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Release pipeline v1.0.0 #279

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Release pipeline v1.0.0

Release pipeline v1.0.0 #279

Triggered via pull request February 4, 2025 12:53
@kubranarcikubranarci
opened #148
dev
Status Failure
Total duration 13m 52s
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ci.yml

on: pull_request
Matrix: test
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84 errors and 12 warnings
24.04.2 | docker | 2/6
Process completed with exit code 1.
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.-stub: Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'snv' --method 'sompy': Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 1 of 1 assertions failed
latest-everything | singularity | 2/6
Process completed with exit code 1.
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.-stub: Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'snv' --method 'sompy': Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 1 of 1 assertions failed
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools': Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for indel somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'indel' --method 'sompy': Test pipeline for indel somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
24.04.2 | singularity | 1/6
Process completed with exit code 1.
latest-everything | conda | 2/6
Process completed with exit code 1.
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.-stub: Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'snv' --method 'sompy': Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 1 of 1 assertions failed
24.04.2 | conda | 1/6
Process completed with exit code 1.
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools': Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for indel somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'indel' --method 'sompy': Test pipeline for indel somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
24.04.2 | conda | 2/6
Process completed with exit code 1.
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.-stub: Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'snv' --method 'sompy': Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 1 of 1 assertions failed
latest-everything | conda | 3/6
Process completed with exit code 1.
Test pipeline for structural germline variants, tested benchmarking methods are truvari, svbenchmark and wittyer.Params: --analysis 'germline' --variant_type 'structural' --method 'truvari,svbenchmark,wittyer': Test pipeline for structural germline variants, tested benchmarking methods are truvari, svbenchmark and wittyer#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.-stub: Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
latest-everything | docker | 1/6
Process completed with exit code 1.
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools': Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for indel somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'indel' --method 'sompy': Test pipeline for indel somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
latest-everything | conda | 6/6
Process completed with exit code 1.
Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools' --liftover 'truth': Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for structural germline variants, tested benchmarking methods is svanalyzer.-stub: Test pipeline for structural germline variants, tested benchmarking methods is svanalyzer#L1
Assertion failed: 2 of 2 assertions failed
latest-everything | conda | 1/6
Process completed with exit code 1.
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools': Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for indel somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'indel' --method 'sompy': Test pipeline for indel somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for structural germline variants, tested benchmarking methods are truvari, svbenchmark and wittyer.-stub: Test pipeline for structural germline variants, tested benchmarking methods are truvari, svbenchmark and wittyer#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for structural somatic variants, tested benchmarking methods are truvari and svbenchmark.Params: --analysis 'somatic' --variant_type 'structural' --method 'truvari,svbenchmark': Test pipeline for structural somatic variants, tested benchmarking methods are truvari and svbenchmark#L1
Assertion failed: 2 of 2 assertions failed
latest-everything | conda | 4/6
Process completed with exit code 1.
24.04.2 | docker | 1/6
Process completed with exit code 1.
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools': Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for indel somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'indel' --method 'sompy': Test pipeline for indel somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
24.04.2 | conda | 3/6
Process completed with exit code 1.
Test pipeline for structural germline variants, tested benchmarking methods are truvari, svbenchmark and wittyer.Params: --analysis 'germline' --variant_type 'structural' --method 'truvari,svbenchmark,wittyer': Test pipeline for structural germline variants, tested benchmarking methods are truvari, svbenchmark and wittyer#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.-stub: Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools': Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for indel somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'indel' --method 'sompy': Test pipeline for indel somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
latest-everything | singularity | 1/6
Process completed with exit code 1.
latest-everything | docker | 6/6
Process completed with exit code 1.
Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools' --liftover 'truth': Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.-stub: Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'snv' --method 'sompy': Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 1 of 1 assertions failed
24.04.2 | singularity | 2/6
Process completed with exit code 1.
latest-everything | singularity | 6/6
Process completed with exit code 1.
Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools' --liftover 'truth': Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
24.04.2 | singularity | 6/6
Process completed with exit code 1.
Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools' --liftover 'truth': Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari.Params: --analysis 'germline' --variant_type 'structural' --method 'truvari' --liftover 'test': Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for structural germline variants, tested benchmarking methods is svanalyzer.Params: --analysis 'germline' --variant_type 'structural' --method 'svanalyzer': Test pipeline for structural germline variants, tested benchmarking methods is svanalyzer#L1
Assertion failed: 2 of 2 assertions failed
24.04.2 | conda | 5/6
Process completed with exit code 1.
24.04.2 | docker | 6/6
Process completed with exit code 1.
Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools' --liftover 'truth': Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools.Params: --analysis 'germline' --variant_type 'small' --method 'happy,rtgtools' --liftover 'truth': Test pipeline for liftover small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for structural germline variants, tested benchmarking methods is svanalyzer.-stub: Test pipeline for structural germline variants, tested benchmarking methods is svanalyzer#L1
Assertion failed: 2 of 2 assertions failed
24.04.2 | conda | 6/6
Process completed with exit code 1.
latest-everything | singularity | 5/6
Process completed with exit code 1.
Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari.Params: --analysis 'germline' --variant_type 'structural' --method 'truvari' --liftover 'test': Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari#L1
Assertion failed: 2 of 2 assertions failed
24.04.2 | conda | 4/6
Process completed with exit code 1.
Test pipeline for structural germline variants, tested benchmarking methods are truvari, svbenchmark and wittyer.-stub: Test pipeline for structural germline variants, tested benchmarking methods are truvari, svbenchmark and wittyer#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for structural somatic variants, tested benchmarking methods are truvari and svbenchmark.Params: --analysis 'somatic' --variant_type 'structural' --method 'truvari,svbenchmark': Test pipeline for structural somatic variants, tested benchmarking methods are truvari and svbenchmark#L1
Assertion failed: 2 of 2 assertions failed
latest-everything | conda | 5/6
Process completed with exit code 1.
Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari.Params: --analysis 'germline' --variant_type 'structural' --method 'truvari' --liftover 'test': Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for structural germline variants, tested benchmarking methods is svanalyzer.Params: --analysis 'germline' --variant_type 'structural' --method 'svanalyzer': Test pipeline for structural germline variants, tested benchmarking methods is svanalyzer#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari.Params: --analysis 'germline' --variant_type 'structural' --method 'truvari' --liftover 'test': Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari#L1
Assertion failed: 2 of 2 assertions failed
24.04.2 | singularity | 5/6
Process completed with exit code 1.
latest-everything | docker | 5/6
Process completed with exit code 1.
Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari.Params: --analysis 'germline' --variant_type 'structural' --method 'truvari' --liftover 'test': Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari#L1
Assertion failed: 2 of 2 assertions failed
24.04.2 | singularity | 3/6
Process completed with exit code 1.
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.-stub: Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
24.04.2 | docker | 5/6
Process completed with exit code 1.
Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari.Params: --analysis 'germline' --variant_type 'structural' --method 'truvari' --liftover 'test': Test pipeline for liftover structural germline variants, tested benchmarking methods are truvari#L1
Assertion failed: 2 of 2 assertions failed
latest-everything | singularity | 3/6
Process completed with exit code 1.
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.-stub: Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
latest-everything | docker | 3/6
Process completed with exit code 1.
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.-stub: Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
24.04.2 | docker | 3/6
Process completed with exit code 1.
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.-stub: Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 2 of 2 assertions failed
latest-everything | docker | 2/6
Process completed with exit code 1.
Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools.-stub: Test pipeline for small germline variants, tested benchmarking methods are happy and rtgtools#L1
Assertion failed: 2 of 2 assertions failed
Test pipeline for snv somatic variants, tested benchmarking methods are sompy.Params: --analysis 'somatic' --variant_type 'snv' --method 'sompy': Test pipeline for snv somatic variants, tested benchmarking methods are sompy#L1
Assertion failed: 1 of 1 assertions failed
latest-everything | conda | 2/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
24.04.2 | conda | 1/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
24.04.2 | conda | 2/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
latest-everything | conda | 3/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
latest-everything | conda | 6/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
latest-everything | conda | 1/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
latest-everything | conda | 4/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
24.04.2 | conda | 3/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
24.04.2 | conda | 5/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
24.04.2 | conda | 6/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
24.04.2 | conda | 4/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(
latest-everything | conda | 5/6
/home/runner/miniconda3/lib/python3.12/site-packages/conda/base/context.py:201: FutureWarning: Adding 'defaults' to channel list implicitly is deprecated and will be removed in 25.3. To remove this warning, please choose a default channel explicitly with conda's regular configuration system, e.g. by adding 'defaults' to the list of channels: conda config --add channels defaults For more information see https://docs.conda.io/projects/conda/en/stable/user-guide/configuration/use-condarc.html deprecated.topic(