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MetazoaPhylogenomicsLab / FANTASIA

GNU General Public License v3.0
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Issues with nohup #4

Closed fka21 closed 2 weeks ago

fka21 commented 8 months ago

Hello @gmartinezredondo,

Thanks for developing this great tool! I am very excited to test it on my own species, but I ran into some difficulties while running it. I am using a local high-performance computer and installed FANTASIA with both singularity and also the precompiled version of it after standard installation steps. With both versions, I attempted to run it with nohup, but I different error messages. I might have misunderstood something with the running instructions, if so please correct me.

Anyhow, here is the command used with the singularity version: nohup ./fantasia_sha256.06f759be1e48bf4f72aed0d4bb4fe2fd6e05774bb58131b131f0128c7b0efc84.sif --infile schMedA2_h1.pep --outpath ./ --prefix asmed &

And the error message from the nohup file: nohup_singularity_version.txt

For the precompiled version I used the commands: ../FANTASIA/generate_gopredsim_input_files.sh -i schMedA2_h1.pep -p -x asmed -o /projects/ferenc.kagan/Tools/FANTASIA/sandbox/ The above command finished without any errors (gopredsim conda environment was active while running).

After config file generation I used the following command: nohup ../FANTASIA/launch_gopredsim_pipeline.sh -m prott5 -x asmed -o /projects/ferenc.kagan/Tools/FANTASIA/sandbox &

And here is the error message from the nohup file: nohup_precompiled_version.txt

Any help is very welcome!

Cheers, Ferenc

gmartinezredondo commented 8 months ago

Hi, Ferenc! I'm not sure about the error with the singularity. It is not able to find your file. I've just tested it on my computer with nohup (I hadn't tried it before) and it works. I will run some tests to see if I can reproduce your error and find a solution. The second error is my fault. The version you probably have contains an old version of the script with some lines specific for loading libraries in my cluster. I uploaded a fixed version one or two days ago. Sorry for that.

gmartinezredondo commented 8 months ago

When you execute the singularity version, are there any output files in your home directory? I've been told of an issue related to this that gives the same error you get.

fka21 commented 8 months ago

Hi and thanks for the reply.

I have downloaded the most recent singularity image I think (it was uploaded March 13th) using the link in the git (https://cloud.sylabs.io/library/gemma.martinezredondo/fantasia/fantasia). The same is true for the precompiled version. I installed these versions on March 14th if that matters.

Interestingly, yes, there are output files in the home directory. Should I then run the pipeline from the home directory?

Cheers, Ferenc

gmartinezredondo commented 8 months ago

Try running the singularity from the home directory, yes. I'm trying to discover why this is happening and how to fix it.

About the precompiled version, I believe that in lines 14 and 15 in the launch_gopredsim_pipeline.sh script it says something like module load XXX. This has to be deleted. I will change this in the gzip.

fka21 commented 8 months ago

I tried running from the home directory and I am still facing the same issue. It is generating an empty config_files directory with embeddings and gopredsim subdirectories. Additionally, now I am testing to run it with screen and it is working so far.