StainedGlass
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mrvollger
numpy.linalg import error when running cooler_density + temporary fix
Hey there, ever since the parallelization update, I've been able to run StainedGlass on some especially large genomes and that has been such a game changer, thank you! Unfortunately, I'm coming across this error when running cooler_density. My solve was to go into env.yaml and change the numpy version specification from numpy<1.20 to numpy>=1.22.4 and then it ran smoothly. I hope this helps!
Command Run:
snakemake --cores 24 --use-conda --jobs 20 cooler_density --config sample=ChrY fasta=ChrY.fa window=32 cooler_window=100
Error:
[Tue May 14 11:31:57 2024]
localrule cooler_density_d:
input: results/contacts_ChrY_32.gz, /cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/ChrY.fa.fai
output: results/ChrY.32.100.density.cool
log: logs/cooler_density.ChrY.32.100.log
jobid: 2
reason: Missing output files: results/ChrY.32.100.density.cool
wildcards: SM=ChrY, W=32, CW=100
resources: mem_mb=16096, mem_mib=15351, disk_mb=1962, disk_mib=1872, tmpdir=/tmp, runtime=120, mem=64
Activating conda environment: .snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_
/cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_/lib/python3.9/site-packages/cooler/api.py:8: UserWarning: A NumPy version >=1.22.4 and <2.3.0 is required for this version of SciPy (detected version 1.19.5)
from scipy.sparse import coo_matrix
Traceback (most recent call last):
File "/cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_/bin/cooler", line 7, in <module>
from cooler.cli import cli
File "/cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_/lib/python3.9/site-packages/cooler/__init__.py", line 14, in <module>
from .api import Cooler, annotate
File "/cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_/lib/python3.9/site-packages/cooler/api.py", line 8, in <module>
from scipy.sparse import coo_matrix
File "/cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_/lib/python3.9/site-packages/scipy/sparse/__init__.py", line 294, in <module>
from ._base import *
File "/cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_/lib/python3.9/site-packages/scipy/sparse/_base.py", line 5, in <module>
from scipy._lib._util import VisibleDeprecationWarning
File "/cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_/lib/python3.9/site-packages/scipy/_lib/_util.py", line 18, in <module>
from scipy._lib._array_api import array_namespace
File "/cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_/lib/python3.9/site-packages/scipy/_lib/_array_api.py", line 17, in <module>
from scipy._lib.array_api_compat import (
File "/cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_/lib/python3.9/site-packages/scipy/_lib/array_api_compat/numpy/__init__.py", line 16, in <module>
__import__(__package__ + '.linalg')
File "/cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_/lib/python3.9/site-packages/scipy/_lib/array_api_compat/numpy/linalg.py", line 2, in <module>
from numpy.linalg import __all__ as linalg_all
ImportError: cannot import name '__all__' from 'numpy.linalg' (/cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_/lib/python3.9/site-packages/numpy/linalg/__init__.py)
[Tue May 14 11:31:59 2024]
Error in rule cooler_density_d:
jobid: 2
input: results/contacts_ChrY_32.gz, /cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/ChrY.fa.fai
output: results/ChrY.32.100.density.cool
log: logs/cooler_density.ChrY.32.100.log (check log file(s) for error details)
conda-env: /cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/ca1aab6256c939063ad2dad3ce65ab6e_
shell:
cooler cload pairs -c1 1 -p1 2 -c2 4 -p2 5 --chunksize 50000000000 /cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/ChrY.fa.fai:100 --zero-based results/contacts_ChrY_32$
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile logs/cooler_density.ChrY.32.100.log not found.
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-05-14T113004.423661.snakemake.log
WorkflowError:
At least one job did not complete successfully.
Thanks for the report!
Can you share the specific versions of cooler, pandas, and numpy that you installed? I am going to start locking things to specific versions instead of ranges.
