Error loading GFA file

Question

Error loading GFA file

brettChapman opened this issue 4 years ago · comments

Hi

I'm trying to load my GFA file, but I'm getting an error.

gfaestus *.smooth.gfa *.smooth.chop.og.lay
loading GFA
loading GFA with 734 nodes, 1003 edges
adding nodes
adding edges
adding paths
created path handles
thread 'main' panicked at 'called `Result::unwrap()` on an `Err` value: stream did not contain valid UTF-8', src/main.rs:116:61
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

echo $RUST_BACKTRACE
1

I've also set the environment variable RUST_BACKTRACE=1 but still get no more information about the error.

I'm trying to visualise graphs produced from PGGB (https://github.com/pangenome/pggb). At the moment I'm only looking at small graphs representing a gene region. Thanks for any help you can provide.

Christian Fischer · Answer 1 · Fri Mar 12 2021 13:12:58 GMT+0800 (China Standard Time)

You need to have odgi output the layout file in TSV format (I think it's the -T command line flag) // Christian

…

-------- Original Message --------

On Mar 11, 2021, 9:59 PM, Brett Chapman wrote: Hi I'm trying to load my GFA file, but I'm getting an error. gfaestus *.smooth.gfa *.smooth.chop.og.lay loading GFA loading GFA with 734 nodes, 1003 edges adding nodes adding edges adding paths created path handles thread 'main' panicked at 'called `Result::unwrap()` on an `Err` value: stream did not contain valid UTF-8', src/main.rs:116:61 note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace echo $RUST_BACKTRACE 1 I've also set the environment variable RUST_BACKTRACE=1 but still get no more information about the error. I'm trying to visualise graphs produced from PGGB (https://github.com/pangenome/pggb). At the moment I'm only looking at small graphs representing a gene region. Thanks for any help you can provide. — You are receiving this because you are subscribed to this thread. Reply to this email directly, [view it on GitHub](#2), or [unsubscribe](https://github.com/notifications/unsubscribe-auth/AA6IDQGQFMCYQWYSFLSGPH3TDGGRXANCNFSM4ZBQQXZQ).

Brett Chapman · Answer 2 · Mon Mar 15 2021 16:00:24 GMT+0800 (China Standard Time)

Thanks. I managed to generate a TSV formatted layout file.

After running I now get a different error message:

gfaestus *.smooth-w400000-j10000-e10000-I0.9-p1_4_6_2_26_1.gfa *.smooth-w400000-j10000-e10000-I0.9-p1_4_6_2_26_1.chop.og.lay.tsv
loading GFA
loading GFA with 791 nodes, 1083 edges
adding nodes
adding edges
adding paths
created path handles
layout bounding box	(1000.00, 1000.00)	(6212.05, 1051.36)
layout width: 5212.05	height: 51.36
GFA loaded in 0.016 sec
Loaded 791 nodes	1582 points
thread 'main' panicked at 'called `Result::unwrap()` on an `Err` value: LoadingError(LibraryLoadFailure("dlopen(libvulkan.1.dylib, 1): image not found"))', src/main.rs:152:59
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Christian Fischer · Answer 3 · Mon Mar 15 2021 23:19:27 GMT+0800 (China Standard Time)

If you're on Mac, you need to have MoltenVK installed https://github.com/KhronosGroup/MoltenVK // Christian

…

-------- Original Message --------

On Mar 15, 2021, 3:00 AM, Brett Chapman wrote: Thanks. I managed to generate a TSV formatted layout file. After running I now get a different error message: gfaestus *.smooth-w400000-j10000-e10000-I0.9-p1_4_6_2_26_1.gfa *.smooth-w400000-j10000-e10000-I0.9-p1_4_6_2_26_1.chop.og.lay.tsv loading GFA loading GFA with 791 nodes, 1083 edges adding nodes adding edges adding paths created path handles layout bounding box (1000.00, 1000.00) (6212.05, 1051.36) layout width: 5212.05 height: 51.36 GFA loaded in 0.016 sec Loaded 791 nodes 1582 points thread 'main' panicked at 'called `Result::unwrap()` on an `Err` value: LoadingError(LibraryLoadFailure("dlopen(libvulkan.1.dylib, 1): image not found"))', src/main.rs:152:59 note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace — You are receiving this because you commented. Reply to this email directly, [view it on GitHub](#2 (comment)), or [unsubscribe](https://github.com/notifications/unsubscribe-auth/AA6IDQDLUFL4U255ZDRH53LTDW5CRANCNFSM4ZBQQXZQ).

Brett Chapman · Answer 4 · Mon Apr 12 2021 16:06:35 GMT+0800 (China Standard Time)

Hi, I've been trying to get the MoltenVK libraries installed on my Mac with no success. It doesn't look very straight forward to install the libraries.

I've tried:

xcodebuild build -quiet -project MoltenVKPackaging.xcodeproj -scheme "MoltenVK Package (macOS only)" -configuration "Debug"

And then running gfaestus again, but I still get the same error about loading libvulkan.1.dylib.

My MacBook Pro is running Catalina 10.15.7.

Is there a more straight forward way to install, perhaps through homebrew or similar? Thanks.

Brett Chapman · Answer 5 · Mon Apr 12 2021 16:50:34 GMT+0800 (China Standard Time)

I realised I hadn't installed dependencies. So I tried this:

./fetchDependencies --macos
sudo make macos
sudo make install

I still get the same error about libvulkan.1.dylib image not found.

Simon Heumos · Answer 6 · Wed May 05 2021 18:25:55 GMT+0800 (China Standard Time)

I have a similar problem with today's master, rust 1.51.0 and Archlinux:

gfaestus cerevisiae.pan.fa.aed9ce4.34ee7b1.891e76b.smooth.gfa cerevisiae.pan.fa.aed9ce4.34ee7b1.891e76b.smooth.og.lay.tsv
loading GFA
loading GFA with 636434 nodes, 878055 edges
adding nodes
adding edges
adding paths
created path handles
layout bounding box	(1000.00, 1000.00)	(1533269.38, 1849298.75)
layout width: 1532269.38	height: 1848298.75
GFA loaded in 4.641 sec
Loaded 636434 nodes	1272868 points
thread 'main' panicked at 'Validation layer not supported: VK_LAYER_KHRONOS_validation', src/vulkan/debug.rs:73:13
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Currently happening with all data sets I tried. Happy to share if you need some.

Christian Fischer · Answer 7 · Thu May 06 2021 09:38:14 GMT+0800 (China Standard Time)

I realised I hadn't installed dependencies. So I tried this:
./fetchDependencies --macos
sudo make macos
sudo make install
I still get the same error about libvulkan.1.dylib image not found.

I don't have a Mac, so I can't really help. I'd suggest trying another Vulkan app (these examples are easy to build: https://github.com/SaschaWillems/Vulkan); if they work, there's probably something wrong with gfaestus

Christian Fischer · Answer 8 · Thu May 06 2021 09:41:01 GMT+0800 (China Standard Time)

I have a similar problem with today's master, rust 1.51.0 and Archlinux:

gfaestus cerevisiae.pan.fa.aed9ce4.34ee7b1.891e76b.smooth.gfa cerevisiae.pan.fa.aed9ce4.34ee7b1.891e76b.smooth.og.lay.tsv
loading GFA
loading GFA with 636434 nodes, 878055 edges
adding nodes
adding edges
adding paths
created path handles
layout bounding box	(1000.00, 1000.00)	(1533269.38, 1849298.75)
layout width: 1532269.38	height: 1848298.75
GFA loaded in 4.641 sec
Loaded 636434 nodes	1272868 points
thread 'main' panicked at 'Validation layer not supported: VK_LAYER_KHRONOS_validation', src/vulkan/debug.rs:73:13
note: run with `RUST_BACKTRACE=1` environment variable to display a backtrace

Currently happening with all data sets I tried. Happy to share if you need some.

I think it's because it needs the Vulkan SDK, I'd accidentally set it up so even release builds use the debug features from the SDK.

Latest master should work without the SDK (though you may still need it to compile the shaders)

Simon Heumos · Answer 9 · Thu May 06 2021 15:58:00 GMT+0800 (China Standard Time)

Got it. Now it works for me, thank you very much @chfi !