Sorry to bother you, but for the life of me I cannot figure out the reason for my docker submission failing. I am running it locally just fine, and have really hit a dead end in my attempts at troubleshooting it before contacting you. Any guidance you might have would be super helpful!
Submission ID
```
id: 9723804
```
Thanks,
Michael
```
STDERR: 2022-08-11T20:38:53.550807720Z Log from job 'file:///var/lib/docker/volumes/workflow_orchestrator_shared/_data/483a6872-9cf4-44d0-9145-449db00fd96e/mod-microbiome-2022-main/steps/validate.cwl' validate.py kind-file_var_lib_docker_volumes_workflow_orchestrator_shared__data_483a6872-9cf4-44d0-9145-449db00fd96e_mod-microbiome-2022-main_steps_validate.cwl/instance-knl0c0kk follows:
STDERR: 2022-08-11T20:38:53.550810456Z =========>
STDERR: 2022-08-11T20:38:53.550812502Z INFO:toil.worker:---TOIL WORKER OUTPUT LOG---
STDERR: 2022-08-11T20:38:53.550814555Z INFO:toil:Running Toil version 4.1.0-5ad5e77d98e1456b4f70f5b00e688a43cdce2ebe.
STDERR: 2022-08-11T20:38:53.550816707Z Traceback (most recent call last):
STDERR: 2022-08-11T20:38:53.550818801Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2022-08-11T20:38:53.550821157Z raise WorkflowException(
STDERR: 2022-08-11T20:38:53.550823158Z cwltool.errors.WorkflowException: Missing required input parameter 'input_file'
STDERR: 2022-08-11T20:38:53.550825298Z
STDERR: 2022-08-11T20:38:53.550827231Z The above exception was the direct cause of the following exception:
STDERR: 2022-08-11T20:38:53.550829320Z
STDERR: 2022-08-11T20:38:53.550831362Z Traceback (most recent call last):
STDERR: 2022-08-11T20:38:53.550833410Z File "/usr/local/lib/python3.8/site-packages/toil/worker.py", line 366, in workerScript
STDERR: 2022-08-11T20:38:53.550835593Z job._runner(jobGraph=jobGraph, jobStore=jobStore, fileStore=fileStore, defer=defer)
STDERR: 2022-08-11T20:38:53.550837724Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1392, in _runner
STDERR: 2022-08-11T20:38:53.550839859Z returnValues = self._run(jobGraph, fileStore)
STDERR: 2022-08-11T20:38:53.550841925Z File "/usr/local/lib/python3.8/site-packages/toil/job.py", line 1329, in _run
STDERR: 2022-08-11T20:38:53.550844104Z return self.run(fileStore)
STDERR: 2022-08-11T20:38:53.550846115Z File "/usr/local/lib/python3.8/site-packages/toil/cwl/cwltoil.py", line 880, in run
STDERR: 2022-08-11T20:38:53.550848254Z fill_in_defaults(
STDERR: 2022-08-11T20:38:53.550850265Z File "/usr/local/lib/python3.8/site-packages/cwltool/process.py", line 454, in fill_in_defaults
STDERR: 2022-08-11T20:38:53.550852434Z raise WorkflowException(
STDERR: 2022-08-11T20:38:53.550854469Z File "/usr/local/lib/python3.8/site-packages/schema_salad/sourceline.py", line 305, in __exit__
STDERR: 2022-08-11T20:38:53.550859353Z raise self.makeError(str(exc_value)) from exc_value
STDERR: 2022-08-11T20:38:53.550861619Z cwltool.errors.WorkflowException: mod-microbiome-2022-main/steps/validate.cwl:11:3: Missing required input parameter 'input_file'
```
Created by Michael Jochum MADscientist314 Hi @MADscientist314
Here is the part of your logs. It seems there are NAs produced. Hope it helps. Thank you!
```
[1] "2022-08-12 21:43:32 LOG: Importing the Models "
[1] "2022-08-12 21:44:12 LOG: Data Wrangling Started"
[1] "2022-08-12 21:44:12 LOG: Data Wrangling: Metadata Preprocessing Started"
Warning message:
Problem while computing `age = as.numeric(gsub("Unknown", NA, age))`.
? NAs introduced by coercion
[1] "2022-08-12 21:44:12 LOG: Data Wrangling: Categorical Preprocessing Completed"
Joining, by = "specimen"
Warning message:
Expected 2 pieces. Missing pieces filled with `NA`.
[1] "2022-08-12 21:44:12 LOG: Joining datasets"
[1] "2022-08-12 21:44:17 LOG: Data Wrangling: One Hot Encoding Started"
[1] "2022-08-12 21:44:17 LOG: Data Wrangling: Numeric Preprocessing Started"
Killed
```
Thank you! I can send you an invite to my private github repo where I have the code if it helps Hi @MADscientist314 , thanks for reaching out- we are still looking into your error and will get back to you soon!