dysgu
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kcleal
Error installing with conda
Hi!
I have an error when running dysgu test. I get this message:
2024-04-29 14:47:56,143 [INFO ] [dysgu-test] Version: 1.6.2
Traceback (most recent call last):
File "/home/j/jbruxaux/miniconda3/envs/dysgu/bin/dysgu", line 11, in <module>
sys.exit(cli())
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/dysgu/main.py", line 534, in test_command
v = run(shlex.split(c), shell=False, capture_output=True, check=True)
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/subprocess.py", line 526, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command '['dysgu', 'fetch', '-x', '/pfs/stor10/projects/projnb10/snic2019-29-3/wd_test', '/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/dysgu/tests/small.bam']' returned non-zero exit status 1.
I have installed dysgu using conda. I have all the packages requested:
# packages in environment at /home/j/jbruxaux/miniconda3/envs/dysgu:
#
# Name Version Build Channel
_libgcc_mutex 0.1 conda_forge conda-forge
_openmp_mutex 4.5 2_gnu conda-forge
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
click 8.1.7 unix_pyh707e725_0 conda-forge
cython 3.0.10 py310hc6cd4ac_0 conda-forge
dysgu 1.6.2 py310h770aed0_0 bioconda
htslib 1.20 h81da01d_0 bioconda
joblib 1.4.0 pyhd8ed1ab_0 conda-forge
keyutils 1.6.1 h166bdaf_0 conda-forge
krb5 1.21.2 h659d440_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
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
libffi 3.4.2 h7f98852_5 conda-forge
libgcc-ng 13.2.0 hc881cc4_6 conda-forge
libgfortran-ng 13.2.0 h69a702a_6 conda-forge
libgfortran5 13.2.0 h43f5ff8_6 conda-forge
libgomp 13.2.0 hc881cc4_6 conda-forge
liblapack 3.9.0 22_linux64_openblas 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
libsqlite 3.45.3 h2797004_0 conda-forge
libssh2 1.11.0 h0841786_0 conda-forge
libstdcxx-ng 13.2.0 h95c4c6d_6 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
lightgbm 4.3.0 py310hc6cd4ac_0 conda-forge
ncurses 6.4.20240210 h59595ed_0 conda-forge
networkx 3.3 pyhd8ed1ab_1 conda-forge
numpy 1.26.4 py310hb13e2d6_0 conda-forge
openssl 3.2.1 hd590300_1 conda-forge
pandas 2.2.2 py310hcc13569_0 conda-forge
pip 24.0 pyhd8ed1ab_0 conda-forge
pysam 0.22.0 py310h41dec4a_1 bioconda
python 3.10.14 hd12c33a_0_cpython conda-forge
python-dateutil 2.9.0 pyhd8ed1ab_0 conda-forge
python-edlib 1.3.9 py310h0dbaff4_6 bioconda
python-tzdata 2024.1 pyhd8ed1ab_0 conda-forge
python_abi 3.10 4_cp310 conda-forge
pytz 2024.1 pyhd8ed1ab_0 conda-forge
readline 8.2 h8228510_1 conda-forge
scikit-learn 1.4.2 py310h1fdf081_0 conda-forge
scipy 1.13.0 py310hb13e2d6_0 conda-forge
setuptools 69.5.1 pyhd8ed1ab_0 conda-forge
six 1.16.0 pyh6c4a22f_0 conda-forge
sortedcontainers 2.4.0 pyhd8ed1ab_0 conda-forge
threadpoolctl 3.4.0 pyhc1e730c_0 conda-forge
tk 8.6.13 noxft_h4845f30_101 conda-forge
tzdata 2024a h0c530f3_0 conda-forge
wheel 0.43.0 pyhd8ed1ab_1 conda-forge
xz 5.2.6 h166bdaf_0 conda-forge
zlib 1.2.13 hd590300_5 conda-forge
zstd 1.5.5 hfc55251_0 conda-forge
I use conda 24.3.0 in case it matters.
Any suggestion?
Thanks in advance!
Hi @jbruxaux,
Thanks for reporting this. The reason for the error is not really specified in the output message, dysgu test only reports an error with one of the commands. To get a better output log for the failing command, would you be able to run the command manually, and send me the output log of the command? The failing command from the log is:
dysgu fetch -x /pfs/stor10/projects/projnb10/snic2019-29-3/wd_test /home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/dysgu/tests/small.bam
Thanks for your quick reply! Here is the log:
2024-04-29 16:48:08,211 [INFO ] [dysgu-fetch] Version: 1.6.2
Traceback (most recent call last):
File "/home/j/jbruxaux/miniconda3/envs/dysgu/bin/dysgu", line 11, in <module>
sys.exit(cli())
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/core.py", line 1157, in __call__
return self.main(*args, **kwargs)
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/core.py", line 1078, in main
rv = self.invoke(ctx)
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/core.py", line 1688, in invoke
return _process_result(sub_ctx.command.invoke(sub_ctx))
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/core.py", line 1434, in invoke
return ctx.invoke(self.callback, **ctx.params)
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/core.py", line 783, in invoke
return __callback(*args, **kwargs)
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/click/decorators.py", line 33, in new_func
return f(get_current_context(), *args, **kwargs)
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/dysgu/main.py", line 303, in get_reads
return sv2bam.process(ctx.obj)
File "dysgu/sv2bam.pyx", line 165, in dysgu.sv2bam.process
File "dysgu/sv2bam.pyx", line 166, in dysgu.sv2bam.process
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/pkg_resources/__init__.py", line 937, in require
needed = self.resolve(parse_requirements(requirements))
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/pkg_resources/__init__.py", line 798, in resolve
dist = self._resolve_dist(
File "/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages/pkg_resources/__init__.py", line 844, in _resolve_dist
raise VersionConflict(dist, req).with_context(dependent_req)
pkg_resources.ContextualVersionConflict: (pysam 0.22.0 (/pfs/stor10/users/home/j/jbruxaux/miniconda3/envs/dysgu/lib/python3.10/site-packages), Requirement.parse('pysam==0.21.0'), {'dysgu'})
Should I try to use pysam v.0.21.0 instead of 0.22.0 that was in the requirement file?
Ah interesting. Im not sure where the requirement for 0.21 is from. The conda recipe if for pysam >= 0.19 and the master branch is pysam == 0.22. Are you able to using pip install?
It works with pip install:
2024-04-29 17:04:24,989 [INFO ] [dysgu-test] Version: 1.6.3
PASS: dysgu fetch -x /pfs/stor10/projects/projnb10/snic2019-29-3/wd_test /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/small.bam
PASS: dysgu run -x --drop-gaps False -o /pfs/stor10/projects/projnb10/snic2019-29-3/test.dysgu1.6.3.vcf /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/ref.fa /pfs/stor10/projects/projnb10/snic2019-29-3/wd_test /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/small.bam
PASS: dysgu run -x --drop-gaps False --regions /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/targets.bed -o /pfs/stor10/projects/projnb10/snic2019-29-3/test_regions.dysgu1.6.3.vcf /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/ref.fa /pfs/stor10/projects/projnb10/snic2019-29-3/wd_test2 /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/small.bam
PASS: dysgu run -x --drop-gaps False --procs 2 --regions /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/targets.bed -o /pfs/stor10/projects/projnb10/snic2019-29-3/test_regions.dysgu1.6.3.vcf /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/ref.fa /pfs/stor10/projects/projnb10/snic2019-29-3/wd_test2 /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/small.bam
PASS: dysgu run -x --drop-gaps False --mode pacbio -o /pfs/stor10/projects/projnb10/snic2019-29-3/test2.dysgu1.6.3.vcf /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/ref.fa /pfs/stor10/projects/projnb10/snic2019-29-3/wd_test /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/small.bam
PASS: dysgu call -x --drop-gaps False -o /pfs/stor10/projects/projnb10/snic2019-29-3/test2.dysgu1.6.3.vcf /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/ref.fa /pfs/stor10/projects/projnb10/snic2019-29-3/wd_test /home/j/jbruxaux/.local/lib/python3.11/site-packages/dysgu/tests/small.bam
PASS: dysgu merge /pfs/stor10/projects/projnb10/snic2019-29-3/test.dysgu1.6.3.vcf /pfs/stor10/projects/projnb10/snic2019-29-3/test2.dysgu1.6.3.vcf -o /pfs/stor10/projects/projnb10/snic2019-29-3/test.merge.dysgu1.6.3.vcf
2024-04-29 17:05:07,258 [INFO ] Run test complete
Thanks! Let me know if you want to explore more the conda issue in the meantime.
Great! It's ok, there is an update for dysgu on the way so I can try and make sure the conda build is correct for the next release.
Thanks!