Germany.1252
#>
#> attached base packages:
#> [1] stats4 parallel stats graphics grDevices utils datasets
#> [8] methods base
#>
#> other attached packages:
#> [1] RNAmodR.Data_0.99.5 ExperimentHubData_1.10.0
#> [3] AnnotationHubData_1.14.0 ExperimentHub_1.10.0
#> [5] AnnotationHub_2.17.0 BiocFileCache_1.8.0
#> [7] dbplyr_1.4.1 futile.logger_1.4.3
#> [9] GenomicAlignments_1.20.0 Rsamtools_2.0.0
#> [11] Biostrings_2.52.0 XVector_0.24.0
#> [13] SummarizedExperiment_1.14.0 DelayedArray_0.10.0
#> [15] BiocParallel_1.17.18 matrixStats_0.54.0
#> [17] Biobase_2.44.0 GenomicRanges_1.36.0
#> [19] GenomeInfoDb_1.20.0 IRanges_2.18.1
#> [21] S4Vectors_0.22.0 BiocGenerics_0.30.0
#>
#> loaded via a namespace (and not attached):
#> [1] bitops_1.0-6 bit64_0.9-7
#> [3] progress_1.2.2 httr_1.4.0
#> [5] tools_3.6.0 R6_2.4.0
#> [7] DBI_1.0.0 tidyselect_0.2.5
#> [9] prettyunits_1.0.2 bit_1.1-14
#> [11] curl_3.3 compiler_3.6.0
#> [13] graph_1.62.0 BiocCheck_1.20.0
#> [15] formatR_1.7 rtracklayer_1.44.0
#> [17] RBGL_1.60.0 rappdirs_0.3.1
#> [19] stringr_1.4.0 digest_0.6.19
#> [21] rmarkdown_1.13 stringdist_0.9.5.2
#> [23] AnnotationForge_1.26.0 rBiopaxParser_2.24.0
#> [25] pkgconfig_2.0.2 htmltools_0.3.6
#> [27] highr_0.8 rlang_0.3.4
#> [29] RSQLite_2.1.1 shiny_1.3.2
#> [31] jsonlite_1.6 dplyr_0.8.1
#> [33] RCurl_1.95-4.12 magrittr_1.5
#> [35] GenomeInfoDbData_1.2.1 Matrix_1.2-17
#> [37] Rcpp_1.0.1 stringi_1.4.3
#> [39] yaml_2.2.0 zlibbioc_1.30.0
#> [41] biocViews_1.52.2 grid_3.6.0
#> [43] blob_1.1.1 promises_1.0.1
#> [45] crayon_1.3.4 lattice_0.20-38
#> [47] GenomicFeatures_1.36.1 hms_0.4.2
#> [49] knitr_1.23 pillar_1.4.1
#> [51] optparse_1.6.2 RUnit_0.4.32
#> [53] codetools_0.2-16 biomaRt_2.40.0
#> [55] futile.options_1.0.1 XML_3.98-1.20
#> [57] glue_1.3.1 evaluate_0.14
#> [59] lambda.r_1.2.3 data.table_1.12.2
#> [61] BiocManager_1.30.4 httpuv_1.5.1
#> [63] getopt_1.20.3 purrr_0.3.2
#> [65] assertthat_0.2.1 xfun_0.7
#> [67] mime_0.6 xtable_1.8-4
#> [69] later_0.8.0 tibble_2.1.3
#> [71] OrganismDbi_1.26.0 AnnotationDbi_1.46.0
#> [73] memoise_1.1.0 interactiveDisplayBase_1.22.0
GenomicAlignments (1.32.0)
I have trouble to subset a cigar string for a region larger than 100,000 in length.
Is this a memory issue on my PC or a know limitation of cigarNarrow function?
cg <- "7=1X4=1X2=1X19=2X3=2X2=1X6=1X14=1X3=1X18=1X39=1X7=1D90=1X3=1X13=1X4=1X13=6I97=1X213=4D24=1X50=1X151=18I166=1X16=1X4=1X46=3D58=1X144=1X182=1X13=1X127=1X4=1X35=1X66=1X141=1X119=1X42=1X35=6I126=1X23=1X12=1X35=1X9=1X12=1X71=255D8=1X57=2X24=1X22=1X3=1X54=1X4=1X22=1X30=1X66=2X107=1X3=1X112=1X257=1X7=1X21=1X126=1X55=1X174=3D137=1X186=1X54=1X30=1X42=1X55=1X40=2I2X133=1X59=1X73=1D103=1X8=1X101=1X22=1X71=1X56=1X35=1X33=2X14=1X185=1X32=1X47=1X11=4I5=3X33=1X38=1X69=1X60=4I30=1X9=1X34=2X100=1X1=1X68=1X14=1X7=1X53=1X25=5I1X52=5I7=1X302=1X240=1X105=1X41=1X29=1X34=1X27=3D246=1X56=1X210=1X144=1X116=1X166=1X59=1X1=1X13=5I66=1X107=1X48=1X8=2X12=1X6=1X45=1X93=1X43=1X11=1X73=1X27=1X26=1X26=1X7=1X9=1D13=1X49=1X106=2D1=1X147=1X81=1X51=1X78=1X36=9523D11=1X6=1X23=1X108=1X49=1X7=2X11=1I179=1D62=1X85=1X27=1X21=1X11=1X2=1X208=1X16=1X24=1X2=1X9=1X39=1X90=1I13=5I84=1X46=1X93=1X124=1X7=1X22=10I24=1X35=1X53=1X80=1X6=1X67=1X73=1I3=1X3=1X8=11I91=1X242=2X51=1X165=1X103=1X21=1X152=1I34=1X153=1X29=1X20=1X25=1X71=1X12=1X117=2D32=1X72=1X93=1X1=1X3=1X34=1X49=1X10=1X17=1X39=1X26=1X15=1X35=9I28=1X6=1X43=1X57=1X10=1X190=1X149=1X52=1X32=1X1=1X59=2X50=1X339=1X24=1X42=1I11=5I9=1X584=1X216=1X15=1X11=1X60=1X5=1X245=1X140=1X15=1I204=1X448=1X26=1X24=1X35=1X37=1X16=1X52=1X10=1X93=1X87=1X91=1X53=1X5=1X24=1X115=1X74=1X249=1X25=1I65=1X145=1X177=1X11=1X1=1X20=1I1X107=1X47=1X9=1X2=2D21=1D101=1X48=1X119=1X24=1X78=1X61=1X1=1X4=1X2=1X6=1X1=1X10=2X8=2X2=2I1X1=1X5=1X2=1X3=1X4=1X106=1I161=1D109=1X68=1X2=1X384=1X64=1X145=1X38=1X49=4D31=1X205=2X17=1X19=1X2=1X72=1X86=1X71=5I264=1X13=2X150=1X33=1X253=1X29=1X159=1X28=1X19=1X2=1X7=1X42=1X24=1X25=1D15=6I62=1X86=1X155=1X44=1X5=1X277=1X48=1X224=1X248=1X358=1X65=1X98=1X107=1X216=1X23=1X120=1X41=1X54=1D60=1X55=1X27=1X17=2D1=1X12=1X30=1X1=1X2=1X5=1D6=1X12=1X4=2D36=12I5=1X7=1X12=1X6=1X3=1X7=12I212=4D73=1X14=1X39=1X96=1X99=2X169=1X53=1X237=1X37=1X14=1X63=1X222=1X32=1X12=2X80=1X4=10I20=1X120=1X68=1X18=1X50=1X2=4D256=1X421=1X91=3I67=1X6=1X28=1X14=1X3=1X45=1X38=1X19=2D189=3D92=2X43=1X74=1X92=1X165=1X155=5D1X15=1X1=1X67=1X101=1X24=1X61=1X58=1I187=1X1=3D7=2X241=1X24=1X70=1X69=1X25=1X143=6I15=1X96=1X1=1X45=1X27=1X19=1X29=1X46=1X188=1X154=1X78=1X84=1I13=1X78=1X39=1X343=1X2=1X61=1X143=1X20=1X41=1X30=1X16=25I15=1X16=1X1=1X44=1X43=1X17=8I183=9D113=1X41=1X42=1X7=1X2=1X7=1X133=1X17=1X63=1X42