job.txt:
22/11/17 19:07:56 Executing Job installation....
22/11/17 19:07:57 Preparing Application 'Genotype Imputation (Minimac4)'...
22/11/17 19:07:57 Installing Application imputationserver@1.4.1...
22/11/17 19:08:00 Installation finished.
22/11/17 19:08:00 Preparing Application 'HapMap 2'...
22/11/17 19:08:01 Installing Application hapmap-2@2.0.0...
22/11/17 19:08:16 Installation finished.
22/11/17 19:08:16 Executing Job setups....
22/11/17 19:08:17 Planner: WDL evaluated.
22/11/17 19:08:17 Planner: DAG created.
22/11/17 19:08:17 Nodes: 3
22/11/17 19:08:17 Input Validation
22/11/17 19:08:17 Inputs:
22/11/17 19:08:17 Outputs:
22/11/17 19:08:17 Quality Control
22/11/17 19:08:17 Inputs:
22/11/17 19:08:17 Outputs: mafFile chunkFileDir statisticDir
22/11/17 19:08:17 Quality Control (Report)
22/11/17 19:08:17 Inputs: mafFile myseparator
22/11/17 19:08:17 Outputs: qcreport
22/11/17 19:08:17 Dependencies: 2
22/11/17 19:08:17 Input Validation->Quality Control
22/11/17 19:08:17 Quality Control->Quality Control (Report)
22/11/17 19:08:17 Executor: execute DAG...
22/11/17 19:08:17 ------------------------------------------------------
22/11/17 19:08:17 Input Validation
22/11/17 19:08:17 ------------------------------------------------------
22/11/17 19:08:17 Versions:
22/11/17 19:08:17 Pipeline: michigan-imputationserver-1.4.1
22/11/17 19:08:17 Imputation-Engine: minimac4-1.0.2
22/11/17 19:08:17 Phasing-Engine: eagle-2.4
22/11/17 19:08:17 Configuration file '/data/apps/imputationserver/1.4.1/job.config' not available. Use default values.
22/11/17 19:08:28 Input Validation [10 sec]
22/11/17 19:08:28 ------------------------------------------------------
22/11/17 19:08:28 Quality Control
22/11/17 19:08:28 ------------------------------------------------------
22/11/17 19:08:28 Configuration file '/data/apps/imputationserver/1.4.1/job.config' not available. Use default values.
22/11/17 19:08:28 Reference Panel Ranges: genome-wide
22/11/17 19:09:14 Quality Control [45 sec]
22/11/17 19:09:14 Exporting parameter statisticDir...
22/11/17 19:09:14 Added 3 downloads.
22/11/17 19:09:14 Added 0 custom downloads.
22/11/17 19:09:14 ------------------------------------------------------
22/11/17 19:09:14 Quality Control (Report)
22/11/17 19:09:14 ------------------------------------------------------
22/11/17 19:09:14 Running script /data/apps/imputationserver/1.4.1/qc-report.Rmd...
22/11/17 19:09:14 Working Directory: /data/apps/imputationserver/1.4.1
22/11/17 19:09:14 Output: /data/jobs/job-20221117-190738-049/qcreport/qcreport.html
22/11/17 19:09:14 Parameters:
22/11/17 19:09:14 /data/jobs/job-20221117-190738-049/temp/mafFile/mafFile
22/11/17 19:09:14 Creating RMarkdown report from /data/apps/imputationserver/1.4.1/qc-report.Rmd...
22/11/17 19:09:15 Quality Control (Report) [ERROR]
22/11/17 19:09:15 Exporting parameter qcreport...
22/11/17 19:09:15 Added 0 downloads.
22/11/17 19:09:15 Added 0 custom downloads.
22/11/17 19:09:15 Executing onFailure...
22/11/17 19:09:15 ------------------------------------------------------
22/11/17 19:09:15 Send Notification on Failure
22/11/17 19:09:15 ------------------------------------------------------
22/11/17 19:09:15 Configuration file '/data/apps/imputationserver/1.4.1/job.config' not available. Use default values.
22/11/17 19:09:15 Send Notification on Failure [ERROR]
22/11/17 19:09:15 onFailure execution failed.
22/11/17 19:09:15 Job execution failed: Job Execution failed.
22/11/17 19:09:15 Cleaning up...
22/11/17 19:09:15 Cleaning up uploaded local files...
22/11/17 19:09:15 Cleaning up temporary local files...
22/11/17 19:09:15 Cleaning up temporary hdfs files...
22/11/17 19:09:15 Cleaning up hdfs files...
22/11/17 19:09:15 Cleanup successful.
std.out:
Export parameter 'statisticDir'...
Error: package or namespace load failed for 'graphics' in registerS3methods(nsInfo$S3methods, package, env):
read failed on /usr/lib/R/library/graphics/R/graphics.rdb
Export parameter 'qcreport'...
No action required. Email notification has been disabled in job.config```
Hi, i am getting the below error in the logs: