m6Anet inference output missing probability_modified values

[nickst85]

Hi,

I ran the m6Anet inference and the one output file data.result.csv file does not include any values in probabity_modified column. I used the default parameters and I ran the inference over the default human model trained on the HCT116 cell line. Is there any explanation?

Thanks

[yuukiiwa]

Hi @nickst85,

It will be great if you can try running m6anet with the modified eventalign.txt file from the xpore issue. Also, please do reinstall m6anet as data.result.csv is deprecated.

Thanks!

Best wishes, Yuk Kei

[nickst85]

Hi Yuk Kei,

Thank you for you reply. I remember, I initially tried to install m6Anet through a virtual conda environment but it failed. Thus I installed it with pip install. Have you fixed the anaconda package? Should I try to install it again or uninstall the pip and re-install it?

A couple more things. I noticed that in your test/data folder the eventalign.txt file that you have in that folder includes two more columns at the end ( start_idx and end_idx) that my nanopolish eventalign output does not. How did you create these two columns? Does it matter that mine doesn’t have them?

When the m6anet inference command runs with the default parameters where it gets the baseline no methylation data signal from? Do I have to direct it to a specific file?

Best,

Nick From: Yuk Kei Wan @.> Date: Tuesday, January 23, 2024 at 8:16 PM To: GoekeLab/m6anet @.> Cc: Settas, Nikolaos @.>, Mention @.> Subject: [EXT] Re: [GoekeLab/m6anet] m6Anet inference output missing probability_modified values (Issue #147) ATTENTION: External Email! Do not click attachments/links unless sender is known.

---

Hi @nickst85 [github. com], It will be great if you can try running m6anet with the modified eventalign. txt file from the xpore issue. Also, please do reinstall m6anet as data. result. csv is deprecated. Thanks! Best wishes, Yuk Kei —Reply

Hi @nickst85 [github.com]https://urldefense.com/v3/__https:/github.com/nickst85__;!!FMDslA!e16QM84B5z8G7yLBqC-XS-fkXjL_IDyNOqS7V0pW45avl46fWQKe88N6jywEcQDG7eKPKZCSPGSvDuDYWNiNnfiOxVOmn8M$,

It will be great if you can try running m6anet with the modified eventalign.txt file from the xpore issue. Also, please do reinstall m6anet as data.result.csv is deprecated.

Thanks!

Best wishes, Yuk Kei

— Reply to this email directly, view it on GitHub [github.com]https://urldefense.com/v3/__https:/github.com/GoekeLab/m6anet/issues/147*issuecomment-1907187240__;Iw!!FMDslA!e16QM84B5z8G7yLBqC-XS-fkXjL_IDyNOqS7V0pW45avl46fWQKe88N6jywEcQDG7eKPKZCSPGSvDuDYWNiNnfiOJuPores$, or unsubscribe [github.com]https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/A5QGITTJNU5O77FLRN2T2ALYQBOEXAVCNFSM6AAAAABCA6IWRGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMBXGE4DOMRUGA__;!!FMDslA!e16QM84B5z8G7yLBqC-XS-fkXjL_IDyNOqS7V0pW45avl46fWQKe88N6jywEcQDG7eKPKZCSPGSvDuDYWNiNnfiOtIqMPug$. You are receiving this because you were mentioned.Message ID: @.***>

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[yuukiiwa]

Hi @nickst85,

The conda package points to the latest version of m6anet automatically after each of our releases. You will have to uninstall your current m6anet and install the new one which should give you data.indv_proba.csv and data.site_proba.csv as outputs instead

Yes, you need to have start_idx and end_idx for xpore dataprep and m6anet dataprep to run through. xPore's documentation shows how you can obtain those columns:

nanopolish index -d <PATH/TO/FAST5_DIR> <PATH/TO/FASTQ_FILE>
nanopolish eventalign --reads <PATH/TO/FASTQ_FILE> \
--bam <PATH/TO/BAM_FILE> \
--genome <PATH/TO/FASTA_FILE \
--signal-index \
--scale-events \
--summary <PATH/TO/summary.txt> \
--threads 32 > <PATH/TO/eventalign.txt>

Thanks!