=1X1=3I7X21=1X92=1X191=1X86=5I129=1X8=1X25=1I34=1X137=1X21=4D131=1X127=1X68=1X238=1X135=1X36=1X16=1X83=1X7=1I8=2X93=1X13=1X20=1X68=1D4=1X52=1X20=1X40=1X44=1X1=1X41=5I48=1X112=1X33=1X81=1X18=1X33=1X50=1X47=1X87=5I10=1X7=13I13=1X4=1X64=1X75=1X92=1X11=2X137=1X108=1X12=1D19=1X112=3D32=1X40=1X81=5I59=1X21=1X60=1I19=1X26=1X67=1X44=4D56=1X90=1X2=8D243=1X28=1X150=1X392=1X27=2D64=1X453=2D14=1X49=1X119=1X27=1I2=1X542=1X78=1I50=1X49=1X86=1X53=1X18=1X14=1X1=1X4=1X25=1X18=2I175=1X37=4D57=1X105=6D176=1X55=1X184=1X1=1X40=1X91=1X40=1X28=1X13=1X66=1X2=1X72=1X112=1X63=1X207=1X65=1X157=1X362=1X8=1X16=1X29=1X16=1X6=1X290=2X15=1X34=1X286=1X224=1X111=1X66=1X12=1X59=1X80=1X4=1I62=1X153=1X138=1X40=1X77=1X184=1X140=5D74=1X38=1X32=1X62=1X20=1X24=1X110=4D36=1X44=1X79=1X78=1X246=1X45=1X17=1X62=1X79=1X146=1X41=8I1=1X100=1X156=1X79=1X121=1X80=1X23=1X24=1X339=1X190=1X69=1X216=25I73=1X186=1X54=1X98=1X152=1X7=1X71=1X29=1X9=1X9=15D109=1X30=5D111=1X48=1X20=4I104=4I243=1X14=1X55=1X152=1X138=1X106=1I117=1X152=1X15=1X100=1X7=1X5=12D188=1X14=1I28=1X36=1X106=1X187=1X37=1X6=1X3=2X3=6I29=1X31=1X39=1X42=1X50=1X104=2X14=1X29=1X16=1X76=3X8=14I109=1X20=1X48=1X60=1X9=1X37=2X76=1X7=1X58=1X186=1X77=1X83=1X91=1X44=1X84=1X27=1X212=1X80=1X6=1X78=1X3=1X65=1X5=1I158=1X64=1X46=1X62=1X7=2D22=1X41=1X3=1X71=1X13=1X2=1X23=1X27=1X30=1X27=1X4=1X69=1I2=1X32=1D19=1X109=1X19=1X25=1X368=5I13=1X120=1X44=1X54=1X66=9I2=1X100=1X94=7D94=1X6=1X10=1X13=1X64=1X21=1X33=1X4=1X69=1X79=1X349=1X150=1X18=1X121=1X87=1X6=1X1=1X63=3D209=1I8=1X7=1X93=1X38=1X78=1X48=1X15=1D53=1X14=1X129=1X110=1X18=5I64=1X31=2X94=1X26=1X3=1X6=1X58=1X3=1X4=2X31=1X152=1X111=1X63=1X144=1X32=11D6=1X11=1X59=1X23=1D6=1X212=1X91=1X8=1X14=1X31=1X10=1X94=1X5=1X28=3D3=1X3=1X135=142D2=1X17=1I119=1X123=6D160=1X163=1X19=10I65=1X53=1X1040=1X98=1X38=1X253=1X233=1X17=1D13=11D9=1X63=1X23=1X21=1X306=1X7=1X9=1X1=1X57=1X13=1D95=1I1X55=1X220=1X35=1X277=1X52=2D2=1X44=1X13=3D257=1X4=1X72=1X117=1X162=1X37=1X130=1X5=1X45=1X182=25D80=1I41=5D45=1X49=1X103=1X75=1X6=1X88=1X99=1X76=1I2=1X8=1D7=2I2=1X4=2I186=1X147=1X75=1X44=1X56=1X80=1X22=1I51=1X28=1X4=2D24=2X70=2X4=1D4=1X36=1X36=1I122=1X12=1X31=1X36=1X66=2I155=1X241=3I24=1X359=1X96=1X72=1X467=1I168=8I143=1X27=1I412=1X219=1X134=1X424=1X225=1X486=1X258=1X2=1X50=1X88=1X125=1X70=4I1222=1X1342=1X554=1X22=1X34=1D570=1D64=1X119=1X213=1X1=1X20=1X66=1X22=1X905=1X25=1X221=3D518=1D86=1X1135=1X729=2D80=1X132=1X24=1I213=1X63=1X7=1X80=1X77=1X53=3D13=1X125=1X13=1X39=1X158=1X16=1X15=1X53=3D5=2X37=1X51=1X57=1X11=1X10=3D210=2X396=1X227=1X102=1X6=1X166=1X110=1X19=1X51=2X16=1X134=1X132=1X46=1X197=1X194=1X60=3I193=1X130=2X60=1X110=1X9=1X56=1X18=1X167=1X62=1X11=3D52=1X8=1X39=1X29=1X125=1X27=1X43=1X65=1X9=1X213=2I53=1X12=2D116=1X62=1X32=1X213=1X43=1X98=1X35=1D57=1X122=1X75=1X45=2X21=2I12=1X2=1X18=1X54=1X19=1X35=1X17=1X48=1X13=1X4=3D31=1X8=1X75=1X17=1X200=1X11=1X9=1X83=1X70=1D92=1X14=1X31=1X28=1X86=1X154=1X3=1X30=1X22=1X130=1X13=1X1=1I129=1X12=2X130=1X13=1X9=1X8=1X11=1X63=5D7=1X261=1X290=1X9=1X1=1X173=7D30=1X10=1X121=1X58=1X42=7I9=3X25=1X24=1X100=1X27=1X30=3I171=2I52=1X31=1X155=1X16=1X18=1X39=2X4=1X637=1X5=1X60=1X49=4I40=1X11=1X204=1X30=1X98=1X8=1X43=1X151=1D141=1X14=1X95=1X14=1X83=1X647=1X69=1X53=1X285=1X418=1I29=1X181=1X41=1X44=1X89=1X104=1X525=1X78=1X180=5I159=1X2=1X5=621D14=1X8=1X30=1X2=1X5=2X112=1I191=1X287=1X46=6D88=1X3=1X107=1X54=1X872=1X461=1X1521=1X666=1X226=1X89=1X66=1X211=1X4=1X1290=1X299=1I158=1X39=1X197=1X113=22D79=1X18=15I48=1X78=1X157=16D3=2D18=1X124=4I11=1X408=1X265=2D120=1X18=1X18=1X49=1X156=1X115=1X6=1X4=1X55=1X12=1D103=1X2=2I41=1X235=1X7=1X106=1X111=1X3=1X112=1X7=1X169=10I1=1X99=1X140=1X5=1X100=1X3=1X579=6D90=1X41=22D77=1X98=1X2=1X61=1X69=1I249=1X34=1X1=1X17=1X94=2D8=1X118=1X29=1X133=2X341=1X28=2D248=1X25=1X106=1X67=1X115=1X133=1X41=1X135=1X444=1X153=3D53=1X104=4I2=1X15=1X331=1D176=2I202=1X47=1X27=2X41=1X9=1D114=1X60=14I8=1X28=2I20=2D147=1X153=1X205=1X40=1X40=1X16=5D154=1X49=3D13=1X581=1X612=4I49=1X1=28I263=2D50=1X57=1X38=1X327=1X65=1X515=1X98=1X3=4D126=1X18=1X81=1X10=1I88=1X156=1X30=1X82=1X4=1X86=1D271=1X53=1X38=1X67=1X11=4D115=1X59=1X2=1X175=1X195=1X107=1X90=1X166=1I86=1X154=1X411=1X136=1X33=1X75=1X114=1X110=1X413=1X58=1X335=1X266=1X88=6I32=1X1521=1X701=1X186=9D257=1X154=1X106=1X41=1I387=1X79=1X91=2D2007=12D226=1X58=1X262=1X1585=1X63=1X264=1X301=1X180=1X106=1X558=1X178=1X44=3D84=1X25=1X20=1X8=1X212=2X148=1I88=1X168=1X8=1X535=2I51=3D1X421=1X124=1X1=1X32=1X94=1X110=3D33=1X12=1X17=1X291=1X433=1X1596=1X111=1X212=1X122=1X55=1D81=1X326=1X137=1X261=1I131="
GenomicAlignments::cigarNarrow(cigar = cg, start = 8703, end = 124563)[1]
*** caught segfault ***
address 0x7f879f4ed000, cause 'invalid permissions'
