zouaghiyassine
commented
8 months ago I am having the exact same issue here and no attempts over the last few days resolved the problem for me
Closed davidfstein closed 7 months ago
zouaghiyassine
commented
8 months ago I am having the exact same issue here and no attempts over the last few days resolved the problem for me
davidfstein
commented
8 months ago Yes I've tried various workarounds, but can't seem to get it installed. Hopefully it will be resolved soon since the website can't process bulk requests right now
ThorbenMaa
commented
8 months ago Hi and thanks a lot for reaching out! I have tried to reproduce the errors from a clean environment and for me everything works. Could you try to do the following?:
EDIT: You could also try to use micormamba, as it may be better in resolving the environments. This was pointed out in the issue here (https://github.com/kircherlab/CADD-scripts/issues/54)
If you have problems with scoring large files on our webserver, I can offer you to reach out to us via E-Mail. I am sure we can find a convenient solution!
All the best Thorben
zouaghiyassine
commented
7 months ago Hi, this is very strange. I went back and removed all the previous installations starting fresh and creating an mmsplice environment even individually doesn't work. trried using conda, mamba and micromamba but all failed with more or less the same errors. Suspecting it was due to WSL2 on windows I went on a computing cluster and tried from there using mamba but I still get exactly the same error as above. I also tried to fiddle with the packages individually to find a combination of versions that would work but always arrived at a conflict in the pip dependancies, most of the time related to pybedtools.
davidfstein
commented
7 months ago @ThorbenMaa I've just gotten to trying your suggestions. I was already using micromamba, but I wiped it and freshly installed. I also had conda installed and I removed it. Unfortunately, now I am running into an issue with the installer which seems to be relying explicitly on conda
Setting up virtual environments for CADD v1.7
Building DAG of jobs...
/usr/bin/bash: line 1: conda: command not found
Traceback (most recent call last):
File "/home/david/micromamba/lib/python3.11/site-packages/snakemake/__init__.py", line 792, in snakemake
success = workflow.execute(
^^^^^^^^^^^^^^^^^
File "/home/david/micromamba/lib/python3.11/site-packages/snakemake/workflow.py", line 1078, in execute
dag.create_conda_envs(
File "/home/david/micromamba/lib/python3.11/site-packages/snakemake/dag.py", line 359, in create_conda_envs
env.create(dryrun)
File "/home/david/micromamba/lib/python3.11/site-packages/snakemake/deployment/conda.py", line 393, in create
pin_file = self.pin_file
^^^^^^^^^^^^^
File "/home/david/micromamba/lib/python3.11/site-packages/snakemake/common/__init__.py", line 217, in __get__
value = self.method(instance)
^^^^^^^^^^^^^^^^^^^^^
File "/home/david/micromamba/lib/python3.11/site-packages/snakemake/deployment/conda.py", line 103, in pin_file
f".{self.conda.platform}.pin.txt"
^^^^^^^^^^
File "/home/david/micromamba/lib/python3.11/site-packages/snakemake/common/__init__.py", line 217, in __get__
value = self.method(instance)
^^^^^^^^^^^^^^^^^^^^^
File "/home/david/micromamba/lib/python3.11/site-packages/snakemake/deployment/conda.py", line 96, in conda
return Conda(
^^^^^^
File "/home/david/micromamba/lib/python3.11/site-packages/snakemake/deployment/conda.py", line 653, in __init__
shell.check_output(self._get_cmd("conda info --json"), text=True)
File "/home/david/micromamba/lib/python3.11/site-packages/snakemake/shell.py", line 61, in check_output
return sp.check_output(cmd, shell=True, executable=executable, **kwargs)
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/david/micromamba/lib/python3.11/subprocess.py", line 466, in check_output
return run(*popenargs, stdout=PIPE, timeout=timeout, check=True,
^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^^
File "/home/david/micromamba/lib/python3.11/subprocess.py", line 571, in run
raise CalledProcessError(retcode, process.args,
subprocess.CalledProcessError: Command 'conda info --json' returned non-zero exit status 127.I tried aliasing micromamba to conda, but I still run into the same error.
Running conda info --json produces:
{
"base environment": "/home/david/micromamba",
"channels": [
"https://conda.anaconda.org/conda-forge/linux-64",
"https://conda.anaconda.org/conda-forge/noarch",
"https://conda.anaconda.org/nodefaults/linux-64",
"https://conda.anaconda.org/nodefaults/noarch"
],
"curl version": "libcurl/8.5.0 OpenSSL/3.2.1 zlib/1.2.13 zstd/1.5.5 libssh2/1.11.0 nghttp2/1.58.0",
"env location": "/home/david/micromamba",
"environment": "base (active)",
"envs directories": [
"/home/david/micromamba/envs"
],
"libarchive version": "libarchive 3.7.2 zlib/1.2.13 bz2lib/1.0.8 libzstd/1.5.5",
"libmamba version": "1.5.7",
"micromamba version": "1.5.7",
"package cache": [
"/home/david/micromamba/pkgs",
"/home/david/.mamba/pkgs"
],
"platform": "linux-64",
"populated config files": [
"/home/david/.condarc"
],
"user config files": [
"/home/david/.mambarc"
],
"virtual packages": [
"__unix=0=0",
"__linux=6.5.0=0",
"__glibc=2.35=0",
"__archspec=1=x86_64-v3",
"__cuda=12.2=0"
]
}@ThorbenMaa I uninstalled and reinstalled mamba this time via miniforge as suggested. After installation I ran ./CADD.sh test/input.vcf and again encountered the following:
CADD-v1.7 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health at Charité - Universitätsmedizin Berlin 2013-2023. All rights reserved.
Running snakemake pipeline:
snakemake /tmp/tmp.zFz7bfFfkT/input.tsv.gz --use-conda --conda-prefix /home/david/Projects/CADD-scripts-1.7-master/envs/conda --cores 1
--configfile /home/david/Projects/CADD-scripts-1.7-master/config/config_GRCh38_v1.7_noanno.yml --snakefile /home/david/Projects/CADD-scripts-1.7-master/Snakefile -q
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: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count
-------- -------
join 1
prepare 1
prescore 1
total 3
Select jobs to execute...
Activating conda environment: envs/conda/6286c07397830d220a93727bfb2db5d3_
Select jobs to execute...
Activating conda environment: envs/conda/6286c07397830d220a93727bfb2db5d3_
Creating conda environment envs/mmsplice.yml...
Downloading and installing remote packages.
CreateCondaEnvironmentException:
Could not create conda environment from /home/david/Projects/CADD-scripts-1.7-master/envs/mmsplice.yml:
Command:
mamba env create --quiet --file "/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_.yaml" --prefix "/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_"
Output:
Preparing transaction: ...working... done
Verifying transaction: ...working... done
Executing transaction: ...working... done
Installing pip dependencies: ...working... Pip subprocess error:
Running command git clone --filter=blob:none -q https://github.com/Aerval/SpliceAI.git /tmp/pip-req-build-p8fssr76
ERROR: Command errored out with exit status 1:
command: /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/python /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/lib/python3.6/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-q07_2605/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=61.0.0' wheel cython 'setuptools_scm[toml]>=6.2'
cwd: None
Complete output (2 lines):
ERROR: Could not find a version that satisfies the requirement setuptools>=61.0.0 (from versions: 0.6b1, 0.6b2, 0.6b3, 0.6b4, 0.6rc1, 0.6rc2, 0.6rc3, 0.6rc4, 0.6rc5, 0.6rc6, 0.6rc7, 0.6rc8, 0.6rc9, 0.6rc10, 0.6rc11, 0.7.2, 0.7.3, 0.7.4, 0.7.5, 0.7.6, 0.7.7, 0.7.8, 0.8, 0.9, 0.9.1, 0.9.2, 0.9.3, 0.9.4, 0.9.5, 0.9.6, 0.9.7, 0.9.8, 1.0, 1.1, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5, 1.1.6, 1.1.7, 1.2, 1.3, 1.3.1, 1.3.2, 1.4, 1.4.1, 1.4.2, 2.0, 2.0.1, 2.0.2, 2.1, 2.1.1, 2.1.2, 2.2, 3.0, 3.0.1, 3.0.2, 3.1, 3.2, 3.3, 3.4, 3.4.1, 3.4.2, 3.4.3, 3.4.4, 3.5, 3.5.1, 3.5.2, 3.6, 3.7, 3.7.1, 3.8, 3.8.1, 4.0, 4.0.1, 5.0, 5.0.1, 5.0.2, 5.1, 5.2, 5.3, 5.4, 5.4.1, 5.4.2, 5.5, 5.5.1, 5.6, 5.7, 5.8, 6.0.1, 6.0.2, 6.1, 7.0, 8.0, 8.0.1, 8.0.2, 8.0.3, 8.0.4, 8.1, 8.2, 8.2.1, 8.3, 9.0, 9.0.1, 9.1, 10.0, 10.0.1, 10.1, 10.2, 10.2.1, 11.0, 11.1, 11.2, 11.3, 11.3.1, 12.0, 12.0.1, 12.0.2, 12.0.3, 12.0.4, 12.0.5, 12.1, 12.2, 12.3, 12.4, 13.0.1, 13.0.2, 14.0, 14.1, 14.1.1, 14.2, 14.3, 14.3.1, 15.0, 15.1, 15.2, 16.0, 17.0, 17.1, 17.1.1, 18.0, 18.0.1, 18.1, 18.2, 18.3, 18.3.1, 18.3.2, 18.4, 18.5, 18.6, 18.6.1, 18.7, 18.7.1, 18.8, 18.8.1, 19.0, 19.1, 19.1.1, 19.2, 19.3, 19.4, 19.4.1, 19.5, 19.6, 19.6.1, 19.6.2, 19.7, 20.0, 20.1, 20.1.1, 20.2.2, 20.3, 20.3.1, 20.4, 20.6.6, 20.6.7, 20.6.8, 20.7.0, 20.8.0, 20.8.1, 20.9.0, 20.10.1, 21.0.0, 21.1.0, 21.2.0, 21.2.1, 21.2.2, 22.0.0, 22.0.1, 22.0.2, 22.0.4, 22.0.5, 23.0.0, 23.1.0, 23.2.0, 23.2.1, 24.0.0, 24.0.1, 24.0.2, 24.0.3, 24.1.0, 24.1.1, 24.2.0, 24.2.1, 24.3.0, 24.3.1, 25.0.0, 25.0.1, 25.0.2, 25.1.0, 25.1.1, 25.1.2, 25.1.3, 25.1.4, 25.1.5, 25.1.6, 25.2.0, 25.3.0, 25.4.0, 26.0.0, 26.1.0, 26.1.1, 27.0.0, 27.1.0, 27.1.2, 27.2.0, 27.3.0, 27.3.1, 28.0.0, 28.1.0, 28.2.0, 28.3.0, 28.4.0, 28.5.0, 28.6.0, 28.6.1, 28.7.0, 28.7.1, 28.8.0, 28.8.1, 29.0.0, 29.0.1, 30.0.0, 30.1.0, 30.2.0, 30.2.1, 30.3.0, 30.4.0, 31.0.0, 31.0.1, 32.0.0, 32.1.0, 32.1.1, 32.1.2, 32.1.3, 32.2.0, 32.3.0, 32.3.1, 33.1.0, 33.1.1, 34.0.0, 34.0.1, 34.0.2, 34.0.3, 34.1.0, 34.1.1, 34.2.0, 34.3.0, 34.3.1, 34.3.2, 34.3.3, 34.4.0, 34.4.1, 35.0.0, 35.0.1, 35.0.2, 36.0.1, 36.1.0, 36.1.1, 36.2.0, 36.2.1, 36.2.2, 36.2.3, 36.2.4, 36.2.5, 36.2.6, 36.2.7, 36.3.0, 36.4.0, 36.5.0, 36.6.0, 36.6.1, 36.7.0, 36.7.1, 36.7.2, 36.8.0, 37.0.0, 38.0.0, 38.1.0, 38.2.0, 38.2.1, 38.2.3, 38.2.4, 38.2.5, 38.3.0, 38.4.0, 38.4.1, 38.5.0, 38.5.1, 38.5.2, 38.6.0, 38.6.1, 38.7.0, 39.0.0, 39.0.1, 39.1.0, 39.2.0, 40.0.0, 40.1.0, 40.1.1, 40.2.0, 40.3.0, 40.4.0, 40.4.1, 40.4.2, 40.4.3, 40.5.0, 40.6.0, 40.6.1, 40.6.2, 40.6.3, 40.7.0, 40.7.1, 40.7.2, 40.7.3, 40.8.0, 40.9.0, 41.0.0, 41.0.1, 41.1.0, 41.2.0, 41.3.0, 41.4.0, 41.5.0, 41.5.1, 41.6.0, 42.0.0, 42.0.1, 42.0.2, 43.0.0, 44.0.0, 44.1.0, 44.1.1, 45.0.0, 45.1.0, 45.2.0, 45.3.0, 46.0.0, 46.1.0, 46.1.1, 46.1.2, 46.1.3, 46.2.0, 46.3.0, 46.3.1, 46.4.0, 47.0.0, 47.1.0, 47.1.1, 47.2.0, 47.3.0, 47.3.1, 47.3.2, 48.0.0, 49.0.0, 49.0.1, 49.1.0, 49.1.1, 49.1.2, 49.1.3, 49.2.0, 49.2.1, 49.3.0, 49.3.1, 49.3.2, 49.4.0, 49.5.0, 49.6.0, 50.0.0, 50.0.1, 50.0.2, 50.0.3, 50.1.0, 50.2.0, 50.3.0, 50.3.1, 50.3.2, 51.0.0, 51.1.0, 51.1.0.post20201221, 51.1.1, 51.1.2, 51.2.0, 51.3.0, 51.3.1, 51.3.2, 51.3.3, 52.0.0, 53.0.0, 53.1.0, 54.0.0, 54.1.0, 54.1.1, 54.1.2, 54.1.3, 54.2.0, 56.0.0, 56.1.0, 56.2.0, 57.0.0, 57.1.0, 57.2.0, 57.3.0, 57.4.0, 57.5.0, 58.0.0, 58.0.1, 58.0.2, 58.0.3, 58.0.4, 58.1.0, 58.2.0, 58.3.0, 58.4.0, 58.5.0, 58.5.1, 58.5.2, 58.5.3, 59.0.1, 59.1.0, 59.1.1, 59.2.0, 59.3.0, 59.4.0, 59.5.0, 59.6.0)
ERROR: No matching distribution found for setuptools>=61.0.0
----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/88/b8/210d5cb1fa85c7675323aacbd52af11553dc190aad1c15584699f40797f1/ncls-0.0.68.tar.gz#sha256=81aaa5abb123bb21797ed2f8ef921e20222db14a3ecbc61ccf447532f2b7ba93 (from https://pypi.org/simple/ncls/). Command errored out with exit status 1: /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/python /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/lib/python3.6/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-q07_2605/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=61.0.0' wheel cython 'setuptools_scm[toml]>=6.2' Check the logs for full command output.
ERROR: Command errored out with exit status 1:
command: /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/python /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/lib/python3.6/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-znk7tcy7/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=61.0.0' wheel cython 'setuptools_scm[toml]>=6.2'
cwd: None
Complete output (2 lines):
ERROR: Could not find a version that satisfies the requirement setuptools>=61.0.0 (from versions: 0.6b1, 0.6b2, 0.6b3, 0.6b4, 0.6rc1, 0.6rc2, 0.6rc3, 0.6rc4, 0.6rc5, 0.6rc6, 0.6rc7, 0.6rc8, 0.6rc9, 0.6rc10, 0.6rc11, 0.7.2, 0.7.3, 0.7.4, 0.7.5, 0.7.6, 0.7.7, 0.7.8, 0.8, 0.9, 0.9.1, 0.9.2, 0.9.3, 0.9.4, 0.9.5, 0.9.6, 0.9.7, 0.9.8, 1.0, 1.1, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5, 1.1.6, 1.1.7, 1.2, 1.3, 1.3.1, 1.3.2, 1.4, 1.4.1, 1.4.2, 2.0, 2.0.1, 2.0.2, 2.1, 2.1.1, 2.1.2, 2.2, 3.0, 3.0.1, 3.0.2, 3.1, 3.2, 3.3, 3.4, 3.4.1, 3.4.2, 3.4.3, 3.4.4, 3.5, 3.5.1, 3.5.2, 3.6, 3.7, 3.7.1, 3.8, 3.8.1, 4.0, 4.0.1, 5.0, 5.0.1, 5.0.2, 5.1, 5.2, 5.3, 5.4, 5.4.1, 5.4.2, 5.5, 5.5.1, 5.6, 5.7, 5.8, 6.0.1, 6.0.2, 6.1, 7.0, 8.0, 8.0.1, 8.0.2, 8.0.3, 8.0.4, 8.1, 8.2, 8.2.1, 8.3, 9.0, 9.0.1, 9.1, 10.0, 10.0.1, 10.1, 10.2, 10.2.1, 11.0, 11.1, 11.2, 11.3, 11.3.1, 12.0, 12.0.1, 12.0.2, 12.0.3, 12.0.4, 12.0.5, 12.1, 12.2, 12.3, 12.4, 13.0.1, 13.0.2, 14.0, 14.1, 14.1.1, 14.2, 14.3, 14.3.1, 15.0, 15.1, 15.2, 16.0, 17.0, 17.1, 17.1.1, 18.0, 18.0.1, 18.1, 18.2, 18.3, 18.3.1, 18.3.2, 18.4, 18.5, 18.6, 18.6.1, 18.7, 18.7.1, 18.8, 18.8.1, 19.0, 19.1, 19.1.1, 19.2, 19.3, 19.4, 19.4.1, 19.5, 19.6, 19.6.1, 19.6.2, 19.7, 20.0, 20.1, 20.1.1, 20.2.2, 20.3, 20.3.1, 20.4, 20.6.6, 20.6.7, 20.6.8, 20.7.0, 20.8.0, 20.8.1, 20.9.0, 20.10.1, 21.0.0, 21.1.0, 21.2.0, 21.2.1, 21.2.2, 22.0.0, 22.0.1, 22.0.2, 22.0.4, 22.0.5, 23.0.0, 23.1.0, 23.2.0, 23.2.1, 24.0.0, 24.0.1, 24.0.2, 24.0.3, 24.1.0, 24.1.1, 24.2.0, 24.2.1, 24.3.0, 24.3.1, 25.0.0, 25.0.1, 25.0.2, 25.1.0, 25.1.1, 25.1.2, 25.1.3, 25.1.4, 25.1.5, 25.1.6, 25.2.0, 25.3.0, 25.4.0, 26.0.0, 26.1.0, 26.1.1, 27.0.0, 27.1.0, 27.1.2, 27.2.0, 27.3.0, 27.3.1, 28.0.0, 28.1.0, 28.2.0, 28.3.0, 28.4.0, 28.5.0, 28.6.0, 28.6.1, 28.7.0, 28.7.1, 28.8.0, 28.8.1, 29.0.0, 29.0.1, 30.0.0, 30.1.0, 30.2.0, 30.2.1, 30.3.0, 30.4.0, 31.0.0, 31.0.1, 32.0.0, 32.1.0, 32.1.1, 32.1.2, 32.1.3, 32.2.0, 32.3.0, 32.3.1, 33.1.0, 33.1.1, 34.0.0, 34.0.1, 34.0.2, 34.0.3, 34.1.0, 34.1.1, 34.2.0, 34.3.0, 34.3.1, 34.3.2, 34.3.3, 34.4.0, 34.4.1, 35.0.0, 35.0.1, 35.0.2, 36.0.1, 36.1.0, 36.1.1, 36.2.0, 36.2.1, 36.2.2, 36.2.3, 36.2.4, 36.2.5, 36.2.6, 36.2.7, 36.3.0, 36.4.0, 36.5.0, 36.6.0, 36.6.1, 36.7.0, 36.7.1, 36.7.2, 36.8.0, 37.0.0, 38.0.0, 38.1.0, 38.2.0, 38.2.1, 38.2.3, 38.2.4, 38.2.5, 38.3.0, 38.4.0, 38.4.1, 38.5.0, 38.5.1, 38.5.2, 38.6.0, 38.6.1, 38.7.0, 39.0.0, 39.0.1, 39.1.0, 39.2.0, 40.0.0, 40.1.0, 40.1.1, 40.2.0, 40.3.0, 40.4.0, 40.4.1, 40.4.2, 40.4.3, 40.5.0, 40.6.0, 40.6.1, 40.6.2, 40.6.3, 40.7.0, 40.7.1, 40.7.2, 40.7.3, 40.8.0, 40.9.0, 41.0.0, 41.0.1, 41.1.0, 41.2.0, 41.3.0, 41.4.0, 41.5.0, 41.5.1, 41.6.0, 42.0.0, 42.0.1, 42.0.2, 43.0.0, 44.0.0, 44.1.0, 44.1.1, 45.0.0, 45.1.0, 45.2.0, 45.3.0, 46.0.0, 46.1.0, 46.1.1, 46.1.2, 46.1.3, 46.2.0, 46.3.0, 46.3.1, 46.4.0, 47.0.0, 47.1.0, 47.1.1, 47.2.0, 47.3.0, 47.3.1, 47.3.2, 48.0.0, 49.0.0, 49.0.1, 49.1.0, 49.1.1, 49.1.2, 49.1.3, 49.2.0, 49.2.1, 49.3.0, 49.3.1, 49.3.2, 49.4.0, 49.5.0, 49.6.0, 50.0.0, 50.0.1, 50.0.2, 50.0.3, 50.1.0, 50.2.0, 50.3.0, 50.3.1, 50.3.2, 51.0.0, 51.1.0, 51.1.0.post20201221, 51.1.1, 51.1.2, 51.2.0, 51.3.0, 51.3.1, 51.3.2, 51.3.3, 52.0.0, 53.0.0, 53.1.0, 54.0.0, 54.1.0, 54.1.1, 54.1.2, 54.1.3, 54.2.0, 56.0.0, 56.1.0, 56.2.0, 57.0.0, 57.1.0, 57.2.0, 57.3.0, 57.4.0, 57.5.0, 58.0.0, 58.0.1, 58.0.2, 58.0.3, 58.0.4, 58.1.0, 58.2.0, 58.3.0, 58.4.0, 58.5.0, 58.5.1, 58.5.2, 58.5.3, 59.0.1, 59.1.0, 59.1.1, 59.2.0, 59.3.0, 59.4.0, 59.5.0, 59.6.0)
ERROR: No matching distribution found for setuptools>=61.0.0
----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/1d/53/0fc3eb65e7f940422dc0f54910e36d5b88d6c0ac9ed391dfbc98567e4050/pyrle-0.0.39.tar.gz#sha256=1be4be7814d3941db907aaf19f311bd46a407244316cadbf4b73109685c055c5 (from https://pypi.org/simple/pyrle/). Command errored out with exit status 1: /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/python /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/lib/python3.6/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-znk7tcy7/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=61.0.0' wheel cython 'setuptools_scm[toml]>=6.2' Check the logs for full command output.
ERROR: Command errored out with exit status 1:
command: /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/python /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/lib/python3.6/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-wayo8pjg/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=61.0.0' wheel cython 'setuptools_scm[toml]>=6.2'
cwd: None
Complete output (2 lines):
ERROR: Could not find a version that satisfies the requirement setuptools>=61.0.0 (from versions: 0.6b1, 0.6b2, 0.6b3, 0.6b4, 0.6rc1, 0.6rc2, 0.6rc3, 0.6rc4, 0.6rc5, 0.6rc6, 0.6rc7, 0.6rc8, 0.6rc9, 0.6rc10, 0.6rc11, 0.7.2, 0.7.3, 0.7.4, 0.7.5, 0.7.6, 0.7.7, 0.7.8, 0.8, 0.9, 0.9.1, 0.9.2, 0.9.3, 0.9.4, 0.9.5, 0.9.6, 0.9.7, 0.9.8, 1.0, 1.1, 1.1.1, 1.1.2, 1.1.3, 1.1.4, 1.1.5, 1.1.6, 1.1.7, 1.2, 1.3, 1.3.1, 1.3.2, 1.4, 1.4.1, 1.4.2, 2.0, 2.0.1, 2.0.2, 2.1, 2.1.1, 2.1.2, 2.2, 3.0, 3.0.1, 3.0.2, 3.1, 3.2, 3.3, 3.4, 3.4.1, 3.4.2, 3.4.3, 3.4.4, 3.5, 3.5.1, 3.5.2, 3.6, 3.7, 3.7.1, 3.8, 3.8.1, 4.0, 4.0.1, 5.0, 5.0.1, 5.0.2, 5.1, 5.2, 5.3, 5.4, 5.4.1, 5.4.2, 5.5, 5.5.1, 5.6, 5.7, 5.8, 6.0.1, 6.0.2, 6.1, 7.0, 8.0, 8.0.1, 8.0.2, 8.0.3, 8.0.4, 8.1, 8.2, 8.2.1, 8.3, 9.0, 9.0.1, 9.1, 10.0, 10.0.1, 10.1, 10.2, 10.2.1, 11.0, 11.1, 11.2, 11.3, 11.3.1, 12.0, 12.0.1, 12.0.2, 12.0.3, 12.0.4, 12.0.5, 12.1, 12.2, 12.3, 12.4, 13.0.1, 13.0.2, 14.0, 14.1, 14.1.1, 14.2, 14.3, 14.3.1, 15.0, 15.1, 15.2, 16.0, 17.0, 17.1, 17.1.1, 18.0, 18.0.1, 18.1, 18.2, 18.3, 18.3.1, 18.3.2, 18.4, 18.5, 18.6, 18.6.1, 18.7, 18.7.1, 18.8, 18.8.1, 19.0, 19.1, 19.1.1, 19.2, 19.3, 19.4, 19.4.1, 19.5, 19.6, 19.6.1, 19.6.2, 19.7, 20.0, 20.1, 20.1.1, 20.2.2, 20.3, 20.3.1, 20.4, 20.6.6, 20.6.7, 20.6.8, 20.7.0, 20.8.0, 20.8.1, 20.9.0, 20.10.1, 21.0.0, 21.1.0, 21.2.0, 21.2.1, 21.2.2, 22.0.0, 22.0.1, 22.0.2, 22.0.4, 22.0.5, 23.0.0, 23.1.0, 23.2.0, 23.2.1, 24.0.0, 24.0.1, 24.0.2, 24.0.3, 24.1.0, 24.1.1, 24.2.0, 24.2.1, 24.3.0, 24.3.1, 25.0.0, 25.0.1, 25.0.2, 25.1.0, 25.1.1, 25.1.2, 25.1.3, 25.1.4, 25.1.5, 25.1.6, 25.2.0, 25.3.0, 25.4.0, 26.0.0, 26.1.0, 26.1.1, 27.0.0, 27.1.0, 27.1.2, 27.2.0, 27.3.0, 27.3.1, 28.0.0, 28.1.0, 28.2.0, 28.3.0, 28.4.0, 28.5.0, 28.6.0, 28.6.1, 28.7.0, 28.7.1, 28.8.0, 28.8.1, 29.0.0, 29.0.1, 30.0.0, 30.1.0, 30.2.0, 30.2.1, 30.3.0, 30.4.0, 31.0.0, 31.0.1, 32.0.0, 32.1.0, 32.1.1, 32.1.2, 32.1.3, 32.2.0, 32.3.0, 32.3.1, 33.1.0, 33.1.1, 34.0.0, 34.0.1, 34.0.2, 34.0.3, 34.1.0, 34.1.1, 34.2.0, 34.3.0, 34.3.1, 34.3.2, 34.3.3, 34.4.0, 34.4.1, 35.0.0, 35.0.1, 35.0.2, 36.0.1, 36.1.0, 36.1.1, 36.2.0, 36.2.1, 36.2.2, 36.2.3, 36.2.4, 36.2.5, 36.2.6, 36.2.7, 36.3.0, 36.4.0, 36.5.0, 36.6.0, 36.6.1, 36.7.0, 36.7.1, 36.7.2, 36.8.0, 37.0.0, 38.0.0, 38.1.0, 38.2.0, 38.2.1, 38.2.3, 38.2.4, 38.2.5, 38.3.0, 38.4.0, 38.4.1, 38.5.0, 38.5.1, 38.5.2, 38.6.0, 38.6.1, 38.7.0, 39.0.0, 39.0.1, 39.1.0, 39.2.0, 40.0.0, 40.1.0, 40.1.1, 40.2.0, 40.3.0, 40.4.0, 40.4.1, 40.4.2, 40.4.3, 40.5.0, 40.6.0, 40.6.1, 40.6.2, 40.6.3, 40.7.0, 40.7.1, 40.7.2, 40.7.3, 40.8.0, 40.9.0, 41.0.0, 41.0.1, 41.1.0, 41.2.0, 41.3.0, 41.4.0, 41.5.0, 41.5.1, 41.6.0, 42.0.0, 42.0.1, 42.0.2, 43.0.0, 44.0.0, 44.1.0, 44.1.1, 45.0.0, 45.1.0, 45.2.0, 45.3.0, 46.0.0, 46.1.0, 46.1.1, 46.1.2, 46.1.3, 46.2.0, 46.3.0, 46.3.1, 46.4.0, 47.0.0, 47.1.0, 47.1.1, 47.2.0, 47.3.0, 47.3.1, 47.3.2, 48.0.0, 49.0.0, 49.0.1, 49.1.0, 49.1.1, 49.1.2, 49.1.3, 49.2.0, 49.2.1, 49.3.0, 49.3.1, 49.3.2, 49.4.0, 49.5.0, 49.6.0, 50.0.0, 50.0.1, 50.0.2, 50.0.3, 50.1.0, 50.2.0, 50.3.0, 50.3.1, 50.3.2, 51.0.0, 51.1.0, 51.1.0.post20201221, 51.1.1, 51.1.2, 51.2.0, 51.3.0, 51.3.1, 51.3.2, 51.3.3, 52.0.0, 53.0.0, 53.1.0, 54.0.0, 54.1.0, 54.1.1, 54.1.2, 54.1.3, 54.2.0, 56.0.0, 56.1.0, 56.2.0, 57.0.0, 57.1.0, 57.2.0, 57.3.0, 57.4.0, 57.5.0, 58.0.0, 58.0.1, 58.0.2, 58.0.3, 58.0.4, 58.1.0, 58.2.0, 58.3.0, 58.4.0, 58.5.0, 58.5.1, 58.5.2, 58.5.3, 59.0.1, 59.1.0, 59.1.1, 59.2.0, 59.3.0, 59.4.0, 59.5.0, 59.6.0)
ERROR: No matching distribution found for setuptools>=61.0.0
----------------------------------------
WARNING: Discarding https://files.pythonhosted.org/packages/9e/76/52c6604084cf37240ff1450272ee97a8969b7b943833bff923ed9e45400d/pyrle-0.0.38.tar.gz#sha256=8b382947a18c73eb4aeaa9e731cb89d0b755f85f75ccb49fc7e121ae3fb984be (from https://pypi.org/simple/pyrle/). Command errored out with exit status 1: /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/python /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/lib/python3.6/site-packages/pip install --ignore-installed --no-user --prefix /tmp/pip-build-env-wayo8pjg/overlay --no-warn-script-location --no-binary :none: --only-binary :none: -i https://pypi.org/simple -- 'setuptools>=61.0.0' wheel cython 'setuptools_scm[toml]>=6.2' Check the logs for full command output.
ERROR: Command errored out with exit status 1:
command: /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-3zh8w4aj/pybedtools_588c351c9448496ca96851490932caee/setup.py'"'"'; __file__='"'"'/tmp/pip-install-3zh8w4aj/pybedtools_588c351c9448496ca96851490932caee/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-88ioqp1e
cwd: /tmp/pip-install-3zh8w4aj/pybedtools_588c351c9448496ca96851490932caee/
Complete output (148 lines):
/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
warnings.warn(msg)
running bdist_wheel
The [wheel] section is deprecated. Use [bdist_wheel] instead.
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/settings.py -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/filenames.py -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/paths.py -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/stats.py -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/parallel.py -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/version.py -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/bedtool.py -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/logger.py -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/genome_registry.py -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/helpers.py -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools
creating build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/test_contrib.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/test_helpers.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/test_issues.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/regression_tests.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/test_cbedtools.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/test_len_leak.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/test_iter.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/test_1.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/tfuncs.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/test_gzip_support.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/genomepy_integration.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/test_pathlib.py -> build/lib.linux-x86_64-3.6/pybedtools/test
copying pybedtools/test/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools/test
