Error installing with conda

[jbruxaux]

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!

[kcleal]

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

[jbruxaux]

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?

[kcleal]

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?

[jbruxaux]

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.

[kcleal]

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!