conda environment installation issues

[sjfleck]

Hello,
I want to use HERRO for its experimental R9.4.1 correction model, but I'm having issues running this command to set up the conda environment:

conda env create --file scripts/herro-env.yml

I get an error saying that some dependencies are not available from conda-forge and bioconda. I went into the .yml file and searched through the list of dependencies and version numbers and was able to find many of the missing ones in the intel, anaconda, cctbx202211, popiclab-dev channels. I assume I can add these to the "channels:" section and that would fix that issue.

I updated it in the file by adding (please ignore the github format change):

channels:

• conda-forge
• bioconda
• intel
• anaconda
• cctbx202211
• popiclab-dev

That said, there are still some dependencies that are no longer available with their listed version. These are:

• libsqlite=3.44.0 (version 3.45.0 is available in the mark.harfouche channel)
• openssl=3.1.4 (version 3.1.3 is available in the intel channel)
• python=3.10.13 (version 3.10.14 is available in the intel channel)
• seqkit=2.5.1 (version 2.8.2 is available in the bioconda channel)
• setuptools=68.2.2 (version 75.1.0 is available in the conda-forge channel)

I'm new to running singularity images, but if I'm understanding correctly, I will need this conda environment active for when I run this command:

singularity run --nv --bind <host_path>:<dest_path> herro.sif inference

Do you either have an updated herro-env.yml file or is it advisable for me to change the unavailable dependency versions to available ones (even though this may not have been tested) and try to finish installing the conda environment?

Thank you for any help you're able to provide on this

[sjfleck]

This problem is worse than I thought because many of the software versions were only available on the intel channel, which isn't around anymore. That makes many more dependencies unavailable.

I was able to access an old conda environment for herro that someone installed on our system in May and only needed to manually install porechop and duplex_tools using pip in order to do the preprocessing steps without any errors.

When I finally ran herro, this was my command:
singularity run --nv --bind ${host_path}:${dest_path} herro.sif inference
--read-alns ${directory_alignment_batches}
-t ${feat_gen_threads_per_device}
-d 0,1
-m ${model_path}
-b ${batch_size}
${output_prefix}.fastq.gz ${fasta_output}

and I ended up with this error:
[W graph_fuser.cpp:108] Warning: operator() profile_node %1243 : int[] = prim::profile_ivalue(%1241)
does not have profile information (function operator())
[00:01:22] Processed 205217 reads.

the low number of reads is because I'm using a small input fastq .gz file (5.7Gb with no reads smaller than 5kb since 10kb eliminated too much) as a test to get herro working. I will note that the original file started with 434,739 reads. The "preprocess_cont.sh" command appeared to utilize all the reads and this was the output from that command:

[10:34:19 - SplitOnAdapters] Split 6145 reads
Kept 428597 reads
[10:34:19 - SplitOnAdapters] Wrote a total of 12388 reads
�[33m[WARN]�[0m you may switch on flag -g/--remove-gaps to remove spaces

When I ran "create_batched_alignments.sh", this was the output:

0it [00:00, ?it/s][M::mm_idx_gen::89.4011.61] collected minimizers
[M::mm_idx_gen::90.9882.16] sorted minimizers
[M::main::90.9882.16] loaded/built the index for 244684 target sequence(s)
[M::mm_mapopt_update::96.7382.09] mid_occ = 13
[M::mm_idx_stat] kmer size: 25; skip: 17; is_hpc: 0; #seq: 244684
[M::mm_idx_stat::100.1562.05] distinct minimizers: 307960901 (75.75% are singletons); average occurrences: 1.720; average spacing: 8.896; total length: 4711813619
...
[M::worker_pipeline::209.95110.52] mapped 244684 sequences
[M::main] Version: 2.26-r1175
[M::main] CMD: minimap2 -K8g -cx ava-ont -k25 -w17 -e200 -r150 -m2500 -z200 -f 0.005 -t64 --dual=yes preprocessed.fastq.gz preprocessed.fastq.gz
[M::main] Real time: 210.432 sec; CPU: 2209.777 sec; Peak RSS: 34.926 GB

Is the error I got from running herro concerning or can I ignore it? Any help with this would be greatly appreciated. Thank you,
Steve

[byebrid]

I was installing herro for someone else, and just wanted to pop in and say that I was able to create the conda environment just fine. I've attached the full output below.

@sjfleck, could you please say which exact packages are failing to be found for you? I'm not sure why it would be failing unless you are e.g. stuck with some outdated mirrors of these repos. But I'm certainly not a conda expert.

Details

Using mamba (replacement for conda) from miniforge3:

(base) [lexg@m3-login3 herro (main)]$ mamba --version
mamba 1.5.8
conda 24.3.0

My condarc:

(base) [lexg@m3-login3 herro (main)]$ cat ~/.condarc 
envs_dirs:
  - /path/to/conda/envs
channels:
  - conda-forge
  - defaults
pkgs_dirs:
  - /path/to/conda/pkgs
non_admin_enabled: true
channel_priority: flexible

I used latest commit 01eab1d on main branch. Note https://github.com/lbcb-sci/herro/blob/main/scripts/herro-env.yml hasn't been updated in 10 months, well before you encountered your issue.