creating build/lib.linux-x86_64-3.6/pybedtools/contrib
copying pybedtools/contrib/long_range_interaction.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib
copying pybedtools/contrib/bigbed.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib
copying pybedtools/contrib/plotting.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib
copying pybedtools/contrib/bigwig.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib
copying pybedtools/contrib/venn_maker.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib
copying pybedtools/contrib/intersection_matrix.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib
copying pybedtools/contrib/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools/contrib
creating build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/__init__.py -> build/lib.linux-x86_64-3.6/pybedtools/test/data
running egg_info
creating pybedtools.egg-info
writing pybedtools.egg-info/PKG-INFO
writing dependency_links to pybedtools.egg-info/dependency_links.txt
writing requirements to pybedtools.egg-info/requires.txt
writing top-level names to pybedtools.egg-info/top_level.txt
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
reading manifest file 'pybedtools.egg-info/SOURCES.txt'
adding license file 'LICENSE.txt'
writing manifest file 'pybedtools.egg-info/SOURCES.txt'
copying pybedtools/cbedtools.cpp -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/featurefuncs.cpp -> build/lib.linux-x86_64-3.6/pybedtools
creating build/lib.linux-x86_64-3.6/pybedtools/include
copying pybedtools/include/bedFile.cpp -> build/lib.linux-x86_64-3.6/pybedtools/include
copying pybedtools/include/fileType.cpp -> build/lib.linux-x86_64-3.6/pybedtools/include
copying pybedtools/include/gzstream.cpp -> build/lib.linux-x86_64-3.6/pybedtools/include
copying pybedtools/test/data/test.fa -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/hg38-base.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/m1.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/democonfig.yaml -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam.bai -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/tag_test2.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/Cp190_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/venn.b.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/mm9.bed12 -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/v.vcf -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/test_tsses.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/BEAF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/hg38-problem.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.1.100.bam.bai -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/venn.c.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/c.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.gff.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/reads.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/issue319.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/issue319.vcf.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/Cp190_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.cram -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/issue_121.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/SuHw_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/CTCF_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/a.links.html -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/bedpe2.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M.gff.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.sorted.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/vcf-stderr-test.vcf -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/test.fa.fai -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/small.fastq -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/expand_test.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/a.bed.gz.tbi -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/rmsk.hg18.chr21.small.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/a.bed.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/d.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/small.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/BEAF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/y.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/exons.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/x.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/issue319.out.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/dm3-chr2L-5M-invalid.gff.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.othersort.bam -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/example.narrowPeak -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/164.gtf -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/genome.fa -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/a.igv_script -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/hg19.gff -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/test_bedpe.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/b.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/test_peaks.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/tag_test1.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/SuHw_Mbn2_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/CTCF_Kc_Bushey_2009.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/a.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/snps.bed.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/gdc.50.200.bam.bai -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/x.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/bedpe.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/multibamcov_test.bed -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/test/data/1000genomes-example.vcf.gz -> build/lib.linux-x86_64-3.6/pybedtools/test/data
copying pybedtools/featurefuncs.pyx -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/_Window.pyx -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/cbedtools.pyx -> build/lib.linux-x86_64-3.6/pybedtools
copying pybedtools/cbedtools.pxd -> build/lib.linux-x86_64-3.6/pybedtools
running build_ext
building 'pybedtools.cbedtools' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/pybedtools
creating build/temp.linux-x86_64-3.6/pybedtools/include
/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include -fPIC -Ipybedtools/include/ -I/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include/python3.6m -c pybedtools/cbedtools.cpp -o build/temp.linux-x86_64-3.6/pybedtools/cbedtools.o
cc1plus: warning: command-line option '-Wstrict-prototypes' is valid for C/ObjC but not for C++
In file included from pybedtools/cbedtools.cpp:35:
/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include/python3.6m/Python.h:39:10: fatal error: crypt.h: No such file or directory
39 | #include <crypt.h>
| ^~~~~~~~~
compilation terminated.
