Configuration file '/data/apps/imputationserver/1.4.1 /job.config' not available.

[EdinH]

We encountered a problem with running jobs on the Michigan Imputation Server locally.
We followed the steps from the README file and successfully ran the Docker image.

We tried both Hapmap2 and 1000 Genomes Phase 3, but in both cases got the following message:

Configuration file '/data/apps/imputationserver/1.5.7/job.config' not available. Use default values.

We have also tried 1.4.1 and 1.5.7 Genotype Imputation (Minimac4) versions, but we got the same error.

Just to note that the files we used as an input for the locally run imputation job were imputed using the Michigan Server UI.

Full log:

job.txt:

21/01/29 09:38:28 Executing Job installation....
21/01/29 09:38:28   Preparing Application 'Genotype Imputation (Minimac4)'...
21/01/29 09:38:28   Application 'Genotype Imputation (Minimac4)'is already installed.
21/01/29 09:38:28   Preparing Application 'HapMap 2'...
21/01/29 09:38:28   Application 'HapMap 2'is already installed.
21/01/29 09:38:28 Executing Job setups....
21/01/29 09:38:28 Planner: WDL evaluated.
21/01/29 09:38:28 Planner: DAG created.
21/01/29 09:38:28   Nodes: 3
21/01/29 09:38:28     Input Validation
21/01/29 09:38:28       Inputs: 
21/01/29 09:38:28       Outputs: 
21/01/29 09:38:28     Quality Control
21/01/29 09:38:28       Inputs: 
21/01/29 09:38:28       Outputs: mafFile chunkFileDir statisticDir 
21/01/29 09:38:28     Quality Control (Report)
21/01/29 09:38:28       Inputs: mafFile myseparator 
21/01/29 09:38:28       Outputs: qcreport 
21/01/29 09:38:28   Dependencies: 2
21/01/29 09:38:28     Input Validation->Quality Control
21/01/29 09:38:28     Quality Control->Quality Control (Report)
21/01/29 09:38:28 Executor: execute DAG...
21/01/29 09:38:28 ------------------------------------------------------
21/01/29 09:38:28 Input Validation
21/01/29 09:38:28 ------------------------------------------------------
21/01/29 09:38:28 Versions:
21/01/29 09:38:28   Pipeline: michigan-imputationserver-1.5.7
21/01/29 09:38:28   Imputation-Engine: minimac4-1.0.2
21/01/29 09:38:28   Phasing-Engine: eagle-2.4
21/01/29 09:38:28 Configuration file '/data/apps/imputationserver/1.5.7/job.config' not available. Use default values.
21/01/29 09:38:28   Input Validation [ERROR]
21/01/29 09:38:28 Executing onFailure... 
21/01/29 09:38:28 ------------------------------------------------------
21/01/29 09:38:28 Send Notification on Failure
21/01/29 09:38:28 ------------------------------------------------------
21/01/29 09:38:28 Configuration file '/data/apps/imputationserver/1.5.7/job.config' not available. Use default values.
21/01/29 09:38:28   Send Notification on Failure [ERROR]
21/01/29 09:38:28 onFailure execution failed.
21/01/29 09:38:28 Job execution failed: Job Execution failed.
21/01/29 09:38:28 Cleaning up...
21/01/29 09:38:28 Cleaning up uploaded local files...
21/01/29 09:38:28 Cleaning up temporary local files...
21/01/29 09:38:28 Cleaning up temporary hdfs files...
21/01/29 09:38:28 Cleaning up hdfs files...
21/01/29 09:38:28 Cleanup successful.


std.out:

No action required. Email notification has been disabled in job.config

CC: @enazunic

[HippocampusGirl]

I have the same issue. It would be great if you could provide an example job.config file and/or document how to make one.

[cristianrohr]

Hello, I'm having the exact same issue, can you give us some guidance?
thanks!

[HippocampusGirl]

My solution was to delete everything and recreate my Hadoop instance, recreate the HDFS from scratch, and reinstall the imputation server app. Then it somehow worked :-)

[EdinH]

in the end, I decided to build an in-house imputation pipeline using the following protocol.