Hi,
thank you in advance for your help and support!
Our submissions 9724478 and 9724479 were made with the same docker image.
- Submission 9724479 was made to the fast lane and it yields no error (status ACCEPTED)
- Submission 9724478 was made to the task 1 queue and is INVALID
I am unable to decipher the logs from submission 9724478. This seems to be the error but it does not appear to be related to our code:
```
STDERR: 2022-08-28T17:17:17.922466751Z =========>
STDERR: 2022-08-28T17:17:17.922470383Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2022-08-28T17:17:17.922473791Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2022-08-28T17:17:17.922477203Z Traceback (most recent call last):
STDERR: 2022-08-28T17:17:17.922480625Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2022-08-28T17:17:17.922507067Z raise WorkflowException(
STDERR: 2022-08-28T17:17:17.922511088Z cwltool.errors.WorkflowException: Missing required input parameter 'infile'
STDERR: 2022-08-28T17:17:17.922514512Z
STDERR: 2022-08-28T17:17:17.922517643Z The above exception was the direct cause of the following exception:
STDERR: 2022-08-28T17:17:17.922520950Z
STDERR: 2022-08-28T17:17:17.922524093Z Traceback (most recent call last):
STDERR: 2022-08-28T17:17:17.922527264Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2022-08-28T17:17:17.922531031Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2022-08-28T17:17:17.922534554Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2022-08-28T17:17:17.922538235Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2022-08-28T17:17:17.922541525Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run
STDERR: 2022-08-28T17:17:17.922544925Z return self.run(fileStore)
STDERR: 2022-08-28T17:17:17.922548082Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 880, in run
STDERR: 2022-08-28T17:17:17.922551918Z fill_in_defaults(
STDERR: 2022-08-28T17:17:17.922555014Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2022-08-28T17:17:17.922558529Z raise WorkflowException(
STDERR: 2022-08-28T17:17:17.922561745Z File "/usr/local/lib/python3.8/site-packages/schema_salad/sourceline.py", line 305, in __exit__
STDERR: 2022-08-28T17:17:17.922565341Z raise self.makeError(str(exc_value)) from exc_value
```
Thank you again!
Francesco and Alonso
Created by Francesco Cremonesi sharkovsky @sharkovsky ,
No worries! Let us know if you come across any other issues :) --@vchung sorry to bother you again, as a follow up could you please share with me the logs from submission 9724607?--
--Thank you!--
Never mind, I figured out my mistake, sorry for the noise and thank you for your great support!
Thank you Verena!
It's my fault, you did explain that the logs weren't made available, but somehow I confused myself by reading the (wrong) log file and the fact that the fast lane submission was valid.
Thank you for your help and for reminding me about the outcome columns.
Francesco and Alonso Hi @sharkovsky ,
Docker logs for the Task 1 and Task 2 queues will not be available; the logs you have attached are for the workflow. Specifically: the workflow is expecting a predictions file but it wasn't found. Apologies if this point about the logs was not made more clear!
I looked at your invalid submission, and its error is:
```python
Traceback (most recent call last):
File "main.py", line 56, in
complete_df.drop(["was_preterm", "was_term", "project", "participant_id", "delivery_wk", "was_early_preterm", "collect_wk"], axis=1, inplace=True)
File "/usr/local/lib/python3.8/dist-packages/pandas/util/_decorators.py", line 311, in wrapper
return func(*args, **kwargs)
File "/usr/local/lib/python3.8/dist-packages/pandas/core/frame.py", line 4954, in drop
return super().drop(
File "/usr/local/lib/python3.8/dist-packages/pandas/core/generic.py", line 4267, in drop
obj = obj._drop_axis(labels, axis, level=level, errors=errors)
File "/usr/local/lib/python3.8/dist-packages/pandas/core/generic.py", line 4311, in _drop_axis
new_axis = axis.drop(labels, errors=errors)
File "/usr/local/lib/python3.8/dist-packages/pandas/core/indexes/base.py", line 6644, in drop
raise KeyError(f"{list(labels[mask])} not found in axis")
KeyError: "['was_preterm', 'was_term', 'delivery_wk', 'was_early_preterm'] not found in axis"
```
A quick reminder that the test set does not contain any of the "outcome" columns in metadata.csv:
* was_preterm
* was_early_preterm
* was_term
* delivery_wk
Hope this helps!
Drop files to upload
Submission is valid in fast lane but not valid in regular queue page is loading…