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raw-lab / MetaCerberus

Python code for versatile Functional Ontology Assignments for Metagenomes searching via Hidden Markov Model (HMM) with environmental focus of shotgun metaomics data
BSD 3-Clause "New" or "Revised" License
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IOError: [RayletClient] Unable to register worker with raylet #17

Closed ereyred closed 4 months ago

ereyred commented 4 months ago

Hello, I don't know what this RAY problem is, but when I try to run my predictions: metacerberus.py --prodigal preds.faa --illumina --meta --dir_out /out/ OR metacerberus.py --prodigal preds.faa --hmm ALL --dir_out /out/ --meta it gives me this error: Initializing RAY 2024-06-04 15:27:40,142 ERROR services.py:1329 -- Failed to start the dashboard , return code -11 2024-06-04 15:27:40,143 ERROR services.py:1354 -- Error should be written to 'dashboard.log' or 'dashboard.err'. We are printing the last 20 lines for you. See 'https://docs.ray.io/en/master/ray-observability/ray-logging.html#logging-directory-structure' to find where the log file is. 2024-06-04 15:27:40,143 ERROR services.py:1398 -- The last 20 lines of /tmp/ray/session_2024-06-04_15-27-38_566097_2044722/logs/dashboard.log (it contains the error message from the dashboard): 2024-06-04 15:27:39,995 INFO head.py:254 -- Starting dashboard metrics server on port 44227

2024-06-04 15:27:40,291 INFO worker.py:1673 -- Started a local Ray instance. [2024-06-04 15:27:42,626 E 2044722 2044722] core_worker.cc:205: Failed to register worker 01000000ffffffffffffffffffffffffffffffffffffffffffffffff to Raylet. IOError: [RayletClient] Unable to register worker with raylet. No such file or directory

Is there a way to run MetaCerberus without this RAY thing? Could you explain a bit more what it is? Also, I want to run MetaCerberus with my ORF predictions file (pipeline option 3) and output functional annotations and visualise them on pathview. Which code should I use? Are the two I wrote above wrong for this? I was trying with only one sample, should I try with 4 samples? If so, how do I input these? Do I input all samples in one directory? metacerberus.py --prodigal [preds.faa directory] --illumina --meta --dir_out /out/

Thank you! E

raw-lab commented 4 months ago

Version of metacerberus: Version of os:

We fixed this in the new conda 1.3. Re-install metacerberus 1.3 manually should fix it.

ereyred commented 4 months ago

Hey, so I did install 1.3, I followed the installation instructions you gave w conda to install 1.3

raw-lab commented 4 months ago

You will need to delete and re-install. We included a software patch for Ray.

You should be able to use the standard mamba install as 1.3 is finally on bioconda.

Sorry for this. It is unfortunately conda and Ray issues that are beyond our control.

Let us know if you have any further issues?

Thank you for using MetaCerberus

ereyred commented 4 months ago

Sorry if I was unclear, I mean that I had already installed 1.3 via conda when I got this error. I installed it today and followed the most up to date conda install instructions with v1.3

ereyred commented 4 months ago

Do you mean I have to install with mamba and not conda?

raw-lab commented 4 months ago

Which install did you use: Option 1: git clone https://github.com/raw-lab/MetaCerberus.git cd MetaCerberus bash install_metacerberus.sh conda activate MetaCerberus-1.3.0 metacerberus.py --download

Or option 2: mamba create -n metacerberus -c bioconda -c conda-forge metacerberus conda activate metacerberus metacerberus.py --setup

As we fixed it in the straight mamba version option 2.

I can double check manual.

ereyred commented 4 months ago

Oh I did Option 1. But I don't have mamba so I edited install_metacerberus.sh to say conda install instead of mamba install. Should I do Option 2?

raw-lab commented 4 months ago

Are you on a Mac? Or linux? Try option 2 and let me know? Install mamba.

ereyred commented 4 months ago

I'm on Linux. I installed mamba through miniforge3 and then installed metacerberus 1.3.0 again through mamba using Option 2 and it still gives me the same error:

Initializing RAY 2024-06-05 11:02:05,887 ERROR services.py:1329 -- Failed to start the dashboard , return code -11 2024-06-05 11:02:05,887 ERROR services.py:1354 -- Error should be written to 'dashboard.log' or 'dashboard.err'. We are printing the last 20 lines for you. See 'https://docs.ray.io/en/master/ray-observability/ray-logging.html#logging-directory-structure' to find where the log file is. 2024-06-05 11:02:05,888 ERROR services.py:1398 -- The last 20 lines of /tmp/ray/session_2024-06-05_11-02-04_250334_3035553/logs/dashboard.log (it contains the error message from the dashboard): 2024-06-05 11:02:05,756 INFO head.py:254 -- Starting dashboard metrics server on port 44227

2024-06-05 11:02:06,040 INFO worker.py:1673 -- Started a local Ray instance. [2024-06-05 11:02:08,585 E 3035553 3035553] core_worker.cc:205: Failed to register worker 01000000ffffffffffffffffffffffffffffffffffffffffffffffff to Raylet. IOError: [RayletClient] Unable to register worker with raylet. No such file or directory

metacerberus.py --version

MetaCerberus: version: 1.3.0 March 2024

raw-lab commented 4 months ago

Delete and try again. We just added a software patch to bioconda. Let us know? I am closing for now.

If it still has the same error let us know?

This may also help if your running on slurm. https://docs.ray.io/en/latest/cluster/vms/user-guides/community/slurm.html#slurm-network-ray