Alignment file loading error

[jhnath21]

I installed pavian on an Rstudio server (running on Centos 7 on an AWS EC2 instance, R version 4.1.2 is installed). I followed the installation and deployment instructions and install the Rsamtools as well. After logging into the instance and launching firefox, I navigated to http://127.0.0.1:5000. The application opens and I can import the example data fine and can view the Sankey visualization for all the samples in both datasets. However, when I try to import the example alignment files I get an error.

This is the output when I try to load the example data for the alignment: Loaded PT5-JC_polyomavirus.bam . Click on a row to see the genome coverage.

Error: Some column names in the 'escape' argument not found in data

Any help would be appreciated. I have tried reinstalling both Rsamtools and pavian but have not had any success.

Here is the output from the About tab within the Pavian webpage: R version 4.1.2 (2021-11-01) Platform: x86_64-pc-linux-gnu (64-bit) Running under: CentOS Linux 7 (Core)

Matrix products: default BLAS/LAPACK: /usr/lib64/libopenblasp-r0.3.3.so

locale: [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=en_US.UTF-8
[4] LC_COLLATE=en_US.UTF-8 LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
[7] LC_PAPER=en_US.UTF-8 LC_NAME=C LC_ADDRESS=C
[10] 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] pavian_1.2.0 shiny_1.7.1 Rsamtools_2.10.0 Biostrings_2.62.0 XVector_0.34.0
[6] GenomicRanges_1.46.1 GenomeInfoDb_1.30.1 IRanges_2.28.0 S4Vectors_0.32.4 BiocGenerics_0.40.0

loaded via a namespace (and not attached): [1] Rcpp_1.0.8.3 shinyWidgets_0.6.4 digest_0.6.29 utf8_1.2.2
[5] mime_0.12 plyr_1.8.7 R6_2.5.1 d3r_1.0.0
[9] ggplot2_3.3.5 pillar_1.7.0 zlibbioc_1.40.0 rlang_1.0.2
[13] rstudioapi_0.13 fontawesome_0.2.2 jquerylib_0.1.4 DT_0.22
[17] shinyFileTree_0.0.0.9000 shinyjs_2.1.0 BiocParallel_1.28.3 htmlwidgets_1.5.4
[21] RCurl_1.98-1.6 munsell_0.5.0 compiler_4.1.2 httpuv_1.6.5
[25] pkgconfig_2.0.3 htmltools_0.5.2 tidyselect_1.1.2 tibble_3.1.6
[29] GenomeInfoDbData_1.2.7 fansi_1.0.3 crayon_1.5.1 dplyr_1.0.8
[33] later_1.3.0 bitops_1.0-7 grid_4.1.2 jsonlite_1.8.0
[37] xtable_1.8-4 gtable_0.3.0 lifecycle_1.0.1 magrittr_2.0.3
[41] scales_1.1.1 cli_3.2.0 cachem_1.0.6 promises_1.2.0.1
[45] rhandsontable_0.3.8 bslib_0.3.1 ellipsis_0.3.2 generics_0.1.2
[49] vctrs_0.4.0 RColorBrewer_1.1-3 tools_4.1.2 glue_1.6.2
[53] purrr_0.3.4 sankeyD3_0.3.2 crosstalk_1.2.0 parallel_4.1.2
[57] fastmap_1.1.0 yaml_2.3.5 colorspace_2.0-3 shinydashboard_0.7.2
[61] sass_0.4.1

[jrumore]

I am also having a similar issue.

Any assistance would be greatly appreciated! Many thanks!

[derekstein]

Has this been solved? Also getting the same error!

[tigerxu]

I am meeting the same error! Thanks a lot if anyone would help!