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ENCODE-DCC / chip-seq-pipeline2

ENCODE ChIP-seq pipeline
MIT License
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caper.wdl_parser|ERROR| Failed to parse WDL with miniwdl. #288

Closed wbszhu closed 1 year ago

wbszhu commented 1 year ago

Hi, I am trying to use this pipeline for the first time. And I meet this error. when i follow the README.md. the command like this : $ caper run chip.wdl -i "${INPUT_JSON}" --singularity docker://ubuntu:latest

2022-11-04 21:47:02,661|caper.cli|INFO| Cromwell stdout: /public/home/luzhang/tmp/test/cromwell.out.3
2022-11-04 21:47:02,663|caper.caper_base|INFO| Creating a timestamped temporary directory. /public/home/luzhang/caper_tmp/chip/20221104_214702_663539
2022-11-04 21:47:02,664|caper.caper_runner|INFO| Localizing files on work_dir. /public/home/luzhang/caper_tmp/chip/20221104_214702_663539
2022-11-04 21:47:03,922|caper.wdl_parser|ERROR| Failed to parse WDL with miniwdl.
2022-11-04 21:47:03,931|caper.cromwell|INFO| Validating WDL/inputs/imports with Womtool...
2022-11-04 21:47:05,600|caper.nb_subproc_thread|ERROR| Subprocess failed. returncode=1
Traceback (most recent call last):
  File "/public/home/luzhang/miniconda3/bin/caper", line 13, in <module>
    main()
  File "/public/home/luzhang/miniconda3/lib/python3.8/site-packages/caper/cli.py", line 713, in main
    return runner(parsed_args, nonblocking_server=nonblocking_server)
  File "/public/home/luzhang/miniconda3/lib/python3.8/site-packages/caper/cli.py", line 255, in runner
    subcmd_run(c, args)
  File "/public/home/luzhang/miniconda3/lib/python3.8/site-packages/caper/cli.py", line 386, in subcmd_run
    thread = caper_runner.run(
  File "/public/home/luzhang/miniconda3/lib/python3.8/site-packages/caper/caper_runner.py", line 462, in run
    self._cromwell.validate(wdl=wdl, inputs=inputs, imports=imports)
  File "/public/home/luzhang/miniconda3/lib/python3.8/site-packages/caper/cromwell.py", line 160, in validate
    raise WomtoolValidationFailed(
caper.cromwell.WomtoolValidationFailed: RC=1
STDERR=Unrecognized token on line 28, column 46:

