Closed Vy5HAGit closed 3 years ago
I aslo tried to upload a kraken2 report with a custom database. I don't know do you only suport default db or only bracken reports?
Hi! I installed Pavian and I'm trying to use Metaphlan3 output files which are .txt. But I get this : "The following files did not conform the report format". Were you able to find a solution?
Error message: Warning: File C:/Users/MARIAE~1/AppData/Local/Temp/Rtmpa04HKP/d5cbd7a481490ec0ee8c0a05/X.profile.txt does not have the required format 'data.frame': 5 obs. of 4 variables: $ kBacteria: chr "kBacteria|pFirmicutes" "kBacteria|pBacteroidetes" "kBacteria|pProteobacteria" "kBacteria|p__Verrucomicrobia" ... $ 2 : chr "2|1239" "2|976" "2|1224" "2|74201" ... $ 100.0 : num 61.963 33.352 3.213 1.016 0.456 $ : logi NA NA NA NA NA
Hi! I installed Pavian and I'm trying to use Metaphlan3 output files which are .txt. But I get this : "The following files did not conform the report format". Were you able to find a solution?
Error message: Warning: File C:/Users/MARIAE~1/AppData/Local/Temp/Rtmpa04HKP/d5cbd7a481490ec0ee8c0a05/X.profile.txt does not have the required format 'data.frame': 5 obs. of 4 variables: $ kBacteria: chr "kBacteria|pFirmicutes" "kBacteria|pBacteroidetes" "kBacteria|pProteobacteria" "kBacteria|p__Verrucomicrobia" ... $ 2 : chr "2|1239" "2|976" "2|1224" "2|74201" ... $ 100.0 : num 61.963 33.352 3.213 1.016 0.456 $ : logi NA NA NA NA NA
I also tried this : https://github.com/fbreitwieser/pavian/issues/48
Same problem here. Tested with a file that previously worked. This file does not work anymore. Seems that this occurred after dependencies for the shiny app were updated
Hi @Vy5HAGit , @SilasK , @evezeyl , can you provide example files that don't work? Thanks!
61225_report.txt
I previously could make report with this file. Because I encountered a problem with a new run, I used it to test if it was a problem with my new run (with kraken2 output) or with pavian. It is not read anymore.
Some package have been updated, unfortunately I do not have session Info when it worked.
Screenshot of the error message I get when trying to upload the report file, and current R session Info bellow. I hope this helps. All the best. Eve
Here is R session info R version 4.0.0 (2020-04-24) Platform: x86_64-pc-linux-gnu (64-bit) Running under: Ubuntu 18.04.5 LTS
Matrix products: default BLAS: /home/evezeyl/bin/R/4.0.0_GWAS/lib/R/lib/libRblas.so LAPACK: /home/evezeyl/bin/R/4.0.0_GWAS/lib/R/lib/libRlapack.so
locale:
[1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C LC_TIME=nb_NO.UTF-8 LC_COLLATE=en_US.UTF-8 LC_MONETARY=nb_NO.UTF-8
[6] LC_MESSAGES=en_US.UTF-8 LC_PAPER=nb_NO.UTF-8 LC_NAME=C LC_ADDRESS=C LC_TELEPHONE=C
[11] LC_MEASUREMENT=nb_NO.UTF-8 LC_IDENTIFICATION=C
attached base packages: [1] stats graphics grDevices utils datasets methods base
other attached packages: [1] shiny_1.6.0 pavian_1.0.0
loaded via a namespace (and not attached):
[1] Rcpp_1.0.6 jquerylib_0.1.3 bslib_0.2.4 pillar_1.6.0 compiler_4.0.0
[6] later_1.1.0.1 shinyWidgets_0.6.0 shinyjs_2.0.0 tools_4.0.0 digest_0.6.27
[11] jsonlite_1.7.2 lifecycle_1.0.0 tibble_3.1.0 gtable_0.3.0 pkgconfig_2.0.3
[16] rlang_0.4.10 DBI_1.1.1 crosstalk_1.1.1 yaml_2.2.1 fastmap_1.1.0
[21] dplyr_1.0.5 sass_0.3.1 generics_0.1.0 vctrs_0.3.7 htmlwidgets_1.5.3
[26] DT_0.17 shinydashboard_0.7.1 grid_4.0.0 tidyselect_1.1.0 shinyFileTree_0.0.0.9000
[31] glue_1.4.2 R6_2.5.0 fansi_0.4.2 ggplot2_3.3.3 purrr_0.3.4
[36] magrittr_2.0.1 sankeyD3_0.3.2 scales_1.1.1 promises_1.2.0.1 ellipsis_0.3.1
[41] htmltools_0.5.1.1 assertthat_0.2.1 xtable_1.8-4 rhandsontable_0.3.7 mime_0.10
[46] colorspace_2.0-0 httpuv_1.5.5 utf8_1.2.1 munsell_0.5.0 cachem_1.0.4
[51] crayon_1.4.1
Hi @evezeyl , can you try updating once more? Pavian v1.1.0 should fix your issue again. Thanks!
Thanks! This is updated and working fine. Tested with large number of samples, no problem. All the best Eve
On Wed, Apr 14, 2021 at 9:17 AM Florian Breitwieser < @.***> wrote:
Hi @evezeyl https://github.com/evezeyl , can you try updating once more? Pavian v1.1.0 should fix your issue again. Thanks!
— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/fbreitwieser/pavian/issues/68#issuecomment-819289613, or unsubscribe https://github.com/notifications/unsubscribe-auth/AK3TRDNSAU7EJ4NIPEUR5TTTIU6Q5ANCNFSM4QEAED6A .
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Med vennlig hilsen/ best regards
Eve Zeyl Fiskebeck
Mobil: +47 45 41 56 90 email: @.*** https://no.linkedin.com/in/eve-fiskebeck-73a29bb
Thanks for the info @evezeyl .
@SilasK , @Vy5HAGit , I'll close this issue , but please feel free to open a new one with a sample file if it doesn't work for you
Hello I am trying to upload my report into pavian and it;s saying it can read the file format
it's a .txt file