Traceback:
1: .Call2("cigar_narrow", cigar, width(threeranges$left), width(threeranges$right), PACKAGE = "GenomicAlignments")
2: GenomicAlignments::cigarNarrow(cigar = paf.aln$cg, start = 8703, end = 124563)
Possible actions:
1: abort (with core dump, if enabled)
2: normal R exit
3: exit R without saving workspace
4: exit R saving workspace
Selection:
R version 4.1.1 (2021-08-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 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=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
loaded via a namespace (and not attached):
[1] rstudioapi_0.13 XVector_0.34.0 GenomicRanges_1.46.1 BiocGenerics_0.40.0
[5] zlibbioc_1.40.0 GenomicAlignments_1.32.0 IRanges_2.28.0 BiocParallel_1.28.3
[9] lattice_0.20-45 GenomeInfoDb_1.30.1 tools_4.1.1 SummarizedExperiment_1.24.0
[13] parallel_4.1.1 grid_4.1.1 Biobase_2.54.0 matrixStats_0.62.0
[17] crayon_1.5.1 Matrix_1.3-4 GenomeInfoDbData_1.2.7 S4Vectors_0.32.4
[21] bitops_1.0-7 RCurl_1.98-1.7 DelayedArray_0.20.0 compiler_4.1.1
[25] MatrixGenerics_1.6.0 Biostrings_2.62.0 Rsamtools_2.10.0 stats4_4.1.1
hi there,
I am getting a core dump trying to use readGAlignmentPairs to read in a bam file (actually a set of bam files). I can use readGAlignments on the same bam file without any trouble.
I get a similar issue whether I'm running R on a node of our linux cluster or on my mac. On the linux cluster it seems to happen every time I try to read the file, and on the mac it's a bit more hit and miss - sometimes it works fine, but repeating the same command a few seconds later causes R to crash. Weird.
Some code is below. I think I'm using the latest release versions of everything. I'm happy to upload a bam file somewhere if that's useful.
thanks!
Janet
library(GenomicAlignments)
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 14.04.5 LTS
Matrix products: default
BLAS/LAPACK: /app/easybuild/software/OpenBLAS/0.2.18-GCC-5.4.0-2.26-LAPACK-3.6.1/lib/libopenblas_prescottp-r0.2.18.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 parallel stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] GenomicAlignments_1.22.1 Rsamtools_2.2.1
[3] Biostrings_2.54.0 XVector_0.26.0
[5] SummarizedExperiment_1.16.1 DelayedArray_0.12.2
[7] BiocParallel_1.20.1 matrixStats_0.55.0
[9] Biobase_2.46.0 GenomicRanges_1.38.0
[11] GenomeInfoDb_1.22.0 IRanges_2.20.2
[13] S4Vectors_0.24.3 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] lattice_0.20-38 bitops_1.0-6 grid_3.6.2
[4] zlibbioc_1.32.0 Matrix_1.2-18 tools_3.6.2
[7] RCurl_1.95-4.12 compiler_3.6.2 GenomeInfoDbData_1.2.2
temp1 <- readGAlignments("mapToCombinedFlyYeastHumanGenomes_ATfiltReads/just_dm6_reads/zz_testR/Nnk_chip_rep3.ATfilt.combined.dm6.chr4.bam")
temp1
# GAlignments object with 421653 alignments and 0 metadata columns:
# seqnames strand cigar qwidth start end width
# <Rle> <Rle> <character> <integer> <integer> <integer> <integer>
# [1] chr4 - 151M 151 7 157 151
# [2] chr4 + 54M97H 54 24 77 54
## etc
temp2 <- readGAlignmentPairs("mapToCombinedFlyYeastHumanGenomes_ATfiltReads/just_dm6_reads/zz_testR/Nnk_chip_rep3.ATfilt.combined.dm6.chr4.bam")
## Floating point exception (core dumped)
library(GenomicAlignments)
sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-apple-darwin15.6.0 (64-bit)
Running under: macOS Mojave 10.14.6
Matrix products: default
BLAS: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.0.dylib
LAPACK: /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
locale:
[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 parallel stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicAlignments_1.22.1 Rsamtools_2.2.1 Biostrings_2.54.0
[4] XVector_0.26.0 SummarizedExperiment_1.16.1 DelayedArray_0.12.2
[7] BiocParallel_1.20.1 matrixStats_0.55.0 Biobase_2.46.0
[10] GenomicRanges_1.38.0 GenomeInfoDb_1.22.0 IRanges_2.20.2
[13] S4Vectors_0.24.3 BiocGenerics_0.32.0
loaded via a namespace (and not attached):
[1] lattice_0.20-38 bitops_1.0-6 grid_3.6.2 zlibbioc_1.32.0
[5] Matrix_1.2-18 tools_3.6.2 RCurl_1.95-4.13 compiler_3.6.2
[9] GenomeInfoDbData_1.2.2
temp1 <- readGAlignments("Desktop/test/again/Nnk_chip_rep3.ATfilt.combined.dm6.chr4.bam")
temp2 <- readGAlignmentPairs("Desktop/test/again/Nnk_chip_rep3.ATfilt.combined.dm6.chr4.bam")
# worked right after I copied the file into this location.
# BUT after R crashes and I restart it and try it again, it does NOT work
# the the issue is sporadic - sometimes it works, sometimes it crashes R
here's the crazy long R-crash message my mac shows (it's a lot more verbose than the linux crash was....)
Process: R [5060]
Path: /Applications/R.app/Contents/MacOS/R
Identifier: org.R-project.R
Version: R 3.6.2 GUI 1.70 El Capitan build (7735)
Code Type: X86-64 (Native)
Parent Process: ??? [1]
Responsible: R [5060]
User ID: 504
Date/Time: 2020-01-29 17:54:41.837 -0800
OS Version: Mac OS X 10.14.6 (18G2022)
Report Version: 12
Anonymous UUID: C98D92BF-E276-1288-F466-4F0DA6071B06
Time Awake Since Boot: 21000 seconds
System Integrity Protection: enabled
Crashed Thread: 0 Dispatch queue: com.apple.main-thread
Exception Type: EXC_ARITHMETIC (SIGFPE)
Exception Codes: EXC_I386_DIV (divide by zero)
Exception Note: EXC_CORPSE_NOTIFY
Termination Signal: Floating point exception: 8
Termination Reason: Namespace SIGNAL, Code 0x8
Terminating Process: exc handler [5060]
Thread 0 Crashed:: Dispatch queue: com.apple.main-thread
0 Rsamtools.so 0x000000010c6c5ea3 Template::is_mate(bam1_t const*, bam1_t const*, unsigned int const*) const + 51
1 Rsamtools.so 0x000000010c6c5b59 Template::mate(std::__1::queue<std::__1::list<bam1_t const*, std::__1::allocator<bam1_t const*> >, std::__1::deque<std::__1::list<bam1_t const*, std::__1::allocator<bam1_t const*> >, std::__1::allocator<std::__1::list<bam1_t const*, std::__1::allocator<bam1_t const*> > > > >&, unsigned int const*) + 441
2 Rsamtools.so 0x000000010c6c55e8 BamIterator::mate_touched_templates() + 168
3 Rsamtools.so 0x000000010c6c71b4 BamFileIterator::iterate_inprogress(BGZF*) + 164
4 Rsamtools.so 0x000000010c6c1f6a BamIterator::yield(BGZF*, bam_mates_t*) + 90
5 Rsamtools.so 0x000000010c6c2763 samread_mate + 147
6 Rsamtools.so 0x000000010c6d949b _do_scan_bam + 619
7 Rsamtools.so 0x000000010c6d9a18 _scan_bam + 360
8 libR.dylib 0x00000001042a7f54 R_doDotCall + 2996
9 libR.dylib 0x00000001042a95f3 do_dotcall + 323 (dotcode.c:1252)
10 libR.dylib 0x00000001042dfc61 bcEval + 27617 (eval.c:6721)
11 libR.dylib 0x00000001042d894d Rf_eval + 445
12 libR.dylib 0x00000001042f58c3 forcePromise + 179 (eval.c:516)
13 libR.dylib 0x000000010430014c getvar + 828
14 libR.dylib 0x00000001042dcef4 bcEval + 15988 (eval.c:6517)
15 libR.dylib 0x00000001042d894d Rf_eval + 445
16 libR.dylib 0x00000001042f58c3 forcePromise + 179 (eval.c:516)
17 libR.dylib 0x000000010430014c getvar + 828
18 libR.dylib 0x00000001042dcef4 bcEval + 15988 (eval.c:6517)
19 libR.dylib 0x00000001042d894d Rf_eval + 445
20 libR.dylib 0x00000001042f58c3 forcePromise + 179 (eval.c:516)
21 libR.dylib 0x000000010430014c getvar + 828
22 libR.dylib 0x00000001042dcef4 bcEval + 15988 (eval.c:6517)
23 libR.dylib 0x00000001042d894d Rf_eval + 445
24 libR.dylib 0x00000001042f58c3 forcePromise + 179 (eval.c:516)
25 libR.dylib 0x000000010430014c getvar + 828
26 libR.dylib 0x00000001042dcef4 bcEval + 15988 (eval.c:6517)
27 libR.dylib 0x00000001042d894d Rf_eval + 445
28 libR.dylib 0x00000001042f7209 R_execClosure + 2153
29 libR.dylib 0x00000001042f610a Rf_applyClosure + 346 (eval.c:1716)
30 libR.dylib 0x00000001042dfd71 bcEval + 27889 (eval.c:6740)
31 libR.dylib 0x00000001042d894d Rf_eval + 445
32 libR.dylib 0x00000001042f7209 R_execClosure + 2153
33 libR.dylib 0x00000001042f610a Rf_applyClosure + 346 (eval.c:1716)
34 libR.dylib 0x00000001042dfd71 bcEval + 27889 (eval.c:6740)
35 libR.dylib 0x00000001042d894d Rf_eval + 445
36 libR.dylib 0x00000001042f7209 R_execClosure + 2153
37 libR.dylib 0x00000001042f610a Rf_applyClosure + 346 (eval.c:1716)
38 libR.dylib 0x00000001042dfd71 bcEval + 27889 (eval.c:6740)
39 libR.dylib 0x00000001042d894d Rf_eval + 445
40 libR.dylib 0x00000001042f7209 R_execClosure + 2153
41 libR.dylib 0x00000001042f610a Rf_applyClosure + 346 (eval.c:1716)
42 libR.dylib 0x00000001042dfd71 bcEval + 27889 (eval.c:6740)
43 libR.dylib 0x00000001042d894d Rf_eval + 445
44 libR.dylib 0x00000001042f7209 R_execClosure + 2153
45 libR.dylib 0x00000001042f610a Rf_applyClosure + 346 (eval.c:1716)
46 libR.dylib 0x00000001042dfd71 bcEval + 27889 (eval.c:6740)
47 libR.dylib 0x00000001042d894d Rf_eval + 445
48 libR.dylib 0x00000001042f7209 R_execClosure + 2153
49 libR.dylib 0x00000001042f7f43 R_execMethod + 611 (eval.c:1954)
50 methods.so 0x000000010fb698e7 R_dispatchGeneric + 2455
51 libR.dylib 0x000000010433dec3 do_standardGeneric + 675 (objects.c:1287)
52 libR.dylib 0x00000001042dfc61 bcEval + 27617 (eval.c:6721)
53 libR.dylib 0x00000001042d894d Rf_eval + 445
54 libR.dylib 0x00000001042f7209 R_execClosure + 2153
55 libR.dylib 0x00000001042f610a Rf_applyClosure + 346 (eval.c:1716)
56 libR.dylib 0x00000001042dfd71 bcEval + 27889 (eval.c:6740)
57 libR.dylib 0x00000001042d894d Rf_eval + 445
58 libR.dylib 0x00000001042f7209 R_execClosure + 2153
59 libR.dylib 0x00000001042f610a Rf_applyClosure + 346 (eval.c:1716)
60 libR.dylib 0x00000001042dfd71 bcEval + 27889 (eval.c:6740)
61 libR.dylib 0x00000001042d894d Rf_eval + 445
62 libR.dylib 0x00000001042f7209 R_execClosure + 2153
63 libR.dylib 0x00000001042f7f43 R_execMethod + 611 (eval.c:1954)
64 methods.so 0x000000010fb698e7 R_dispatchGeneric + 2455
65 libR.dylib 0x000000010433dec3 do_standardGeneric + 675 (objects.c:1287)
66 libR.dylib 0x00000001042dfc61 bcEval + 27617 (eval.c:6721)
67 libR.dylib 0x00000001042d894d Rf_eval + 445
68 libR.dylib 0x00000001042f7209 R_execClosure + 2153
69 libR.dylib 0x00000001042f610a Rf_applyClosure + 346 (eval.c:1716)
70 libR.dylib 0x00000001042dfd71 bcEval + 27889 (eval.c:6740)
71 libR.dylib 0x00000001042d894d Rf_eval + 445
72 libR.dylib 0x00000001042f7209 R_execClosure + 2153
73 libR.dylib 0x00000001042f7f43 R_execMethod + 611 (eval.c:1954)
74 methods.so 0x000000010fb698e7 R_dispatchGeneric + 2455
75 libR.dylib 0x000000010433dec3 do_standardGeneric + 675 (objects.c:1287)
76 libR.dylib 0x00000001042dfc61 bcEval + 27617 (eval.c:6721)
77 libR.dylib 0x00000001042d894d Rf_eval + 445
78 libR.dylib 0x00000001042f7209 R_execClosure + 2153
79 libR.dylib 0x00000001042f610a Rf_applyClosure + 346 (eval.c:1716)
80 libR.dylib 0x00000001042dfd71 bcEval + 27889 (eval.c:6740)
81 libR.dylib 0x00000001042d894d Rf_eval + 445
82 libR.dylib 0x00000001042f7209 R_execClosure + 2153
83 libR.dylib 0x00000001042f7f43 R_execMethod + 611 (eval.c:1954)
84 methods.so 0x000000010fb698e7 R_dispatchGeneric + 2455
85 libR.dylib 0x000000010433dec3 do_standardGeneric + 675 (objects.c:1287)
86 libR.dylib 0x00000001042dfc61 bcEval + 27617 (eval.c:6721)
87 libR.dylib 0x00000001042d894d Rf_eval + 445
88 libR.dylib 0x00000001042f7209 R_execClosure + 2153
