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vinisalazar / metaphor

Metaphor: a general-purpose workflow for assembly and binning of metagenomes
https://metaphor-workflow.readthedocs.io/
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Metaphor execution cancelled #59

Closed o-enric closed 4 months ago

o-enric commented 10 months ago

Hello,

I managed to install and run Metaphor smoothly; however, when I noticed that the assembly quality was not satisfactory, I decided to interrupt the process and run it again as a coassembly.

After that, Metaphor didn't work, not even the test command. I've tried uninstalling everything and reinstalling it. I have also tried some functions from the troubleshooting section, such as "--unlock" and "--rerun-incomplete," but I haven't been successful.

Erro

metaphor test

Directory exists, skipping. Skipped 8 files.

Input file 'samples.csv' already exists. Skipping creation.

Starting Snakemake. This may require the installation of conda environments which should take a while.

You can suppress this confirmation message by running the Metaphor command with the -y flag.

Snakemake will start with 3 cores and 8192 MB RAM. Ok to continue? [y/N]

Metaphor execution cancelled. An error occurred while running Metaphor. Please check the traceback below.

There is no traceback below not even a snakemake.log in this directory.

vinisalazar commented 9 months ago

@otaviopin apologies for the delayed reply, somehow I missed this issue. Are you running Metaphor as a script? If you are, did you try adding the -y option to prevent the confirmation prompt?

Best, Vini

o-enric commented 9 months ago

Hi Vini Salazar, thank you very much for your attention.

I've already tried several things, including using the -y flag.

In this case, something like the problem described with the Atlas pipeline is happening, where the program remains stuck on 'Downloading and installing remote packages' indefinitely.

https://github.com/metagenome-atlas/atlas/issues/390

[image: image.png][image: image.png]

After many attempts, the root of my server installed a version in another conda environment that appears to work. With this version, I can run the test, but I'm encountering permission issues when attempting to run the samples.

Em ter., 26 de set. de 2023 às 01:44, Vini Salazar @.***> escreveu:

@otaviopin https://github.com/otaviopin apologies for the delayed reply, somehow I missed this issue. Are you running Metaphor as a script? If you are, did you try adding the -y option to prevent the confirmation prompt?

Best, Vini

— Reply to this email directly, view it on GitHub https://github.com/vinisalazar/metaphor/issues/59#issuecomment-1734822698, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCI5K7NH4FOYAAOKKVZCFBTX4JMRLANCNFSM6AAAAAA4NWR7OY . You are receiving this because you were mentioned.Message ID: @.***>

o-enric commented 9 months ago

Hi Vini Salazar, thank you very much for your attention.

I've already tried several things, including using the -y flag.

In this case, something like the problem described with the Atlas pipeline is happening, where the program remains stuck on 'Downloading and installing remote packages' indefinitely.

https://github.com/metagenome-atlas/atlas/issues/390

[image: image.png][image: image.png]

After many attempts, the root of my server installed a version in another conda environment that appears to work. With this version, I can run the test, but I'm encountering permission issues when attempting to run the samples.

[image: image.png]

Best,

Otavio

Em ter., 26 de set. de 2023 às 01:44, Vini Salazar @.***> escreveu:

@otaviopin https://github.com/otaviopin apologies for the delayed reply, somehow I missed this issue. Are you running Metaphor as a script? If you are, did you try adding the -y option to prevent the confirmation prompt?

Best, Vini

— Reply to this email directly, view it on GitHub https://github.com/vinisalazar/metaphor/issues/59#issuecomment-1734822698, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCI5K7NH4FOYAAOKKVZCFBTX4JMRLANCNFSM6AAAAAA4NWR7OY . You are receiving this because you were mentioned.Message ID: @.***>

vinisalazar commented 9 months ago

Hi @otaviopin,

thank you for your response. This does look like a permission issue or complications from a shared conda installation. Could you please provide more details on your computing environment? What's the OS, is it an individual or shared system, how was conda installed?

Best, Vini

o-enric commented 9 months ago

Hello Vini Salazar,

I'm using Ubuntu 22.04.2 LTS on a shared system.

To begin, I installed Conda by running the command bash Miniconda3-latest-Linux-x86_64.sh within my user account.

As I previously mentioned, the Metaphor software was initially functioning smoothly. It successfully completed the stage involving quality filters and successfully assembled six metagenomes. However, when I interrupted the program and subsequently restarted it, the first error message emerged.

To resolve the issue, I went ahead and uninstalled everything, including Conda and Metaphor. I then reinstalled Conda and Metaphor, and explored a few other troubleshooting steps. Unfortunately, none of these efforts yielded positive results.

Recognizing the persistence of the issue, I reached out to our server administrator for assistance. They installed Conda using the SH file obtained from anaconda.com, placing it in a shared directory alongside Metaphor. However, this installation attempt resulted in the appearance of a second error message, which appeared to be related to permission issues.

If you need further information or have any suggestions, please feel free to let me know.

Em ter., 26 de set. de 2023 às 22:57, Vini Salazar @.***> escreveu:

Hi @otaviopin https://github.com/otaviopin,

thank you for your response. This does look like a permission issue or complications from a shared conda installation. Could you please provide more details on your computing environment? What's the OS, is it an individual or shared system, how was conda installed?

Best, Vini

— Reply to this email directly, view it on GitHub https://github.com/vinisalazar/metaphor/issues/59#issuecomment-1736551257, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCI5K7IXXXEGY6VUSWODC63X4OBY3ANCNFSM6AAAAAA4NWR7OY . You are receiving this because you were mentioned.Message ID: @.***>

vinisalazar commented 9 months ago

Hello @otaviopin,

This does look like a problem related to your system/OS setup rather than a Metaphor problem. Personally, I would suggest having your own, user-level installation of Conda, especially if Metaphor was running smoothly that way before.

Did you try using the --unlock flag when restarting Metaphor after it crashed?

Thank you, Vini

o-enric commented 9 months ago

Hello Vini Salazar,

Thank you very much for your assistance.

I am currently continuing my work within my user-level Conda environment, following a pipeline that requires running several programs separately, including MEGAHIT and MetaPhlAn 4.

I've already tried to address the issue by using the '--unlock' flag.

Thank you,

Otavio

Em dom., 1 de out. de 2023 às 23:47, Vini Salazar @.***> escreveu:

Hello @otaviopin https://github.com/otaviopin,

This does look like a problem related to your system/OS setup rather than a Metaphor problem. Personally, I would suggest having your own, user-level installation of Conda, especially if Metaphor was running smoothly that way before.

Did you try using the --unlock flag when restarting Metaphor after it crashed?

Thank you, Vini

— Reply to this email directly, view it on GitHub https://github.com/vinisalazar/metaphor/issues/59#issuecomment-1742332692, or unsubscribe https://github.com/notifications/unsubscribe-auth/BCI5K7LPVP7NUX57CPCYE4TX5ITK5ANCNFSM6AAAAAA4NWR7OY . You are receiving this because you were mentioned.Message ID: @.***>

vinisalazar commented 4 months ago

I'll be closing this issue for now, but don't hesitate to reopen it if needed.