use docker to run the test

gq1 commented 5 months ago

PR checklist

[ ] This comment contains a description of changes (with reason).
[ ] If you've fixed a bug or added code that should be tested, add tests!
[ ] If you've added a new tool - have you followed the pipeline conventions in the contribution docs
[ ] Make sure your code lints (nf-core lint).
[ ] Ensure the test suite passes (nextflow run . -profile test,docker --outdir <OUTDIR>).
[ ] Usage Documentation in docs/usage.md is updated.
[ ] Output Documentation in docs/output.md is updated.
[ ] CHANGELOG.md is updated.
[ ] README.md is updated (including new tool citations and authors/contributors).

github-actions[bot] commented 5 months ago

`nf-core lint` overall result: Passed :white_check_mark: :warning:

Posted for pipeline commit ca02b41

+| ✅ 127 tests passed       |+
#| ❔  20 tests were ignored |#
!| ❗   4 tests had warnings |!

### :heavy_exclamation_mark: Test warnings: * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``manifest.version`` should end in ``dev``: ``'1.0.2'`` * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `methods_description_template.yml`: _## Update the HTML below to your prefered methods description, e.g. add publication citation for this pipeline_ * [pipeline_todos](https://nf-co.re/tools-docs/lint_tests/pipeline_todos.html) - TODO string in `WorkflowMain.groovy`: _Add Zenodo DOI for pipeline after first release_ * [system_exit](https://nf-co.re/tools-docs/lint_tests/system_exit.html) - `System.exit` in WorkflowTreeval.groovy: _System.exit(1)_ [line 17] ### :grey_question: Tests ignored: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `assets/nf-core-treeval_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `conf/test_full.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-treeval_logo_light.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `docs/images/nf-core-treeval_logo_dark.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `conf/igenomes.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awstest.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File is ignored: `.github/workflows/awsfulltest.yml` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ignored: `manifest.name` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ignored: `manifest.homePage` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/CONTRIBUTING.md` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.github/workflows/linting.yml` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `assets/sendmail_template.txt` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `assets/nf-core-treeval_logo_light.png` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `docs/images/nf-core-treeval_logo_light.png` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File does not exist: `docs/images/nf-core-treeval_logo_dark.png` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `lib/NfcoreTemplate.groovy` * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - File ignored due to lint config: `.gitignore` or `.prettierignore` or `pyproject.toml` * [actions_awstest](https://nf-co.re/tools-docs/lint_tests/actions_awstest.html) - 'awstest.yml' workflow not found: `/home/runner/work/treeval/treeval/.github/workflows/awstest.yml` ### :white_check_mark: Tests passed: * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitattributes` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.gitignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.nf-core.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.editorconfig` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.prettierignore` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.prettierrc.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CHANGELOG.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CITATIONS.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `CODE_OF_CONDUCT.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `LICENSE` or `LICENSE.md` or `LICENCE` or `LICENCE.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow_schema.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `nextflow.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/.dockstore.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/CONTRIBUTING.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/bug_report.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/ISSUE_TEMPLATE/feature_request.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/PULL_REQUEST_TEMPLATE.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/branch.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/ci.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting_comment.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `.github/workflows/linting.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.html` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/email_template.txt` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/sendmail_template.txt` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/modules.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/test.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/output.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/README.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `docs/usage.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/nfcore_external_java_deps.jar` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/NfcoreSchema.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/NfcoreTemplate.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/Utils.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/WorkflowMain.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `main.nf` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `assets/multiqc_config.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `conf/base.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `lib/WorkflowTreeval.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `modules.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File found: `pyproject.toml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `Singularity` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `parameters.settings.json` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.nf-core.yaml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `bin/markdown_to_html.r` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `conf/aws.config` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/workflows/push_dockerhub.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/ISSUE_TEMPLATE/bug_report.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.github/ISSUE_TEMPLATE/feature_request.md` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `docs/images/nf-core-treeval_logo.png` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.markdownlint.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.yamllint.yml` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `lib/Checks.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `lib/Completion.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `lib/Workflow.groovy` * [files_exist](https://nf-co.re/tools-docs/lint_tests/files_exist.html) - File not found check: `.travis.yml` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.nextflowVersion` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.description` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `timeline.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.enabled` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.cpus` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.memory` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `process.time` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.outdir` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.input` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.show_hidden_params` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `params.schema_ignore_params` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `manifest.mainScript` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `timeline.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `trace.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `report.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable found: `dag.file` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.nf_required_version` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.container` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.singleEnd` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.igenomesIgnore` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.name` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable (correctly) not found: `params.enable_conda` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``timeline.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``report.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``trace.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``dag.enabled`` had correct value: ``true`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config ``dag.file`` ended with ``.html`` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config variable ``manifest.nextflowVersion`` started with >= or !>= * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config `params.custom_config_version` is set to `master` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Config `params.custom_config_base` is set to `https://raw.githubusercontent.com/nf-core/configs/master` * [nextflow_config](https://nf-co.re/tools-docs/lint_tests/nextflow_config.html) - Lines for loading custom profiles found * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.gitattributes` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.prettierrc.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/.dockstore.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/ISSUE_TEMPLATE/feature_request.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/PULL_REQUEST_TEMPLATE.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/branch.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `.github/workflows/linting_comment.yml` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.html` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `assets/email_template.txt` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `docs/README.md` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/nfcore_external_java_deps.jar` matches the template * [files_unchanged](https://nf-co.re/tools-docs/lint_tests/files_unchanged.html) - `lib/NfcoreSchema.groovy` matches the template * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - '.github/workflows/ci.yml' is triggered on expected events * [actions_ci](https://nf-co.re/tools-docs/lint_tests/actions_ci.html) - '.github/workflows/ci.yml' checks minimum NF version * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README Nextflow minimum version badge matched config. Badge: `22.10.1`, Config: `22.10.1` * [readme](https://nf-co.re/tools-docs/lint_tests/readme.html) - README Zenodo placeholder was replaced with DOI. * [pipeline_name_conventions](https://nf-co.re/tools-docs/lint_tests/pipeline_name_conventions.html) - Name adheres to nf-core convention * [template_strings](https://nf-co.re/tools-docs/lint_tests/template_strings.html) - Did not find any Jinja template strings (343 files) * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema lint passed * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Schema title + description lint passed * [schema_lint](https://nf-co.re/tools-docs/lint_tests/schema_lint.html) - Input mimetype lint passed: 'text/yaml' * [schema_params](https://nf-co.re/tools-docs/lint_tests/schema_params.html) - Schema matched params returned from nextflow config * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: branch.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: fix-linting.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: sanger_test_full.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: ci.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: clean-up.yml * [actions_schema_validation](https://nf-co.re/tools-docs/lint_tests/actions_schema_validation.html) - Workflow validation passed: linting_comment.yml * [merge_markers](https://nf-co.re/tools-docs/lint_tests/merge_markers.html) - No merge markers found in pipeline files * [modules_json](https://nf-co.re/tools-docs/lint_tests/modules_json.html) - Only installed modules found in `modules.json` * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' follows the ordering scheme of the minimally required plugins. * [multiqc_config](https://nf-co.re/tools-docs/lint_tests/multiqc_config.html) - 'assets/multiqc_config.yml' contains 'export_plots: true'. * [modules_structure](https://nf-co.re/tools-docs/lint_tests/modules_structure.html) - modules directory structure is correct 'modules/nf-core/TOOL/SUBTOOL' ### Run details * nf-core/tools version 2.8 * Run at `2024-01-31 17:02:33`