Absolutely! Here's the output of conda list for the environment used during the successful run:
conda activate /cluster/home/lasmith/centromeres/neo/hap1/chromosomes/ChrY/StainedGlass/.snakemake/conda/4018f50b65bd0a625849ad987adee327_
conda list
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
asciitree 0.3.3 py_2 conda-forge
aws-c-auth 0.7.20 h5f1c8d9_0 conda-forge
aws-c-cal 0.6.12 h2ba76a8_0 conda-forge
aws-c-common 0.9.17 h4ab18f5_0 conda-forge
aws-c-compression 0.2.18 h36a0aea_4 conda-forge
aws-c-event-stream 0.4.2 h161de36_10 conda-forge
aws-c-http 0.8.1 h63f54a0_13 conda-forge
aws-c-io 0.14.8 h96d4d28_0 conda-forge
aws-c-mqtt 0.10.4 hcc7299c_2 conda-forge
aws-c-s3 0.5.8 h10bd90f_3 conda-forge
aws-c-sdkutils 0.1.16 h36a0aea_0 conda-forge
aws-checksums 0.1.18 h36a0aea_4 conda-forge
aws-crt-cpp 0.26.8 h02fd9b4_10 conda-forge
aws-sdk-cpp 1.11.267 h51dfee4_8 conda-forge
bedtools 2.31.1 hf5e1c6e_1 bioconda
biopython 1.83 py310h2372a71_0 conda-forge
bokeh 3.4.1 pyhd8ed1ab_0 conda-forge
brotli-python 1.1.0 py310hc6cd4ac_1 conda-forge
bwa 0.7.18 he4a0461_0 bioconda
bzip2 1.0.8 hd590300_5 conda-forge
c-ares 1.28.1 hd590300_0 conda-forge
ca-certificates 2024.2.2 hbcca054_0 conda-forge
cached-property 1.5.2 hd8ed1ab_1 conda-forge
cached_property 1.5.2 pyha770c72_1 conda-forge
click 8.1.7 unix_pyh707e725_0 conda-forge
cloudpickle 3.0.0 pyhd8ed1ab_0 conda-forge
contourpy 1.2.1 py310hd41b1e2_0 conda-forge
cooler 0.8.11 pyh7cba7a3_2 bioconda
cytoolz 0.12.3 py310h2372a71_0 conda-forge
dask 2024.2.1 pyhd8ed1ab_0 conda-forge
dask-core 2024.2.1 pyhd8ed1ab_1 conda-forge
dill 0.3.8 pyhd8ed1ab_0 conda-forge
distributed 2024.2.1 pyhd8ed1ab_0 conda-forge
freetype 2.12.1 h267a509_2 conda-forge
fsspec 2024.3.1 pyhca7485f_0 conda-forge
gflags 2.2.2 he1b5a44_1004 conda-forge
glog 0.7.0 hed5481d_0 conda-forge
h5py 3.11.0 nompi_py310h65828d5_100 conda-forge
hdf5 1.14.3 nompi_h4f84152_101 conda-forge
htslib 1.20 h81da01d_0 bioconda
importlib-metadata 7.1.0 pyha770c72_0 conda-forge
importlib_metadata 7.1.0 hd8ed1ab_0 conda-forge
jinja2 3.1.4 pyhd8ed1ab_0 conda-forge
k8 0.2.5 hdcf5f25_4 bioconda
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_0 conda-forge
lcms2 2.15 h7f713cb_2 conda-forge
ld_impl_linux-64 2.40 h55db66e_0 conda-forge
lerc 4.0.0 h27087fc_0 conda-forge
libabseil 20240116.2 cxx17_h59595ed_0 conda-forge
libaec 1.1.3 h59595ed_0 conda-forge
libarrow 16.0.0 hefa796f_1_cpu conda-forge
libarrow-acero 16.0.0 hac33072_1_cpu conda-forge
libarrow-dataset 16.0.0 hac33072_1_cpu conda-forge
libarrow-substrait 16.0.0 h7e0c224_1_cpu conda-forge
libblas 3.9.0 22_linux64_openblas conda-forge
libbrotlicommon 1.1.0 hd590300_1 conda-forge
libbrotlidec 1.1.0 hd590300_1 conda-forge
libbrotlienc 1.1.0 hd590300_1 conda-forge
libcblas 3.9.0 22_linux64_openblas conda-forge
libcrc32c 1.1.2 h9c3ff4c_0 conda-forge
libcurl 8.7.1 hca28451_0 conda-forge
libdeflate 1.18 h0b41bf4_0 conda-forge
libedit 3.1.20191231 he28a2e2_2 conda-forge
libev 4.33 hd590300_2 conda-forge
libevent 2.1.12 hf998b51_1 conda-forge
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 h77fa898_7 conda-forge
libgfortran-ng 13.2.0 h69a702a_7 conda-forge
