Not open my vcf file?

Question

Not open my vcf file?

Gon1976 opened this issue 3 years ago · 20 comments

Gon1976 commented 3 years ago

Hi
I am trying to run viva on windows after intall Julia 1.7.2 .

I launch viva in the powershell with:
viva -f AMvsJJref.vcf -s pdf -o .

After a julia open and load packages, only 1 second after close thw window. I can see the message using PrintScreen and the only I can see after "Finished leading packages!" is "required option --vcf_file was not provided"

My first lines of vcf file are:
V tig00000057_pilon_pilon 165830 165830 1 60 - ttttttttttt tig00000271_pilon_pilon 111839 111850 +
V tig00000057_pilon_pilon 165870 165871 1 60 t c tig00000271_pilon_pilon 111890 111891 +
V tig00000057_pilon_pilon 165903 165905 1 60 tc - tig00000271_pilon_pilon 111923 111923 +

thanks for you support
Gonzalo

Answer 1 · 2022-03-25T20:34:24.000Z

@Gon1976 Hi Gonzalo,

Lets solve this! It looks like the argument parsing function is throwing an error. Can you send me the compete output you get when running viva -h?

Also, can you try adding the compete filepath to the vcf file in the command?

Answer 2 · 2022-03-29T17:49:43.000Z

Hi
when I run viva -h after select Julia1.7 to run the comand a new windows open but the window closes inmedately.

I can, only make a screen capture.
I am launching viva from the directory I have the vcf file. But I try also include all the filepath.
I am view two warnings also. Now I make de vcf file using sniffles2.0.
Thanks
gonzalo

Answer 3 · 2022-03-29T17:57:24.000Z

I can solve the first warning running powershell as administrator. But still can run viva

Answer 4 · 2022-03-29T18:02:48.000Z

Hi @Gon1976 ,

Thank you, this is helpful. Are you using 64-bit or 32-bit version of Windows?

The second warning (ORCA.jl) should not be affecting the run. We may make changes to replace the deprecated functionality in the future but this shouldn't affect the run currently.

I see that when you ran viva -h, a new windows appears with the script output and closes when the help message is displayed, which is expected. When you ran the other viva commands in your screenshot (like viva -f <your_file.vcf> -o . -m read_depth) did they also open the temporary window and display any message?

Last, have you tried running the full viva commands to produce plots administrator yet so that the Kaledio package is available for plotting? Or did you only run viva -h as administrator? When you run the full viva command to produce plots as administrator, what output do you see? Can you attach the complete text of the output?

Thank you,
George

Answer 5 · 2022-03-29T18:19:11.000Z

Hi George,
I am using Windows 64-bit.

When I run viva -f myfile.vcf -s pdf -o . the same happened (the windows open and closes after the help message is displayed). The only I can see is "required option --vcf_file was not provided". I try running the full viva command as administrator. No plots were produced. The complete text of the ouput is the same as I send in the print screen image.
Gonzalo

Answer 6 · 2022-03-29T18:33:38.000Z

Thanks @Gon1976,

Can you try running the same commands using the test VCF file called test_4X_191.vcf which we provide here: https://github.com/compbiocore/VariantVisualization.jl/tree/master/test/test_files and let me know what the output message says?

Answer 7 · 2022-03-29T18:37:42.000Z

I download the file and the same output message (no output generated)

Answer 8 · 2022-03-29T19:34:07.000Z

I see. I think what's going on here is that when the command is run, the command is not receiving any of the argument inputs. I think this is the case because, when looking back on your output screenshot, I see that when you ran viva -h, it did not show the expected -h help response but rather it showed that it expected the required VCF input.

I have a few questions about your set up. Are you running on a personal windows computer or shared server? What version of Windows are you using? Are you using PowerShell or Windows Command Prompt to run the Julia executable?

