marcos-diazg / musica Goto Github PK

While MAF or TSV type was chosen, the program still takes it as vcf and throws out the error "Wrong vcf types".

Update README with information about the R version use for development for users to select as preferred

When only one sample is selected, the sample name does not appear in the plots or table, it says "my_contributions[30:1,]"

bioclite is depricated, consider updateing README.md with BiocManager

I have uploaded 109 files trying to run mutational signatures analysis, but an error occurs and I cannot get the results. it seems that the server is very busy?

Submit button is missing.

In bowser:

An error has occurred!
shinyjs: extendShinyjs: functions argument must not contain any of the following function names: refresh

In command line:

$ echo 'shiny::runApp()' | Rscript -
Loading required package: shiny

Listening on http://127.0.0.1:5351

Attaching package: ‘shinysky’

The following object is masked from ‘package:shiny’:

actionButton

Attaching package: ‘shinyjs’

The following object is masked from ‘package:shiny’:

runExample

The following objects are masked from ‘package:methods’:

removeClass, show

Using V8 engine 8.9.83
Loading required package: ggplot2

Attaching package: ‘plotly’

The following object is masked from ‘package:ggplot2’:

last_plot

The following object is masked from ‘package:stats’:

filter

The following object is masked from ‘package:graphics’:

layout

Warning: Error in : shinyjs: extendShinyjs: functions argument must not contain any of the following function names:
refresh
70: stop
69: errMsg
68: shinyjs::extendShinyjs
1: shiny::runApp
Warning: Error in : shinyjs: extendShinyjs: functions argument must not contain any of the following function names:
refresh
70: stop
69: errMsg
68: shinyjs::extendShinyjs
1: shiny::runApp

Hi,

Thank you for developing such a useful tool. I am trying to analyze mutation signatures using somatic data downloaded from TCGA in the maf format. I realized that the files were too loarge for the web app and have installed the R app but after I select my maf files for analysis, I get errors.

Specifically I am getting:

Warning: Error in scanBcfHeader: no 'header' line "#CHROM POS ID..."?
Warning: Error in if: argument is of length zero
Warning: Error in round: non-numeric argument to mathematical function

The maf files are the raw files from the TCGA, so do I have to do any manipulation or changes before uploading them in the app for analysis

Thanks, would appreciate your feedback

Hi,

Could not install musica on my Ubuntu machine due to dependency issues. While changing the entries in musica_env.yml to linux-x64 seemed to resolve al lot of it, some still remain. Is it possible, those packages are MacOS specific?

Best,
Jan

Hello,

Thanks for making this useful tool.
I met an issue for online analysis. After I click "Run" (I tried vcf and tsp format, no problem with upload). I got "Disconnected from the server" on the screen and no results comes out.

Thanks,
Shan

Hi,

I am trying to run musica on multiple .tsv files, but I get the following error. I could not easily pinpoint the problem. Any help with this error message is appreciated:

[E::COMPAT_bcf_hdr_read] Input is not detected as bcf or vcf format
Warning: Error in scanBcfHeader: no 'header' line "#CHROM POS ID..."?
  167: scanBcfHeader
  165: <Anonymous>
  164: mapply
  163: Map
  158: Map
  157: scanBcfHeader
  155: scanVcfHeader
  153: .scanVcfToVCF
  152: .readVcf
  151: .local
  150: readVcf
  147: FUN
  146: lapply
  145: mclapply
  144: read_vcfs_as_granges
  143: eventReactiveHandler [C:\...\shinyapp4b705a323111\musica-master/server.R#223]
   99: vcfs
   98: renderUI [C:\...\shinyapp4b705a323111\musica-master/server.R#473]
   97: func
   84: origRenderFunc
   83: output$selected_samples
    3: runApp
    2: runUrl
    1: runGitHub

My input tsv files comply with the proposed file structure:

CHROM	POS	REF	ALT
chr1	43869309	G	C
chr6	46111021	G	T
chr4	88996682	G	A
chr14	94845810	T	C
chr14	51192683	T	G
chr1	31744245	T	C
chr6	15496431	G	T
chr15	64017683	A	G

> sessionInfo()
R Under development (unstable) (2019-02-13 r76098)
Platform: x86_64-w64-mingw32/x64 (64-bit)
Running under: Windows >= 8 x64 (build 9200)