error: command '/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/x86_64-conda-linux-gnu-cc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for pybedtools
ERROR: Command errored out with exit status 1:
command: /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-3zh8w4aj/pybedtools_588c351c9448496ca96851490932caee/setup.py'"'"'; __file__='"'"'/tmp/pip-install-3zh8w4aj/pybedtools_588c351c9448496ca96851490932caee/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' clean --all
cwd: /tmp/pip-install-3zh8w4aj/pybedtools_588c351c9448496ca96851490932caee
Complete output (8 lines):
/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/lib/python3.6/distutils/dist.py:261: UserWarning: Unknown distribution option: 'language_level'
warnings.warn(msg)
usage: setup.py [global_opts] cmd1 [cmd1_opts] [cmd2 [cmd2_opts] ...]
or: setup.py --help [cmd1 cmd2 ...]
or: setup.py --help-commands
or: setup.py cmd --help
error: option --all not recognized
----------------------------------------
ERROR: Failed cleaning build dir for pybedtools
ERROR: Command errored out with exit status 1:
command: /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/python -u -c 'import io, os, sys, setuptools, tokenize; sys.argv[0] = '"'"'/tmp/pip-install-3zh8w4aj/ncls_0a845ba45d51429db21c3e645e8eccd5/setup.py'"'"'; __file__='"'"'/tmp/pip-install-3zh8w4aj/ncls_0a845ba45d51429db21c3e645e8eccd5/setup.py'"'"';f = getattr(tokenize, '"'"'open'"'"', open)(__file__) if os.path.exists(__file__) else io.StringIO('"'"'from setuptools import setup; setup()'"'"');code = f.read().replace('"'"'\r\n'"'"', '"'"'\n'"'"');f.close();exec(compile(code, __file__, '"'"'exec'"'"'))' bdist_wheel -d /tmp/pip-wheel-4t6vvrnj
cwd: /tmp/pip-install-3zh8w4aj/ncls_0a845ba45d51429db21c3e645e8eccd5/
Complete output (40 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/ncls
copying ncls/version.py -> build/lib.linux-x86_64-3.6/ncls
copying ncls/__init__.py -> build/lib.linux-x86_64-3.6/ncls
creating build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/__init__.py -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/ncls32.pyx -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/fncls.pyx -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/ncls.pyx -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/cfncls.pxd -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/cncls.pxd -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/cncls32.pxd -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/cgraph.h -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/intervaldb32.h -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/utarray.h -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/fintervaldb.h -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/default.h -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/intervaldb.h -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/ncls32.c -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/fintervaldb.c -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/intervaldb32.c -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/fncls.c -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/intervaldb.c -> build/lib.linux-x86_64-3.6/ncls/src
copying ncls/src/ncls.c -> build/lib.linux-x86_64-3.6/ncls/src
running build_ext
building 'ncls.src.ncls' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/ncls
creating build/temp.linux-x86_64-3.6/ncls/src
/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include -fPIC -I/tmp/pip-install-3zh8w4aj/ncls_0a845ba45d51429db21c3e645e8eccd5/ncls/src -I/tmp/pip-install-3zh8w4aj/ncls_0a845ba45d51429db21c3e645e8eccd5 -I. -I/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include/python3.6m -c ncls/src/ncls.c -o build/temp.linux-x86_64-3.6/ncls/src/ncls.o
In file included from ncls/src/ncls.c:36:
/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include/python3.6m/Python.h:39:10: fatal error: crypt.h: No such file or directory
39 | #include <crypt.h>
| ^~~~~~~~~
compilation terminated.
error: command '/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/x86_64-conda-linux-gnu-cc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for ncls
ERROR: Command errored out with exit status 1:
command: /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/python /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/lib/python3.6/site-packages/pip/_vendor/pep517/in_process/_in_process.py build_wheel /tmp/tmpmma3ozvs
cwd: /tmp/pip-install-3zh8w4aj/pyrle_8b0a1872b87441a39b26a1713735aaa9
Complete output (38 lines):
running bdist_wheel
running build
running build_py
creating build
creating build/lib.linux-x86_64-3.6
creating build/lib.linux-x86_64-3.6/tests
copying tests/test_subset_coverage.py -> build/lib.linux-x86_64-3.6/tests
copying tests/hypothesis_helper.py -> build/lib.linux-x86_64-3.6/tests
copying tests/helpers.py -> build/lib.linux-x86_64-3.6/tests
copying tests/test_hypothesis_coverage.py -> build/lib.linux-x86_64-3.6/tests
copying tests/__init__.py -> build/lib.linux-x86_64-3.6/tests
copying tests/test_hypothesis.py -> build/lib.linux-x86_64-3.6/tests
creating build/lib.linux-x86_64-3.6/pyrle
copying pyrle/rledict.py -> build/lib.linux-x86_64-3.6/pyrle
copying pyrle/version.py -> build/lib.linux-x86_64-3.6/pyrle
copying pyrle/methods.py -> build/lib.linux-x86_64-3.6/pyrle
copying pyrle/rle.py -> build/lib.linux-x86_64-3.6/pyrle
copying pyrle/__init__.py -> build/lib.linux-x86_64-3.6/pyrle
creating build/lib.linux-x86_64-3.6/pyrle/src
copying pyrle/src/__init__.py -> build/lib.linux-x86_64-3.6/pyrle/src
copying pyrle/src/getitem.pyx -> build/lib.linux-x86_64-3.6/pyrle/src
copying pyrle/src/rle.pyx -> build/lib.linux-x86_64-3.6/pyrle/src
copying pyrle/src/coverage.pyx -> build/lib.linux-x86_64-3.6/pyrle/src
copying pyrle/src/rle.c -> build/lib.linux-x86_64-3.6/pyrle/src
copying pyrle/src/coverage.c -> build/lib.linux-x86_64-3.6/pyrle/src
copying pyrle/src/getitem.c -> build/lib.linux-x86_64-3.6/pyrle/src
running build_ext
building 'pyrle.src.rle' extension
creating build/temp.linux-x86_64-3.6
creating build/temp.linux-x86_64-3.6/pyrle
creating build/temp.linux-x86_64-3.6/pyrle/src
/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/x86_64-conda-linux-gnu-cc -DNDEBUG -fwrapv -O2 -Wall -Wstrict-prototypes -march=nocona -mtune=haswell -ftree-vectorize -fPIC -fstack-protector-strong -fno-plt -O2 -ffunction-sections -pipe -isystem /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include -DNDEBUG -D_FORTIFY_SOURCE=2 -O2 -isystem /home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include -fPIC -I. -I/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include/python3.6m -c pyrle/src/rle.c -o build/temp.linux-x86_64-3.6/pyrle/src/rle.o
In file included from pyrle/src/rle.c:29:
/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/include/python3.6m/Python.h:39:10: fatal error: crypt.h: No such file or directory
39 | #include <crypt.h>
| ^~~~~~~~~
compilation terminated.
