Question: Error while creating txDb from gtf file
0
gravatar for bioinagesh
3 months ago by
bioinagesh0
bioinagesh0 wrote:

Hello,

I am trying to create TxDb object from gtf file but end up with the following error. I have loaded required libraries abd gtf file.

> gtf <-system.file("annotation_merged.gtf.gz", package = "jcc")                                               > bam <- system.file("../sad_merged/salmon_output/mapping.bam", package = "jcc")                               > biasMod <- fitAlpineBiasModel(gtf = gtf, bam = bam, organism = "Oryza_indica", minLength = 230, maxLength = 7000, minCount = 10, maxCount = 10000, subsample = TRUE, nbrSubsample = 30, seed = 1, minSize = NULL, maxSize = 220, verbose = TRUE)

Creating TxDb object...
Importing GTF file ... Import genomic features from the file as a GRanges object ... Error in connectionForResource(manager, resource(x), open = open) :
  path cannot be an empty string

> sessionInfo()
R version 3.6.1 (2019-07-05)
Platform: x86_64-conda_cos6-linux-gnu (64-bit)
Running under: CentOS Linux 7 (Core)

Matrix products: default
BLAS/LAPACK: /mnt/du-synology/v1shr1/scratch/ns43567/apps/conda/lib/libopenblasp-r0.3.7.so

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] stats4    parallel  stats     graphics  grDevices utils     datasets
[8] methods   base

other attached packages:
 [1] dplyr_0.8.3                   BSgenome.Oindica.ASM465v1_1.0
 [3] BSgenome_1.52.0               rtracklayer_1.44.3
 [5] Biostrings_2.52.0             XVector_0.24.0
 [7] GenomicRanges_1.36.0          GenomeInfoDb_1.20.0
 [9] IRanges_2.18.2                S4Vectors_0.22.0
[11] BiocGenerics_0.30.0           jcc_0.1.0

loaded via a namespace (and not attached):
 [1] ProtGenerics_1.16.0         bitops_1.0-6
 [3] matrixStats_0.54.0          bit64_0.9-7
 [5] RColorBrewer_1.1-2          progress_1.2.2
 [7] httr_1.4.1                  tools_3.6.1
 [9] backports_1.1.4             R6_2.4.0
[11] rpart_4.1-15                Hmisc_4.2-0
[13] DBI_1.0.0                   lazyeval_0.2.2
[15] Gviz_1.28.0                 colorspace_1.4-1
[17] nnet_7.3-12                 tidyselect_0.2.5
[19] gridExtra_2.3               prettyunits_1.0.2
[21] bit_1.1-14                  curl_4.0
[23] compiler_3.6.1              graph_1.62.0
[25] Biobase_2.44.0              htmlTable_1.13.1
[27] scatterpie_0.1.2            DelayedArray_0.10.0
[29] scales_1.0.0                checkmate_1.9.4
[31] RBGL_1.60.0                 speedglm_0.3-2
[33] stringr_1.4.0               digest_0.6.20
[35] Rsamtools_2.0.0             foreign_0.8-71
[37] base64enc_0.1-3             dichromat_2.0-0
[39] pkgconfig_2.0.2             htmltools_0.3.6
[41] ensembldb_2.8.0             htmlwidgets_1.3
[43] rlang_0.4.0                 rstudioapi_0.10
[45] RSQLite_2.1.2               farver_1.1.0
[47] BiocParallel_1.18.1         acepack_1.4.1
[49] VariantAnnotation_1.30.1    RCurl_1.95-4.12
[51] magrittr_1.5                GenomeInfoDbData_1.2.1
[53] Formula_1.2-3               Matrix_1.2-17
[55] Rcpp_1.0.2                  munsell_0.5.0
[57] stringi_1.4.3               MASS_7.3-51.4
[59] SummarizedExperiment_1.14.1 zlibbioc_1.30.0
[61] grid_3.6.1                  blob_1.2.0
[63] crayon_1.3.4                lattice_0.20-38
[65] cowplot_1.0.0               alpine_1.10.0
[67] splines_3.6.1               GenomicFeatures_1.36.4
[69] hms_0.5.1                   zeallot_0.1.0
[71] knitr_1.24                  pillar_1.4.2
[73] biomaRt_2.40.3              XML_3.98-1.20
[75] glue_1.3.1                  biovizBase_1.32.0
[77] latticeExtra_0.6-28         data.table_1.12.2
[79] tweenr_1.0.1                vctrs_0.2.0
[81] tidyr_0.8.3                 polyclip_1.10-0
[83] gtable_0.3.0                purrr_0.3.2
[85] assertthat_0.2.1            ggplot2_3.2.1
[87] ggforce_0.3.1               xfun_0.9
[89] AnnotationFilter_1.8.0      survival_2.44-1.1
[91] tibble_2.1.3                rvcheck_0.1.3
[93] GenomicAlignments_1.20.1    AnnotationDbi_1.46.1
[95] memoise_1.1.0               cluster_2.1.0

I appreciate every suggestion, thanks in advance.

genomicfeatures • 135 views
ADD COMMENTlink written 3 months ago by bioinagesh0

Do gtf and bam contain valid file paths?

ADD REPLYlink written 3 months ago by Michael Lawrence11k

Thanks Michael, file path is the problem and worked on it.

ADD REPLYlink written 3 months ago by bioinagesh0
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