no subcommand mhl

[ifishlin]

Hi

I used conda to install Meteor by running 'conda install -c dohlee metheor'.
The version that was installed is 0.0.3, but it appears that this version only includes four subcommands: lpmd, me, pdr, and pm. I did not find any mention of the 'mhl' subcommand in the README.

Additionally, I have been running the 'pm' command for 48 hours on a 30G BAM file, but it has not completed yet. Can you provide an estimate of how long it might take to finish?

Thanks

[dohlee]

If there isn't any specific reason to use version 0.0.3, could you please update metheor to the latest version (0.1.6) with conda update -c dohlee metheor=0.1.6 and try again?

Thanks,
Dohoon

[ifishlin]

Hello

I used the 'conda install -c dohlee metheor=0.1.6' to install it and have some trouble.
The log indicate that I should have a libstdcxx-ng > 12 installed, but I had.

Can you please help me about it? thanks

The log

(/omics/groups/OE0219/internal/yuyu/miniconda_envs/meth) -bash-4.2$ conda install -c dohlee metheor=0.1.6
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with a past
explicit spec that is not an explicit spec in this operation (libstdcxx-ng):

  - metheor=0.1.6 -> libstdcxx-ng[version='>=12']

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.17=0
  - feature:|@/linux-64::__glibc==2.17=0

Your installed version is: 2.17


(/omics/groups/OE0219/internal/yuyu/miniconda_envs/meth) -bash-4.2$ conda install -c conda-forge libstdcxx-ng=12.2.0
Collecting package metadata (current_repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
  current version: 4.10.1
  latest version: 23.3.1

Please update conda by running

    $ conda update -n base conda



All requested packages already installed.

[dohlee]

Thank you for sharing the log. It seems that there is a dependency conflict with metheor and some packages already installed in your environment. There is no simple way to resolve it, so I usually make a separate environment when I run into this kind of errors. Would you give it a try?

In your (base) environment, run
conda create -n metheor && conda activate metheor && conda install -c dohlee metheor=0.1.6 -y

By the way, it seems that your version of conda is too old! Updating it to the latest version may solve it, although it is not very likely :)

[ifishlin]

Hello

I create a clear VM to install it. and it comes out more warning.
I think it's too difficult to solve the conflicts like this.

Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: /
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

ResolvePackageNotFound:
  - libgcc-ng[version='>=12']

Then I install "conda install -c conda-forge libgcc-ng"

(metheor) [y306n@benchmarking01 ~]$ conda install -c dohlee metheor=0.1.6 -y
Collecting package metadata (current_repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: failed with repodata from current_repodata.json, will retry with next repodata source.
Collecting package metadata (repodata.json): done
Solving environment: failed with initial frozen solve. Retrying with flexible solve.
Solving environment: \
Found conflicts! Looking for incompatible packages.
This can take several minutes.  Press CTRL-C to abort.
failed

UnsatisfiableError: The following specifications were found to be incompatible with a past
explicit spec that is not an explicit spec in this operation (libgcc-ng):

  - metheor=0.1.6 -> libgcc-ng[version='>=12']

The following specifications were found to be incompatible with each other:

Output in format: Requested package -> Available versions

Package libgomp conflicts for:
_openmp_mutex -> libgomp[version='>=7.5.0']
libgomp
libgcc-ng -> _openmp_mutex[version='>=4.5'] -> libgomp[version='>=7.5.0']

Package _libgcc_mutex conflicts for:
metheor=0.1.6 -> libgcc-ng[version='>=12'] -> _libgcc_mutex==0.1=conda_forge
_openmp_mutex -> _libgcc_mutex==0.1[build='main|conda_forge']
libgcc-ng -> _libgcc_mutex[version='*|0.1',build='main|main|conda_forge']
_libgcc_mutex

Package _openmp_mutex conflicts for:
_openmp_mutex
metheor=0.1.6 -> libgcc-ng[version='>=12'] -> _openmp_mutex[version='>=4.5']
libgcc-ng -> _openmp_mutex[version='>=4.5']The following specifications were found to be incompatible with your system:

  - feature:/linux-64::__glibc==2.28=0
  - feature:|@/linux-64::__glibc==2.28=0
  - libgcc-ng -> __glibc[version='>=2.17']

Your installed version is: 2.28

[dohlee]

That's strange. Please share your operating system and results of conda --version and conda config --show.

[ifishlin]

Here is it. Thanks

(base) [y306n@benchmarking01 ~]$ conda --version
conda 23.1.0
(base) [y306n@benchmarking01 ~]$ conda config --show
add_anaconda_token: True
add_pip_as_python_dependency: True
aggressive_update_packages:
  - ca-certificates
  - certifi
  - openssl
allow_conda_downgrades: False
allow_cycles: True
allow_non_channel_urls: False
allow_softlinks: False
allowlist_channels: []
always_copy: False
always_softlink: False
always_yes: None
anaconda_upload: None
auto_activate_base: True
auto_stack: 0
auto_update_conda: True
bld_path:
changeps1: True
channel_alias: https://conda.anaconda.org
channel_priority: flexible
channels:
  - defaults
client_ssl_cert: None
client_ssl_cert_key: None
clobber: False
conda_build: {}
create_default_packages: []
croot: /home/y306n/miniconda3/conda-bld
custom_channels:
  pkgs/main: https://repo.anaconda.com
  pkgs/r: https://repo.anaconda.com
  pkgs/pro: https://repo.anaconda.com
custom_multichannels:
  defaults:
    - https://repo.anaconda.com/pkgs/main
    - https://repo.anaconda.com/pkgs/r
  local:
debug: False
default_channels:
  - https://repo.anaconda.com/pkgs/main
  - https://repo.anaconda.com/pkgs/r
default_python: 3.10
default_threads: None
deps_modifier: not_set
dev: False
disallowed_packages: []
download_only: False
dry_run: False
enable_private_envs: False
env_prompt: ({default_env})
envs_dirs:
  - /home/y306n/miniconda3/envs
  - /home/y306n/.conda/envs
 error_upload_url: https://conda.io/conda-post/unexpected-error
execute_threads: 1
extra_safety_checks: False
fetch_threads: 5
force: False
force_32bit: False
force_reinstall: False
force_remove: False
ignore_pinned: False
json: False
local_repodata_ttl: 1
migrated_channel_aliases: []
migrated_custom_channels: {}
non_admin_enabled: True
notify_outdated_conda: True
number_channel_notices: 5
offline: False
override_channels_enabled: True
path_conflict: clobber
pinned_packages: []
pip_interop_enabled: False
pkgs_dirs:
  - /home/y306n/miniconda3/pkgs
  - /home/y306n/.conda/pkgs
proxy_servers: {}
quiet: False
remote_backoff_factor: 1
remote_connect_timeout_secs: 9.15
remote_max_retries: 3
remote_read_timeout_secs: 60.0
repodata_fns:
  - current_repodata.json
  - repodata.json
repodata_threads: None
report_errors: None
restore_free_channel: False
rollback_enabled: True
root_prefix: /home/y306n/miniconda3
safety_checks: warn
sat_solver: pycosat
separate_format_cache: False
shortcuts: True
show_channel_urls: None
signing_metadata_url_base: None
solver: classic
solver_ignore_timestamps: False
ssl_verify: True
subdir: linux-64
subdirs:
  - linux-64
  - noarch
target_prefix_override:
track_features: []
unsatisfiable_hints: True
unsatisfiable_hints_check_depth: 2
update_modifier: update_specs
use_index_cache: False
use_local: False
use_only_tar_bz2: False
verbosity: 0
verify_threads: 1

[dohlee]

This seems to be a bad conda issue regarding glibc, and unfortunately I cannot give you a clear solution that'll definitely work at the moment. I suspect that it may be due to the glibc supported by your OS.

These are some references that might help you, please give them a try:
conda/conda#8823
KevinMusgrave/pytorch-metric-learning#55
automl/auto-sklearn#1240
https://stackoverflow.com/questions/71678461/conda-unsatisfiableerror-with-linux64-and-glibc

Anyway, what is the result from ldd --version on your system?

[ifishlin]

Thanks for your help.

Could it possible that you can wrapper metheor as a docker image?
I think it will be of great help to users.

(base) [y306n@benchmarking01 ~]$ ldd --version
ldd (GNU libc) 2.28
Copyright (C) 2018 Free Software Foundation, Inc.
This is free software; see the source for copying conditions.  There is NO
warranty; not even for MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.
Written by Roland McGrath and Ulrich Drepper.

[dohlee]

Great idea! I'll try composing a Docker image and let you know by next week. Thanks for the suggestion.
Please let me know if you solve your problem until then.

Thanks,
Dohoon