Conda env create output

(base) [lexg@m3-login3 herro (main)]$ mamba env create -y --file=scripts/herro-env.yml --name=herro-env
Retrieving notices: ...working... done
Channels:
 - conda-forge
 - bioconda
 - defaults
Platform: linux-64
Collecting package metadata (repodata.json): done
Solving environment: done


==> WARNING: A newer version of conda exists. <==
    current version: 24.3.0
    latest version: 24.9.2

Please update conda by running

    $ conda update -n base -c conda-forge conda



Downloading and Extracting Packages:

Preparing transaction: done
Verifying transaction: done
Executing transaction: done
Installing pip dependencies: \ Ran pip subprocess with arguments:
['/scratch/nq46/lexg/conda_envs/conda/envs/herro-env/bin/python', '-m', 'pip', 'install', '-U', '-r', '/fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt', '--exists-action=b']
Pip subprocess output:
Collecting git+https://github.com/dehui333/Porechop.git (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 31))
  Cloning https://github.com/dehui333/Porechop.git to /tmp/pip-req-build-vnd4bmtn
  Resolved https://github.com/dehui333/Porechop.git to commit d2e77c669a7ebcb3e605bd792408d0975dcd7419
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting contourpy==1.2.0 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 1))
  Downloading contourpy-1.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting cycler==0.12.1 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 2))
  Using cached cycler-0.12.1-py3-none-any.whl.metadata (3.8 kB)
Collecting duplex-tools==0.3.3 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 3))
  Downloading duplex_tools-0.3.3.tar.gz (30 kB)
  Preparing metadata (setup.py): started
  Preparing metadata (setup.py): finished with status 'done'
Collecting edlib==1.3.9 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 4))
  Using cached edlib-1.3.9-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (9.0 kB)
Collecting fonttools==4.44.0 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 5))
  Downloading fonttools-4.44.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (153 kB)
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Collecting h5py==3.8.0 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 6))
  Downloading h5py-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (2.5 kB)
Collecting iso8601==2.1.0 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 7))
  Downloading iso8601-2.1.0-py3-none-any.whl.metadata (3.7 kB)
Collecting kiwisolver==1.4.5 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 8))
  Using cached kiwisolver-1.4.5-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl.metadata (6.4 kB)
Collecting lib-pod5==0.2.4 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 9))
  Downloading lib_pod5-0.2.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (1.1 kB)
Collecting mappy==2.26 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 10))
  Downloading mappy-2.26.tar.gz (135 kB)
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  Installing build dependencies: started
  Installing build dependencies: finished with status 'done'
  Getting requirements to build wheel: started
  Getting requirements to build wheel: finished with status 'done'
  Preparing metadata (pyproject.toml): started
  Preparing metadata (pyproject.toml): finished with status 'done'
Collecting matplotlib==3.8.1 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 11))
  Downloading matplotlib-3.8.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (5.8 kB)
Collecting more-itertools==10.1.0 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 12))
  Downloading more_itertools-10.1.0-py3-none-any.whl.metadata (33 kB)
Collecting natsort==8.4.0 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 13))
  Using cached natsort-8.4.0-py3-none-any.whl.metadata (21 kB)
Collecting numpy==1.26.1 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 14))
  Downloading numpy-1.26.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (61 kB)
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Collecting packaging==23.2 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 15))
  Downloading packaging-23.2-py3-none-any.whl.metadata (3.2 kB)
Collecting pandas==2.1.2 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 16))
  Downloading pandas-2.1.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (18 kB)
Collecting parasail==1.3.4 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 17))
  Using cached parasail-1.3.4-py2.py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (21 kB)
Collecting pillow==10.1.0 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 18))
  Downloading Pillow-10.1.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (9.5 kB)
Collecting pod5==0.2.4 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 19))
  Downloading pod5-0.2.4-py3-none-any.whl.metadata (20 kB)
Collecting polars==0.17.15 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 20))
  Downloading polars-0.17.15-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (14 kB)
Collecting pyarrow==11.0.0 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 21))
  Downloading pyarrow-11.0.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (3.0 kB)
Collecting pyfastx==2.0.1 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 22))
  Downloading pyfastx-2.0.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl.metadata (30 kB)
Collecting pyparsing==3.1.1 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 23))