gq1 commented 5 months ago

@yumisims Error message from Github action runner when using docker:

2024-01-31T17:02:51.6288222Z ERROR ~ Error executing process > 'SANGERTOL_TREEVAL:TREEVAL:HIC_MAPPING:GENERATE_CRAM_CSV (grTriPseu1_1)'
2024-01-31T17:02:51.6289658Z 
2024-01-31T17:02:51.6290958Z Caused by:
2024-01-31T17:02:51.6435629Z   Process `SANGERTOL_TREEVAL:TREEVAL:HIC_MAPPING:GENERATE_CRAM_CSV (grTriPseu1_1)` terminated with an error exit status (1)
2024-01-31T17:02:51.6460025Z 
2024-01-31T17:02:51.6460679Z Command executed:
2024-01-31T17:02:51.6465426Z 
2024-01-31T17:02:51.6466563Z   generate_cram_csv.sh hic-arima >> grTriPseu1_1_cram.csv
2024-01-31T17:02:51.6470423Z   
2024-01-31T17:02:51.6471218Z   cat <<-END_VERSIONS > versions.yml
2024-01-31T17:02:51.6475335Z   "SANGERTOL_TREEVAL:TREEVAL:HIC_MAPPING:GENERATE_CRAM_CSV":
2024-01-31T17:02:51.6477357Z       samtools: $(echo $(samtools --version 2>&1) | sed 's/^.*samtools //; s/Using.*$//' )
2024-01-31T17:02:51.6478967Z   END_VERSIONS
2024-01-31T17:02:51.6568206Z 
2024-01-31T17:02:51.6568763Z Command exit status:
2024-01-31T17:02:51.6569822Z   1
2024-01-31T17:02:51.6570129Z 
2024-01-31T17:02:51.6570889Z Command output:
2024-01-31T17:02:51.6571720Z   (empty)
2024-01-31T17:02:51.6572033Z 
2024-01-31T17:02:51.6572206Z Command error:
2024-01-31T17:02:51.6573526Z   Unable to find image 'quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1' locally
2024-01-31T17:02:51.6575047Z   0.001-c1: Pulling from sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl
2024-01-31T17:02:51.6575960Z   97518928ae5f: Pulling fs layer
2024-01-31T17:02:51.6576655Z   55ddb9fee572: Pulling fs layer
2024-01-31T17:02:51.6577588Z   b0e5c2566bb2: Pulling fs layer
2024-01-31T17:02:51.6578214Z   003bbdddb0bb: Pulling fs layer
2024-01-31T17:02:51.6578916Z   77a8cd211416: Pulling fs layer
2024-01-31T17:02:51.6579806Z   4f4fb700ef54: Pulling fs layer
2024-01-31T17:02:51.6580342Z   003bbdddb0bb: Waiting
2024-01-31T17:02:51.6580988Z   77a8cd211416: Waiting
2024-01-31T17:02:51.6581490Z   4f4fb700ef54: Waiting
2024-01-31T17:02:51.6581974Z   97518928ae5f: Verifying Checksum
2024-01-31T17:02:51.6582707Z   97518928ae5f: Download complete
2024-01-31T17:02:51.6583315Z   55ddb9fee572: Verifying Checksum
2024-01-31T17:02:51.6583889Z   55ddb9fee572: Download complete
2024-01-31T17:02:51.6584592Z   97518928ae5f: Pull complete
2024-01-31T17:02:51.6585165Z   77a8cd211416: Download complete
2024-01-31T17:02:51.6585726Z   4f4fb700ef54: Verifying Checksum
2024-01-31T17:02:51.6586455Z   4f4fb700ef54: Download complete
2024-01-31T17:02:51.6587051Z   55ddb9fee572: Pull complete
2024-01-31T17:02:51.6587589Z   b0e5c2566bb2: Verifying Checksum
2024-01-31T17:02:51.6588303Z   b0e5c2566bb2: Download complete
2024-01-31T17:02:51.6588907Z   003bbdddb0bb: Verifying Checksum
2024-01-31T17:02:51.6589475Z   003bbdddb0bb: Download complete
2024-01-31T17:02:51.6590189Z   b0e5c2566bb2: Pull complete
2024-01-31T17:02:51.6590762Z   003bbdddb0bb: Pull complete
2024-01-31T17:02:51.6591307Z   77a8cd211416: Pull complete
2024-01-31T17:02:51.6591951Z   4f4fb700ef54: Pull complete
2024-01-31T17:02:51.6592836Z   Digest: sha256:8602c0c667d490a3ba672e223da8c1c0fd2fd076c049dd3c4b53617625523d0b
2024-01-31T17:02:51.6594435Z   Status: Downloaded newer image for quay.io/sanger-tol/cramfilter_bwamem2_minimap2_samtools_perl:0.001-c1
2024-01-31T17:02:51.6595749Z   touch: .command.trace: Permission denied
2024-01-31T17:02:51.6596200Z 
2024-01-31T17:02:51.6596409Z Work dir:
2024-01-31T17:02:51.6597148Z   /home/runner/work/treeval/treeval/work/29/4e6dd1c94763af0871cb4da9dfea05
2024-01-31T17:02:51.6597998Z 
2024-01-31T17:02:51.6598955Z Tip: when you have fixed the problem you can continue the execution adding the option `-resume` to the run command line
2024-01-31T17:02:51.6599982Z 
2024-01-31T17:02:51.6600332Z  -- Check '.nextflow.log' file for details
2024-01-31T17:02:51.6601266Z Execution cancelled -- Finishing pending tasks before exit
2024-01-31T17:02:51.7026574Z ERROR ~ Invalid method invocation `call` with arguments: [[id:grTriPseu1_1, class:fungi, project_type:DTOL], /home/runner/work/treeval/treeval/TreeValTinyData/assembly/draft/grTriPseu1.fa] (java.util.LinkedList) on _closure16 type

gq1 commented 5 months ago

@yumisims Error message on farm when running with Singularity

ERROR ~ Error executing process > 'SANGERTOL_TREEVAL:TREEVAL:KMER_READ_COVERAGE:FASTK_FASTK (grTriPseu1_1)'

Caused by:
  Process `SANGERTOL_TREEVAL:TREEVAL:KMER_READ_COVERAGE:FASTK_FASTK (grTriPseu1_1)` terminated with an error exit status (1)

Command executed:

  FastK \
      -k31 -t \
      -T2 \
      -M6 \
      -NgrTriPseu1_1_fk \
      grTriPseu1_1.fasta.gz

  cat <<-END_VERSIONS > versions.yml
  "SANGERTOL_TREEVAL:TREEVAL:KMER_READ_COVERAGE:FASTK_FASTK":
      fastk: f18a4e6d2207539f7b84461daebc54530a9559b0
  END_VERSIONS

Command exit status:
  1

Command output:
  (empty)

Command error:
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T10': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T11': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T12': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T13': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T14': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T15': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T16': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T17': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T18': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T19': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T2': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T20': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T21': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T22': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T23': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T24': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T3': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T4': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T5': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T6': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T7': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T8': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T9': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T0': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T1': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T10': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T11': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T12': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T13': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T14': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T15': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T16': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T17': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T18': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T19': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T2': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T20': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T21': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T22': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T23': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T24': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T3': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T4': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T5': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T6': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T7': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T8': Operation not permitted
  rm: cannot remove '/tmp/grTriPseu1_1_fk.0.T9': Operation not permitted

     Could not clean up !

Work dir:
  /lustre/scratch123/tol/teams/tolit/users/gq2/treeval/work/af/99a9bc0b09a5bed4fd2a4d526a8a4a

Tip: you can try to figure out what's wrong by changing to the process work dir and showing the script file named `.command.sh`

sanger-tol / treeval