Entering edit mode
Daniel E. Weeks
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30
@daniel-e-weeks-10677
Last seen 4 months ago
Pittsburgh, Pennsylvania, United States…
Previously working coMET epigenetic plotting code now fails. It appears that this is because now UcscTrack fails when trying to pull information from the GC Percent track, generating the error "Error fetching data from UCSC".
Minimal Working Example
While the initial error was encountered trying to pull a "GC Percent' track for human 'hg19' (second example below) , this first example is directly based on
https://xiaonilee.github.io/post/ucscgenebrowser2/
where this code looks like it previously worked as of 2021-02-14.
library(Gviz)
from <- 65921878
to <- 65980988
knownGenes <- UcscTrack(genome = "mm9", chromosome = "chrX",
track = "knownGene", from = from, to = to,
trackType = "GeneRegionTrack",
rstarts = "exonStarts", rends = "exonEnds",
gene = "name", symbol = "name",
transcript = "name", strand = "strand",
fill = "#8282d2", name = "UCSC Genes")
knownGenes
# This plot works:
# plotTracks(list(knownGenes),
# from = from, to = to, showTitle = TRUE)
gcContent <- UcscTrack(genome = "mm9", chromosome = "chrX",
track = "GC Percent", table = "gc5Base",
from = from, to = to, trackType = "DataTrack",
start = "start", end = "end", data = "score",
type = "hist", window = -1, windowSize = 1500,
fill.histogram = "black", col.histogram = "black",
ylim = c(30, 70), name = "GC Percent")
gcContent
# Human example based on call that coMET generated
chr <- 7
gen <- "hg19"
genTrunk <- "hg19"
title <- "GC Percent"
start <- 33567324
# end <- 33722324
end <- start + 3000
GCTrack <- UcscTrack(genome = genTrunk, chromosome = chr, track = "GC Percent",
table = "gc5Base", from = start, to = end, trackType = "DataTrack",
start = "start", end = "end", data = "score", type = "hist",
window = -1, windowSize = 1500, fill.histogram = "black",
col.histogram = "red", ylim = c(30, 70), name = title,
col.line = NULL, col = NULL, fontfamily = "sans", fontfamily.title = "sans")
sessionInfo()
Result of running the code above
> suppressMessages(library(Gviz))
> from <- 65921878
> to <- 65980988
>
> knownGenes <- UcscTrack(genome = "mm9", chromosome = "chrX",
+ track = "knownGene", from = from, to = to,
+ trackType = "GeneRegionTrack",
+ rstarts = "exonStarts", rends = "exonEnds",
+ gene = "name", symbol = "name",
+ transcript = "name", strand = "strand",
+ fill = "#8282d2", name = "UCSC Genes")
Warning messages:
1: In curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) :
Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x10effe590): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
2: In .local(x, ...) :
'track' parameter is deprecated now you go by the 'table' instead
Use ucscTables(genome, track) to retrieve the list of tables for a track
3: In .local(x, ...) :
'track' parameter is deprecated now you go by the 'table' instead
Use ucscTables(genome, track) to retrieve the list of tables for a track
4: In curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) :
Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x13b817be0): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
>
> knownGenes
GeneRegionTrack 'UCSC Genes'
| genome: mm9
| active chromosome: chrX
| annotation features: 76
> # This plot works:
> # plotTracks(list(knownGenes),
> # from = from, to = to, showTitle = TRUE)
>
>
> gcContent <- UcscTrack(genome = "mm9", chromosome = "chrX",
+ track = "GC Percent", table = "gc5Base",
+ from = from, to = to, trackType = "DataTrack",
+ start = "start", end = "end", data = "score",
+ type = "hist", window = -1, windowSize = 1500,
+ fill.histogram = "black", col.histogram = "black",
+ ylim = c(30, 70), name = "GC Percent")
Error in UcscTrack(genome = "mm9", chromosome = "chrX", track = "GC Percent", :
Error fetching data from UCSC
In addition: Warning messages:
1: In .local(x, ...) :
'track' parameter is deprecated now you go by the 'table' instead
Use ucscTables(genome, track) to retrieve the list of tables for a track
2: In .local(x, ...) :
'track' parameter is deprecated now you go by the 'table' instead
Use ucscTables(genome, track) to retrieve the list of tables for a track
3: In curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) :
Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x295c40830): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
4: In UcscTrack(genome = "mm9", chromosome = "chrX", track = "GC Percent", :
Error in errorHandler(responseError) : Too Many Requests
> gcContent
Error: object 'gcContent' not found
> # Human example based on call that coMET generated
> chr <- 7
> gen <- "hg19"
> genTrunk <- "hg19"
> title <- "GC Percent"
> start <- 33567324
> # end <- 33722324
> end <- start + 3000
>
> GCTrack <- UcscTrack(genome = genTrunk, chromosome = chr, track = "GC Percent",
+ table = "gc5Base", from = start, to = end, trackType = "DataTrack",
+ start = "start", end = "end", data = "score", type = "hist",
+ window = -1, windowSize = 1500, fill.histogram = "black",
+ col.histogram = "red", ylim = c(30, 70), name = title,
+ col.line = NULL, col = NULL, fontfamily = "sans", fontfamily.title = "sans")
Error in UcscTrack(genome = genTrunk, chromosome = chr, track = "GC Percent", :
Error fetching data from UCSC
In addition: Warning messages:
1: In .local(x, ...) :
'track' parameter is deprecated now you go by the 'table' instead
Use ucscTables(genome, track) to retrieve the list of tables for a track
2: In .local(x, ...) :
'track' parameter is deprecated now you go by the 'table' instead
Use ucscTables(genome, track) to retrieve the list of tables for a track
3: In curlSetOpt(..., .opts = .opts, curl = h, .encoding = .encoding) :
Error setting the option for # 3 (status = 43) (enum = 81) (value = 0x16fd92240): A libcurl function was given a bad argument CURLOPT_SSL_VERIFYHOST no longer supports 1 as value!
