ERROR: No matching distribution found for scipy==1.14.0

[cheong cheong]

Hi,

How are you?

I am trying to install majiq on HPC cluster and this error message shows up:

ERROR: Could not find a version that satisfies the requirement scipy==1.14.0 (from rna-majiq) (from versions: 0.8.0, 0.9.0, 0.10.0, 0.10.1, 0.11.0, 0.12.0, 0.12.1, 0.13.0, 0.13.1, 0.13.2, 0.13.3, 0.14.0, 0.14.1, 0.15.0, 0.15.1, 0.16.0, 0.16.1, 0.17.0, 0.17.1, 0.18.0, 0.18.1, 0.19.0, 0.19.1, 1.0.0, 1.0.1, 1.1.0, 1.2.0, 1.2.1, 1.2.2, 1.2.3, 1.3.0, 1.3.1, 1.3.2, 1.3.3, 1.4.0, 1.4.1, 1.5.0, 1.5.1, 1.5.2, 1.5.3, 1.5.4, 1.6.0, 1.6.1, 1.6.2, 1.6.3, 1.7.0, 1.7.1, 1.7.2, 1.7.3, 1.8.0rc1, 1.8.0rc2, 1.8.0rc3, 1.8.0rc4, 1.8.0, 1.8.1, 1.9.0rc1, 1.9.0rc2, 1.9.0rc3, 1.9.0, 1.9.1, 1.9.2, 1.9.3, 1.10.0rc1, 1.10.0rc2, 1.10.0, 1.10.1, 1.11.0rc1, 1.11.0rc2, 1.11.0, 1.11.1, 1.11.2, 1.11.3, 1.11.4, 1.12.0rc1, 1.12.0rc2, 1.12.0, 1.13.0rc1, 1.13.0, 1.13.1)

ERROR: No matching distribution found for scipy==1.14.0

how to resolve this?

Thank you.

[San Jewell]

Hi Cheong, are you using the recommended python version 3.10 on your cluster?

If so, please post the full output of the pip command.

Thanks,

-San

[cheong cheong]

Hi San,

Installed now but at the end of the installation message there are warnings like:

WARNING: The script waitress-serve is installed in '/home/cheong/.local/bin' which is not on PATH.

Consider adding this directory to PATH or, if you prefer to suppress this warning, use --no-warn-script-location.

should I do something about that?

Thank you.

[San Jewell]

Hi Cheong,

I would highly recommend that you install majiq/voila into a virtual environment, rather than your global user python packages location, that is $ python3.10 -m venv env ; source env/bin/activate ; pip install ...   This helps keep the requirements of each python software from conflicting with each other.

In regards to that message, if you'd like to keep using the installation in your global python packages installation  location anyway, you can address the warning by exporting a new path like $ export PATH=$PATH:/home/chrong/.local/bin   (this will only work for the current shell, you can put it somewhere like ~/.bashrc if you'd like the change to be permanent for all shells that you open)

Let me know if it makes sense,

Thanks,

-San

[cheong cheong]

Hi San

Yes i installed in a virtual environment now, and i tried to run majiq :

majiq --license /scratch/project/genetic_data_analysis/cheong/majiq/majiq_license_academic_official.lic build /scratch/project/genetic_data_analysis/cheong/geneannotations/gencode.v45.primary_assembly.annotation.gff3 --conf /scratch/project/genetic_data_analysis/cheong/majiq/config.txt --output /scratch/project/genetic_data_analysis/cheong/majiq/output

then i got the error:

Traceback (most recent call last):

  File "/scratch/project_mnt/S0007/cheong/majiq/majiq/lib/python3.10/site-packages/rna_majiq/src/config.py", line 76, in __init__

    sam_dirlist = general["bamdirs"].split(",")

KeyError: 'bamdirs'

During handling of the above exception, another exception occurred:

Traceback (most recent call last):

  File "/scratch/project_mnt/S0007/cheong/majiq/majiq/bin/majiq", line 8, in <module>

    sys.exit(main())