89 libR.dylib 0x00000001042f610a Rf_applyClosure + 346 (eval.c:1716)
90 libR.dylib 0x00000001042d8e7d Rf_eval + 1773 (eval.c:743)
91 libR.dylib 0x00000001042fa41d do_set + 2125 (eval.c:2807)
92 libR.dylib 0x00000001042d8b40 Rf_eval + 944 (eval.c:695)
93 libR.dylib 0x0000000104329641 R_ReplDLLdo1 + 449 (main.c:393)
94 org.R-project.R 0x0000000103e09ddf run_REngineRmainloop + 287
95 org.R-project.R 0x0000000103dfde31 -[REngine runREPL] + 225
96 org.R-project.R 0x0000000103decba1 main + 817
97 libdyld.dylib 0x00007fff594d23d5 start + 1
Thread 1:
0 libsystem_pthread.dylib 0x00007fff596c53f0 start_wqthread + 0
Thread 2:: JavaScriptCore bmalloc scavenger
0 libsystem_kernel.dylib 0x00007fff5960a866 __psynch_cvwait + 10
1 libsystem_pthread.dylib 0x00007fff596c956e _pthread_cond_wait + 722
2 libc++.1.dylib 0x00007fff56703a0a std::__1::condition_variable::wait(std::__1::unique_lock<std::__1::mutex>&) + 18
3 com.apple.JavaScriptCore 0x00007fff30a2cc42 void std::__1::condition_variable_any::wait<std::__1::unique_lock<bmalloc::Mutex> >(std::__1::unique_lock<bmalloc::Mutex>&) + 82
4 com.apple.JavaScriptCore 0x00007fff30a30d4b bmalloc::Scavenger::threadRunLoop() + 139
5 com.apple.JavaScriptCore 0x00007fff30a30579 bmalloc::Scavenger::threadEntryPoint(bmalloc::Scavenger*) + 9
6 com.apple.JavaScriptCore 0x00007fff30a31ee7 void* std::__1::__thread_proxy<std::__1::tuple<std::__1::unique_ptr<std::__1::__thread_struct, std::__1::default_delete<std::__1::__thread_struct> >, void (*)(bmalloc::Scavenger*), bmalloc::Scavenger*> >(void*) + 39
7 libsystem_pthread.dylib 0x00007fff596c62eb _pthread_body + 126
8 libsystem_pthread.dylib 0x00007fff596c9249 _pthread_start + 66
9 libsystem_pthread.dylib 0x00007fff596c540d thread_start + 13
Thread 3:
0 libsystem_kernel.dylib 0x00007fff5960e616 __select + 10
1 org.R-project.R 0x0000000103def867 -[RController readThread:] + 647
2 com.apple.Foundation 0x00007fff2f7a60e2 __NSThread__start__ + 1194
3 libsystem_pthread.dylib 0x00007fff596c62eb _pthread_body + 126
4 libsystem_pthread.dylib 0x00007fff596c9249 _pthread_start + 66
5 libsystem_pthread.dylib 0x00007fff596c540d thread_start + 13
Thread 4:: com.apple.NSEventThread
0 libsystem_kernel.dylib 0x00007fff5960721a mach_msg_trap + 10
1 libsystem_kernel.dylib 0x00007fff59607768 mach_msg + 60
2 com.apple.CoreFoundation 0x00007fff2d54b99e __CFRunLoopServiceMachPort + 328
3 com.apple.CoreFoundation 0x00007fff2d54af0c __CFRunLoopRun + 1612
4 com.apple.CoreFoundation 0x00007fff2d54a66e CFRunLoopRunSpecific + 455
5 com.apple.AppKit 0x00007fff2ab484a2 _NSEventThread + 175
6 libsystem_pthread.dylib 0x00007fff596c62eb _pthread_body + 126
7 libsystem_pthread.dylib 0x00007fff596c9249 _pthread_start + 66
8 libsystem_pthread.dylib 0x00007fff596c540d thread_start + 13
Thread 5:
0 libsystem_pthread.dylib 0x00007fff596c53f0 start_wqthread + 0
Thread 6:
0 libsystem_pthread.dylib 0x00007fff596c53f0 start_wqthread + 0
Thread 0 crashed with X86 Thread State (64-bit):
rax: 0x0000000003541387 rbx: 0x0000000000000004 rcx: 0x00006000022ec580 rdx: 0x0000000000000000
rdi: 0x0000600003724600 rsi: 0x000060000371b800 rbp: 0x00007ffeebe053c0 rsp: 0x00007ffeebe053a0
r8: 0x000000000004fe5a r9: 0x0000000003541387 r10: 0x00000000000034d0 r11: 0xffffffffffffffff
r12: 0x0000000000000081 r13: 0x0000000000000001 r14: 0x000060000220f000 r15: 0x0000000000000851
rip: 0x000000010c6c5ea3 rfl: 0x0000000000010246 cr2: 0x000000012fcd3000
Logical CPU: 0
Error Code: 0x00000000
Trap Number: 0
Binary Images:
0x103deb000 - 0x103e77ff3 +org.R-project.R (R 3.6.2 GUI 1.70 El Capitan build - 7735) <095FA1C7-116A-3F07-BE3E-8AC323BABCAD> /Applications/R.app/Contents/MacOS/R
0x103ef7000 - 0x103f21ff7 +libRblas.dylib (0) <CEB0747F-EC57-3430-A81F-E229A6C8B7BC> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRblas.dylib
0x103f26000 - 0x104045fff +libgfortran.3.dylib (0) <53830B74-39EA-3EA7-8673-3CC9F041F6B7> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgfortran.3.dylib
0x1040b1000 - 0x1040e8fe7 +libquadmath.0.dylib (0) <F6B458A7-8193-3831-B86E-DD832A5A19BE> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libquadmath.0.dylib
0x1040f7000 - 0x104121fd9 +libreadline.5.2.dylib (5.2) /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libreadline.5.2.dylib
0x104135000 - 0x10414afef +libgcc_s.1.dylib (0) <20CA2D94-AB72-312A-ADD8-7912FE2574A0> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libgcc_s.1.dylib
0x104159000 - 0x1041c370f dyld (655.1.1) <B3D9DDCB-5AA7-3674-9608-16B5AA4AA494> /usr/lib/dyld
0x104224000 - 0x1044eefff +libR.dylib (0) <7E5EB822-A174-35A9-B626-8AAEAE85C797> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libR.dylib
0x1046ae000 - 0x104716fff +libomp.dylib (0) <5F2A02FB-2D20-3D6C-BEEE-40CA5EE3618C> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libomp.dylib
0x10619e000 - 0x1061a6ff3 +utils.so (0) <F4773C49-D219-3C39-B2E8-91DE6A437805> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/utils/libs/utils.so
0x1069de000 - 0x1069e1047 libobjc-trampolines.dylib (756.2) <5795A048-3940-3801-90CE-33D1B1AF81F4> /usr/lib/libobjc-trampolines.dylib
0x107dd3000 - 0x107dd5ff3 +bitops.so (0) <97B61BB0-6CB3-3045-BAAD-117408467B9A> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/bitops/libs/bitops.so
0x107dd8000 - 0x107ddaff3 +lattice.so (0) <AF1D8EBC-EFCF-3431-B915-A8AD02714353> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/lattice/libs/lattice.so
0x10b03d000 - 0x10b041ffb +Biobase.so (0) <910F69B3-87FE-3955-80D2-BC2D481EB269> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biobase/libs/Biobase.so
0x10b045000 - 0x10b049ff7 +DelayedArray.so (0) <F658D4FF-F3B5-3A4D-B369-77B2FE942FF3> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/DelayedArray/libs/DelayedArray.so
0x10b2b7000 - 0x10b2c5fff +BiocParallel.so (0) <BF940EEC-4FF0-3422-B117-9404AA6DF653> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/BiocParallel/libs/BiocParallel.so
0x10b47c000 - 0x10b485ffb +RCurl.so (0) <A34226CB-90EC-3BD9-85B3-150AC5163FE4> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/RCurl/libs/RCurl.so
0x10b728000 - 0x10b761ff7 +graphics.so (0) <0AA83284-0B38-3F36-AFA5-5D52AA5F7787> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/graphics/libs/graphics.so
0x10b811000 - 0x10b81bffb +lapack.so (0) <FD42543E-FAED-384E-9238-143E5D5C3919> /Library/Frameworks/R.framework/Resources/modules/lapack.so