Best wishes, Yuk Kei

[nickst85]

Hi Yuk Kei,

I tried to install the m6anet through conda install -c bioconda m6anet

and after trying to solve the environment it found some conflicts.

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 each other:

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

-feature:/linux64::__glibc==2.28=0

• feature:|@/linux64::__glibc==2.28=0

Do you know which version of glibc is compatible?

Thanks,

Nick

[yuukiiwa]

Hi @nickst85,

You can create a new environment for m6anet

conda create --name env_for_m6anet python=3.9

Then you can install m6anet there with

pip install m6anet

Thanks!

Best wishes, Yuk Kei

[nickst85]

Hi Yuk Kei,

I followed your guidelines and I got the following errors:

Collecting m6anet

Using cached m6anet-2.0.1-py3-none-any.whl (135 kB)

Collecting numpy==1.18.0 (from m6anet)

Using cached numpy-1.18.0.zip (5.4 MB)

Installing build dependencies ... done

Getting requirements to build wheel ... done

Preparing metadata (pyproject.toml) ... error

error: subprocess-exited-with-error

× Preparing metadata (pyproject.toml) did not run successfully.

│ exit code: 1

╰─> [54 lines of output]

  Running from numpy source directory.

  <string>:425: UserWarning: Unrecognized setuptools command, proceeding with generating Cython sources and expanding templates

  /tmp/pip-install-irghmet8/numpy_89a385817c67487c9c54a936211f364d/tools/cythonize.py:75: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.

    required_version = LooseVersion('0.29.13')

  /tmp/pip-install-irghmet8/numpy_89a385817c67487c9c54a936211f364d/tools/cythonize.py:77: DeprecationWarning: distutils Version classes are deprecated. Use packaging.version instead.

    if LooseVersion(cython_version) < required_version:

  Error compiling Cython file:

  ------------------------------------------------------------

  ...

          for i in range(1, RK_STATE_LEN):

              self.rng_state.key[i] = val[i]

          self.rng_state.pos = i

          self._bitgen.state = &self.rng_state

          self._bitgen.next_uint64 = &mt19937_uint64

                                     ^

  ------------------------------------------------------------

  _mt19937.pyx:138:35: Cannot assign type 'uint64_t (*)(void *) except? -1 nogil' to 'uint64_t (*)(void *) noexcept nogil'. Exception values are incompatible. Suggest adding 'noexcept' to type 'uint64_t (void *) except? -1 nogil'.

  Processing numpy/random/_bounded_integers.pxd.in

  Processing numpy/random/_mt19937.pyx

  Traceback (most recent call last):

    File "/tmp/pip-install-irghmet8/numpy_89a385817c67487c9c54a936211f364d/tools/cythonize.py", line 238, in <module>

      main()

    File "/tmp/pip-install-irghmet8/numpy_89a385817c67487c9c54a936211f364d/tools/cythonize.py", line 234, in main

      find_process_files(root_dir)

    File "/tmp/pip-install-irghmet8/numpy_89a385817c67487c9c54a936211f364d/tools/cythonize.py", line 225, in find_process_files

      process(root_dir, fromfile, tofile, function, hash_db)

    File "/tmp/pip-install-irghmet8/numpy_89a385817c67487c9c54a936211f364d/tools/cythonize.py", line 191, in process

      processor_function(fromfile, tofile)

    File "/tmp/pip-install-irghmet8/numpy_89a385817c67487c9c54a936211f364d/tools/cythonize.py", line 80, in process_pyx

      subprocess.check_call(

    File "/home/nsettas/.conda/envs/m6anet_env/lib/python3.9/subprocess.py", line 373, in check_call

      raise CalledProcessError(retcode, cmd)

  subprocess.CalledProcessError: Command '['/home/nsettas/.conda/envs/m6anet_env/bin/python', '-m', 'cython', '-3', '--fast-fail', '-o', '_mt19937.c', '_mt19937.pyx']' returned non-zero exit status 1.