    <meta name="optimizely-datafile" content="{&quot;groups&quot;: [], &quot;environmentKey&quot;: &quot;production&quot;, &quot;rollouts&quot;: [], &quot;typedAudiences&quot;: [], &quot;projectId&quot;: &quot;16737760170&quot;, &quot;variables&quot;: [], &quot;featureFlags&quot;: [], &quot;experiments&quot;: [], &quot;version&quot;: &quot;4&quot;, &quot;audiences&quot;: [{&quot;conditions&quot;: &quot;[\&quot;or\&quot;, {\&quot;match\&quot;: \&quot;exact\&quot;, \&quot;name\&quot;: \&quot;$opt_dummy_attribute\&quot;, \&quot;type\&quot;: \&quot;custom_attribute\&quot;, \&quot;value\&quot;: \&quot;$opt_dummy_value\&quot;}]&quot;, &quot;id&quot;: &quot;$opt_dummy_audience&quot;, &quot;name&quot;: &quot;Optimizely-Generated Audience for Backwards Compatibility&quot;}], &quot;anonymizeIP&quot;: true, &quot;sdkKey&quot;: &quot;WTc6awnGuYDdG98CYRban&quot;, &quot;attributes&quot;: [{&quot;id&quot;: &quot;16822470375&quot;, &quot;key&quot;: &quot;user_id&quot;}, {&quot;id&quot;: &quot;17143601254&quot;, &quot;key&quot;: &quot;spammy&quot;}, {&quot;id&quot;: &quot;18175660309&quot;, &quot;key&quot;: &quot;organization_plan&quot;}, {&quot;id&quot;: &quot;18813001570&quot;, &quot;key&quot;: &quot;is_logged_in&quot;}, {&quot;id&quot;: &quot;19073851829&quot;, &quot;key&quot;: &quot;geo&quot;}, {&quot;id&quot;: &quot;20175462351&quot;, &quot;key&quot;: &quot;requestedCurrency&quot;}, {&quot;id&quot;: &quot;20785470195&quot;, &quot;key&quot;: &quot;country_code&quot;}, {&quot;id&quot;: &quot;21656311196&quot;, &quot;key&quot;: &quot;opened_downgrade_dialog&quot;}], &quot;botFiltering&quot;: false, &quot;accountId&quot;: &quot;16737760170&quot;, &quot;events&quot;: [{&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;17911811441&quot;, &quot;key&quot;: &quot;hydro_click.dashboard.teacher_toolbox_cta&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18124116703&quot;, &quot;key&quot;: &quot;submit.organizations.complete_sign_up&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18145892387&quot;, &quot;key&quot;: &quot;no_metric.tracked_outside_of_optimizely&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18178755568&quot;, &quot;key&quot;: &quot;click.org_onboarding_checklist.add_repo&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18180553241&quot;, &quot;key&quot;: &quot;submit.repository_imports.create&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18186103728&quot;, &quot;key&quot;: &quot;click.help.learn_more_about_repository_creation&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18188530140&quot;, &quot;key&quot;: &quot;test_event&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18191963644&quot;, &quot;key&quot;: &quot;click.empty_org_repo_cta.transfer_repository&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18195612788&quot;, &quot;key&quot;: &quot;click.empty_org_repo_cta.import_repository&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18210945499&quot;, &quot;key&quot;: &quot;click.org_onboarding_checklist.invite_members&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18211063248&quot;, &quot;key&quot;: &quot;click.empty_org_repo_cta.create_repository&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18215721889&quot;, &quot;key&quot;: &quot;click.org_onboarding_checklist.update_profile&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18224360785&quot;, &quot;key&quot;: &quot;click.org_onboarding_checklist.dismiss&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18234832286&quot;, &quot;key&quot;: &quot;submit.organization_activation.complete&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18252392383&quot;, &quot;key&quot;: &quot;submit.org_repository.create&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18257551537&quot;, &quot;key&quot;: &quot;submit.org_member_invitation.create&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18259522260&quot;, &quot;key&quot;: &quot;submit.organization_profile.update&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18564603625&quot;, &quot;key&quot;: &quot;view.classroom_select_organization&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18568612016&quot;, &quot;key&quot;: &quot;click.classroom_sign_in_click&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18572592540&quot;, &quot;key&quot;: &quot;view.classroom_name&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18574203855&quot;, &quot;key&quot;: &quot;click.classroom_create_organization&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18582053415&quot;, &quot;key&quot;: &quot;click.classroom_select_organization&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18589463420&quot;, &quot;key&quot;: &quot;click.classroom_create_classroom&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18591323364&quot;, &quot;key&quot;: &quot;click.classroom_create_first_classroom&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18591652321&quot;, &quot;key&quot;: &quot;click.classroom_grant_access&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18607131425&quot;, &quot;key&quot;: &quot;view.classroom_creation&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;18831680583&quot;, &quot;key&quot;: &quot;upgrade_account_plan&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19064064515&quot;, &quot;key&quot;: &quot;click.signup&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19075373687&quot;, &quot;key&quot;: &quot;click.view_account_billing_page&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19077355841&quot;, &quot;key&quot;: &quot;click.dismiss_signup_prompt&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19079713938&quot;, &quot;key&quot;: &quot;click.contact_sales&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19120963070&quot;, &quot;key&quot;: &quot;click.compare_account_plans&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19151690317&quot;, &quot;key&quot;: &quot;click.upgrade_account_cta&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19424193129&quot;, &quot;key&quot;: &quot;click.open_account_switcher&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19520330825&quot;, &quot;key&quot;: &quot;click.visit_account_profile&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19540970635&quot;, &quot;key&quot;: &quot;click.switch_account_context&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19730198868&quot;, &quot;key&quot;: &quot;submit.homepage_signup&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19820830627&quot;, &quot;key&quot;: &quot;click.homepage_signup&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;19988571001&quot;, &quot;key&quot;: &quot;click.create_enterprise_trial&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20036538294&quot;, &quot;key&quot;: &quot;click.create_organization_team&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20040653299&quot;, &quot;key&quot;: &quot;click.input_enterprise_trial_form&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20062030003&quot;, &quot;key&quot;: &quot;click.continue_with_team&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20068947153&quot;, &quot;key&quot;: &quot;click.create_organization_free&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20086636658&quot;, &quot;key&quot;: &quot;click.signup_continue.username&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20091648988&quot;, &quot;key&quot;: &quot;click.signup_continue.create_account&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20103637615&quot;, &quot;key&quot;: &quot;click.signup_continue.email&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20111574253&quot;, &quot;key&quot;: &quot;click.signup_continue.password&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20120044111&quot;, &quot;key&quot;: &quot;view.pricing_page&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20152062109&quot;, &quot;key&quot;: &quot;submit.create_account&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20165800992&quot;, &quot;key&quot;: &quot;submit.upgrade_payment_form&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20171520319&quot;, &quot;key&quot;: &quot;submit.create_organization&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20222645674&quot;, &quot;key&quot;: &quot;click.recommended_plan_in_signup.discuss_your_needs&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20227443657&quot;, &quot;key&quot;: &quot;submit.verify_primary_user_email&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20234607160&quot;, &quot;key&quot;: &quot;click.recommended_plan_in_signup.try_enterprise&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20238175784&quot;, &quot;key&quot;: &quot;click.recommended_plan_in_signup.team&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20239847212&quot;, &quot;key&quot;: &quot;click.recommended_plan_in_signup.continue_free&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20251097193&quot;, &quot;key&quot;: &quot;recommended_plan&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20438619534&quot;, &quot;key&quot;: &quot;click.pricing_calculator.1_member&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20456699683&quot;, &quot;key&quot;: &quot;click.pricing_calculator.15_members&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20467868331&quot;, &quot;key&quot;: &quot;click.pricing_calculator.10_members&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20476267432&quot;, &quot;key&quot;: &quot;click.trial_days_remaining&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20476357660&quot;, &quot;key&quot;: &quot;click.discover_feature&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20479287901&quot;, &quot;key&quot;: &quot;click.pricing_calculator.custom_members&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20481107083&quot;, &quot;key&quot;: &quot;click.recommended_plan_in_signup.apply_teacher_benefits&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20483089392&quot;, &quot;key&quot;: &quot;click.pricing_calculator.5_members&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20484283944&quot;, &quot;key&quot;: &quot;click.onboarding_task&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20484996281&quot;, &quot;key&quot;: &quot;click.recommended_plan_in_signup.apply_student_benefits&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20486713726&quot;, &quot;key&quot;: &quot;click.onboarding_task_breadcrumb&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20490791319&quot;, &quot;key&quot;: &quot;click.upgrade_to_enterprise&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20491786766&quot;, &quot;key&quot;: &quot;click.talk_to_us&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20494144087&quot;, &quot;key&quot;: &quot;click.dismiss_enterprise_trial&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20499722759&quot;, &quot;key&quot;: &quot;completed_all_tasks&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20500710104&quot;, &quot;key&quot;: &quot;completed_onboarding_tasks&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20513160672&quot;, &quot;key&quot;: &quot;click.read_doc&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20516196762&quot;, &quot;key&quot;: &quot;actions_enabled&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20518980986&quot;, &quot;key&quot;: &quot;click.dismiss_trial_banner&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20535446721&quot;, &quot;key&quot;: &quot;click.issue_actions_prompt.dismiss_prompt&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20557002247&quot;, &quot;key&quot;: &quot;click.issue_actions_prompt.setup_workflow&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20595070227&quot;, &quot;key&quot;: &quot;click.pull_request_setup_workflow&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20626600314&quot;, &quot;key&quot;: &quot;click.seats_input&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20642310305&quot;, &quot;key&quot;: &quot;click.decrease_seats_number&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20662990045&quot;, &quot;key&quot;: &quot;click.increase_seats_number&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20679620969&quot;, &quot;key&quot;: &quot;click.public_product_roadmap&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20761240940&quot;, &quot;key&quot;: &quot;click.dismiss_survey_banner&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20767210721&quot;, &quot;key&quot;: &quot;click.take_survey&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20795281201&quot;, &quot;key&quot;: &quot;click.archive_list&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20966790249&quot;, &quot;key&quot;: &quot;contact_sales.submit&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20996500333&quot;, &quot;key&quot;: &quot;contact_sales.existing_customer&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;20996890162&quot;, &quot;key&quot;: &quot;contact_sales.blank_message_field&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21000470317&quot;, &quot;key&quot;: &quot;contact_sales.personal_email&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21002790172&quot;, &quot;key&quot;: &quot;contact_sales.blank_phone_field&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21354412592&quot;, &quot;key&quot;: &quot;click.dismiss_create_readme&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21366102546&quot;, &quot;key&quot;: &quot;click.dismiss_zero_user_content&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21370252505&quot;, &quot;key&quot;: &quot;account_did_downgrade&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21370840408&quot;, &quot;key&quot;: &quot;click.cta_create_readme&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21375451068&quot;, &quot;key&quot;: &quot;click.cta_create_new_repository&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21385390948&quot;, &quot;key&quot;: &quot;click.zero_user_content&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21467712175&quot;, &quot;key&quot;: &quot;click.downgrade_keep&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21484112202&quot;, &quot;key&quot;: &quot;click.downgrade&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21495292213&quot;, &quot;key&quot;: &quot;click.downgrade_survey_exit&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21508241468&quot;, &quot;key&quot;: &quot;click.downgrade_survey_submit&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21512030356&quot;, &quot;key&quot;: &quot;click.downgrade_support&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21539090022&quot;, &quot;key&quot;: &quot;click.downgrade_exit&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21543640644&quot;, &quot;key&quot;: &quot;click_fetch_upstream&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21646510300&quot;, &quot;key&quot;: &quot;click.move_your_work&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21656151116&quot;, &quot;key&quot;: &quot;click.add_branch_protection_rule&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21663860599&quot;, &quot;key&quot;: &quot;click.downgrade_dialog_open&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21687860483&quot;, &quot;key&quot;: &quot;click.learn_about_protected_branches&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21689050333&quot;, &quot;key&quot;: &quot;click.dismiss_protect_this_branch&quot;}, {&quot;experimentIds&quot;: [], &quot;id&quot;: &quot;21864370109&quot;, &quot;key&quot;: &quot;click.sign_in&quot;}], &quot;revision&quot;: &quot;1367&quot;}" />
                                             ^

~/.caper/default.conf

backend=lsf

# Local directory for localized files and Cromwell's intermediate files.
# If not defined then Caper will make .caper_tmp/ on CWD or `local-out-dir`.
# /tmp is not recommended since Caper store localized data files here.
local-loc-dir=/public/home/luzhang/caper_tmp

cromwell=/public/home/luzhang/.caper/cromwell_jar/cromwell-82.jar
womtool=/public/home/luzhang/.caper/womtool_jar/womtool-82.jar

Hope you can help me. many thanks.

leepc12 commented 1 year ago

It looks like your WDL didn't pass Womtool's validation. Check your WDL.

$ java -jar /public/home/luzhang/.caper/womtool_jar/womtool-82.jar validate YOUR_WDL
wbszhu commented 1 year ago

Thanks a lot, I have solved it~ Luzhang