0x10b822000 - 0x10b856ff3 +grDevices.so (0) <D7F27905-D7DD-3BA0-989F-E30012633D9C> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/grDevices/libs/grDevices.so
0x10b8c1000 - 0x10b96bfff +stats.so (0) <0B71BE67-63E5-3F29-B3AD-8B151500979C> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/stats/libs/stats.so
0x10c38b000 - 0x10c39cffb +tools.so (0) <4E4A55A5-B974-3FFA-961C-F1AB71811219> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/tools/libs/tools.so
0x10c6b3000 - 0x10c763fff +Rsamtools.so (0) <8F52EFE1-9EB1-3D3A-A0CA-A83B73E70EA2> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Rsamtools/libs/Rsamtools.so
0x10caeb000 - 0x10caf4fff +GenomicAlignments.so (0) <C038A525-7CAB-30F4-9FD2-6155CEFFD097> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/GenomicAlignments/libs/GenomicAlignments.so
0x10fb67000 - 0x10fb6cfff +methods.so (0) <01339C07-2C9C-38B2-B3A2-FDD55B73CC56> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/methods/libs/methods.so
0x10fd25000 - 0x10fd29ff3 +parallel.so (0) <CA7EE20B-9E6A-3667-9B5F-D6EE12077089> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/parallel/libs/parallel.so
0x10fd69000 - 0x10fd7cfff +IRanges.so (0) <26D70259-7288-3C38-B7BB-4B9DA415B200> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/IRanges/libs/IRanges.so
0x10ff1e000 - 0x11011ffff +libRlapack.dylib (0) <61C208F7-2A76-35AC-97F1-B3F0CB57057A> /Library/Frameworks/R.framework/Versions/3.6/Resources/lib/libRlapack.dylib
0x110193000 - 0x1101a4fff +XVector.so (0) <FA6186D7-E6FA-39F3-91CA-F06DBDA249F7> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/XVector/libs/XVector.so
0x11045b000 - 0x110460ff7 +GenomicRanges.so (0) <7BBF99F9-59DA-37B8-B3FC-B83F5CE534D2> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/GenomicRanges/libs/GenomicRanges.so
0x1105e2000 - 0x1105fcffb +grid.so (0) <E4EB1B95-5E8B-353F-B543-E8F00F5CE425> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/grid/libs/grid.so
0x112a24000 - 0x112a40ff7 +S4Vectors.so (0) <D0A6522A-F114-36C0-A491-50B95D98385D> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/S4Vectors/libs/S4Vectors.so
0x1132cc000 - 0x1134e4fff +matrixStats.so (0) <407BC54B-A660-3E8A-A4BD-1729EF91C9A5> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/matrixStats/libs/matrixStats.so
0x113864000 - 0x113925ffb +Matrix.so (0) <2E7B3643-1BE7-3746-806A-F2738620947A> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Matrix/libs/Matrix.so
0x11d689000 - 0x11d6aeff7 +Biostrings.so (0) <C18502AB-FE8C-3544-9A3E-5DDFD8FC0AEC> /Library/Frameworks/R.framework/Versions/3.6/Resources/library/Biostrings/libs/Biostrings.so
0x7fff21c73000 - 0x7fff21fccfff com.apple.RawCamera.bundle (8.15.0 - 1031.4.4) <AB6E8A8F-0BFE-37EE-A135-44ABA4FCB559> /System/Library/CoreServices/RawCamera.bundle/Contents/MacOS/RawCamera
0x7fff21fcf000 - 0x7fff220dbfff com.apple.AMDMTLBronzeDriver (2.11.21 - 2.1.1) <D0034ABB-2AD7-3227-B34C-5038871E4D98> /System/Library/Extensions/AMDMTLBronzeDriver.bundle/Contents/MacOS/AMDMTLBronzeDriver
0x7fff29548000 - 0x7fff29724ffb com.apple.avfoundation (2.0 - 1550.4) <5854207B-6106-3DA4-80B6-36C42D042F26> /System/Library/Frameworks/AVFoundation.framework/Versions/A/AVFoundation
0x7fff29725000 - 0x7fff297eafff com.apple.audio.AVFAudio (1.0 - ???) <D454A339-2FC6-3EF6-992F-D676046612DB> /System/Library/Frameworks/AVFoundation.framework/Versions/A/Frameworks/AVFAudio.framework/Versions/A/AVFAudio
0x7fff298f2000 - 0x7fff298f2fff com.apple.Accelerate (1.11 - Accelerate 1.11) <762942CB-CFC9-3A0C-9645-A56523A06426> /System/Library/Frameworks/Accelerate.framework/Versions/A/Accelerate
0x7fff298f3000 - 0x7fff29909ff7 libCGInterfaces.dylib (506.22) <1B6C92D9-F4B8-37BA-9635-94C4A56098CE> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/Libraries/libCGInterfaces.dylib
0x7fff2990a000 - 0x7fff29fa3fef com.apple.vImage (8.1 - ???) <53FA3611-894E-3158-A654-FBD2F70998FE> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vImage.framework/Versions/A/vImage
0x7fff29fa4000 - 0x7fff2a21dff3 libBLAS.dylib (1243.200.4) <417CA0FC-B6CB-3FB3-ACBC-8914E3F62D20> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib
0x7fff2a21e000 - 0x7fff2a290ffb libBNNS.dylib (38.250.1) <538D12A2-9B9D-3E22-9896-F90F6E69C06E> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBNNS.dylib
0x7fff2a291000 - 0x7fff2a63aff3 libLAPACK.dylib (1243.200.4) <92175DF4-863A-3780-909A-A3E5C410F2E9> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLAPACK.dylib
0x7fff2a63b000 - 0x7fff2a650feb libLinearAlgebra.dylib (1243.200.4) <CB671EE6-DEA1-391C-9B2B-AA09A46B4D7A> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libLinearAlgebra.dylib
0x7fff2a651000 - 0x7fff2a656ff3 libQuadrature.dylib (3.200.2) <1BAE7E22-2862-379F-B334-A3756067730F> /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libQuadrature.dylib
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Hi, I trid to install the package and met an error. My OS is Red Hat and GCC vresion is 8.3.0 and the package version is GenomicAlignments_1.10.1. I can't install the new version because of the limit of Rsamtools vresion could you help me fix this problem ? Thank you very much .
encodeOverlaps_methods.c: In function 'CharAE_append_int':
encodeOverlaps_methods.c:49:2: warning: implicit declaration of function 'append_string_to_CharAE' [-Wimplicit-function-declaration]
append_string_to_CharAE(char_ae, buf);
^~~~~~~~~~~~~~~~~~~~~~~
gcc -std=gnu99 -shared -fPIC -L/ds3512/home/panyp/ruanjian/packages/lib -o GenomicAlignments.so IRanges_stubs.o R_init_GenomicAlignments.o S4Vectors_stubs.o cigar_utils.o coordinate_mapping_methods.o encodeOverlaps_methods.o
installing to /ds3512/home/panyp/ruanjian/R-4.0.3/lib64/R/library/00LOCK-GenomicAlignments/00new/GenomicAlignments/libs
** R
** inst
** byte-compile and prepare package for lazy loading
Warning: undefined slot classes in definition of "GAlignments": NAMES(class "characterORNULL")
Error in rematchDefinition(definition, fdef, mnames, fnames, signature) :
methods can add arguments to the generic 'seqinfo<-' only if '...' is an argument to the generic
Error: unable to load R code in package 'GenomicAlignments'
Execution halted
ERROR: lazy loading failed for package 'GenomicAlignments'
I have developed a package that uses GenomicAlignments and I am trying to submit my package to cran. However, the tests on r-devel-windows-ix86+x86_64 are failing with a backtrace that points to GenomicAlignments::readGAlignments. Can you please help?
