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knights-lab / SHOGUN

SHallow shOtGUN profiler
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Error Running UTREE with SHOGUN-BUGBASE #3

Closed cmstaley closed 7 years ago

cmstaley commented 7 years ago

I'm trying to run shogun_bugbase with the command

shogun_bugbase -i /panfs/roc/scratch/staleyc/byron/ssg/ -o /panfs/roc/scratch/staleyc/byron/ssg/shogun/ -u /home/sadowsky/staleyc/shogun_bugbase_db

Everything seems to have installed properly and is extracted. I think all of the paths are linked in the .bashrc. I have R ver 3.3.1 loaded and all of the packages (except grid) installed. I get the following error

Traceback (most recent call last): File "/home/sadowsky/staleyc/miniconda3/envs/shogun/bin/shogun_bugbase", line 11, in load_entry_point('ninja-shogun==0.0.1.dev0', 'console_scripts', 'shogun_bugbase')() File "/home/sadowsky/staleyc/miniconda3/envs/shogun/lib/python3.5/site-packages/click/core.py", line 716, in call return self.main(args, kwargs) File "/home/sadowsky/staleyc/miniconda3/envs/shogun/lib/python3.5/site-packages/click/core.py", line 696, in main rv = self.invoke(ctx) File "/home/sadowsky/staleyc/miniconda3/envs/shogun/lib/python3.5/site-packages/click/core.py", line 889, in invoke return ctx.invoke(self.callback, ctx.params) File "/home/sadowsky/staleyc/miniconda3/envs/shogun/lib/python3.5/site-packages/click/core.py", line 534, in invoke return callback(args, **kwargs) File "/home/sadowsky/staleyc/miniconda3/envs/shogun/lib/python3.5/site-packages/ninja_shogun/scripts/shogun_bugbase.py", line 51, in shogun_bugbase with open(utree_tsv) as inf: FileNotFoundError: [Errno 2] No such file or directory: '/panfs/roc/scratch/staleyc/byron/ssg/017.baseline.S12.utree.tsv'

I tried installing UTREE again using the compilation instructions with the shogun environment up and also copied the UTREE scripts into /miniconda3/envs/shogun/bin.

The only files in the input directory are .fna files and the log file from shi7en.

Any thoughts on how to fix this?

bhillmann commented 7 years ago

Can I get access to:

/panfs/roc/scratch/staleyc/byron/ssg/shogun

To see if anything is in there?

cmstaley commented 7 years ago

You should have access now, but I don't see anything there. The command failed pretty quickly.

bhillmann commented 7 years ago

I don't think UTree is working from those binaries.

Try running this with your environment active and let me know:

utree-search

@GabeAl Can you add you add 'static' compile to the makefile for UTree? The release binaries zip folder isn't working correctly because the binaries are a bit small.

cmstaley commented 7 years ago

UTree is not working: utree-search: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by utree-search)

GabeAl commented 7 years ago

Got it. Yes, for some reason the binary wasn't static. I will upload the static binaries within the hour.

Thanks for the report!

On Nov 22, 2016 10:42 AM, "Chris Staley" notifications@github.com wrote:

UTree is not working: utree-search: /lib64/libc.so.6: version `GLIBC_2.14' not found (required by utree-search)

— You are receiving this because you were mentioned. Reply to this email directly, view it on GitHub https://github.com/knights-lab/SHOGUN/issues/3#issuecomment-262293887, or mute the thread https://github.com/notifications/unsubscribe-auth/AHrXBuhVQMxMep_kpjGrSUuY3Tfxtnjhks5rAxuLgaJpZM4K4pcT .

cmstaley commented 7 years ago

Thanks. I reinstalled UTree this morning and the command worked.

bhillmann commented 7 years ago

I am closing this issue. It sounds like everything worked.