error: command '/home/david/Projects/CADD-scripts-1.7-master/envs/conda/5f65d8c3cbefdd415a813fdb4930385a_/bin/x86_64-conda-linux-gnu-cc' failed with exit status 1
----------------------------------------
ERROR: Failed building wheel for pyrle
ERROR: Could not build wheels for pyrle, which is required to install pyproject.toml-based projects
failed
CondaEnvException: Pip failedIf you start from a fresh mamba install and clone the repository from master, are you able to successfully build the mmsplice environment? Based on the required packages it does seem that there are unresolvable conflicts
ThorbenMaa
commented
7 months ago Hi David,
sorry for the inconvenience, I hope this time I have a better solution that actually works for you. Can you try to replace the content in /home/david/Projects/CADD-scripts-1.7-master/envs/mmsplice.yml with what is shown below and let me know whether it worked out this time?
---
name: mmsplice
channels:
- bioconda
- conda-forge
dependencies:
- _libgcc_mutex=0.1=conda_forge
- _openmp_mutex=4.5=2_gnu
- binutils_impl_linux-64=2.40=hf600244_0
- binutils_linux-64=2.40=hbdbef99_2
- blas=1.1=openblas
- bzip2=1.0.8=hd590300_5
- c-ares=1.11.0=h470a237_1
- ca-certificates=2023.11.17=hbcca054_0
- click=8.0.1=py36h5fab9bb_0
- coloredlogs=15.0.1=py36h5fab9bb_1
- curl=7.71.1=he644dc0_8
- cython=0.29.13=py36he1b5a44_0
- cyvcf2=0.8.4=py36h355e19c_4
- dataclasses=0.8=pyh787bdff_2
- gcc_impl_linux-64=13.2.0=h338b0a0_3
- gcc_linux-64=13.2.0=h112eaf3_2
- gxx_impl_linux-64=13.2.0=h338b0a0_3
- gxx_linux-64=13.2.0=hc53e3bf_2
- h5py=2.10.0=nompi_py36hecadee3_104
- hdf5=1.10.6=nompi_h7c3c948_1111
- htslib=1.9=ha228f0b_7
- humanfriendly=10.0=py36h5fab9bb_0
- importlib-metadata=4.8.1=py36h5fab9bb_0
- joblib=1.2.0=pyhd8ed1ab_0
- keras=2.2.4=py36_1
- keras-applications=1.0.8=py_1
- keras-preprocessing=1.1.2=pyhd8ed1ab_0
- kernel-headers_linux-64=2.6.32=he073ed8_16
- krb5=1.17.2=h926e7f8_0
- ld_impl_linux-64=2.40=h41732ed_0
- libblas=3.9.0=1_h6e990d7_netlib
- libcblas=3.9.0=3_h893e4fe_netlib
- libcurl=7.71.1=hcdd3856_8
- libdeflate=1.0=h14c3975_1
- libedit=3.1.20191231=he28a2e2_2
- libev=4.33=hd590300_2
- libffi=3.4.2=h7f98852_5
- libgcc=7.2.0=h69d50b8_2
- libgcc-devel_linux-64=13.2.0=ha9c7c90_103
- libgcc-ng=13.2.0=h807b86a_3
- libgfortran-ng=7.5.0=h14aa051_20
- libgfortran4=7.5.0=h14aa051_20
- libgomp=13.2.0=h807b86a_3
- libgpuarray=0.7.6=h7f98852_1003
- liblapack=3.9.0=3_h893e4fe_netlib
- libnghttp2=1.41.0=hab1572f_1
- libnsl=2.0.1=hd590300_0
- libprotobuf=3.18.0=h780b84a_1
- libsanitizer=13.2.0=h7e041cc_3
- libsqlite=3.44.2=h2797004_0
- libssh2=1.10.0=haa6b8db_3
- libstdcxx-devel_linux-64=13.2.0=ha9c7c90_103
- libstdcxx-ng=13.2.0=h7e041cc_3
- libzlib=1.2.13=hd590300_5
- mako=1.3.0=pyhd8ed1ab_0
- markupsafe=2.0.1=py36h8f6f2f9_0
- mock=5.1.0=pyhd8ed1ab_0
- natsort=8.2.0=pyhd8ed1ab_0
- ncurses=6.4=h59595ed_2
- numpy=1.16.1=py36_blas_openblash1522bff_0
- openblas=0.3.3=h9ac9557_1001
- openssl=1.1.1w=hd590300_0
- pandas=0.24.2=py36hb3f55d8_1
- pip=21.3.1=pyhd8ed1ab_0
- protobuf=3.18.0=py36hc4f0c31_0
- pygpu=0.7.6=py36h785e9b2_1001
- pyranges=0.0.51=py36h516909a_1
- pysam=0.15.3=py36hda2845c_1
- python=3.6.15=hb7a2778_0_cpython
- python-dateutil=2.8.2=pyhd8ed1ab_0
- python_abi=3.6=2_cp36m
- pytz=2023.3.post1=pyhd8ed1ab_0
- pyyaml=5.4.1=py36h8f6f2f9_1
- readline=8.2=h8228510_1
- scipy=1.5.1=py36h2d22cac_0
- setuptools=58.0.4=py36h5fab9bb_2
- six=1.16.0=pyh6c4a22f_0
- sorted_nearest=0.0.37=py36h91eb985_1
- sqlite=3.44.2=h2c6b66d_0
- sysroot_linux-64=2.12=he073ed8_16
- tabulate=0.8.10=pyhd8ed1ab_0
- tensorflow=1.1.0=py36_0
- theano=1.0.4=py36hf484d3e_1000
- threadpoolctl=3.1.0=pyh8a188c0_0
- tk=8.6.13=noxft_h4845f30_101
- typing_extensions=4.1.1=pyha770c72_0
- werkzeug=2.0.2=pyhd8ed1ab_0
- wheel=0.37.1=pyhd8ed1ab_0
- xz=5.2.6=h166bdaf_0
- yaml=0.2.5=h7f98852_2
- zipp=3.6.0=pyhd8ed1ab_0
- zlib=1.2.13=hd590300_5
- pip:
- argcomplete==3.1.2
- argh==0.27.2
- arrow==1.2.3
- attrs==21.4.0
- binaryornot==0.4.4
- certifi==2023.11.17
- chardet==5.0.0
- charset-normalizer==2.0.12
- colorlog==6.8.0
- concise==0.6.9
- cookiecutter==1.7.3
- cycler==0.11.0
- deprecation==2.1.0
- descartes==1.1.0
- future==0.18.3
- gffutils==0.12
- gtfparse==2.0.1
- idna==3.6
- importlib-resources==5.4.0
- jinja2==3.0.3
- jinja2-time==0.2.0
- kipoi==0.8.6
- kipoi-conda==0.3.1
- kipoi-utils==0.7.7
- kipoiseq==0.2.5
- kiwisolver==1.3.1
- matplotlib==3.3.4
- mmsplice==1.0.1
- ncls==0.0.67
- packaging==21.3
- pillow==8.4.0
- polars==0.12.5
- poyo==0.5.0
- pybedtools==0.9.1
- pyfaidx==0.7.1
- pyparsing==3.1.1
- pyrle==0.0.37
- python-slugify==6.1.2
- related==0.7.3
- requests==2.27.1
- scikit-learn==0.19.2
- shapely==1.8.5.post1
- simplejson==3.19.2
- spliceai==1.3
- text-unidecode==1.3
- tinydb==4.7.0
- tqdm==4.64.1
- urllib3==1.26.18
Thanks Thorben, that fixed the mmsplice issue! And it appears that all the environments are being created successfully now. Unfortunately, I'm still running into an issue with the test script:
CADD-v1.7 (c) University of Washington, Hudson-Alpha Institute for Biotechnology and Berlin Institute of Health at Charité - Universitätsmedizin Berlin 2013-2023. All rights reserved.
Running snakemake pipeline:
snakemake /tmp/tmp.SqcUs6aYmH/input.tsv.gz --use-conda --conda-prefix /home/david/Projects/CADD-scripts-1.7-master/envs/conda --cores 1
--configfile /home/david/Projects/CADD-scripts-1.7-master/config/config_GRCh38_v1.7_noanno.yml --snakefile /home/david/Projects/CADD-scripts-1.7-master/Snakefile -q
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: 1 (use --cores to define parallelism)
Rules claiming more threads will be scaled down.
Job stats:
job count
-------- -------
join 1
prepare 1
prescore 1
total 3
Select jobs to execute...
Activating conda environment: envs/conda/6286c07397830d220a93727bfb2db5d3_
Select jobs to execute...
Activating conda environment: envs/conda/6286c07397830d220a93727bfb2db5d3_
Creating conda environment envs/mmsplice.yml...
Downloading and installing remote packages.
Environment for /home/david/Projects/CADD-scripts-1.7-master/envs/mmsplice.yml created (location: envs/conda/314d47aafa9d70164634814e1c15c0b6_)
Creating conda environment envs/esm.yml...
Downloading and installing remote packages.
Environment for /home/david/Projects/CADD-scripts-1.7-master/envs/esm.yml created (location: envs/conda/2708e22ad39a84f1657b8582098aec8c_)
Creating conda environment envs/vep.yml...
Downloading and installing remote packages.
Environment for /home/david/Projects/CADD-scripts-1.7-master/envs/vep.yml created (location: envs/conda/49b0bd0c0764f34655987e41beb1d3d0_)
Creating conda environment envs/regulatorySequence.yml...
Downloading and installing remote packages.
Environment for /home/david/Projects/CADD-scripts-1.7-master/envs/regulatorySequence.yml created (location: envs/conda/c1e6153218582c24ef7133fa74016642_)
Removing temporary output /tmp/tmp.SqcUs6aYmH/input.prepared.vcf.
Select jobs to execute...
Activating conda environment: envs/conda/49b0bd0c0764f34655987e41beb1d3d0_
Smartmatch is experimental at /home/david/Projects/CADD-scripts-1.7-master/envs/conda/49b0bd0c0764f34655987e41beb1d3d0_/share/ensembl-vep-110.1-0/modules/Bio/EnsEMBL/VEP/AnnotationSource/File.pm line 472.
Removing temporary output /tmp/tmp.SqcUs6aYmH/input.novel.vcf.
Select jobs to execute...
Activating conda environment: envs/conda/2708e22ad39a84f1657b8582098aec8c_
Removing temporary output /tmp/tmp.SqcUs6aYmH/input.vep.vcf.gz.
Removing temporary output /tmp/tmp.SqcUs6aYmH/input.esm_missens.vcf.gz.
Removing temporary output /tmp/tmp.SqcUs6aYmH/input.esm_frameshift.vcf.gz.
Select jobs to execute...
Activating conda environment: envs/conda/c1e6153218582c24ef7133fa74016642_
[Wed Mar 20 10:18:23 2024]
Error in rule annotate_regseq:
jobid: 9
input: /tmp/tmp.SqcUs6aYmH/input.esm.vcf.gz, data/annotations/GRCh38_v1.7/regseq/reference.fa, data/annotations/GRCh38_v1.7/regseq/reference.fa.genome, data/annotations/GRCh38_v1.7/regseq/Hyperopt400InclNegatives.json, data/annotations/GRCh38_v1.7/regseq/Hyperopt400InclNegatives.h5
output: /tmp/tmp.SqcUs6aYmH/input.regseq.vcf.gz
log: /tmp/tmp.SqcUs6aYmH/input.annotate_regseq.log (check log file(s) for error details)
conda-env: /home/david/Projects/CADD-scripts-1.7-master/envs/conda/c1e6153218582c24ef7133fa74016642_
shell:
python /home/david/Projects/CADD-scripts-1.7-master/src/scripts/lib/tools/regulatorySequence/predictVariants.py --variants /tmp/tmp.SqcUs6aYmH/input.esm.vcf.gz --model data/annotations/GRCh38_v1.7/regseq/Hyperopt400InclNegatives.json --weights data/annotations/GRCh38_v1.7/regseq/Hyperopt400InclNegatives.h5 --reference data/annotations/GRCh38_v1.7/regseq/reference.fa --genome data/annotations/GRCh38_v1.7/regseq/reference.fa.genome --output /tmp/tmp.SqcUs6aYmH/input.regseq.vcf.gz &> /tmp/tmp.SqcUs6aYmH/input.annotate_regseq.log
(one of the commands exited with non-zero exit code; note that snakemake uses bash strict mode!)
Shutting down, this might take some time.
Exiting because a job execution failed. Look above for error message
Complete log: .snakemake/log/2024-03-20T100840.128547.snakemake.logLet me know if you'd like me to make a separate issue for this.
ThorbenMaa
commented
7 months ago Hmmm, this is most likely related to your variants. Can you try to sort them using
sort -k1,1 -k2,2n
? Also, try to avoid using, e.g., chr7 and just use 7 instead. Note that we are not supporting the MT chromosome. If you already considered all these things, and you are using the right genome version (there is a CADD for GRCh37 and one for 38, as you probably already know), than it would be nice if you could create a new issue and provide me with some example variants for that you get this error. I will than try to reproduce it and fix the problem.
All the best, Thorben
The mmsplice environment tries to install python 3.6. Most packages successfully install, but mmsplice relies on a few packages which require setuptools>=61.0.0 which is not available for python 3.6. Any advice on how to get around this issue?
mamba env create -f mmsplice.yml