Question

Question: Exception( "Failed to extract job." )

1

2.7 years ago by

northcoted • 30

northcoted • 30 wrote:

HI,

I get the following error when attempting to create a workflow:

*'Failed to find matching implicit job - job is %s, jobs are %s, assoc_name is %s.'*

Followed by:

Exception( "Failed to extract job." )

The workflow consists of 12 input datasets which were then created as a "dataset list" as input into the subsequent steps.

Cheers.

software error • 898 views

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written 2.7 years ago by northcoted • 30

Hello, Where did this occur? http://usegalaxy.org (Main public Galaxy server) or your own local or cloud server?

Meanwhile, I am testing this out on main to see if I can independently reproduce there.

If your history is on Main (or you can recreate the problem there) and would like to share it, that will help, as the dataset collection list may not be the core issue. Rather, there could be a specific tool triggering the problem. Send a shared history link to galaxy-bugs@lists.galaxyproject.org along with a link to this post to help with that broader testing.

Thanks, Jen, Galaxy team

ADD REPLY • link written 2.7 years ago by Jennifer Hillman Jackson ♦ 25k

1

I seem to have found the following:

In extract.py:

The variables assoc_name and query_assoc_name

 if job in summary.implicit_map_jobs:
            hid = None
            for implicit_pair in jobs[ job ]:
                query_assoc_name, dataset_collection = implicit_pair
                **if query_assoc_name == assoc_name**
                    hid = dataset_collection.hid
            if hid is None:
                template = "Failed to find matching implicit job - job is %s, jobs are %s, assoc_name is %s."
                message = template % ( job.id, jobs, assoc.name )
                log.warn( message )
                raise Exception( "**Failed to extract job**." )

By changing the code:

template = "Failed to find matching implicit job - job is %s, jobs are %s, assoc_name is %s." message = template % ( job.id, jobs, assoc.name )

to the following:

template = "Failed to find matching implicit job - job is %s, jobs are %s, assoc_name is %s, query_assoc_name is %s message = template % ( job.id, jobs, assoc.name, query_assoc_name )

This returns assoc_name with the value "txt_file" whereas query_assoc_name holds the value "html_file" which breaks the comparison.

In wrapper file FastQC.xml

<outputs>
    <data format="html" name="html_file" label="${tool.name} on ${on_string}: Webpage" />
    <data format="txt" name="text_file"  label="${tool.name} on ${on_string}: RawData" />
</outputs>

So it seems that the 2 output file types may be causing this failure in the if query_assoc_name == assoc_name: test.

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by northcoted • 30

Thank you for providing the details. We are still looking into this in more detail to determine if this is an unknown bug (there were cluster issues over the last several days hindering effective testing). I will write back with more details (and possibly an issue ticket) within the next few days. Thanks, Jen, Galaxy team

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by Jennifer Hillman Jackson ♦ 25k

As an added note.

This same failure occurs when attempting to extract any workflow built under "analyze data" using "Dataset Collections" as input.

ADD REPLY • link modified 2.6 years ago • written 2.6 years ago by northcoted • 30

Thanks for posting this, I just ran into the exact same thing (also with FastQC) and it looks like the cause is the same.

ADD REPLY • link modified 2.5 years ago • written 2.5 years ago by Devon Ryan • 1.9k

Update: Our local user who ran into this was able to resolve it by noting that in the selection window some of the steps appeared multiple times (I'm guessing this is due to the multiple output entries in the history). He then ensured that only one such instance of these was selected and then the workflow creation worked.

ADD REPLY • link written 2.5 years ago by Devon Ryan • 1.9k

Excellent. Many thanks. I'll give it a try.

ADD REPLY • link written 2.5 years ago by northcoted • 30

Hi.

It occurred on a local Galaxy server which is unfortunately firewalled.

Basically I have 12 .bam datasets from which I have created a dataset list as input to fastqc

( FastQC Read Quality reports (Galaxy Version 0.63) ( devteam 2d094334f61e) on Galaxy Server v16.01-516-g45bd65f.

I can extract the workflow at the point after the dataset list has been created, however after completion of the fastqc is when the "export workflow" error occurs.

Also, in the "export Workflow" gui, I have the following message under the "Dataset Collection Creation" dialogue box.

"Dataset collection created in a way not compatible with workflows"

Unfortunately I am unable to share as it is patient data that I am using.

Regards

Derek

ADD REPLY • link modified 2.7 years ago • written 2.7 years ago by northcoted • 30

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