  Downloading pyparsing-3.1.1-py3-none-any.whl.metadata (5.1 kB)
Collecting pysam==0.22.0 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 24))
  Downloading pysam-0.22.0-cp310-cp310-manylinux_2_28_x86_64.whl.metadata (1.5 kB)
Collecting python-dateutil==2.8.2 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 25))
  Downloading python_dateutil-2.8.2-py2.py3-none-any.whl.metadata (8.2 kB)
Collecting pytz==2023.3.post1 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 26))
  Downloading pytz-2023.3.post1-py2.py3-none-any.whl.metadata (22 kB)
Collecting six==1.16.0 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 27))
  Using cached six-1.16.0-py2.py3-none-any.whl.metadata (1.8 kB)
Collecting tqdm==4.66.1 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 28))
  Downloading tqdm-4.66.1-py3-none-any.whl.metadata (57 kB)
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Collecting tzdata==2023.3 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 29))
  Downloading tzdata-2023.3-py2.py3-none-any.whl.metadata (1.4 kB)
Collecting vbz-h5py-plugin==1.0.1 (from -r /fs03/nq46/lexg/herro/herro/scripts/condaenv.gboykt9j.requirements.txt (line 30))
  Downloading vbz_h5py_plugin-1.0.1-py3-none-any.whl.metadata (1.7 kB)
Downloading contourpy-1.2.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (310 kB)
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Using cached cycler-0.12.1-py3-none-any.whl (8.3 kB)
Using cached edlib-1.3.9-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (363 kB)
Downloading fonttools-4.44.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.5 MB)
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Downloading h5py-3.8.0-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (4.6 MB)
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Downloading iso8601-2.1.0-py3-none-any.whl (7.5 kB)
Using cached kiwisolver-1.4.5-cp310-cp310-manylinux_2_12_x86_64.manylinux2010_x86_64.whl (1.6 MB)
Downloading lib_pod5-0.2.4-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (2.9 MB)
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Downloading matplotlib-3.8.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (11.6 MB)
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Downloading more_itertools-10.1.0-py3-none-any.whl (55 kB)
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Using cached natsort-8.4.0-py3-none-any.whl (38 kB)
Downloading numpy-1.26.1-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
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Downloading packaging-23.2-py3-none-any.whl (53 kB)
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Downloading pandas-2.1.2-cp310-cp310-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (12.3 MB)
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Using cached parasail-1.3.4-py2.py3-none-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (15.6 MB)
Downloading Pillow-10.1.0-cp310-cp310-manylinux_2_28_x86_64.whl (3.6 MB)
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Downloading pod5-0.2.4-py3-none-any.whl (66 kB)
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Downloading polars-0.17.15-cp37-abi3-manylinux_2_17_x86_64.manylinux2014_x86_64.whl (18.2 MB)
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Building wheels for collected packages: duplex-tools, mappy, porechop
  Building wheel for duplex-tools (setup.py): started
  Building wheel for duplex-tools (setup.py): finished with status 'done'
  Created wheel for duplex-tools: filename=duplex_tools-0.3.3-py3-none-any.whl size=33169 sha256=f1a616cee13513946d33ebbd23d98fe117edd41573096b54b61f30b3101f5b2e
  Stored in directory: /fs03/nq46/lexg/pip-cache/wheels/fd/27/31/9815526a3aab7e566250832a543f038a9a362da8a38052aee5
  Building wheel for mappy (pyproject.toml): started
  Building wheel for mappy (pyproject.toml): finished with status 'done'
  Created wheel for mappy: filename=mappy-2.26-cp310-cp310-linux_x86_64.whl size=168303 sha256=77b54a1c876754488ab5615a4db213f4de1e9ace7a087ee2cce4d7689e212ae5
  Stored in directory: /fs03/nq46/lexg/pip-cache/wheels/58/c3/d8/fd22344af6bd1318fa6817937cc083c8ce06d3fc50364dfb73
  Building wheel for porechop (setup.py): started
  Building wheel for porechop (setup.py): finished with status 'done'
  Created wheel for porechop: filename=porechop-0.2.4-py3-none-any.whl size=86212 sha256=8c95ba13f3ae0c49d0b7883973bc895ae9f35cdd2ac7f956da9a6b29a269ecaa
  Stored in directory: /tmp/pip-ephem-wheel-cache-08077c3m/wheels/a0/a4/f4/98d67d6f8a488e6b420b71fbc45de0b995bde9d93b522be7df
Successfully built duplex-tools mappy porechop
Installing collected packages: pytz, pyfastx, porechop, mappy, edlib, tzdata, tqdm, six, pysam, pyparsing, polars, pillow, packaging, numpy, natsort, more-itertools, kiwisolver, iso8601, fonttools, cycler, python-dateutil, pyarrow, parasail, lib-pod5, h5py, cont
ourpy, vbz-h5py-plugin, pandas, matplotlib, pod5, duplex-tools
Successfully installed contourpy-1.2.0 cycler-0.12.1 duplex-tools-0.3.3 edlib-1.3.9 fonttools-4.44.0 h5py-3.8.0 iso8601-2.1.0 kiwisolver-1.4.5 lib-pod5-0.2.4 mappy-2.26 matplotlib-3.8.1 more-itertools-10.1.0 natsort-8.4.0 numpy-1.26.1 packaging-23.2 pandas-2.1.2
 parasail-1.3.4 pillow-10.1.0 pod5-0.2.4 polars-0.17.15 porechop-0.2.4 pyarrow-11.0.0 pyfastx-2.0.1 pyparsing-3.1.1 pysam-0.22.0 python-dateutil-2.8.2 pytz-2023.3.post1 six-1.16.0 tqdm-4.66.1 tzdata-2023.3 vbz-h5py-plugin-1.0.1

done
#
# To activate this environment, use
#
#     $ conda activate herro-env
#
# To deactivate an active environment, use
#
#     $ conda deactivate