  Cythonizing sources

  Traceback (most recent call last):

    File "/home/xxxx/.conda/envs/m6anet_env/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 353, in <module>

      main()

    File "/home/xxxx/.conda/envs/m6anet_env/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 335, in main

      json_out['return_val'] = hook(**hook_input['kwargs'])

    File "/home/xxxx/.conda/envs/m6anet_env/lib/python3.9/site-packages/pip/_vendor/pyproject_hooks/_in_process/_in_process.py", line 149, in prepare_metadata_for_build_wheel

      return hook(metadata_directory, config_settings)

    File "/tmp/pip-build-env-mtymf410/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 366, in prepare_metadata_for_build_wheel

      self.run_setup()

    File "/tmp/pip-build-env-mtymf410/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 480, in run_setup

      super(_BuildMetaLegacyBackend, self).run_setup(setup_script=setup_script)

    File "/tmp/pip-build-env-mtymf410/overlay/lib/python3.9/site-packages/setuptools/build_meta.py", line 311, in run_setup

      exec(code, locals())

    File "<string>", line 450, in <module>

    File "<string>", line 433, in setup_package

    File "<string>", line 240, in generate_cython

  RuntimeError: Running cythonize failed!

  [end of output]

note: This error originates from a subprocess, and is likely not a problem with pip.

error: metadata-generation-failed

× Encountered error while generating package metadata.

╰─> See above for output.

note: This is an issue with the package mentioned above, not pip.

hint: See above for details.

Do you have any idea what caused this? (where you see xxxx is my folder

Thanks,

Nick

From: Yuk Kei Wan @.> Date: Monday, January 29, 2024 at 1:52 AM To: GoekeLab/m6anet @.> Cc: Settas, Nikolaos @.>, Mention @.> Subject: [EXT] Re: [GoekeLab/m6anet] m6Anet inference output missing probability_modified values (Issue #147) ATTENTION: External Email! Do not click attachments/links unless sender is known.

---

Hi @nickst85 [github. com], You can create a new environment for m6anet conda create --name env_for_m6anet python=3. 9 Then you can install m6anet there with pip install m6anet Thanks! Best wishes, Yuk Kei — Reply to this email directly,

Hi @nickst85 [github.com]https://urldefense.com/v3/__https:/github.com/nickst85__;!!FMDslA!fyH7w9172STeYrydKC1c3CLP07TAqXiMQ4zDuB4FBHoubKYJH2VoTo_Y4hzhCY1ufZjVUubcSDm2vhtdmmV-2R6UXRn5IlI$,

You can create a new environment for m6anet

conda create --name env_for_m6anet python=3.9

Then you can install m6anet there with

pip install m6anet

Thanks!

Best wishes, Yuk Kei

— Reply to this email directly, view it on GitHub [github.com]https://urldefense.com/v3/__https:/github.com/GoekeLab/m6anet/issues/147*issuecomment-1914067264__;Iw!!FMDslA!fyH7w9172STeYrydKC1c3CLP07TAqXiMQ4zDuB4FBHoubKYJH2VoTo_Y4hzhCY1ufZjVUubcSDm2vhtdmmV-2R6Ujt79Ly0$, or unsubscribe [github.com]https://urldefense.com/v3/__https:/github.com/notifications/unsubscribe-auth/A5QGITTGZ37VBTRU2CEM3WDYQ5BIVAVCNFSM6AAAAABCA6IWRGVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMYTSMJUGA3DOMRWGQ__;!!FMDslA!fyH7w9172STeYrydKC1c3CLP07TAqXiMQ4zDuB4FBHoubKYJH2VoTo_Y4hzhCY1ufZjVUubcSDm2vhtdmmV-2R6UezYEOKs$. You are receiving this because you were mentioned.Message ID: @.***>

Confidentiality Notice: This e-mail message, including any attachments, is for the sole use of the intended recipient(s) and may contain confidential and privileged information. Any unauthorized review, use, disclosure or distribution is prohibited. If you are not the intended recipient, please contact the sender by reply e-mail and destroy all copies of the original message.

[nickst85]

Hi Yuk Kei,

The latest version of m6anet was successfully installed when I used python 3.7. Please discard the previous email.

Have a great day,

N

[nickst85]

The tool also gave me the right outputs after modifying the nanopolish eventalign outputs.

Thanks for you help,

N