Matrix products: default

locale:
[1] LC_COLLATE=English_United States.1252  LC_CTYPE=English_United States.1252    LC_MONETARY=English_United States.1252
[4] LC_NUMERIC=C                           LC_TIME=English_United States.1252    

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base     

other attached packages:
 [1] BSgenome.Hsapiens.UCSC.hg38_1.4.1 BSgenome_1.51.0                   rtracklayer_1.43.2                stringr_1.4.0                    
 [5] dplyr_0.8.0.1                     Seurat_3.0.0                      ggrepel_0.8.0                     readxl_1.2.0                     
 [9] openxlsx_4.1.0                    gplots_3.0.1.1                    heatmaply_0.16.0                  viridis_0.5.1                    
[13] viridisLite_0.3.0                 VariantAnnotation_1.30.0          Rsamtools_1.99.1                  Biostrings_2.51.2                
[17] XVector_0.23.0                    SummarizedExperiment_1.13.0       DelayedArray_0.9.8                BiocParallel_1.17.13             
[21] matrixStats_0.54.0                data.table_1.12.0                 reshape2_1.4.3                    MutationalPatterns_1.10.0        
[25] NMF_0.21.0                        Biobase_2.43.1                    cluster_2.0.7-1                   rngtools_1.3.1                   
[29] pkgmaker_0.27                     registry_0.5                      GenomicRanges_1.35.1              GenomeInfoDb_1.19.2              
[33] IRanges_2.17.4                    S4Vectors_0.21.10                 BiocGenerics_0.29.1               plotly_4.8.0                     
[37] ggplot2_3.1.0                     shinythemes_1.1.2                 V8_2.2                            shinyjs_1.0                      
[41] shinysky_0.1.2                    plyr_1.8.4                        RJSONIO_1.3-1.1                   shinyBS_0.61                     
[45] shiny_1.2.0                      

loaded via a namespace (and not attached):
  [1] igraph_1.2.4             lazyeval_0.2.1           splines_3.6.0            listenv_0.7.0            gridBase_0.4-7          
  [6] digest_0.6.18            foreach_1.4.4            htmltools_0.3.6          rsconnect_0.8.13         gdata_2.18.0            
 [11] magrittr_1.5             memoise_1.1.0            doParallel_1.0.14        ROCR_1.0-7               gclus_1.3.2             
 [16] globals_0.12.4           R.utils_2.8.0            prettyunits_1.0.2        colorspace_1.4-0         blob_1.1.1              
 [21] crayon_1.3.4             RCurl_1.95-4.11          jsonlite_1.6             zoo_1.8-6                survival_2.43-3         
 [26] iterators_1.0.10         ape_5.2                  glue_1.3.1               gtable_0.2.0             zlibbioc_1.29.0         
 [31] webshot_0.5.1            future.apply_1.2.0       scales_1.0.0             DBI_1.0.0                bibtex_0.4.2            
 [36] Rcpp_1.0.1               metap_1.1                xtable_1.8-4             progress_1.2.0           reticulate_1.10         
 [41] rsvd_1.0.0               bit_1.1-14               SDMTools_1.1-221         tsne_0.1-3               htmlwidgets_1.3         
 [46] httr_1.4.0               RColorBrewer_1.1-2       ica_1.0-2                pkgconfig_2.0.2          XML_3.98-1.17           
 [51] R.methodsS3_1.7.1        tidyselect_0.2.5         labeling_0.3             rlang_0.3.4              later_0.8.0             
 [56] AnnotationDbi_1.42.1     munsell_0.5.0            cellranger_1.1.0         tools_3.6.0              RSQLite_2.1.1           
 [61] ggridges_0.5.1           ggdendro_0.1-20          yaml_2.2.0               npsurv_0.4-0             bit64_0.9-7             
 [66] fitdistrplus_1.0-14      zip_1.0.0                caTools_1.17.1.1         purrr_0.3.2              RANN_2.6.1              
 [71] dendextend_1.12.0        pbapply_1.4-0            future_1.12.0            nlme_3.1-137             mime_0.6                
 [76] R.oo_1.22.0              pracma_2.2.5             biomaRt_2.36.1           compiler_3.6.0           rstudioapi_0.9.0        
 [81] png_0.1-7                curl_3.3                 lsei_1.2-0               tibble_2.1.3             stringi_1.2.4           
 [86] GenomicFeatures_1.32.3   lattice_0.20-38          Matrix_1.2-15            pillar_1.3.1             Rdpack_0.10-1           
 [91] lmtest_0.9-36            irlba_2.3.3              cowplot_0.9.4            bitops_1.0-6             gbRd_0.4-11             
 [96] seriation_1.2-3          httpuv_1.4.5.1           R6_2.4.0                 promises_1.0.1           TSP_1.1-6               
[101] KernSmooth_2.23-15       gridExtra_2.3            codetools_0.2-16         MASS_7.3-51.1            gtools_3.8.1            
[106] assertthat_0.2.1         withr_2.1.2              sctransform_0.2.0        GenomicAlignments_1.19.1 GenomeInfoDbData_1.2.0  
[111] hms_0.4.2                grid_3.6.0               tidyr_0.8.2              Rtsne_0.15     

