Entering edit mode
I am trying to create a VariantExperiment object from a VCF, but I am getting this error:
Error in validObject(.Object) : invalid class “DelayedAperm” object:
only dimensions equal to 1 can be dropped
The GDS object is created successfully, so the problem is happening in makeVariantExperimentFromGDS. I see that I am failing a validity check, but not sure where. Any suggestions would be greatly appreciated.
> vcf = VariantExperiment::makeVariantExperimentFromVCF(vcf_path,
+ verbose=TRUE)
Fri Aug 19 16:26:52 2022
Variant Call Format (VCF) Import:
file(s):
BSA6.IGV.vcf (81.1M)
file format: VCFv4.2
genome reference: /scratch/mblab/daniel.agustinho/references/crNeoKN99.fasta
the number of sets of chromosomes (ploidy): 1
the number of samples: 31
genotype storage: bit2
compression method: LZMA_RA
# of samples: 31
Output:
/tmp/RtmphIXgN8/file72ed1219a41ca/se.gds
Parsing 'BSA6.IGV.vcf':
+ genotype/data { Bit2 1x31x52742 LZMA_ra(16.7%), 120.1K }
Digests:
sample.id [md5: 8b287218ba90f14a0f577ab3ad30d8c5]
...
annotation/format/QA [md5: ac3472b499e80085f79add9103ac19d1]
annotation/format/MIN_DP [md5: 6e6dcb39f4b68c5a7dc6ad670c6ff366]
Done.
Fri Aug 19 16:27:08 2022
Optimize the access efficiency ...
Clean up the fragments of GDS file:
open the file '/tmp/RtmphIXgN8/file72ed1219a41ca/se.gds' (19.9M)
# of fragments: 1048
save to '/tmp/RtmphIXgN8/file72ed1219a41ca/se.gds.tmp'
rename '/tmp/RtmphIXgN8/file72ed1219a41ca/se.gds.tmp' (19.9M, reduced: 9.6K)
# of fragments: 231
Fri Aug 19 16:27:08 2022
Error in validObject(.Object) : invalid class “DelayedAperm” object:
only dimensions equal to 1 can be dropped
> sessionInfo()
R version 4.2.1 (2022-06-23)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Ubuntu 20.04.4 LTS
Matrix products: default
BLAS: /usr/lib/x86_64-linux-gnu/atlas/libblas.so.3.10.3
LAPACK: /usr/lib/x86_64-linux-gnu/atlas/liblapack.so.3.10.3
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 stats graphics grDevices utils
[6] datasets methods base
other attached packages:
[1] SeqVarTools_1.34.0
[2] here_1.0.1
[3] SeqArray_1.36.2
[4] gdsfmt_1.32.0
[5] forcats_0.5.1
[6] stringr_1.4.0
[7] dplyr_1.0.9
[8] purrr_0.3.4
[9] readr_2.1.2
[10] tidyr_1.2.0
[11] tibble_3.1.8
[12] ggplot2_3.3.6
[13] tidyverse_1.3.2
[14] VariantExperiment_1.10.0
[15] SummarizedExperiment_1.26.1
[16] Biobase_2.56.0
[17] GenomicRanges_1.48.0
[18] GenomeInfoDb_1.32.3
[19] IRanges_2.30.1
[20] MatrixGenerics_1.8.1
[21] matrixStats_0.62.0
[22] S4Vectors_0.34.0
[23] BiocGenerics_0.42.0
[24] BSA_0.0.0.9000
loaded via a namespace (and not attached):
[1] readxl_1.4.1 backports_1.4.1
[3] BiocFileCache_2.4.0 splines_4.2.1
[5] QTLseqr_0.7.5.2 operator.tools_1.6.3
[7] BiocParallel_1.30.3 usethis_2.1.6
[9] digest_0.6.29 htmltools_0.5.3
[11] fansi_1.0.3 magrittr_2.0.3
[13] memoise_2.0.1 BSgenome_1.64.0
[15] GDSArray_1.16.0 googlesheets4_1.0.1
[17] cluster_2.1.3 tzdb_0.3.0
[19] Biostrings_2.64.1 modelr_0.1.9
[21] formula.tools_1.7.1 stabledist_0.7-1
[23] prettyunits_1.1.1 colorspace_2.0-3
[25] blob_1.2.3 rvest_1.0.2
[27] rappdirs_0.3.3 haven_2.5.0
[29] xfun_0.32 crayon_1.5.1
[31] RCurl_1.98-1.8 jsonlite_1.8.0
[33] VariantAnnotation_1.42.1 iterators_1.0.14
[35] glue_1.6.2 gtable_0.3.0
[37] gargle_1.2.0 zlibbioc_1.42.0
[39] XVector_0.36.0 DelayedArray_0.22.0
[41] DelayedDataFrame_1.12.0 scales_1.2.0
[43] DBI_1.1.3 Rcpp_1.0.9
[45] progress_1.2.2 clue_0.3-61
[47] bit_4.0.4 timeSeries_4021.104
[49] httr_1.4.4 logistf_1.24.1
[51] ellipsis_0.3.2 mice_3.14.0
[53] spatial_7.3-15 pkgconfig_2.0.3
[55] XML_3.99-0.10 dbplyr_2.2.1
[57] locfit_1.5-9.6 utf8_1.2.2
[59] tidyselect_1.1.2 rlang_1.0.4
[61] AnnotationDbi_1.58.0 munsell_0.5.0
[63] cellranger_1.1.0 tools_4.2.1
[65] cachem_1.0.6 cli_3.3.0
[67] generics_0.1.3 RSQLite_2.2.16
[69] broom_1.0.0 evaluate_0.16
[71] fastmap_1.1.0 yaml_2.3.5
[73] knitr_1.39 bit64_4.0.5
[75] fs_1.5.2 KEGGREST_1.36.3
[77] nlme_3.1-159 GWASExactHW_1.01
[79] whisker_0.4 xml2_1.3.3
[81] biomaRt_2.52.0 compiler_4.2.1
[83] rstudioapi_0.13 filelock_1.0.2
[85] curl_4.3.2 png_0.1-7
[87] reprex_2.0.2 stringi_1.7.8
[89] statip_0.2.3 GenomicFeatures_1.48.3
[91] desc_1.4.1 modeest_2.4.0
[93] lattice_0.20-45 fBasics_4021.92
[95] Matrix_1.4-1 vctrs_0.4.1
[97] pillar_1.8.1 lifecycle_1.0.1
[99] BiocManager_1.30.18 data.table_1.14.2
[101] bitops_1.0-7 SNPRelate_1.30.1
[103] rtracklayer_1.56.1 R6_2.5.1
[105] stable_1.1.6 BiocIO_1.6.0
[107] codetools_0.2-18 assertthat_0.2.1
[109] rprojroot_2.0.3 rjson_0.2.21
[111] withr_2.5.0 GenomicAlignments_1.32.1
[113] Rsamtools_2.12.0 GenomeInfoDbData_1.2.8
[115] mgcv_1.8-40 parallel_4.2.1
[117] hms_1.1.2 grid_4.2.1
[119] rpart_4.1.16 timeDate_4021.104
[121] rmarkdown_2.15 rmutil_1.1.9
[123] googledrive_2.0.0 lubridate_1.8.0
[125] restfulr_0.0.15