  File "/scratch/project_mnt/S0007/cheong/majiq/majiq/lib/python3.10/site-packages/rna_majiq/run_majiq.py", line 641, in main

    args.func(args)

  File "rna_majiq/src/build.pyx", line 649, in rna_majiq.src.build.build

  File "/scratch/project_mnt/S0007/cheong/majiq/majiq/lib/python3.10/site-packages/rna_majiq/src/basic_pipeline.py", line 13, in pipeline_run

    return pipeline.run()

  File "rna_majiq/src/build.pyx", line 656, in rna_majiq.src.build.Builder.run

  File "/scratch/project_mnt/S0007/cheong/majiq/majiq/lib/python3.10/site-packages/rna_majiq/src/config.py", line 35, in __new__

    Config.instance = Config.__Config(*argv)

  File "/scratch/project_mnt/S0007/cheong/majiq/majiq/lib/python3.10/site-packages/rna_majiq/src/config.py", line 79, in __init__

    raise UserWarning(

UserWarning: samdir is a deprecated value, please use bamdirs instead

[cheong cheong]

Hi San,

i realized rna_majiq is on the pip list but not the conda list, could it be a problem?

Thanks.

[cheong cheong]

Hi San,

it is running when i changed samdirs to bamdirs in the config file.

but now there is 0 LSV

i checked annoation DB and the bamfiles match eg. chr1. What might be the problem?

Thank you.

[San Jewell]

Hi Cheong,

Another thing I can think of might be that the strandness parameter is set incorrectly in the config file (e.g. https://biociphers.bitbucket.io/majiq-docs/getting-started-guide/builder.html)

I would recommend that you try to verify that is matches your BAM experiments. In the case that this is also not the issue, I cannot think of anything immediately obvious ; would you be opposed to sharing the data with me in a secure manner so that I can take a look at what might be going on for you?

Thanks,

-San

[cheong cheong]

Hi San,

I ran it without setting the experiment parameters (without the whole experiment section). Could this be the problem? 

[San Jewell]

Hi Cheong,

Yes, that would be the cause for a problem. The [experiments] section is required if you don't want an annotation-only run. IF you don't want any build groups, you can just specify every experiment on a different line, like

[experiments]

sample1=sample1

sample2=sample2

etc.

Thanks, -San

[cheong cheong]

Hi San,

my messages have been deleted on this forum....

I ran voila view,  it eventually return with a message saying it is serving on localhost:44979

but i cant reach the site when i put that in my browser, it says the site cant be reached, localhost refused to connect.

[San Jewell]

Hi Cheong,

Are you running voila on the same machine as your browser? Like your local laptop? Or some other machine?

[cheong cheong]

Hi San,

I am running it on HPC, and yes i am using the same computer.

[cheong cheong]

Hi San,

On top of the issue in not being able to view voila result on my broswer, i want to quickly ask if majiq has allowed the option to include covariate yet? Went through some older posts on this forum and saw it was on the way...

Thank you.

Cheong

[Astha Mishra]

Hi Cheong,

I am trying to install Voila and I am seeing the same error. Can you please let me know how you managed to resolve this error?

Thanks,

Astha

[San Jewell]

Hi Cheong,

If you are running voila on the hpc, and then trying to open the link from your local machine, it will not work directly. It depends on how your HPC networking is set up, if they are blocking ports, if you need to go through a bastion node to access the node you are running it on, etc. If you'd like to describe the general architecture of your HPC setup I can try to give some tips on how to connect, though this is unrelated to voila itself and would apply to any web server software that you run on your HPC (for example, a jupyter notebook)

Thanks,

-San

[cheong cheong]

Hi San,

i ran voila view and got the message:

Serving on http://localhost:44979

i put the url in google and got the error message:

This site cant be reached.

localhost refused to connect.

i went through some of the posts in the forum and changed localhost to 0.0.0.0, i still wouldnt work, same error messages.