4: In UcscTrack(genome = genTrunk, chromosome = chr, track = "GC Percent", :
Error in do.call(rbind.data.frame, results) :
second argument must be a list
> sessionInfo()
R version 4.2.2 (2022-10-31)
Platform: aarch64-apple-darwin20 (64-bit)
Running under: macOS Big Sur 11.6.7
Matrix products: default
LAPACK: /Library/Frameworks/R.framework/Versions/4.2-arm64/Versions/4.2-arm64/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] grid stats4 stats graphics grDevices utils datasets
[8] methods base
other attached packages:
[1] Gviz_1.42.0 GenomicRanges_1.50.1 GenomeInfoDb_1.34.4
[4] IRanges_2.32.0 S4Vectors_0.37.2 BiocGenerics_0.44.0
loaded via a namespace (and not attached):
[1] ProtGenerics_1.30.0 bitops_1.0-7
[3] matrixStats_0.63.0 bit64_4.0.5
[5] filelock_1.0.2 RColorBrewer_1.1-3
[7] progress_1.2.2 httr_1.4.4
[9] backports_1.4.1 tools_4.2.2
[11] utf8_1.2.2 R6_2.5.1
[13] rpart_4.1.19 lazyeval_0.2.2
[15] Hmisc_4.7-2 DBI_1.1.3
[17] colorspace_2.0-3 nnet_7.3-18
[19] tidyselect_1.2.0 gridExtra_2.3
[21] prettyunits_1.1.1 bit_4.0.5
[23] curl_4.3.3 compiler_4.2.2
[25] cli_3.4.1 Biobase_2.58.0
[27] htmlTable_2.4.1 xml2_1.3.3
[29] DelayedArray_0.24.0 rtracklayer_1.58.0
[31] checkmate_2.1.0 scales_1.2.1
[33] rappdirs_0.3.3 stringr_1.5.0
[35] digest_0.6.30 Rsamtools_2.14.0
[37] foreign_0.8-84 XVector_0.38.0
[39] dichromat_2.0-0.1 htmltools_0.5.4
[41] base64enc_0.1-3 jpeg_0.1-10
[43] pkgconfig_2.0.3 MatrixGenerics_1.10.0
[45] ensembldb_2.22.0 dbplyr_2.2.1
[47] fastmap_1.1.0 BSgenome_1.66.1
[49] htmlwidgets_1.5.4 rlang_1.0.6
[51] rstudioapi_0.14 RSQLite_2.2.19
[53] BiocIO_1.8.0 generics_0.1.3
[55] BiocParallel_1.32.4 dplyr_1.0.10
[57] VariantAnnotation_1.44.0 RCurl_1.98-1.9
[59] magrittr_2.0.3 GenomeInfoDbData_1.2.9
[61] Formula_1.2-4 interp_1.1-3
[63] Matrix_1.5-3 Rcpp_1.0.9
[65] munsell_0.5.0 fansi_1.0.3
[67] lifecycle_1.0.3 stringi_1.7.8
[69] yaml_2.3.6 SummarizedExperiment_1.28.0
[71] zlibbioc_1.44.0 BiocFileCache_2.6.0
[73] blob_1.2.3 parallel_4.2.2
[75] crayon_1.5.2 deldir_1.0-6
[77] lattice_0.20-45 Biostrings_2.66.0
[79] splines_4.2.2 GenomicFeatures_1.50.2
[81] hms_1.1.2 KEGGREST_1.38.0
[83] knitr_1.41 pillar_1.8.1
[85] rjson_0.2.21 codetools_0.2-18
[87] biomaRt_2.54.0 XML_3.99-0.13
[89] glue_1.6.2 biovizBase_1.46.0
[91] latticeExtra_0.6-30 data.table_1.14.6
[93] png_0.1-8 vctrs_0.5.1
[95] gtable_0.3.1 assertthat_0.2.1
[97] cachem_1.0.6 ggplot2_3.4.0
[99] xfun_0.35 AnnotationFilter_1.22.0
[101] restfulr_0.0.15 survival_3.4-0
[103] tibble_3.1.8 GenomicAlignments_1.34.0
[105] AnnotationDbi_1.60.0 memoise_2.0.1
[107] cluster_2.1.4 ellipsis_0.3.2
Stepping through the
mm9chrXcall above toUcscTrackwith the debugger, we see that it sets up a query which then tries to use thetrackcommand from thertracklayerpackage at this line:This fails with the error message:
as well as with a warning:
How does one change the value of CURLOPT_SSL_VERIFYHOST?
But note that the
knownGenescall above works despite also warning aboutCURLOPT_SSL_VERIFYHOST, suggesting that the relevant error message is the one about therbind.data.frame.Looks like the original source of example code that is failing for me is actually from Section 6 of "The Gvis User Guide"
https://bioconductor.org/packages/devel/bioc/vignettes/Gviz/inst/doc/Gviz.html#6_Track_highlighting_and_overlays
where we see:
Looks like the error is happening in
parseResponseofrtracklayer, where the first few lines are:If we watch this in the debugger, we see when we enter
parseResponse, we have:where the Wiggle track list information is in the
chrXelement of theresponse, but the code is trying to pull out the non-existentgc5Baseelement of theresponseinstead.So the line
sets
resultstoNULL, generating the subsequent error message: