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fbreitwieser / pavian

🌈 Interactive analysis of metagenomics data
https://doi.org/10.1093/bioinformatics/btz715
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centrifuge output won't load #33

Closed tom-dyar closed 5 years ago

tom-dyar commented 6 years ago

Hi,

I made a tsv from centrifuge (latest from github, default options) that I have attached. I try to load this in Pavian, but get this output:

Warning: Error in $<-.data.frame: replacement has 0 rows, data has 5 Stack trace (innermost first): 82: $<-.data.frame 81: $<- [/Users/tdyar/workspace/pavian/R/datainput-read_report.R#556] 80: read_report [/Users/tdyar/workspace/pavian/R/datainput-read_report.R#556] 79: FUN [/Users/tdyar/workspace/pavian/R/datainput-read_sample_data.R#73] 78: lapply 77: sapply 76: read_sample_data [/Users/tdyar/workspace/pavian/R/datainput-read_sample_data.R#73] 75: read_server_directory1 [/Users/tdyar/workspace/pavian/R/datainput-read_server_directory.R#75] 74: read_server_directory2 [/Users/tdyar/workspace/pavian/R/datainput-module.R#229] 73: eval [/Users/tdyar/workspace/pavian/R/datainput-module.R#223] 72: eval 71: withProgress 70: read_server_directory [/Users/tdyar/workspace/pavian/R/datainput-module.R#223] 69: observeEventHandler [/Users/tdyar/workspace/pavian/R/datainput-module.R#382] 2: shiny::runApp 1: runApp [#54] [May18 11:34] Exiting session #1

Thanks! Tom centr_Day11MMVpellet_S1_L004.txt

fbreitwieser commented 5 years ago

Hi @tom-dyar , sorry for the late reply. You need to run centrifuge-kreport - the standard centrifuge output currently is not supported since it does not contain the taxonomic tree.