Closed HaimAshk closed 2 years ago
mnshgl0110
commented
2 years ago Hi Haim, I think the issue is with the conda environment. Have you tried creating a new conda environment and then installing syri there? I think, that would solve the issue.
HaimAshk
commented
2 years ago Thanks for the super quick response! I have tried now with a new and clean conda environment and using the conda SyRI installation, but it failed. In the installation above I installed all the dependencies manually and use the python3 setup.py install with the source files from the git.
Any advice on how it can be solved?
conda create -p /Programs/miniconda3/envs/SyRI_v1.5.4.test/ python=3.8
conda activate /Programs/miniconda3/envs/SyRI_v1.5.4.test
conda install -c bioconda syri
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 each other:
Output in format: Requested package -> Available versionsThe following specifications were found to be incompatible with your system:
- feature:/linux-64::__glibc==2.27=0
- feature:|@/linux-64::__glibc==2.27=0
Your installed version is: 2.27Updating conda should help solve this issue: https://stackoverflow.com/questions/66888763/invalidversionspecerror-invalid-version-spec-2-7.
So something like:
conda create -p /Programs/miniconda3/envs/SyRI_v1.5.4.test/ python=3.8 conda
conda activate /Programs/miniconda3/envs/SyRI_v1.5.4.test
conda install -c bioconda syri should work.
HaimAshk
commented
2 years ago Thanks for the help, Manish! Unfortunately, it still does not work 😢
I managed to install it with the commands you suggested:
conda create -p /Programs/miniconda3/envs/SyRI_v1.5.4.test/ python=3.8 conda
conda activate /Programs/miniconda3/envs/SyRI_v1.5.4.test
conda install -c bioconda syri But when running it, I still get the following runtime error:
multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/Programs/miniconda3/envs/SyRI_v1.5.4.test/lib/python3.8/multiprocessing/pool.py", line 125, in worker
result = (True, func(*args, **kwds))
File "/Programs/miniconda3/envs/SyRI_v1.5.4.test/lib/python3.8/multiprocessing/pool.py", line 48, in mapstar
return list(map(*args))
File "syri/pyxFiles/synsearchFunctions.pyx", line 539, in syri.synsearchFunctions.syri
File "syri/pyxFiles/tdfunc.pyx", line 1198, in syri.tdfunc.blocksdata
File "syri/pyxFiles/tdfunc.pyx", line 304, in syri.tdfunc.mergeTransBlocks
File "/.local/lib/python3.8/site-packages/pandas/core/frame.py", line 490, in __init__
mgr = init_dict({}, index, columns, dtype=dtype)
File "/.local/lib/python3.8/site-packages/pandas/core/internals/construction.py", line 239, in init_dict
val = construct_1d_arraylike_from_scalar(np.nan, len(index), nan_dtype)
File "/.local/lib/python3.8/site-packages/pandas/core/dtypes/cast.py", line 1440, in construct_1d_arraylike_from_scalar
dtype = dtype.dtype
AttributeError: type object 'object' has no attribute 'dtype'
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "/Programs/miniconda3/envs/SyRI_v1.5.4.test/bin/syri", line 6, in <module>
main(sys.argv[1:])
File "/Programs/miniconda3/envs/SyRI_v1.5.4.test/lib/python3.8/site-packages/syri/scripts/syri.py", line 305, in main
syri(args)
File "/Programs/miniconda3/envs/SyRI_v1.5.4.test/lib/python3.8/site-packages/syri/scripts/syri.py", line 195, in syri
startSyri(args, coords[["aStart", "aEnd", "bStart", "bEnd", "aLen", "bLen", "iden", "aDir", "bDir", "aChr", "bChr"]])
File "syri/pyxFiles/synsearchFunctions.pyx", line 451, in syri.synsearchFunctions.startSyri
File "syri/pyxFiles/synsearchFunctions.pyx", line 452, in syri.synsearchFunctions.startSyri
File "/Programs/miniconda3/envs/SyRI_v1.5.4.test/lib/python3.8/multiprocessing/pool.py", line 364, in map
return self._map_async(func, iterable, mapstar, chunksize).get()
File "/Programs/miniconda3/envs/SyRI_v1.5.4.test/lib/python3.8/multiprocessing/pool.py", line 771, in get
raise self._value
AttributeError: type object 'object' has no attribute 'dtype'# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 1_gnu conda-forge
amply 0.1.4 py_0 conda-forge
arpack 3.7.0 hdefa2d7_2 conda-forge
brotlipy 0.7.0 py38h0a891b7_1004 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2022.3.29 h06a4308_0