Finally, can you show the output that you receive when you run the following commands to update VariantVisualization.jl:

julia
]add VariantVisualization
exit()

Thanks,
George

Answer 9 · 2022-03-29T19:54:51.000Z

I am running in a windows computer (Intel Core i7-7700, 3.6GHz with 32 Gb RAM) with Windows 10 Pro.
I am using PowerShell to run Julia.
If I run again ]add Variant Visualization, I have this message:

Updating registry at C:\Users\ggreif\.julia\registries\General.toml
Resolving package versions...
No Changes to C:\Users\ggreif\.julia\environments\v1.7\Project.toml
No Changes to C:\Users\ggreif\.julia\environments\v1.7\Manifest.toml

Answer 10 · 2022-03-29T20:09:24.000Z

Ok, I'll try to think about reasons that the viva script isn't receiving the command line arguments via argparse. This may be a bit out of my wheelhouse, since it seems like a system configuration issue rather than a bug with VIVA, but we'll get to the bottom of it!

Did you add Julia to the PATH using these instructions for Windows 10: https://julialang.org/downloads/platform/

I noticed that when you called julia in Powershell, it did not open the REPL as expected.

Answer 11 · 2022-03-30T15:21:10.000Z

Hi George
I really sorry about the problem.
I add Julia to the PATH. Now I can call Julia in powershell and it start Julia prompt. But viva still not work.
Gonzalo

Answer 12 · 2022-03-30T16:41:57.000Z

@Gon1976 No worries!

Do you have access to a system admin or support service team in your institution? I think whats going on here is that the command line arguments aren't being passed to the script for some reason.

Once you have a proper setup, you should be able to execute viva with the viva -h command to see the help output without specifying a -f option. Once the commands are imported into viva properly and you don't get the required --vcf_file argument not provided message, everything should work ok.

We'll figure this out!

Answer 13 · 2022-03-30T19:45:28.000Z

Hi George
I start julia, and under pkg ( ] ) I check the options and I run "test VariantVisualization" and found some errors, maybe related with the problem. I attach the capture of the screen. What do you think? Can add VariantVisualization from source?
Gonzal

Answer 14 · 2022-03-30T20:14:28.000Z

Hi @Gon1976 ,

It looks like a bug may have been introduced when the Julia version was updated that affected the select_columns function within the VariantVisualization.jl package. However this shouldn't be causing the described argument parsing issue as long as the package was installed without errors.

To be sure, can you update VariantVisualization within the pkg prompt and send me a screenshot or paste of the complete output?

pkg> update Example

Answer 15 · 2022-03-31T11:56:18.000Z

I update Variant Visualization:

(@v1.7) pkg> update VariantVisualization
Updating registry at C:\Users\ggreif\.julia\registries\General.toml
Installed Parsers ─ v2.2.4
No Changes to C:\Users\ggreif\.julia\environments\v1.7\Project.toml
Updating C:\Users\ggreif\.julia\environments\v1.7\Manifest.toml
[69de0a69] ↑ Parsers v2.2.3 ⇒ v2.2.4
Precompiling project...
13 dependencies successfully precompiled in 27 seconds (63 already precompiled)

It's look like Parsers was updated. But I try again test VariantVisualization, and the same errors appears.

Gonzalo

Answer 16 · 2022-04-04T18:29:56.000Z

I send the complete output of : test VariantVisualization
Warning: DataFrame(t::Type, nrows::Integer, ncols::Integer) is deprecated, use DataFrame([Vector{t}(undef, nrows) for i = 1:ncols]) instead.
│ caller = ip:0x0
└ @ Core :-1
┌ Warning: names!(df::AbstractDataFrame, vals::Vector{Symbol}; makeunique::Bool = false) is deprecated, use rename!(df, vals, makeunique = makeunique) instead.
│ caller = sortcols_by_phenotype_matrix(pheno_matrix_filename::String, trait_to_group_by::String, num_array::Matrix{Int64}, sample_names::Matrix{Symbol}) at vcf_utils_complete.jl:856
└ @ VariantVisualization C:\Users\ggreif.julia\packages\VariantVisualization\1yoNl\src\vcf_utils_complete.jl:856
select_columns: Error During Test at C:\Users\ggreif.julia\packages\VariantVisualization\1yoNl\test\new_vcf_utils.jl:247
Got exception outside of a @test
MethodError: no method matching rename!(::DataFrames.DataFrame, ::Base.Generator{Base.Iterators.Zip{Tuple{Vector{String}, Matrix{Symbol}}}, VariantVisualization.var"#44#45"})
Closest candidates are:
rename!(::DataFrames.AbstractDataFrame, ::AbstractVector{Symbol}; makeunique) at C:\Users\ggreif.julia\packages\DataFrames\GtZ1l\src\abstractdataframe\abstractdataframe.jl:169
rename!(::DataFrames.AbstractDataFrame, ::AbstractVector{<:AbstractString}; makeunique) at C:\Users\ggreif.julia\packages\DataFrames\GtZ1l\src\abstractdataframe\abstractdataframe.jl:175
rename!(::DataFrames.AbstractDataFrame, ::AbstractVector{Pair{Symbol, Symbol}}) at C:\Users\ggreif.julia\packages\DataFrames\GtZ1l\src\abstractdataframe\abstractdataframe.jl:181
...
Stacktrace:
[1] select_columns(filename_sample_list::String, num_array::Matrix{Int64}, sample_names::Matrix{Symbol})
@ VariantVisualization C:\Users\ggreif.julia\packages\VariantVisualization\1yoNl\src\vcf_utils_complete.jl:890
[2] macro expansion
@ C:\Users\ggreif.julia\packages\VariantVisualization\1yoNl\test\new_vcf_utils.jl:248 [inlined]
[3] macro expansion
@ D:\Downloads\julia-1.7.2-win64\julia-1.7.2\share\julia\stdlib\v1.7\Test\src\Test.jl:1283 [inlined]
[4] macro expansion
@ C:\Users\ggreif.julia\packages\VariantVisualization\1yoNl\test\new_vcf_utils.jl:248 [inlined]
[5] macro expansion
@ D:\Downloads\julia-1.7.2-win64\julia-1.7.2\share\julia\stdlib\v1.7\Test\src\Test.jl:1283 [inlined]
[6] macro expansion
@ C:\Users\ggreif.julia\packages\VariantVisualization\1yoNl\test\new_vcf_utils.jl:223 [inlined]
[7] macro expansion
@ D:\Downloads\julia-1.7.2-win64\julia-1.7.2\share\julia\stdlib\v1.7\Test\src\Test.jl:1283 [inlined]
[8] macro expansion
@ C:\Users\ggreif.julia\packages\VariantVisualization\1yoNl\test\new_vcf_utils.jl:171 [inlined]
[9] macro expansion
@ D:\Downloads\julia-1.7.2-win64\julia-1.7.2\share\julia\stdlib\v1.7\Test\src\Test.jl:1283 [inlined]
[10] macro expansion
@ C:\Users\ggreif.julia\packages\VariantVisualization\1yoNl\test\new_vcf_utils.jl:158 [inlined]
[11] macro expansion
@ D:\Downloads\julia-1.7.2-win64\julia-1.7.2\share\julia\stdlib\v1.7\Test\src\Test.jl:1283 [inlined]
[12] top-level scope
@ C:\Users\ggreif.julia\packages\VariantVisualization\1yoNl\test\new_vcf_utils.jl:14
[13] include(mod::Module, _path::String)
@ Base .\Base.jl:418
[14] include(x::String)
@ Main.TestVariantVisualization C:\Users\ggreif.julia\packages\VariantVisualization\1yoNl\test\runtests.jl:1
[15] top-level scope
@ C:\Users\ggreif.julia\packages\VariantVisualization\1yoNl\test\runtests.jl:23
[16] include(fname::String)
@ Base.MainInclude .\client.jl:451
[17] top-level scope
@ none:6
[18] eval
@ .\boot.jl:373 [inlined]
[19] exec_options(opts::Base.JLOptions)
@ Base .\client.jl:268
[20] _start()
@ Base .\client.jl:495

Answer 17 · 2022-04-07T12:23:53.000Z

Hi @gtollefson

could you see the test output? Do you see the error? Or any new test I can make to solve the problem?
best
gonzalo

Answer 18 · 2022-04-26T19:05:18.000Z

Hi @gtollefson
do you have any help?

Gonzalo

Answer 19 · 2022-08-25T08:19:20.000Z

I am also facing the same issue. Could you find a solution?
Thanks

Answer 20 · 2022-08-29T16:25:06.000Z

No, I dont have answer to my last comments. And I stop to try work with the package