Error when all samples are selected in mutational profile tab: "subscript out of bounds"

I have a VCF file generated using Mutect2 and filtered using FilterMutectCalls (GATK). It contains all types of mutations (somatic, germline, SNVs, insertions/deletions) and they are labelled. In order to perform a mutational signature analysis using musica, should the germline and indel mutations be filtered out and only SNVs should be given as input?

Also, since I am working on RNA-seq data, would choosing Whole exome sequencing option work?

Hello,

I tried the web vesion of MuSiCa with a multi sample MAF file. However, I got an error :

I emailed you, with the MAF file, but it got rejected by your email security, probably because of the MAF extension.

Could it be a problem with my MAF file ? I tried with one with only one sample and I got the same error.

Thank you for your help,

Pauline

Hi,

I am running the Musica locally and it always failed when I try to upload a TCGA maf files. (tsv files works well)
Just curious, is there a template maf file I can use to modify the TCGA maf files?

Thank you.
Xin

Is there a way to run musica with command line? I'd like to create docker image for it.

Can Musica be used for analysis of Whole Exome Data.??

Hello,
I tried uploading a full maf file, but naturally this was too big. I then cut out only the first sample, and recieved a non-specified error. File type seemed fine.
Any ideas what I can try?
Thanks so much,
Avi

Hi, I understand that we have to include four mandatory columns including CHROM, POS, REF, and ALT. I wonder where to put the sample names. I tried for a couple of times and could not get it to work. Thank you.

Hello,

I explore cancer in a OneHealth manner across numerous species. Can MuSiCa be adapted to other reference genomes and annotations?

When trying to install dependencies, there is a problem installing ShinySky.

Also, web-app is down.

• installing source package 'shinysky' ...
  ** R
  ** inst
  ** byte-compile and prepare package for lazy loading
  Error : (converted from warning) package 'shiny' was built under R version 3.5.3
  ERROR: lazy loading failed for package 'shinysky'
• removing 'C:/Users/lcheung1/Documents/R/R-3.5.2/library/shinysky'
  In R CMD INSTALL
  Error in i.p(...) :
  (converted from warning) installation of package ‘C:/Users/lcheung1/AppData/Local/Temp/RtmporL0QN/file13e6e062211299/shinysky_0.1.2.tar.gz’ had non-zero exit status

131: stop
130: mut_matrix
129: reactive:mut_mat [/home/xie/Workspace/R/musica/server.R#261]
113: mut_mat
111: reactive:fit_res [/home/xie/Workspace/R/musica/server.R#278]
95: fit_res
92: renderUI [/home/xie/Workspace/R/musica/server.R#458]
91: func
78: origRenderFunc
77: output$selected_samples
1: runApp

Installed from git
OS: Ubuntu 18.04
R version 3.4.4 (2018-03-15) -- "Someone to Lean On"

Hi,
first of all thank you for this amazing, intuitive tool. It's so great to be able to detect mutational signature and compare to existing ones using one button!
I would like to report an issue regarding downloaded plots. It seems that some information is cut off, e.g.
prof96_plot: n in Relative contribution, the name of the file if it's longer than ~10 characters
signatures_plot: the name of the file on the bottom, values on the scale are not displayed fully
comparison_with_cancers: names of signatures are pretty tight (that's lower priority) but the names of cancers like nasopharyngeal carcinoma or oral gingivo buccal squamous (cell carcinoma) are cut off, also the name of the file if it's as long
I am using only one sample.
Thanks so much!
Musica_infoCutOff.pdf