New error with read_qza for table.qza?
Closed this issue · 4 comments
Hi,
First, thank you for this package, I've used it a lot in the past and it's saved me a ton of time.
I'm having an issue with the read_qza function when I try to read an ASV table. I'm using qiime2-2020.2 and the latest version of qiime2R. This is a table that I'm generating within R and importing into qiime2. I don't get any issues within qiime, and I recall being able to run this command without issue last time I used this package (months ago), so hopefully this is something we can clear up!
Here's the error:
> SVs <- read_qza("asv_table.qza")
Error in dimnamesGets(x, value) :
invalid dimnames given for “dgCMatrix” object
Calls: read_qza ... colnames<- -> dimnames<- -> dimnames<- -> dimnamesGets
Execution halted
Here's my session info:
_
platform x86_64-pc-linux-gnu
arch x86_64
os linux-gnu
system x86_64, linux-gnu
status
major 3
minor 6.2
year 2019
month 12
day 12
svn rev 77560
language R
version.string R version 3.6.2 (2019-12-12)
nickname Dark and Stormy Night
> library(qiime2R)
> session.info()
Error in session.info() : could not find function "session.info"
> sessionInfo()
R version 3.6.2 (2019-12-12)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Red Hat Enterprise Linux Server 7.7 (Maipo)
Matrix products: default
BLAS: /usr/lib64/libblas.so.3.4.2
LAPACK: /usr/lib64/liblapack.so.3.4.2
locale:
[1] LC_CTYPE=en_US.utf8 LC_NUMERIC=C
[3] LC_TIME=en_US.utf8 LC_COLLATE=en_US.utf8
[5] LC_MONETARY=en_US.utf8 LC_MESSAGES=en_US.utf8
[7] LC_PAPER=en_US.utf8 LC_NAME=C
[9] LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=en_US.utf8 LC_IDENTIFICATION=C
attached base packages:
[1] stats graphics grDevices utils datasets methods base
other attached packages:
[1] qiime2R_0.99.33
loaded via a namespace (and not attached):
[1] Biobase_2.46.0 tidyr_1.0.2 jsonlite_1.6.1
[4] splines_3.6.2 foreach_1.5.0 Formula_1.2-3
[7] assertthat_0.2.1 stats4_3.6.2 phyloseq_1.30.0
[10] latticeExtra_0.6-29 yaml_2.2.1 pillar_1.4.3
[13] backports_1.1.5 lattice_0.20-40 glue_1.4.1
[16] digest_0.6.25 RColorBrewer_1.1-2 XVector_0.26.0
[19] checkmate_2.0.0 colorspace_1.4-1 htmltools_0.4.0
[22] Matrix_1.2-18 plyr_1.8.6 pkgconfig_2.0.3
[25] zlibbioc_1.32.0 purrr_0.3.3 scales_1.1.0
[28] jpeg_0.1-8.1 htmlTable_1.13.3 tibble_3.0.0
[31] mgcv_1.8-31 IRanges_2.20.2 ggplot2_3.3.0
[34] DT_0.13 ellipsis_0.3.0 nnet_7.3-13
[37] BiocGenerics_0.32.0 cli_2.0.2 survival_3.2-3
[40] magrittr_1.5 crayon_1.3.4 fansi_0.4.1
[43] nlme_3.1-145 MASS_7.3-51.5 foreign_0.8-76
[46] truncnorm_1.0-8 vegan_2.5-6 tools_3.6.2
[49] data.table_1.12.8 lifecycle_0.2.0 stringr_1.4.0
[52] Rhdf5lib_1.8.0 S4Vectors_0.24.3 munsell_0.5.0
[55] cluster_2.1.0 Biostrings_2.54.0 ade4_1.7-15
[58] compiler_3.6.2 rlang_0.4.5 rhdf5_2.30.1
[61] grid_3.6.2 iterators_1.0.12 biomformat_1.14.0
[64] rstudioapi_0.11 htmlwidgets_1.5.1 igraph_1.2.5
[67] base64enc_0.1-3 gtable_0.3.0 codetools_0.2-16
[70] multtest_2.42.0 reshape2_1.4.3 R6_2.4.1
[73] gridExtra_2.3 knitr_1.28 dplyr_0.8.5
[76] Hmisc_4.4-0 permute_0.9-5 ape_5.3
[79] stringi_1.4.6 parallel_3.6.2 NADA_1.6-1.1
[82] Rcpp_1.0.4 vctrs_0.2.4 zCompositions_1.3.4
[85] rpart_4.1-15 acepack_1.4.1 png_0.1-7
[88] tidyselect_1.0.0 xfun_0.12
Would you be willing to send me your artifact so I can debug? I changed the method of biom import to avoid another bug in biomformat. I'm wondering if there could be some odd character in your sample names, or perhaps it could be something along the lines of sample names are numbers?
There are underscores and periods in the sample names, but that hasn't been a problem in the past. Also I'm still able to import older projects which have similar sample names. Can I send the artifact to you over email?
That would be great! Please send to jordan.bisanz@gmail.com.
fixed in update