certifi 2021.10.8 py38h578d9bd_2 conda-forge
cffi 1.15.0 py38h3931269_0 conda-forge
charset-normalizer 2.0.12 pyhd8ed1ab_0 conda-forge
coin-or-cbc 2.10.7 h3786ebc_0 conda-forge
coin-or-cgl 0.60.3 he7e83c3_2 conda-forge
coin-or-clp 1.17.6 h256e9bb_3 conda-forge
coin-or-osi 0.108.6 h3b589db_2 conda-forge
coin-or-utils 2.11.6 h573740c_0 conda-forge
coincbc 2.10.7 0_metapackage conda-forge
colorama 0.4.4 pyh9f0ad1d_0 conda-forge
conda 4.12.0 py38h578d9bd_0 conda-forge
conda-package-handling 1.8.1 py38h0a891b7_1 conda-forge
cryptography 36.0.0 py38h9ce1e76_0
docutils 0.18.1 py38h578d9bd_1 conda-forge
glpk 4.65 h9202a9a_1004 conda-forge
gmp 6.2.1 h58526e2_0 conda-forge
icu 70.1 h27087fc_0 conda-forge
idna 3.3 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
ld_impl_linux-64 2.36.1 hea4e1c9_2 conda-forge
libblas 3.9.0 14_linux64_openblas conda-forge
libcblas 3.9.0 14_linux64_openblas conda-forge
libcurl 7.82.0 h7bff187_0 conda-forge
libdeflate 1.10 h7f98852_0 conda-forge
libedit 3.1.20210910 h7f8727e_0
libev 4.33 h516909a_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 11.2.0 h1d223b6_15 conda-forge
libgfortran-ng 11.2.0 h69a702a_15 conda-forge
libgfortran5 11.2.0 h5c6108e_15 conda-forge
libgomp 11.2.0 h1d223b6_15 conda-forge
libiconv 1.16 h516909a_0 conda-forge
liblapack 3.9.0 14_linux64_openblas conda-forge
liblapacke 3.9.0 14_linux64_openblas conda-forge
libnghttp2 1.47.0 h727a467_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.20 pthreads_h78a6416_0 conda-forge
libssh2 1.10.0 ha56f1ee_2 conda-forge
libstdcxx-ng 11.2.0 he4da1e4_15 conda-forge
libuuid 2.32.1 h7f98852_1000 conda-forge
libxml2 2.9.13 h22db469_0 conda-forge
libzlib 1.2.11 h166bdaf_1014 conda-forge
longestrunsubsequence 1.0.1 py_0 bioconda
metis 5.1.0 h58526e2_1006 conda-forge
mpfr 4.1.0 h9202a9a_1 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
numpy 1.22.3 py38h1d589f8_2 conda-forge
openssl 1.1.1n h166bdaf_0 conda-forge
pandas 1.4.2 py38h47df419_1 conda-forge
pip 22.0.4 pyhd8ed1ab_0 conda-forge
psutil 5.9.0 py38h0a891b7_1 conda-forge
pulp 2.6.0 py38h578d9bd_1 conda-forge
pycosat 0.6.3 py38h0a891b7_1010 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyopenssl 22.0.0 pyhd8ed1ab_0 conda-forge
pyparsing 3.0.8 pyhd8ed1ab_0 conda-forge
pysam 0.19.0 py38h8bf8b8d_0 bioconda
pysocks 1.7.1 py38h578d9bd_5 conda-forge
python 3.8.13 h582c2e5_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-igraph 0.9.10 py38hb5c8105_1 conda-forge
python_abi 3.8 2_cp38 conda-forge
pytz 2022.1 pyhd8ed1ab_0 conda-forge
readline 8.1.2 h7f8727e_1
requests 2.27.1 pyhd8ed1ab_0 conda-forge
ruamel_yaml 0.15.100 py38h27cfd23_0
scipy 1.8.0 py38h56a6a73_1 conda-forge
setuptools 62.1.0 py38h578d9bd_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sqlite 3.38.2 h4ff8645_0 conda-forge
suitesparse 5.10.1 h9e50725_1 conda-forge
syri 1.5.4 py38h3a7dea9_0 bioconda
tbb 2021.5.0 h924138e_1 conda-forge
texttable 1.6.4 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tqdm 4.64.0 pyhd8ed1ab_0 conda-forge
urllib3 1.26.9 pyhd8ed1ab_0 conda-forge
wheel 0.37.1 pyhd8ed1ab_0 conda-forge
xz 5.2.5 h516909a_1 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zlib 1.2.11 h166bdaf_1014 conda-forgeJust to update that I was able to fix the error with the solution provided here: https://stackoverflow.com/questions/65998646/pandas-error-for-creating-an-emptydataframe
conda install -c conda-forge numpy==1.19.5
conda install -c conda-forge pandas==0.25.3Many thanks for all the help! Haim
mnshgl0110
commented
2 years ago Great that you made it work.
However, this solution depends on manually installing old versions of numpy and pandas. For future users, using
conda create -n syri_env -c bioconda syrishould install syri properly in a new environment.
Hi,
Thanks for developing SyRI! I am trying to use it with an alignment produced by minimap2 and get the following error. It happens both for my assemblies as well as for the example provided. Could you please advise what could be the problem, and how to solve it?
Many thanks for your help! Haim
The command:
The error message:
The syri log:
My conda enviorment: