Hi!

Forst of all, thanks for such nice pipeline! I got this issue when running PHP. My 2 cents is it is linked to Numpy. I wonder if downgraded it would help… Thanks!

Cheers,

‌

Nico

‌

1- Command used

‌

iphop predict --fa_file selected_virus.fa --out_dir Host_prediction_sel --db_dir /media/nico/MyBook2/iphop_db/Sept_2021_pub_rw/ -t 16

Welcome to iPHoP

Looks like everything is now set up, we will first clean up the input file, and then we will start the host prediction steps themselves
[1/1/Run] Running blastn against genomes...
[1/3/Run] Get relevant blast matches...
[2/1/Run] Running blastn against CRISPR...
[2/2/Run] Get relevant crispr matches...
[3/1/Run] Running (recoded)WIsH...
[3/2/Run] Get relevant WIsH hits...
[4/1/Run] Running VHM s2 similarities...
[4/2/Run] Get relevant VHM hits...
[5/1/Run] Running PHP...
[5/2/Run] Get relevant PHP hits...
Traceback (most recent call last):
File "/home/nico/miniconda3/envs/iphop_env/bin/iphop", line 10, in <module>
sys.exit(cli())
File "/home/nico/miniconda3/envs/iphop_env/lib/python3.8/site-packages/iphop/iphop.py", line 128, in cli
args"func"
File "/home/nico/miniconda3/envs/iphop_env/lib/python3.8/site-packages/iphop/modules/master_predict.py", line 91, in main
php.run_and_parse_php(args)
File "/home/nico/miniconda3/envs/iphop_env/lib/python3.8/site-packages/iphop/modules/php.py", line 28, in run_and_parse_php
get_php_results(args["fasta_file"],args["phprawresult"],args["phpparsed"],logger,args['messages'])
File "/home/nico/miniconda3/envs/iphop_env/lib/python3.8/site-packages/iphop/modules/php.py", line 42, in get_php_results
df_pred = pd.read_csv(pred_file,delimiter=',',quotechar='"', index_col=0)
File "/home/nico/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 912, in read_csv
return _read(filepath_or_buffer, kwds)
File "/home/nico/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 577, in _read
parser = TextFileReader(filepath_or_buffer, **kwds)
File "/home/nico/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1407, in init
self._engine = self._make_engine(f, self.engine)
File "/home/nico/.local/lib/python3.8/site-packages/pandas/io/parsers/readers.py", line 1661, in _make_engine
self.handles = get_handle(
File "/home/nico/.local/lib/python3.8/site-packages/pandas/io/common.py", line 859, in get_handle
handle = open(
FileNotFoundError: [Errno 2] No such file or directory: 'Host_prediction_sel/Wdir/php_results/php_db_Prediction_Allhost.csv'

‌

2- log file

Traceback (most recent call last):
File "/home/nico/miniconda3/envs/iphop_env/lib/python3.8/site-packages/iphop/utils/PHP.py", line 138, in <module>
main()
File "/home/nico/miniconda3/envs/iphop_env/lib/python3.8/site-packages/iphop/utils/PHP.py", line 134, in main
predictVirusHost(scriptPath,bacteriaKmerDir,bacteriaKmerName,outFileDir,dicVirusSeqLength)
File "/home/nico/miniconda3/envs/iphop_env/lib/python3.8/site-packages/iphop/utils/PHP.py", line 7, in predictVirusHost
modelFullLength = joblib.load(scriptPath+'/PHP_src/FullLength/FullLength.m')
File "/home/nico/.local/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 658, in load
obj = _unpickle(fobj, filename, mmap_mode)
File "/home/nico/.local/lib/python3.8/site-packages/joblib/numpy_pickle.py", line 577, in _unpickle
obj = unpickler.load()
File "/home/nico/miniconda3/envs/iphop_env/lib/python3.8/pickle.py", line 1212, in load
dispatchkey[0]
File "/home/nico/miniconda3/envs/iphop_env/lib/python3.8/pickle.py", line 1528, in load_global
klass = self.find_class(module, name)
File "/home/nico/miniconda3/envs/iphop_env/lib/python3.8/pickle.py", line 1579, in find_class
import(module, level=0)
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/mixture/init.py", line 5, in <module>
from ._gaussian_mixture import GaussianMixture
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/mixture/_gaussian_mixture.py", line 11, in <module>
from ._base import BaseMixture, _check_shape
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/mixture/_base.py", line 14, in <module>
from .. import cluster
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/cluster/init.py", line 6, in <module>
from ._spectral import spectral_clustering, SpectralClustering
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/cluster/_spectral.py", line 16, in <module>
from ..neighbors import kneighbors_graph, NearestNeighbors
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/neighbors/init.py", line 17, in <module>
from ._nca import NeighborhoodComponentsAnalysis
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/neighbors/_nca.py", line 22, in <module>
from ..decomposition import PCA
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/decomposition/init.py", line 17, in <module>
from .dict_learning import dict_learning
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/decomposition/dict_learning.py", line 5, in <module>
from . import _dict_learning # type: ignore
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/decomposition/_dict_learning.py", line 21, in <module>
from ..linear_model import Lasso, orthogonal_mp_gram, LassoLars, Lars
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/linear_model/init.py", line 11, in <module>
from ._least_angle import (Lars, LassoLars, lars_path, lars_path_gram, LarsCV,
File "/home/nico/.local/lib/python3.8/site-packages/sklearn/linear_model/_least_angle.py", line 34, in <module>
method='lar', copy_X=True, eps=np.finfo(np.float).eps,
File "/home/nico/.local/lib/python3.8/site-packages/numpy/init.py", line 305, in getattr
raise AttributeError(former_attrs[attr])
AttributeError: module 'numpy' has no attribute 'float'.
np.float was a deprecated alias for the builtin float. To avoid this error in existing code, use float by itself. Doing this will not modify any behavior and is safe. If you specifically wanted the numpy scalar type, use np.float64 here.
The aliases was originally deprecated in NumPy 1.20; for more details and guidance see the original release note at:
https://numpy.org/devdocs/release/1.20.0-notes.html#deprecations

‌

3- Conda env:

‌

packages in environment at /home/nico/miniconda3/envs/iphop_env:

‌

Name Version Build Channel

_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
_r-mutex 1.0.1 anacondar_1 conda-forge
abseil-cpp 20210324.2 h9c3ff4c_0 conda-forge
absl-py 1.4.0 pyhd8ed1ab_0 conda-forge
aiohttp 3.7.4.post0 py38h497a2fe_1 conda-forge
alsa-lib 1.2.8 h166bdaf_0 conda-forge
astunparse 1.6.3 pyhd8ed1ab_0 conda-forge
async-timeout 3.0.1 py_1000 conda-forge
attrs 23.1.0 pyh71513ae_1 conda-forge
binutils_impl_linux-64 2.40 hf600244_0 conda-forge
biopython 1.79 py38h0a891b7_3 conda-forge
blast 2.12.0 hf3cf87c_4 bioconda
blinker 1.6.2 pyhd8ed1ab_0 conda-forge
boltons 23.0.0 pyhd8ed1ab_0 conda-forge
boost-cpp 1.74.0 h75c5d50_8 conda-forge
bottleneck 1.3.7 py38h7e4f40d_0 conda-forge
brotlipy 0.7.0 py38h0a891b7_1005 conda-forge
bwidget 1.9.14 ha770c72_1 conda-forge
bzip2 1.0.8 h7f98852_4 conda-forge
c-ares 1.18.1 h7f98852_0 conda-forge
ca-certificates 2023.5.7 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
cachetools 4.2.4 pyhd8ed1ab_0 conda-forge
cairo 1.16.0 ha61ee94_1014 conda-forge
certifi 2023.5.7 pyhd8ed1ab_0 conda-forge
cffi 1.15.1 py38h4a40e3a_3 conda-forge
chardet 4.0.0 py38h578d9bd_3 conda-forge
charset-normalizer 3.1.0 pyhd8ed1ab_0 conda-forge
click 8.0.4 py38h578d9bd_0 conda-forge
colorama 0.4.6 pyhd8ed1ab_0 conda-forge
conda 23.3.1 py38h578d9bd_0 conda-forge
conda-package-handling 2.0.2 pyh38be061_0 conda-forge
conda-package-streaming 0.7.0 pyhd8ed1ab_1 conda-forge
crisper_recognition_tool 1.2 hdfd78af_2 bioconda
cryptography 39.0.0 py38h1724139_0 conda-forge
curl 7.86.0 h7bff187_1 conda-forge
diamond 2.0.15 hb97b32f_1 bioconda
entrez-direct 16.2 he881be0_1 bioconda
expat 2.5.0 hcb278e6_1 conda-forge
fmt 9.1.0 h924138e_0 conda-forge
font-ttf-dejavu-sans-mono 2.37 hab24e00_0 conda-forge
font-ttf-inconsolata 3.000 h77eed37_0 conda-forge
font-ttf-source-code-pro 2.038 h77eed37_0 conda-forge
font-ttf-ubuntu 0.83 hab24e00_0 conda-forge
fontconfig 2.14.2 h14ed4e7_0 conda-forge
fonts-conda-ecosystem 1 0 conda-forge
fonts-conda-forge 1 0 conda-forge
freetype 2.12.1 hca18f0e_1 conda-forge
fribidi 1.0.10 h36c2ea0_0 conda-forge
gast 0.4.0 pyh9f0ad1d_0 conda-forge
gcc_impl_linux-64 12.2.0 hcc96c02_19 conda-forge
gettext 0.21.1 h27087fc_0 conda-forge
gfortran_impl_linux-64 12.2.0 h55be85b_19 conda-forge
giflib 5.2.1 h0b41bf4_3 conda-forge
google-auth 1.35.0 pyh6c4a22f_0 conda-forge
google-auth-oauthlib 0.4.6 pyhd8ed1ab_0 conda-forge
google-pasta 0.2.0 pyh8c360ce_0 conda-forge
graphite2 1.3.13 h58526e2_1001 conda-forge
grpc-cpp 1.43.2 h9e046d8_3 conda-forge
grpcio 1.43.0 py38hdd6454d_0 conda-forge
gsl 2.7 he838d99_0 conda-forge
gxx_impl_linux-64 12.2.0 hcc96c02_19 conda-forge
h5py 3.8.0 nompi_py38hd5fa8ee_100 conda-forge
harfbuzz 6.0.0 h8e241bc_0 conda-forge
hdf5 1.12.2 nompi_h2386368_100 conda-forge
hmmer 3.3.2 h87f3376_2 bioconda
icu 70.1 h27087fc_0 conda-forge
idna 3.4 pyhd8ed1ab_0 conda-forge
importlib-metadata 6.6.0 pyha770c72_0 conda-forge
iphop 1.3.0 pyhdfd78af_0 bioconda
joblib 1.0.1 pyhd8ed1ab_0 conda-forge
jpeg 9e h0b41bf4_3 conda-forge
jsonpatch 1.32 pyhd8ed1ab_0 conda-forge
jsonpointer 2.0 py_0 conda-forge
keras 2.7.0 pyhd8ed1ab_0 conda-forge
keras-preprocessing 1.1.2 pyhd8ed1ab_0 conda-forge
kernel-headers_linux-64 2.6.32 he073ed8_15 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.19.3 h3790be6_0 conda-forge
lcms2 2.14 h6ed2654_0 conda-forge
ld_impl_linux-64 2.40 h41732ed_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libarchive 3.6.2 hc8874e4_0 conda-forge
libblas 3.9.0 16_linux64_openblas conda-forge
libcblas 3.9.0 16_linux64_openblas conda-forge
libcups 2.3.3 h3e49a29_2 conda-forge
libcurl 7.86.0 h7bff187_1 conda-forge
libdeflate 1.14 h166bdaf_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 h516909a_1 conda-forge
libexpat 2.5.0 hcb278e6_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc 7.2.0 h69d50b8_2 conda-forge
libgcc-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge
libgcc-ng 12.2.0 h65d4601_19 conda-forge
libgfortran-ng 12.2.0 h69a702a_19 conda-forge
libgfortran5 12.2.0 h337968e_19 conda-forge
libglib 2.76.2 hebfc3b9_0 conda-forge
libgomp 12.2.0 h65d4601_19 conda-forge
libiconv 1.17 h166bdaf_0 conda-forge
libidn2 2.3.4 h166bdaf_0 conda-forge
liblapack 3.9.0 16_linux64_openblas conda-forge
libmamba 1.1.0 h83d9b23_3 conda-forge
libmambapy 1.1.0 py38h1f54a8e_3 conda-forge
libnghttp2 1.51.0 hdcd2b5c_0 conda-forge
libnsl 2.0.0 h7f98852_0 conda-forge
libopenblas 0.3.21 pthreads_h78a6416_3 conda-forge
libpng 1.6.39 h753d276_0 conda-forge
libprotobuf 3.19.6 h3eb15da_0 conda-forge
libsanitizer 12.2.0 h46fd767_19 conda-forge
libsolv 0.7.23 h3eb15da_0 conda-forge
libsqlite 3.41.2 h2797004_1 conda-forge
libssh2 1.10.0 haa6b8db_3 conda-forge
libstdcxx-devel_linux-64 12.2.0 h3b97bd3_19 conda-forge
libstdcxx-ng 12.2.0 h46fd767_19 conda-forge
libtiff 4.4.0 h82bc61c_5 conda-forge
libunistring 0.9.10 h7f98852_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.3.0 h0b41bf4_0 conda-forge
libxcb 1.13 h7f98852_1004 conda-forge
libxml2 2.10.3 hca2bb57_4 conda-forge
libzlib 1.2.13 h166bdaf_4 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
lzo 2.10 h516909a_1000 conda-forge
make 4.3 hd18ef5c_1 conda-forge
mamba 1.1.0 py38h1abaa86_3 conda-forge
markdown 3.4.3 pyhd8ed1ab_0 conda-forge
markupsafe 2.1.2 py38h1de0b5d_0 conda-forge
multidict 6.0.4 py38h1de0b5d_0 conda-forge
ncurses 6.3 h27087fc_1 conda-forge
nomkl 1.0 h5ca1d4c_0 conda-forge
numexpr 2.8.4 py38h69a160b_100 conda-forge
numpy 1.23.5 py38h7042d01_0 conda-forge
oauthlib 3.2.2 pyhd8ed1ab_0 conda-forge
openjdk 17.0.3 h58dac75_5 conda-forge
openssl 1.1.1t h0b41bf4_0 conda-forge
opt_einsum 3.3.0 pyhd8ed1ab_1 conda-forge
packaging 23.1 pyhd8ed1ab_0 conda-forge
pandas 1.3.5 py38h8c16a72_0
pango 1.50.14 hd33c08f_0 conda-forge
pcre 8.45 h9c3ff4c_0 conda-forge
pcre2 10.40 hc3806b6_0 conda-forge
perl 5.22.2.1 0 conda-forge
perl-archive-tar 2.18 1 bioconda
perl-bioperl 1.6.924 4 bioconda
perl-common-sense 3.74 0 bioconda
perl-exporter-tiny 0.042 1 bioconda
perl-json 2.90 1 bioconda
perl-json-xs 2.34 0 bioconda
perl-list-moreutils 0.413 1 bioconda
perl-threaded 5.32.1 hdfd78af_1 bioconda
perl-yaml 1.24 pl522_1 bioconda
piler-cr 1.06 h9f5acd7_3 bioconda
pip 23.1.2 pyhd8ed1ab_0 conda-forge
pixman 0.40.0 h36c2ea0_0 conda-forge
platformdirs 3.5.1 pyhd8ed1ab_0 conda-forge
pluggy 1.0.0 pyhd8ed1ab_5 conda-forge
pooch 1.7.0 pyha770c72_3 conda-forge
prodigal 2.6.3 hec16e2b_4 bioconda
protobuf 3.19.6 py38h8dc9893_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyasn1 0.4.8 py_0 conda-forge
pyasn1-modules 0.2.7 py_0 conda-forge
pybind11-abi 4 hd8ed1ab_3 conda-forge
pycosat 0.6.4 py38h0a891b7_1 conda-forge
pycparser 2.21 pyhd8ed1ab_0 conda-forge
