pipeline fails with example json

[atreeneedsaforest]

Hi, I have just cloned the pipeline and tried to run it with the sample data json https://storage.googleapis.com/encode-pipeline-test-samples/encode-chip-seq-pipeline/ENCSR000DYI_subsampled_chr19_only.json but I get the following error:

2020-09-04 13:40:36,300|caper.cromwell|INFO| Validating WDL/inputs/imports with Womtool...
2020-09-04 13:40:41,938|caper.cromwell|INFO| Womtool validation passed.
2020-09-04 13:40:41,938|caper.caper_runner|INFO| launching run: wdl=/home/users/ngs/software/encode/chip-seq-pipeline2/chip.wdl, inputs=/home/users/ngs/software/encode/
tmp/home/users/ngs/DNAnalysis/Chip_test_ENCSR000DYI/ENCSR000DYI_subsampled_chr19_only_fromat.local.json, backend_conf=/home/users/ngs/software/encode/tmp/chip/20200904_
134032_625284/backend.conf
2020-09-04 13:40:54,960|caper.cromwell_workflow_monitor|INFO| Workflow: id=c031f880-6509-40ba-a7e4-65309ea3b7d5, status=Submitted
2020-09-04 13:40:55,032|caper.cromwell_workflow_monitor|INFO| Workflow: id=c031f880-6509-40ba-a7e4-65309ea3b7d5, status=Running
2020-09-04 13:40:58,956|caper.cromwell_workflow_monitor|INFO| Workflow: id=c031f880-6509-40ba-a7e4-65309ea3b7d5, status=Failed
2020-09-04 13:41:04,941|caper.cromwell_metadata|WARNING| Failed to write metadata file. workflowRoot not found. wf_id=c031f880-6509-40ba-a7e4-65309ea3b7d5
2020-09-04 13:41:04,941|caper.cromwell|INFO| Workflow failed. Auto-troubleshooting...
* Started troubleshooting workflow: id=c031f880-6509-40ba-a7e4-65309ea3b7d5, status=Failed
* Found failures JSON object.
[
    {
        "causedBy": [
            {
                "causedBy": [],
                "message": "Task raise_exception has an invalid runtime attribute memory = !! NOT FOUND !!"
            },
            {
                "causedBy": [],
                "message": "Task raise_exception has an invalid runtime attribute memory = !! NOT FOUND !!"
            },
            {
                "message": "Task raise_exception has an invalid runtime attribute memory = !! NOT FOUND !!",
                "causedBy": []
            },
            {
                "message": "Task raise_exception has an invalid runtime attribute memory = !! NOT FOUND !!",
                "causedBy": []
            },
            {
                "causedBy": [],
                "message": "Task raise_exception has an invalid runtime attribute memory = !! NOT FOUND !!"
            },
            {
                "causedBy": [],
                "message": "Task raise_exception has an invalid runtime attribute memory = !! NOT FOUND !!"
            },
            {
                "causedBy": [],
                "message": "Task raise_exception has an invalid runtime attribute memory = !! NOT FOUND !!"
            },
            {
                "causedBy": [],
                "message": "Task raise_exception has an invalid runtime attribute memory = !! NOT FOUND !!"
            }
        ],
        "message": "Runtime validation failed"
    }
]
* Recursively finding failures in calls (tasks)...
2020-09-04 13:41:04,942|caper.nb_subproc_thread|ERROR| Subprocess failed. returncode=1
2020-09-04 13:41:04,942|caper.cli|ERROR| Check stdout/stderr in /home/ngstree/ngs/DNAnalysis/Chip_test_ENCSR000DYI/cromwell.out

can you please help? Best,

Margherita

[leepc12]

https://github.com/ENCODE-DCC/chip-seq-pipeline2/blob/master/chip.wdl#L2878

Please add the following to runtime { } and try again.

        memory : "1 GB"

[atreeneedsaforest]

Hi @leepc12 , thank you so much for your fast answer! That made it run. Best, Margherita

[leepc12]

But you will still see an error. Please post your error here.

[atreeneedsaforest]

@leepc12 actuallly there was no error, the workflow was started and then completed successfully! I am now running it with our data. Thank you again.

[leepc12]

@atreeneedsaforest: That sounds good.