libgfortran5 13.2.0 hca663fb_7 conda-forge
libgomp 13.2.0 h77fa898_7 conda-forge
libgoogle-cloud 2.23.0 h9be4e54_1 conda-forge
libgoogle-cloud-storage 2.23.0 hc7a4891_1 conda-forge
libgrpc 1.62.2 h15f2491_0 conda-forge
libjpeg-turbo 2.1.5.1 hd590300_1 conda-forge
liblapack 3.9.0 22_linux64_openblas conda-forge
libllvm14 14.0.6 hcd5def8_4 conda-forge
libnghttp2 1.58.0 h47da74e_1 conda-forge
libnsl 2.0.1 hd590300_0 conda-forge
libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge
libparquet 16.0.0 h6a7eafb_1_cpu conda-forge
libpng 1.6.43 h2797004_0 conda-forge
libprotobuf 4.25.3 h08a7969_0 conda-forge
libre2-11 2023.09.01 h5a48ba9_2 conda-forge
libsqlite 3.45.3 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 hc0a3c3a_7 conda-forge
libthrift 0.19.0 hb90f79a_1 conda-forge
libtiff 4.6.0 h8b53f26_0 conda-forge
libutf8proc 2.8.0 h166bdaf_0 conda-forge
libuuid 2.38.1 h0b41bf4_0 conda-forge
libwebp-base 1.4.0 hd590300_0 conda-forge
libxcb 1.15 h0b41bf4_0 conda-forge
libxcrypt 4.4.36 hd590300_1 conda-forge
libzlib 1.2.13 hd590300_5 conda-forge
llvmlite 0.42.0 py310h1b8f574_1 conda-forge
locket 1.0.0 pyhd8ed1ab_0 conda-forge
lz4 4.3.3 py310h350c4a5_0 conda-forge
lz4-c 1.9.4 hcb278e6_0 conda-forge
markupsafe 2.1.5 py310h2372a71_0 conda-forge
minimap2 2.18 h5bf99c6_0 bioconda
msgpack-python 1.0.8 py310h25c7140_0 conda-forge
multiprocess 0.70.16 py310h2372a71_0 conda-forge
ncurses 6.5 h59595ed_0 conda-forge
numba 0.59.1 py310h7dc5dd1_0 conda-forge
numpy 1.23.5 py310h53a5b5f_0 conda-forge
openjpeg 2.5.2 h488ebb8_0 conda-forge
openssl 3.3.0 hd590300_0 conda-forge
orc 2.0.0 h17fec99_1 conda-forge
packaging 24.0 pyhd8ed1ab_0 conda-forge
pairix 0.3.8 py310h83093d7_1 bioconda
pandas 1.5.0 py310h769672d_0 conda-forge
partd 1.4.2 pyhd8ed1ab_0 conda-forge
perl 5.32.1 7_hd590300_perl5 conda-forge
pigz 2.8 h2797004_0 conda-forge
pillow 10.0.1 py310h29da1c1_1 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
psutil 5.9.8 py310h2372a71_0 conda-forge
pthread-stubs 0.4 h36c2ea0_1001 conda-forge
pyarrow 16.0.0 py310h17c5347_0 conda-forge
pyarrow-core 16.0.0 py310h6f79a3a_0_cpu conda-forge
pyarrow-hotfix 0.6 pyhd8ed1ab_0 conda-forge
pyfaidx 0.8.1.1 pyhdfd78af_0 bioconda
pysam 0.22.1 py310h41dec4a_0 bioconda
pysocks 1.7.1 pyha2e5f31_6 conda-forge
python 3.10.14 hd12c33a_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python_abi 3.10 4_cp310 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
pyvcf3 1.0.3 pyhdfd78af_0 bioconda
pyyaml 6.0.1 py310h2372a71_1 conda-forge
re2 2023.09.01 h7f4b329_2 conda-forge
readline 8.2 h8228510_1 conda-forge
s2n 1.4.13 he19d79f_0 conda-forge
samtools 1.20 h50ea8bc_0 bioconda
scipy 1.13.0 py310h93e2701_1 conda-forge
setuptools 69.5.1 pyhd8ed1ab_0 conda-forge
simplejson 3.19.2 py310h2372a71_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
snappy 1.2.0 hdb0a2a9_1 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
tblib 3.0.0 pyhd8ed1ab_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
toolz 0.12.1 pyhd8ed1ab_0 conda-forge
tornado 6.4 py310h2372a71_0 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
urllib3 2.2.1 pyhd8ed1ab_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
xorg-libxau 1.0.11 hd590300_0 conda-forge
xorg-libxdmcp 1.1.3 h7f98852_0 conda-forge
xyzservices 2024.4.0 pyhd8ed1ab_0 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
yaml 0.2.5 h7f98852_2 conda-forge
zict 3.0.0 pyhd8ed1ab_0 conda-forge
zipp 3.17.0 pyhd8ed1ab_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.6 ha6fb4c9_0 conda-forge
I have the same error: snakemake --cores 24 cooler_density --config window=32 cooler_window=100 Using workflow specific profile workflow/profiles/default for setting default command line arguments. Thanks for using StainedGlass and please remember to cite the tool! Mitchell R Vollger, Peter Kerpedjiev, Adam M Phillippy, Evan E Eichler. "StainedGlass: Interactive visualization of massive tandem repeat structures with identity heatmaps" Bioinformatics, 2022; https://doi.org/10.1093/bioinformatics/btac018
Config file config/config.yaml is extended by additional config specified via the command line. [INFO] The sequence will be split into 4 batches. Assuming unrestricted shared filesystem usage. Building DAG of jobs... Your conda installation is not configured to use strict channel priorities. This is however crucial for having robust and correct environments (for details, see https://conda-forge.org/docs/user/tipsandtricks.html). Please consider to configure strict priorities by executing 'conda config --set channel_priority strict'. Using shell: /usr/bin/bash Provided cores: 24 Rules claiming more threads will be scaled down. Job stats: job count
cooler_density 1 cooler_density_d 1 cooler_zoomify_d 1 total 3
Select jobs to execute... Execute 1 jobs...
[Thu May 23 13:35:32 2024] localrule cooler_density_d: input: results/contacts_Dm25_32.gz, /home/ggreif/StainedGlass/TcDm25_H1.fasta.fai output: results/Dm25.32.100.density.cool log: logs/cooler_density.Dm25.32.100.log jobid: 2 reason: Missing output files: results/Dm25.32.100.density.cool wildcards: SM=Dm25, W=32, CW=100 resources: mem_mb=16096, mem_mib=15351, disk_mb=1000, disk_mib=954, tmpdir=/tmp, runtime=120, mem=64
Activating conda environment: .snakemake/conda/92fd4fd073b40f84bb5654715f27ce30_
/home/ggreif/StainedGlass/.snakemake/conda/92fd4fd073b40f84bb5654715f27ce30_/lib/python3.9/site-packages/cooler/api.py:8: UserWarning: A NumPy version >=1.22.4 and <2.3.0 is required for this version of SciPy (detected version 1.19.5)
from scipy.sparse import coo_matrix
Traceback (most recent call last):
File "/home/ggreif/StainedGlass/.snakemake/conda/92fd4fd073b40f84bb5654715f27ce30_/bin/cooler", line 6, in
cooler cload pairs -c1 1 -p1 2 -c2 4 -p2 5 --chunksize 50000000000 /home/ggreif/StainedGlass/TcDm25_H1.fasta.fai:100 --zero-based results/contacts_Dm25_32.gz results/Dm25.32.100.density.cool
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Logfile logs/cooler_density.Dm25.32.100.log not found.
Shutting down, this might take some time. Exiting because a job execution failed. Look above for error message Complete log: .snakemake/log/2024-05-23T133531.849068.snakemake.log WorkflowError: At least one job did not complete successfully.
My conda list: conda list
packages in environment at /home/ggreif/miniconda3/envs/snakemake:
Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge _openmp_mutex 4.5 2_gnu conda-forge amply 0.1.6 pyhd8ed1ab_0 conda-forge appdirs 1.4.4 pyh9f0ad1d_0 conda-forge argparse-dataclass 2.0.0 pyhd8ed1ab_0 conda-forge attmap 0.13.2 pyhd8ed1ab_0 conda-forge attrs 23.2.0 pyh71513ae_0 conda-forge brotli-python 1.1.0 py312h30efb56_1 conda-forge bzip2 1.0.8 hd590300_5 conda-forge ca-certificates 2024.2.2 hbcca054_0 conda-forge certifi 2024.2.2 pyhd8ed1ab_0 conda-forge charset-normalizer 3.3.2 pyhd8ed1ab_0 conda-forge coin-or-cbc 2.10.10 h9002f0b_0 conda-forge coin-or-cgl 0.60.7 h516709c_0 conda-forge coin-or-clp 1.17.8 h1ee7a9c_0 conda-forge coin-or-osi 0.108.10 haf5fa05_0 conda-forge coin-or-utils 2.11.11 hee58242_0 conda-forge coincbc 2.10.10 0_metapackage conda-forge colorama 0.4.6 pyhd8ed1ab_0 conda-forge conda-inject 1.3.1 pyhd8ed1ab_0 conda-forge configargparse 1.7 pyhd8ed1ab_0 conda-forge connection_pool 0.0.3 pyhd3deb0d_0 conda-forge datrie 0.8.2 py312h98912ed_7 conda-forge docutils 0.21.2 pyhd8ed1ab_0 conda-forge dpath 2.1.6 pyha770c72_0 conda-forge eido 0.2.2 pyhd8ed1ab_0 conda-forge exceptiongroup 1.2.0 pyhd8ed1ab_2 conda-forge gitdb 4.0.11 pyhd8ed1ab_0 conda-forge gitpython 3.1.43 pyhd8ed1ab_0 conda-forge humanfriendly 10.0 pyhd8ed1ab_6 conda-forge idna 3.7 pyhd8ed1ab_0 conda-forge immutables 0.20 py312h98912ed_1 conda-forge importlib_resources 6.4.0 pyhd8ed1ab_0 conda-forge iniconfig 2.0.0 pyhd8ed1ab_0 conda-forge jinja2 3.1.4 pyhd8ed1ab_0 conda-forge jsonschema 4.22.0 pyhd8ed1ab_0 conda-forge jsonschema-specifications 2023.12.1 pyhd8ed1ab_0 conda-forge jupyter_core 5.7.2 py312h7900ff3_0 conda-forge ld_impl_linux-64 2.40 h55db66e_0 conda-forge libblas 3.9.0 22_linux64_openblas conda-forge libcblas 3.9.0 22_linux64_openblas conda-forge libexpat 2.6.2 h59595ed_0 conda-forge libffi 3.4.2 h7f98852_5 conda-forge libgcc-ng 13.2.0 h77fa898_7 conda-forge libgfortran-ng 13.2.0 h69a702a_7 conda-forge libgfortran5 13.2.0 hca663fb_7 conda-forge libgomp 13.2.0 h77fa898_7 conda-forge liblapack 3.9.0 22_linux64_openblas conda-forge liblapacke 3.9.0 22_linux64_openblas conda-forge libnsl 2.0.1 hd590300_0 conda-forge libopenblas 0.3.27 pthreads_h413a1c8_0 conda-forge libsqlite 3.45.3 h2797004_0 conda-forge libstdcxx-ng 13.2.0 hc0a3c3a_7 conda-forge libuuid 2.38.1 h0b41bf4_0 conda-forge libxcrypt 4.4.36 hd590300_1 conda-forge libzlib 1.2.13 hd590300_5 conda-forge logmuse 0.2.6 pyh8c360ce_0 conda-forge markdown-it-py 3.0.0 pyhd8ed1ab_0 conda-forge markupsafe 2.1.5 py312h98912ed_0 conda-forge mdurl 0.1.2 pyhd8ed1ab_0 conda-forge nbformat 5.10.4 pyhd8ed1ab_0 conda-forge ncurses 6.5 h59595ed_0 conda-forge numpy 1.26.4 py312heda63a1_0 conda-forge openssl 3.3.0 h4ab18f5_3 conda-forge packaging 24.0 pyhd8ed1ab_0 conda-forge pandas 2.2.2 py312h1d6d2e6_1 conda-forge peppy 0.40.1 pyhd8ed1ab_0 conda-forge pip 24.0 pyhd8ed1ab_0 conda-forge pkgutil-resolve-name 1.3.10 pyhd8ed1ab_1 conda-forge plac 1.4.3 pyhd8ed1ab_0 conda-forge platformdirs 4.2.2 pyhd8ed1ab_0 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