pyjwt 2.7.0 pyhd8ed1ab_0 conda-forge
pyopenssl 23.1.1 pyhd8ed1ab_0 conda-forge
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.8.15 h257c98d_0_cpython conda-forge
python-dateutil 2.8.2 pyhd8ed1ab_0 conda-forge
python-flatbuffers 2.0 pyhd8ed1ab_0 conda-forge
python_abi 3.8 3_cp38 conda-forge
pytz 2023.3 pyhd8ed1ab_0 conda-forge
pyu2f 0.1.5 pyhd8ed1ab_0 conda-forge
r-base 4.0.5 hb87df5d_8 conda-forge
r-lattice 0.20_45 r40hcfec24a_0 conda-forge
r-matrix 1.4_1 r40h0154571_0 conda-forge
r-ranger 0.13.1 r40h03ef668_0 conda-forge
r-rcpp 1.0.9 r40h7525677_1 conda-forge
r-rcppeigen 0.3.3.9.2 r40h43535f1_0 conda-forge
re2 2022.02.01 h9c3ff4c_0 conda-forge
readline 8.2 h8228510_1 conda-forge
reproc 14.2.4 h0b41bf4_0 conda-forge
reproc-cpp 14.2.4 hcb278e6_0 conda-forge
requests 2.29.0 pyhd8ed1ab_0 conda-forge
requests-oauthlib 1.3.1 pyhd8ed1ab_0 conda-forge
rsa 4.9 pyhd8ed1ab_0 conda-forge
ruamel.yaml 0.17.26 py38h01eb140_0 conda-forge
ruamel.yaml.clib 0.2.7 py38h1de0b5d_1 conda-forge
scikit-learn 0.22.2.post1 py38hcdab131_0 conda-forge
scipy 1.10.1 py38h59f1b5f_2 conda-forge
sed 4.8 he412f7d_0 conda-forge
setuptools 67.7.2 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.1.10 h9fff704_0 conda-forge
sqlite 3.41.2 h2c6b66d_1 conda-forge
sysroot_linux-64 2.12 he073ed8_15 conda-forge
tensorboard 2.6.0 pyhd8ed1ab_1 conda-forge
tensorboard-data-server 0.6.1 py38h2b5fc30_4 conda-forge
tensorboard-plugin-wit 1.8.1 pyhd8ed1ab_0 conda-forge
tensorflow 2.7.0 pypi_0 pypi
tensorflow-base 2.7.1 cpu_py38ha28dbe6_0 conda-forge
tensorflow-decision-forests 0.2.2 pypi_0 pypi
tensorflow-estimator 2.7.1 cpu_py38h4e23bc6_0 conda-forge
termcolor 2.3.0 pyhd8ed1ab_0 conda-forge
tk 8.6.12 h27826a3_0 conda-forge
tktable 2.10 hb7b940f_3 conda-forge
toolz 0.12.0 pyhd8ed1ab_0 conda-forge
tqdm 4.65.0 pyhd8ed1ab_1 conda-forge
typing-extensions 4.5.0 hd8ed1ab_0 conda-forge
typing_extensions 4.5.0 pyha770c72_0 conda-forge
urllib3 1.26.15 pyhd8ed1ab_0 conda-forge
werkzeug 2.3.4 pyhd8ed1ab_0 conda-forge
wget 1.20.3 ha56f1ee_1 conda-forge
wheel 0.40.0 pyhd8ed1ab_0 conda-forge
wrapt 1.15.0 py38h1de0b5d_0 conda-forge
xorg-fixesproto 5.0 h7f98852_1002 conda-forge
xorg-inputproto 2.3.2 h7f98852_1002 conda-forge
xorg-kbproto 1.0.7 h7f98852_1002 conda-forge
xorg-libice 1.0.10 h7f98852_0 conda-forge
xorg-libsm 1.2.3 hd9c2040_1000 conda-forge
xorg-libx11 1.8.4 h0b41bf4_0 conda-forge
xorg-libxau 1.0.9 h7f98852_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xorg-libxext 1.3.4 h0b41bf4_2 conda-forge
xorg-libxfixes 5.0.3 h7f98852_1004 conda-forge
xorg-libxi 1.7.10 h7f98852_0 conda-forge
xorg-libxrender 0.9.10 h7f98852_1003 conda-forge
xorg-libxt 1.2.1 h7f98852_2 conda-forge
xorg-libxtst 1.2.3 h7f98852_1002 conda-forge
xorg-recordproto 1.14.2 h7f98852_1002 conda-forge
xorg-renderproto 0.11.1 h7f98852_1002 conda-forge
xorg-xextproto 7.3.0 h0b41bf4_1003 conda-forge
xorg-xproto 7.0.31 h7f98852_1007 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml-cpp 0.7.0 h27087fc_2 conda-forge
yarl 1.9.1 py38h01eb140_0 conda-forge
zipp 3.15.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 h166bdaf_4 conda-forge
zstandard 0.19.0 py38h5945529_1 conda-forge
zstd 1.5.2 h3eb15da_6 conda-forge

‌

Welcome to iPHoP

packages in environment at /home/nico/miniconda3/envs/iphop_env:

Name Version Build Channel

Comments (7)