NoModuleFoundError 'seqpy'

[enzovalentino]

Hi,
I've installed strainscan on my computer using the following commands:

conda create --name strainscan --platform osx-64 python=3.7.3
pip install strainscan

I've not actually tried the commands, but when I run

strainscan --help

I see the output. However, when I run

strainscan_build

The following error appears:

Traceback (most recent call last):
  File "/opt/homebrew/Caskroom/miniconda/base/envs/strainscan/bin/strainscan_build", line 5, in <module>
    from StrainScan.StrainScan_build import main
  File "/opt/homebrew/Caskroom/miniconda/base/envs/strainscan/lib/python3.7/site-packages/StrainScan/StrainScan_build.py", line 9, in <module>
    from library import Cluster,Unique_kmer_detect_direct,Build_kmer_sets_unique_region_lasso_test_allinone_sp,select_rep,Build_overlap_matrix_sp,Build_overlap_matrix_sp_jellyfish,Build_tree,Build_tree_mem
  File "/opt/homebrew/Caskroom/miniconda/base/envs/strainscan/lib/python3.7/site-packages/StrainScan/library/Unique_kmer_detect_direct.py", line 8, in <module>
    import seqpy
ModuleNotFoundError: No module named 'seqpy'

Any clues on how to solve this?

Many thanks!

[liaoherui]

Hi, thanks for using StrainScan!

This error can occur if StrainScan is installed via pip instead of conda. You can try installing it using the following commands:

conda create --name strainscan --platform osx-64 python=3.7.3
conda install -c bioconda strainscan

If it still doesn’t work, please let me know and I’ll be happy to help. Thanks!

[enzovalentino]

Thank you!
I've created the environment with Python3.7.3 as suggested, and when I run

conda install -c bioconda -c conda-forge strainscan

I get this:

LibMambaUnsatisfiableError: Encountered problems while solving:
  - nothing provides sibeliaz 1.2.2 needed by strainscan-1.0.10-pyhdfd78af_0

Could not solve for environment specs
The following packages are incompatible
└─ strainscan =* * is not installable because there are no viable options
   ├─ strainscan [1.0.10|1.0.13|1.0.14|1.0.3] would require
   │  └─ sibeliaz ==1.2.2 *, which does not exist (perhaps a missing channel);
   └─ strainscan 1.0.14 would require
      └─ sibeliaz ==1.2.3 *, which does not exist (perhaps a missing channel).

I don't know if there's any channel with sibeliaz.

Thanks

[liaoherui]

Hi, is this a new conda environment or an existing one? If it’s an existing environment, could you try creating a completely new one and then installing the package using the conda install commands? Thanks!

[enzovalentino]

I've deleted the previous one (the one where I installed strainscan through pip) and created a new one with the command you suggested

[liaoherui]

Hi, I just tested this on my end, and the commands below work for me. Maybe you could give it a try?

mamba create -n myenv python=3.7 biopython=1.74
conda activate myenv
mamba install -c bioconda strainscan

Both strainscan -h and strainscan_build -h run successfully.

[enzovalentino]

If I run

mamba create -n strainsca-1.0.13 python=3.7 biopython=1.7

I get this error:

error    libmamba Could not solve for environment specs
    The following packages are incompatible
    ├─ biopython =1.7 * does not exist (perhaps a typo or a missing channel);
    └─ python =3.7 * does not exist (perhaps a typo or a missing channel).
critical libmamba Could not solve for environment specs

so I've tried adding --platform osx-64 and in this case the envrionment is created successfully, but I still get the error about sibeliaz when trying to install strainscan...
thank you!

[liaoherui]

Sorry for the late response. Could you please try biopython=1.74 instead of biopython=1.7?

[enzovalentino]

Hi, sorry, my mistake. Actually I've used biopython=1.7.4 and still got the error

[liaoherui]

Hi, sorry again for the late reply. This error usually indicates that the seqpy module was not built or installed correctly, likely due to installation via pip. Since seqpy is a C extension, compilation can fail depending on the operating system and compiler setup.

However, the installation error you encountered with mamba may suggest a system-level incompatibility. One possible solution would be to try the Option 2 installation method described in the README.

If that still doesn’t work, please let me know. I can try to provide a cleaner YAML file tailored to your setup to help with the installation.

(Oh, I just realized you mentioned your "computer" rather than a Linux cluster. In that case, the issue is more likely due to local system compatibility or missing build dependencies for seqpy. I did test StrainScan on my Mac about two years ago, but I’m not entirely sure it works reliably across different systems or Ubuntu versions. Sorry about this, but you can try Option-2 first!)

[enzovalentino]

Hi.
Yes, I'm sorry, the computer I refer to is a Mac Studio with an Apple Silicon processor (M3 Ultra, 512 GB of RAM).

I've tried installing the tool with the option 2.
I ran

git clone https://github.com/liaoherui/StrainScan.git
cd StrainScan

conda env create -f environment_candidate.yaml

this error pops up

Could not solve for environment specs
The following packages are incompatible
├─ _libgcc_mutex =0.1 * does not exist (perhaps a typo or a missing channel);
├─ binutils_linux-64 =2.36 * does not exist (perhaps a typo or a missing channel);
├─ biopython =1.74 * does not exist (perhaps a typo or a missing channel);
├─ certifi =2021.10.8 * is installable with the potential options
│  ├─ certifi 2021.10.8 would require
│  │  └─ python >=3.8,<3.9.0a0 * with the potential options
│  │     ├─ python [3.10.10|3.10.11|...|3.9.25] would require
│  │     │  └─ libffi >=3.4,<4.0a0 *, which can be installed;
│  │     ├─ python [3.8.10|3.8.6|...|3.9.1rc1] would require
│  │     │  └─ libffi >=3.3,<3.4.0a0 *, which can be installed;
│  │     ├─ python [3.10.0|3.10.1|...|3.9.9] would require
│  │     │  └─ libffi >=3.4.2,<3.5.0a0 *, which can be installed;
│  │     ├─ python [3.8.5|3.8.6] would require
│  │     │  └─ python_abi =3.8 *_cp38, which can be installed;
│  │     └─ python [3.10.0|3.10.3|...|3.9.7] would require
│  │        └─ libffi >=3.3,<4.0a0 *, which can be installed;
│  ├─ certifi 2021.10.8 would require
│  │  └─ python >=3.10,<3.11.0a0 *_cpython, which can be installed (as previously explained);
│  ├─ certifi 2021.10.8 would require
│  │  └─ python >=3.9,<3.10.0a0 * with the potential options
│  │     ├─ python [3.10.10|3.10.11|...|3.9.25], which can be installed (as previously explained);
│  │     ├─ python [3.8.10|3.8.6|...|3.9.1rc1], which can be installed (as previously explained);
│  │     ├─ python [3.10.0|3.10.1|...|3.9.9], which can be installed (as previously explained);
│  │     ├─ python [3.10.0|3.10.3|...|3.9.7], which can be installed (as previously explained);
│  │     ├─ python [3.9.0|3.9.1|...|3.9.7] would require
│  │     │  └─ python_abi =3.9 *_cp39, which can be installed;
│  │     └─ python 3.9.7 would require
│  │        └─ openssl >=3.0.0,<4.0a0 *, which can be installed;
│  └─ certifi 2021.10.8 would require
│     └─ python >=3.10,<3.11.0a0 *, which can be installed (as previously explained);
├─ gcc_impl_linux-64 =7.5.0 * does not exist (perhaps a typo or a missing channel);
├─ gcc_linux-64 =7.5.0 * does not exist (perhaps a typo or a missing channel);
├─ gfortran_impl_linux-64 =7.5.0 * does not exist (perhaps a typo or a missing channel);
├─ gfortran_linux-64 =7.5.0 * does not exist (perhaps a typo or a missing channel);
├─ gxx_impl_linux-64 =7.5.0 * does not exist (perhaps a typo or a missing channel);
├─ gxx_linux-64 =7.5.0 * does not exist (perhaps a typo or a missing channel);
├─ icu =67.1 * is requested and can be installed;
├─ libdeflate =1.0 * does not exist (perhaps a typo or a missing channel);
├─ libffi =3.2.1 * is not installable because it conflicts with any installable versions previously reported;
├─ libgcc-ng =11.2.0 * does not exist (perhaps a typo or a missing channel);
├─ libgfortran-ng =7.5.0 * does not exist (perhaps a typo or a missing channel);
├─ libgfortran4 =7.5.0 * does not exist (perhaps a typo or a missing channel);
├─ libgomp =11.2.0 * does not exist (perhaps a typo or a missing channel);
├─ libstdcxx-ng =11.2.0 * does not exist (perhaps a typo or a missing channel);
├─ numpy =1.17.3 * does not exist (perhaps a typo or a missing channel);
├─ openssl =1.1.1l * is not installable because it conflicts with any installable versions previously reported;
├─ pandas =1.0.1 * does not exist (perhaps a typo or a missing channel);
├─ pcre2 =10.35 * is requested and can be installed;
├─ perl-threaded =5.26.0 * does not exist (perhaps a typo or a missing channel);
├─ pysam =0.15.3 * does not exist (perhaps a typo or a missing channel);
├─ python =3.7.3 * does not exist (perhaps a typo or a missing channel);
├─ python_abi =3.7 * is not installable because there are no viable options
│  ├─ python_abi 3.7 conflicts with any installable versions previously reported;
│  ├─ python_abi 3.7 would require
│  │  └─ python =3.7 *, which does not exist (perhaps a missing channel);
│  └─ python_abi 3.7 would require
│     └─ pypy3.7 =7.3 *, which does not exist (perhaps a missing channel);
├─ r-base =4.0.2 * does not exist (perhaps a typo or a missing channel);
├─ r-nlme =3.1.150 * does not exist (perhaps a typo or a missing channel);
├─ r-withr =2.4.3 * is not installable because there are no viable options
│  ├─ r-withr 2.4.3 would require
│  │  └─ r-base >=4.0,<4.1.0a0 * but there are no viable options
│  │     ├─ r-base 4.0.3 would require
│  │     │  └─ pcre2 >=10.36,<10.37.0a0 *, which conflicts with any installable versions previously reported;
│  │     ├─ r-base [4.0.3|4.0.5|4.1.0|4.1.1] would require
│  │     │  └─ icu >=68.1,<69.0a0 *, which conflicts with any installable versions previously reported;
│  │     ├─ r-base [4.0.5|4.1.1|4.1.2|4.1.3] would require
│  │     │  └─ icu >=69.1,<70.0a0 *, which conflicts with any installable versions previously reported;
│  │     └─ r-base [4.0.5|4.1.3] would require
│  │        └─ icu >=70.1,<71.0a0 *, which conflicts with any installable versions previously reported;
│  └─ r-withr 2.4.3 would require
│     └─ r-base >=4.1,<4.2.0a0 * but there are no viable options
│        ├─ r-base [4.0.3|4.0.5|4.1.0|4.1.1], which cannot be installed (as previously explained);
│        ├─ r-base [4.0.5|4.1.1|4.1.2|4.1.3], which cannot be installed (as previously explained);
│        ├─ r-base [4.0.5|4.1.3], which cannot be installed (as previously explained);
│        ├─ r-base 4.1.3 would require
│        │  └─ icu >=72.1,<73.0a0 *, which conflicts with any installable versions previously reported;
│        ├─ r-base 4.1.3 would require
│        │  └─ icu >=75.1,<76.0a0 *, which conflicts with any installable versions previously reported;
│        └─ r-base 4.1.3 would require
│           └─ icu >=73.2,<74.0a0 *, which conflicts with any installable versions previously reported;
├─ scikit-learn =0.23.1 * does not exist (perhaps a typo or a missing channel);
├─ scipy =1.3.1 * does not exist (perhaps a typo or a missing channel);
├─ sibeliaz =1.2.2 * does not exist (perhaps a typo or a missing channel);
├─ spoa =4.0.3 * does not exist (perhaps a typo or a missing channel);
├─ strainest =1.2.4 * does not exist (perhaps a typo or a missing channel);
└─ twopaco =0.9.4 * does not exist (perhaps a typo or a missing channel).

Then I tried

conda env create --platform osx-64 -f environment_candidate.yaml 

and in this case, this came out:

PackagesNotFoundError: The following packages are not available from current channels:

  - binutils_linux-64=2.36

Thank you again!

[liaoherui]

I see. It looks like Option 2 doesn’t work either and may take even more time to get running. In that case, I have another idea based on the mamba-based installation approach you tried earlier.

For the command you used: mamba create -n strainscan-1.0.13 python=3.7.3 I’m wondering if you could try the following instead: first activate the conda environment, then install biopython==1.74 using pip (pip install biopython==1.74), and afterward run mamba install strainscan biopython=1.74 (mamba install strainscan biopython=1.74). Could you see what happens with this approach? I tested something similar on my end (not StrainScan, but other people's packages), and it worked!

If other dependency packages cause similar issues, you could try the same strategy: install them with pip first, then use mamba to install strainscan along with those packages together. This might help resolve the conflicts.

If this still doesn’t work, please let me know. I’m really sorry for the time this installation has taken and for the less-than-ideal user experience. I’ll consider releasing a new version with fewer fixed dependency constraints, which should make the tool easier to install across different systems. That said, I’m currently tied up with several ongoing projects, so this update may take longer than usual, but I do plan to work on it when time allows! ❤️