pytest-workflow

feat: add MuSE as new somatic variant caller #174

Triggered via pull request December 5, 2024 15:55

famosab

synchronize #1744

famosab:muse

Status Failure

Total duration 46m 55s

Artifacts –

pytest.yml

on: pull_request

Check for changes (pytest)

Matrix: pytest

confirm-pass

Annotations

23 errors and 22 warnings

muse docker NF latest-everything

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:02:00 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:02:01 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:02:02 GMT+0000 (Coordinated Universal Time)

muse docker NF latest-everything

Process completed with exit code 1.

muse docker NF 24.04.2

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:02:54 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:02:56 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:02:57 GMT+0000 (Coordinated Universal Time)

muse docker NF 24.04.2

Process completed with exit code 1.

msisensorpro docker NF 24.04.2

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:01:46 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:04:59 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:06:44 GMT+0000 (Coordinated Universal Time)

msisensorpro docker NF latest-everything

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:03:04 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:06:07 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:07:50 GMT+0000 (Coordinated Universal Time)

tiddit docker NF latest-everything

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:03:07 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:08:09 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:11:31 GMT+0000 (Coordinated Universal Time)

tiddit docker NF 24.04.2

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:02:35 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:07:48 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:11:18 GMT+0000 (Coordinated Universal Time)

concatenate_vcfs docker NF 24.04.2

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:02:14 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:09:37 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:12:48 GMT+0000 (Coordinated Universal Time)

concatenate_vcfs docker NF latest-everything

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:02:38 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:10:15 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:13:25 GMT+0000 (Coordinated Universal Time)

controlfreec docker NF latest-everything

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:00:50 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:07:40 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:12:25 GMT+0000 (Coordinated Universal Time)

mpileup docker NF 24.04.2

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:01:28 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:08:00 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:13:05 GMT+0000 (Coordinated Universal Time)

controlfreec docker NF 24.04.2

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:02:28 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:09:16 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:14:02 GMT+0000 (Coordinated Universal Time)

mpileup docker NF latest-everything

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:03:21 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:09:31 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:14:30 GMT+0000 (Coordinated Universal Time)

manta docker NF latest-everything

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:01:06 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:08:25 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:14:28 GMT+0000 (Coordinated Universal Time)

manta docker NF 24.04.2

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:01:34 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:09:13 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:15:36 GMT+0000 (Coordinated Universal Time)

cnvkit docker NF latest-everything

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:01:09 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:12:13 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:21:05 GMT+0000 (Coordinated Universal Time)

mutect2 docker NF latest-everything

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:03:07 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:13:03 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:21:53 GMT+0000 (Coordinated Universal Time)

cnvkit docker NF 24.04.2

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:01:09 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:12:34 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:21:44 GMT+0000 (Coordinated Universal Time)

mutect2 docker NF 24.04.2

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:03:59 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:14:23 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:23:39 GMT+0000 (Coordinated Universal Time)

freebayes docker NF latest-everything

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:00:59 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:15:45 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:28:26 GMT+0000 (Coordinated Universal Time)

freebayes docker NF 24.04.2

Process returned exit code 2 Launched as "bash --noprofile --norc -eo pipefail /home/runner/work/_actions/Wandalen/wretry.action/v1.4.10_js_action/src/script.sh" Launched at "/home/runner/work/sarek/sarek" Attempts exhausted, made 3 attempts : Attempt #1 started at : 16:01:01 GMT+0000 (Coordinated Universal Time) Attempt #2 started at : 16:16:07 GMT+0000 (Coordinated Universal Time) Attempt #3 started at : 16:29:06 GMT+0000 (Coordinated Universal Time)

confirm-pass

Process completed with exit code 1.

Check for changes (pytest)

ubuntu-latest pipelines will use ubuntu-24.04 soon. For more details, see https://github.com/actions/runner-images/issues/10636

muse docker NF latest-everything

No files were found with the provided path: /home/ubuntu/pytest_workflow_*/*/.nextflow.log /home/ubuntu/pytest_workflow_*/*/log.out /home/ubuntu/pytest_workflow_*/*/log.err /home/ubuntu/pytest_workflow_*/*/work !/home/ubuntu/pytest_workflow_*/*/work/conda !/home/ubuntu/pytest_workflow_*/*/work/singularity !/home/runner/work/sarek/sarek/.singularity. No artifacts will be uploaded.

muse docker NF 24.04.2