My package:
https://github.com/alkodsi/ctDNAtools
The error:
test_check("ctDNAtools")
-- 1. Error: (unknown) (@test-ctDNAtest.R#13) ---------------------------------
trying to get slot "className" from an object of a basic class ("character") with no slots
Backtrace:
1. ctDNAtools::test_ctDNA(...)
2. ctDNAtools::get_mutations_read_names(...)
3. purrr::pmap(...)
4. ctDNAtools:::.f(...)
5. ctDNAtools:::get_mutation_read_names(...)
6. GenomicAlignments::stackStringsFromBam(...)
8. GenomicAlignments::readGAlignments(...)
10. GenomicAlignments::readGAlignments(...)
11. GenomicAlignments:::.bindExtraData(...)
15. methods::is(listData[[1L]], getClass("Annotated"))
I'm contemplating switching over csaw to use GenomicAlignments for BAM file access, rather than continuing to wrestle with Rhtslib and its poor documentation/unreliability on Windows.
I've been looking at the readGAlignments and readGAlignmentPairs functions, which should be swap-in replacements for my main internal BAM reading functions (see LTLA/csaw#4). Currently, csaw runs on sorted BAM files on a chromosome-by-chromosome basis, so I would be calling these functions with which= set to an interval spanning the current chromosome in each iteration.
However, I am concerned about the performance implications of readGAlignmentPairs's obligations to retrieve mates from other chromosomes. Even with indexing, this would seem to require a lot of additional file accesses that would be unnecessary for my use case.
Would it be worthwhile to add an option to ignore paired reads that are not on the same reference sequence? Alternatively, this could feasibly be part of an expanded suite of scanBamParam options based on the INSisize field, e.g., keeping only non-zero INSisize values.
Is there a schedule for the implementation of those functions?
queryLocs2refLocs()
queryLoc2refLoc()
I saw a forum post from 4 years ago with the same question.
Do you take pull requests for this?
Best, Caspar
This example produces a count of 1 which I expected it to, but others might expect a count of zero, because the read spans the query coordinates and none of its matching bases fall within the query. I suppose that the query is typically much bigger (e.g. transcript) than the subject (e.g. read) unlike the example below (e.g. short variant).
GA <- GAlignments(seqnames=Rle("chr1"), pos=1L, cigar="50M10D50M", strand=Rle(factor('+', levels = c('+', '-', '*'))))
countOverlaps(GRanges("chr1", IRanges(51, 60)), GA)Is there somewhere in the vignette that could provide a clarifying explanation in time for the next version?
When I used the software minimap2 to compare the bam files obtained by comparing ont data, I found a problem when I used this package to read the bam files. My main purpose was to obtain each read of the compared bam files. Start and stop site information in the reference genome.
There is a 'cigar_buf' overflow ERROR when trying to subset a fairly large cigar string using GenomicAlignments::cigarNarrow function.
library(GenomicAlignments)
cg <- read.table(file = '<test.cigar.txt>')
cg <- as.character(cg)
matches <- sum(GenomicAlignments::explodeCigarOpLengths(cigar = cg, ops = c('=','M'))[[1]])
GenomicAlignments::cigarNarrow(cigar = cg, start = 1, end = matches)
GenomicAlignments::cigarNarrow(cigar = cg, start = 1, end = 1000000)[[1]]
sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.3 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=en_US.UTF-8 LC_COLLATE=en_US.UTF-8
[5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8 LC_PAPER=en_US.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] stats4 stats graphics grDevices utils datasets methods base
other attached packages:
[1] GenomicAlignments_1.34.0 Rsamtools_2.14.0 Biostrings_2.66.0 XVector_0.38.0
[5] SummarizedExperiment_1.28.0 Biobase_2.58.0 MatrixGenerics_1.10.0 matrixStats_0.63.0
[9] ggbio_1.46.0 ggplot2_3.4.0 GenomicRanges_1.50.2 GenomeInfoDb_1.34.4
[13] IRanges_2.32.0 S4Vectors_0.36.1 BiocGenerics_0.44.0 SVbyEye_0.0.0.9000
loaded via a namespace (and not attached):
[1] backports_1.4.1 Hmisc_4.7-2 BiocFileCache_2.6.0 plyr_1.8.8
[5] lazyeval_0.2.2 splines_4.2.1 BiocParallel_1.32.4 usethis_2.1.6
[9] digest_0.6.31 ensembldb_2.22.0 htmltools_0.5.4 wesanderson_0.3.6
[13] fansi_1.0.3 magrittr_2.0.3 checkmate_2.1.0 memoise_2.0.1
[17] BSgenome_1.66.1 cluster_2.1.4 remotes_2.4.2 ggfittext_0.9.1
[21] prettyunits_1.1.1 jpeg_0.1-10 colorspace_2.0-3 rappdirs_0.3.3
[25] blob_1.2.3 xfun_0.35 dplyr_1.0.10 callr_3.7.3
[29] crayon_1.5.2 RCurl_1.98-1.9 graph_1.76.0 VariantAnnotation_1.44.0
[33] survival_3.4-0 glue_1.6.2 polyclip_1.10-4 gtable_0.3.1
[37] zlibbioc_1.44.0 DelayedArray_0.24.0 pkgbuild_1.4.0 scales_1.2.1
[41] DBI_1.1.3 GGally_2.1.2 miniUI_0.1.1.1 Rcpp_1.0.9
[45] progress_1.2.2 xtable_1.8-4 htmlTable_2.4.1 foreign_0.8-84
[49] bit_4.0.5 OrganismDbi_1.40.0 Formula_1.2-4 profvis_0.3.7
[53] htmlwidgets_1.6.0 httr_1.4.4 RColorBrewer_1.1-3 ellipsis_0.3.2
[57] urlchecker_1.0.1 pkgconfig_2.0.3 reshape_0.8.9 XML_3.99-0.13
[61] farver_2.1.1 dbplyr_2.2.1 nnet_7.3-18 deldir_1.0-6
[65] utf8_1.2.2 tidyselect_1.2.0 labeling_0.4.2 rlang_1.0.6
[69] reshape2_1.4.4 later_1.3.0 AnnotationDbi_1.60.0 munsell_0.5.0
[73] tools_4.2.1 cachem_1.0.6 cli_3.4.1 generics_0.1.3
[77] RSQLite_2.2.19 devtools_2.4.5 evaluate_0.19 stringr_1.5.0
[81] fastmap_1.1.0 yaml_2.3.6 processx_3.8.0 knitr_1.41
[85] bit64_4.0.5 fs_1.5.2 purrr_0.3.5 KEGGREST_1.38.0
[89] AnnotationFilter_1.22.0 RBGL_1.74.0 mime_0.12 xml2_1.3.3
[93] biomaRt_2.54.0 compiler_4.2.1 rstudioapi_0.14 filelock_1.0.2
[97] curl_4.3.3 png_0.1-8 tibble_3.1.8 tweenr_2.0.2
[101] stringi_1.7.8 ps_1.7.2 GenomicFeatures_1.50.3 lattice_0.20-45
[105] ProtGenerics_1.30.0 Matrix_1.5-3 vctrs_0.5.1 pillar_1.8.1
[109] lifecycle_1.0.3 BiocManager_1.30.19 data.table_1.14.6 bitops_1.0-7
[113] httpuv_1.6.7 gggenes_0.4.1 rtracklayer_1.58.0 R6_2.5.1
[117] BiocIO_1.8.0 latticeExtra_0.6-30 promises_1.2.0.1 gridExtra_2.3
[121] sessioninfo_1.2.2 codetools_0.2-18 dichromat_2.0-0.1 MASS_7.3-58.1
[125] assertthat_0.2.1 pkgload_1.3.2 rjson_0.2.21 withr_2.5.0
[129] GenomeInfoDbData_1.2.9 hms_1.1.2 parallel_4.2.1 grid_4.2.1
[133] rpart_4.1.19 rmarkdown_2.19 biovizBase_1.46.0 ggnewscale_0.4.8
[137] ggforce_0.4.1 shiny_1.7.4 base64enc_0.1-3 interp_1.1-3
[141] restfulr_0.0.15
Hi,
I'm getting this error when running readGAlignments on a BamViews object as follows:
readGAlignments(bamfiles,param=ScanBamParam(what=scanBamWhat(),tag=c("rq")),with.which_label=TRUE)
Error: BiocParallel errors
2 remote errors, element index: 1, 2
0 unevaluated and other errors
first remote error: cannot coerce class "list" to a DataFrame
In addition: Warning messages:
1: In readGAlignments(bamfiles, param = ScanBamParam(what = scanBamWhat(), :
'bamRanges(file)' and 'bamWhich(param)' differ; using 'bamRanges(file)'
2: stop worker failed:
wrong args for environment subassignment
I've been trying to debug some performance problems in DiffBind this week and I've traced them back to a few things in GenomicAlignemnts (called in diffbind through summarizeOverlaps). The issues I encountered with summarizeOverlaps are as follows:
In some circumstances, providing a set of intervals twice, both to the 'features' argument and passed in through a 'ScanBamParam' object results in much faster performance (particularly using a small number of intervals e.g. just chromosome 1), which seems counterintuitive since the function should already 'know' which intervals to use.
Using 'singleEnd=FALSE' seems to result in the entire file being read into memory, which is unexpected and can cause serious performance issues.
Combining both of these and passing a set of intervals through ScanBamParam(which=intervals) and also specifying singleEnd=FALSE results in an unrecoverable hang, even in cases where the single-ended function runs in seconds.
Reproducible examples:
library(GenomicAlignments)
library(rtracklayer)
bamfile = "large_file.bam"
bed_file = "peaks_chr1.bed"
intervals = rtracklayer::import(bed_file)
# ISSUE 1
# this runs fine
t1 = system.time({
counts = summarizeOverlaps(features=intervals,reads=bamfile,
ignore.strand=TRUE,singleEnd=TRUE)
})
# but this runs significantly faster, even though intervals are already provided
params = Rsamtools::ScanBamParam(which=intervals)
t2 = system.time({
counts = summarizeOverlaps(features=intervals,reads=bamfile,
ignore.strand=TRUE,singleEnd=TRUE,
param=params)
})
# ISSUE 2
# this causes the entire file to be read into memory
counts = summarizeOverlaps(features=intervals,reads=bamfile,
ignore.strand=TRUE,singleEnd=FALSE)
# ISSUE 3
# this causes an unrecoverable hang, run at your own risk!
# counts = summarizeOverlaps(features=intervals,reads=bamfile,
# ignore.strand=TRUE,singleEnd=FALSE,
# param=params)
sessionInfo:
> sessionInfo()
R version 4.0.5 (2021-03-31)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.2 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_GB.UTF-8 LC_NUMERIC=C
[3] LC_TIME=en_GB.UTF-8 LC_COLLATE=en_GB.UTF-8
[5] LC_MONETARY=en_GB.UTF-8 LC_MESSAGES=en_GB.UTF-8
[7] LC_PAPER=en_GB.UTF-8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_GB.UTF-8 LC_IDENTIFICATION=C
attached base packages:
[1] parallel stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] rtracklayer_1.50.0 DiffBind_3.1.7
[3] SummarizedExperiment_1.20.0 Biobase_2.50.0
[5] MatrixGenerics_1.2.1 matrixStats_0.58.0
[7] GenomicRanges_1.42.0 GenomeInfoDb_1.26.7
[9] IRanges_2.24.1 S4Vectors_0.28.1
[11] BiocGenerics_0.36.1
loaded via a namespace (and not attached):
[1] backports_1.2.1 GOstats_2.56.0 BiocFileCache_1.14.0
[4] plyr_1.8.6 GSEABase_1.52.1 splines_4.0.5
[7] BiocParallel_1.24.1 ggplot2_3.3.3 amap_0.8-18
[10] digest_0.6.27 invgamma_1.1 GO.db_3.12.1
[13] SQUAREM_2021.1 fansi_0.4.2 magrittr_2.0.1
[16] checkmate_2.0.0 memoise_2.0.0 BSgenome_1.58.0
[19] base64url_1.4 limma_3.46.0 Biostrings_2.58.0
[22] annotate_1.68.0 systemPipeR_1.24.3 askpass_1.1
[25] bdsmatrix_1.3-4 prettyunits_1.1.1 jpeg_0.1-8.1
[28] colorspace_2.0-0 blob_1.2.1 rappdirs_0.3.3
[31] apeglm_1.12.0 ggrepel_0.9.1 dplyr_1.0.5
[34] crayon_1.4.1 RCurl_1.98-1.3 jsonlite_1.7.2
[37] graph_1.68.0 genefilter_1.72.1 brew_1.0-6
[40] survival_3.2-10 VariantAnnotation_1.36.0 glue_1.4.2
[43] gtable_0.3.0 zlibbioc_1.36.0 XVector_0.30.0
[46] DelayedArray_0.16.3 V8_3.4.1 Rgraphviz_2.34.0
[49] scales_1.1.1 pheatmap_1.0.12 mvtnorm_1.1-1
[52] DBI_1.1.1 edgeR_3.32.1 Rcpp_1.0.6
[55] xtable_1.8-4 progress_1.2.2 emdbook_1.3.12
[58] bit_4.0.4 rsvg_2.1.1 AnnotationForge_1.32.0
[61] truncnorm_1.0-8 httr_1.4.2 gplots_3.1.1
[64] RColorBrewer_1.1-2 ellipsis_0.3.1 pkgconfig_2.0.3
[67] XML_3.99-0.6 dbplyr_2.1.1 locfit_1.5-9.4
[70] utf8_1.2.1 tidyselect_1.1.0 rlang_0.4.10
[73] AnnotationDbi_1.52.0 munsell_0.5.0 tools_4.0.5
[76] cachem_1.0.4 generics_0.1.0 RSQLite_2.2.7
[79] stringr_1.4.0 fastmap_1.1.0 yaml_2.2.1
[82] bit64_4.0.5 caTools_1.18.2 purrr_0.3.4
[85] RBGL_1.66.0 xml2_1.3.2 biomaRt_2.46.3
[88] compiler_4.0.5 rstudioapi_0.13 curl_4.3
[91] png_0.1-7 tibble_3.1.1 stringi_1.5.3
[94] GenomicFeatures_1.42.3 lattice_0.20-41 Matrix_1.3-2
[97] vctrs_0.3.7 pillar_1.6.0 lifecycle_1.0.0
[100] irlba_2.3.3 data.table_1.14.0 bitops_1.0-7
[103] R6_2.5.0 latticeExtra_0.6-29 hwriter_1.3.2
[106] ShortRead_1.48.0 KernSmooth_2.23-18 MASS_7.3-53.1
[109] gtools_3.8.2 assertthat_0.2.1 openssl_1.4.3
[112] Category_2.56.0 rjson_0.2.20 withr_2.4.2
[115] GenomicAlignments_1.26.0 batchtools_0.9.15 Rsamtools_2.6.0
[118] GenomeInfoDbData_1.2.4 hms_1.0.0 grid_4.0.5
[121] DOT_0.1 coda_0.19-4 GreyListChIP_1.22.0
[124] ashr_2.2-47 mixsqp_0.3-43 bbmle_1.0.23.1
[127] numDeriv_2016.8-1.1
I can provide the original files I used since they are public data but they are quite large, and I'd be interested to know if you can replicate them with different files. I've also attached my session info, which should be pretty up to date since this was a fresh install of both R and Bioconductor from 2 weeks ago.
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