Imputation X-chromosome about imputationserver HOT 6 OPEN

Hi Sebastian, I’m not allowed to upload my data on the MIS server, so I don’t know if it works, but I was able to impute chr 1-22 on the MIS docker. I included the complete log, hopefully it helps. Diana From: Sebastian Schoenherr ***@***.***> Sent: 13 October 2021 15:12 To: genepi/imputationserver ***@***.***> Cc: davanderp ***@***.***>; Author ***@***.***> Subject: Re: [genepi/imputationserver] Imputation X-chromosome (#63) thanks for giving it a try. Does the same job work on MIS? Can you also please send the complete log file. best. Sebastian — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#63 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOIPUSGNW5MZXMQTCWCPZ3DUGWHSZANCNFSM5D5ZOAFA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub> . <https://github.com/notifications/beacon/AOIPUSBLAFEXFGKSKK6L2Q3UGWHSZA5CNFSM5D5ZOAFKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOHAVRRQY.gif> 21/10/13 10:21:46 Executing Job installation.... 21/10/13 10:21:46 Preparing Application 'Genotype Imputation (Minimac4)'... 21/10/13 10:21:46 Application 'Genotype Imputation (Minimac4)'is already installed. 21/10/13 10:21:46 Preparing Application '1000G Phase 3 v5'... 21/10/13 10:21:46 Application '1000G Phase 3 v5'is already installed. 21/10/13 10:21:46 Executing Job setups.... 21/10/13 10:21:46 Planner: WDL evaluated. 21/10/13 10:21:46 Planner: DAG created. 21/10/13 10:21:46 Nodes: 3 21/10/13 10:21:46 Input Validation 21/10/13 10:21:46 Inputs: 21/10/13 10:21:46 Outputs: 21/10/13 10:21:46 Quality Control 21/10/13 10:21:46 Inputs: 21/10/13 10:21:46 Outputs: mafFile chunkFileDir statisticDir 21/10/13 10:21:46 Quality Control (Report) 21/10/13 10:21:46 Inputs: mafFile myseparator 21/10/13 10:21:46 Outputs: qcreport 21/10/13 10:21:46 Dependencies: 2 21/10/13 10:21:46 Input Validation->Quality Control 21/10/13 10:21:46 Quality Control->Quality Control (Report) 21/10/13 10:21:46 Executor: execute DAG... 21/10/13 10:21:46 ------------------------------------------------------ 21/10/13 10:21:46 Input Validation 21/10/13 10:21:46 ------------------------------------------------------ 21/10/13 10:21:46 Versions: 21/10/13 10:21:46 Pipeline: michigan-imputationserver-1.4.1 21/10/13 10:21:46 Imputation-Engine: minimac4-1.0.2 21/10/13 10:21:46 Phasing-Engine: eagle-2.4 21/10/13 10:21:46 Configuration file '/data/apps/imputationserver/1.4.1/job.config' not available. Use default values. 21/10/13 10:21:51 Input Validation [4 sec] 21/10/13 10:21:51 ------------------------------------------------------ 21/10/13 10:21:51 Quality Control 21/10/13 10:21:51 ------------------------------------------------------ 21/10/13 10:21:51 Configuration file '/data/apps/imputationserver/1.4.1/job.config' not available. Use default values. 21/10/13 10:21:51 Reference Panel Ranges: genome-wide 21/10/13 10:23:03 Quality Control [1 min 12 sec] 21/10/13 10:23:03 Exporting parameter statisticDir... 21/10/13 10:23:03 Added 3 downloads. 21/10/13 10:23:03 Added 0 custom downloads. 21/10/13 10:23:03 ------------------------------------------------------ 21/10/13 10:23:03 Quality Control (Report) 21/10/13 10:23:03 ------------------------------------------------------ 21/10/13 10:23:03 Running script /data/apps/imputationserver/1.4.1/qc-report.Rmd... 21/10/13 10:23:03 Working Directory: /data/apps/imputationserver/1.4.1 21/10/13 10:23:03 Output: /data/jobs/job-20211013-102143-529/qcreport/qcreport.html 21/10/13 10:23:03 Parameters: 21/10/13 10:23:03 /data/jobs/job-20211013-102143-529/temp/mafFile/mafFile 21/10/13 10:23:03 Creating RMarkdown report from /data/apps/imputationserver/1.4.1/qc-report.Rmd... 21/10/13 10:23:07 Quality Control (Report) [3 sec] 21/10/13 10:23:07 Exporting parameter qcreport... 21/10/13 10:23:07 Added 1 downloads. 21/10/13 10:23:07 Added 0 custom downloads. 21/10/13 10:23:07 Planner: WDL evaluated. 21/10/13 10:23:10 Planner: WDL evaluated. 21/10/13 10:23:10 Details: 21/10/13 10:23:10 Name: ECRHS_chrX 21/10/13 10:23:10 Job-Id: job-20211013-102143-529 21/10/13 10:23:10 Submitted On: Wed Oct 13 10:21:46 UTC 2021 21/10/13 10:23:10 Completed On: Thu Jan 01 00:00:00 UTC 1970 21/10/13 10:23:10 Inputs: 21/10/13 10:23:10 Reference Panel (<a href="https://imputationserver.sph.umich.edu/start.html#!pages/refpanels" target="_blank">Details</a>): ***@***.***@3.0.0 21/10/13 10:23:10 Input Files (<a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41" target="_blank">VCF</a>): /data/jobs/job-20211013-102143-529/input/files 21/10/13 10:23:10 Array Build: hg19 21/10/13 10:23:10 rsq Filter: 0.3 21/10/13 10:23:10 Phasing: eagle 21/10/13 10:23:10 Population: eur 21/10/13 10:23:10 Mode: imputation 21/10/13 10:23:10 AES 256 encryption: no 21/10/13 10:23:10 null: 21/10/13 10:23:10 Password set by user.: auto 21/10/13 10:23:10 I will not attempt to re-identify or contact research participants.: accepted 21/10/13 10:23:10 I will report any inadvertent data release, security breach or other data management incident of which I become aware.: accepted 21/10/13 10:23:10 Outputs: 21/10/13 10:23:10 Quality-Control Report: /data/jobs/job-20211013-102143-529/qcreport/qcreport 21/10/13 10:23:10 QC Statistics: /data/jobs/job-20211013-102143-529/statisticDir 21/10/13 10:23:10 Imputation Results: /data/jobs/job-20211013-102143-529/local 21/10/13 10:23:10 Logs: /data/jobs/job-20211013-102143-529/logfile 21/10/13 10:23:10 Hadoop Task Logs: /data/jobs/job-20211013-102143-529/hadooplogs 21/10/13 10:23:10 Preparing Job.... 21/10/13 10:23:10 Executing Job.... 21/10/13 10:23:10 Planner: WDL evaluated. 21/10/13 10:23:10 Planner: DAG created. 21/10/13 10:23:10 Nodes: 2 21/10/13 10:23:10 Pre-phasing and Imputation 21/10/13 10:23:10 Inputs: 21/10/13 10:23:10 Outputs: outputimputation local logfile hadooplogs 21/10/13 10:23:10 Data Compression and Encryption 21/10/13 10:23:10 Inputs: 21/10/13 10:23:10 Outputs: 21/10/13 10:23:10 Dependencies: 1 21/10/13 10:23:10 Pre-phasing and Imputation->Data Compression and Encryption 21/10/13 10:23:10 Executor: execute DAG... 21/10/13 10:23:10 ------------------------------------------------------ 21/10/13 10:23:10 Pre-phasing and Imputation 21/10/13 10:23:10 ------------------------------------------------------ 21/10/13 10:23:12 Pre-phasing and Imputation [ERROR] 21/10/13 10:23:12 Exporting parameter hadooplogs... 21/10/13 10:23:12 Added 0 downloads. 21/10/13 10:23:12 Added 0 custom downloads. 21/10/13 10:23:12 Executing onFailure... 21/10/13 10:23:12 ------------------------------------------------------ 21/10/13 10:23:12 Send Notification on Failure 21/10/13 10:23:12 ------------------------------------------------------ 21/10/13 10:23:12 Configuration file '/data/apps/imputationserver/1.4.1/job.config' not available. Use default values. 21/10/13 10:23:12 Send Notification on Failure [ERROR] 21/10/13 10:23:12 onFailure execution failed. 21/10/13 10:23:12 Job Execution failed: Job Execution failed. 21/10/13 10:23:12 Cleaning up... 21/10/13 10:23:12 Cleaning up uploaded local files... 21/10/13 10:23:12 Cleaning up temporary local files... 21/10/13 10:23:12 Cleaning up temporary hdfs files... 21/10/13 10:23:12 Cleaning up hdfs files... 21/10/13 10:23:12 Cleanup successful.

Dear Sebastian, I’m not allowed to share any personal data because of PDRP (data protection laws in EU/UK). Maybe you could send me one sample you know works, so I can check it or otherwise send me a script. Kind regards, Diana van der Plaat From: Sebastian Schoenherr ***@***.***> Sent: 15 October 2021 13:22 To: genepi/imputationserver ***@***.***> Cc: davanderp ***@***.***>; Author ***@***.***> Subject: Re: [genepi/imputationserver] Imputation X-chromosome (#63) Can you provide a minimal example that fails? e.g. one sample included? — You are receiving this because you authored the thread. Reply to this email directly, view it on GitHub <#63 (comment)> , or unsubscribe <https://github.com/notifications/unsubscribe-auth/AOIPUSAFLPY4KOPWNHUIAOTUHAMHPANCNFSM5D5ZOAFA> . Triage notifications on the go with GitHub Mobile for iOS <https://apps.apple.com/app/apple-store/id1477376905?ct=notification-email&mt=8&pt=524675> or Android <https://play.google.com/store/apps/details?id=com.github.android&referrer=utm_campaign%3Dnotification-email%26utm_medium%3Demail%26utm_source%3Dgithub> . <https://github.com/notifications/beacon/AOIPUSENSDUDR7GSB4Q6FOLUHAMHPA5CNFSM5D5ZOAFKYY3PNVWWK3TUL52HS4DFVREXG43VMVBW63LNMVXHJKTDN5WW2ZLOORPWSZGOHBECWHQ.gif>