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post_impute.log
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node01.cluster | 211951 | 2020-02-07 13:21:59.137588 +0100 GMT | | begin drake_config()
node01.cluster | 211951 | 2020-02-07 13:21:59.161409 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node01.cluster | 211951 | 2020-02-07 13:21:59.170084 +0100 GMT | | analyze environment
node01.cluster | 211951 | 2020-02-07 13:21:59.224415 +0100 GMT | | analyze imports
node01.cluster | 211951 | 2020-02-07 13:21:59.883027 +0100 GMT | | get knitr hash
node01.cluster | 211951 | 2020-02-07 13:21:59.902247 +0100 GMT | | analyze commands
node01.cluster | 211951 | 2020-02-07 13:21:59.934015 +0100 GMT | | set knitr files
node01.cluster | 211951 | 2020-02-07 13:21:59.945923 +0100 GMT | | create graph edges
node01.cluster | 211951 | 2020-02-07 13:21:59.953162 +0100 GMT | | connect output files
node01.cluster | 211951 | 2020-02-07 13:21:59.965600 +0100 GMT | file analysis/QC/09_extract_typed | file_out
node01.cluster | 211951 | 2020-02-07 13:21:59.973276 +0100 GMT | file analysis/QC/08_plink_convert | file_out
node01.cluster | 211951 | 2020-02-07 13:21:59.974808 +0100 GMT | file analysis/QC/14_mafcheck | file_out
node01.cluster | 211951 | 2020-02-07 13:21:59.976109 +0100 GMT | file analysis/QC/12_ethnicity_admixture | file_out
node01.cluster | 211951 | 2020-02-07 13:21:59.977325 +0100 GMT | file analysis/QC/10_merge_imputed | file_out
node01.cluster | 211951 | 2020-02-07 13:21:59.978571 +0100 GMT | file analysis/QC/13_hwecheck | file_out
node01.cluster | 211951 | 2020-02-07 13:21:59.984359 +0100 GMT | file analysis/QC/11_relatedness | file_out
node01.cluster | 211951 | 2020-02-07 13:21:59.988603 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node01.cluster | 211951 | 2020-02-07 13:21:59.989858 +0100 GMT | file analysis/QC/15_final_processing | file_out
node01.cluster | 211951 | 2020-02-07 13:21:59.990965 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node01.cluster | 211951 | 2020-02-07 13:21:59.992075 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node01.cluster | 211951 | 2020-02-07 13:22:00.020765 +0100 GMT | | finalize graph edges
node01.cluster | 211951 | 2020-02-07 13:22:00.026366 +0100 GMT | | create igraph
node01.cluster | 211951 | 2020-02-07 13:22:00.028489 +0100 GMT | | trim neighborhoods
node01.cluster | 211951 | 2020-02-07 13:22:00.033201 +0100 GMT | | add igraph attributes
node01.cluster | 211951 | 2020-02-07 13:22:00.036539 +0100 GMT | | finalize igraph
node01.cluster | 211951 | 2020-02-07 13:22:00.049046 +0100 GMT | | end drake_config()
node01.cluster | 211951 | 2020-02-07 13:22:00.049953 +0100 GMT | | begin make()
node01.cluster | 211951 | 2020-02-07 13:22:00.349166 +0100 GMT | processx::run | import
node01.cluster | 211951 | 2020-02-07 13:22:00.433823 +0100 GMT | file code/post_imputation_qc.sh | import
node01.cluster | 211951 | 2020-02-07 13:22:00.590690 +0100 GMT | file code/qc/maf_check.R | import
node01.cluster | 211951 | 2020-02-07 13:22:00.682253 +0100 GMT | file code/qc/ethnicity_check.R | import
node01.cluster | 211951 | 2020-02-07 13:22:00.761783 +0100 GMT | file code/qc/relatedness_filter.R | import
node01.cluster | 211951 | 2020-02-07 13:22:00.842140 +0100 GMT | file code/qc/update_pvar.R | import
node01.cluster | 211951 | 2020-02-07 13:22:00.910641 +0100 GMT | file code/check_imputation.sh | import
node01.cluster | 211951 | 2020-02-07 13:22:01.070101 +0100 GMT | file code/final_processing.sh | import
node01.cluster | 211951 | 2020-02-07 13:22:01.195955 +0100 GMT | | begin outdated()
node01.cluster | 211951 | 2020-02-07 13:22:01.212408 +0100 GMT | | find more outdated targets
node13.cluster | 158958 | 2020-02-07 13:46:30.802932 +0100 GMT | | begin drake_config()
node13.cluster | 158958 | 2020-02-07 13:46:34.340151 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node13.cluster | 158958 | 2020-02-07 13:46:34.343882 +0100 GMT | | analyze environment
node13.cluster | 158958 | 2020-02-07 13:46:34.405364 +0100 GMT | | analyze imports
node13.cluster | 158958 | 2020-02-07 13:46:34.766261 +0100 GMT | | get knitr hash
node13.cluster | 158958 | 2020-02-07 13:46:34.771140 +0100 GMT | | analyze commands
node13.cluster | 158958 | 2020-02-07 13:46:34.816897 +0100 GMT | | set knitr files
node13.cluster | 158958 | 2020-02-07 13:46:34.825479 +0100 GMT | | create graph edges
node13.cluster | 158958 | 2020-02-07 13:46:34.832352 +0100 GMT | | connect output files
node13.cluster | 158958 | 2020-02-07 13:46:34.844021 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node13.cluster | 158958 | 2020-02-07 13:46:34.848772 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node13.cluster | 158958 | 2020-02-07 13:46:34.850298 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node13.cluster | 158958 | 2020-02-07 13:46:34.879037 +0100 GMT | | finalize graph edges
node13.cluster | 158958 | 2020-02-07 13:46:34.880076 +0100 GMT | | create igraph
node13.cluster | 158958 | 2020-02-07 13:46:34.881660 +0100 GMT | | trim neighborhoods
node13.cluster | 158958 | 2020-02-07 13:46:34.886168 +0100 GMT | | add igraph attributes
node13.cluster | 158958 | 2020-02-07 13:46:34.888191 +0100 GMT | | finalize igraph
node13.cluster | 158958 | 2020-02-07 13:46:34.895646 +0100 GMT | | end drake_config()
node13.cluster | 158958 | 2020-02-07 13:46:34.896747 +0100 GMT | | begin make()
node13.cluster | 158958 | 2020-02-07 13:46:35.539215 +0100 GMT | processx::run | import
node13.cluster | 158958 | 2020-02-07 13:46:35.564702 +0100 GMT | file code/check_imputation.sh | import
node13.cluster | 158958 | 2020-02-07 13:46:35.587531 +0100 GMT | file code/final_processing.sh | import
node13.cluster | 158958 | 2020-02-07 13:46:35.599594 +0100 GMT | file code/post_imputation_qc.sh | import
node13.cluster | 158958 | 2020-02-07 13:46:35.611466 +0100 GMT | file code/qc/maf_check.R | import
node13.cluster | 158958 | 2020-02-07 13:46:35.622912 +0100 GMT | file code/qc/ethnicity_check.R | import
node13.cluster | 158958 | 2020-02-07 13:46:35.663187 +0100 GMT | file code/qc/relatedness_filter.R | import
node13.cluster | 158958 | 2020-02-07 13:46:35.675633 +0100 GMT | file code/qc/update_pvar.R | import
node13.cluster | 158958 | 2020-02-07 13:46:35.716931 +0100 GMT | | begin outdated()
node13.cluster | 158958 | 2020-02-07 13:46:35.725955 +0100 GMT | | find more outdated targets
node13.cluster | 158958 | 2020-02-07 13:46:35.735691 +0100 GMT | run_check_imputation | trigger command
node13.cluster | 158958 | 2020-02-07 13:46:35.750820 +0100 GMT | run_final_processing | trigger command
node13.cluster | 158958 | 2020-02-07 13:46:35.768332 +0100 GMT | cp_qc_report | trigger command
node13.cluster | 158958 | 2020-02-07 13:46:35.783697 +0100 GMT | run_post_imputation | trigger command
node13.cluster | 158958 | 2020-02-07 13:46:35.784825 +0100 GMT | | find downstream outdated targets
node13.cluster | 158958 | 2020-02-07 13:46:35.790801 +0100 GMT | | end outdated()
node13.cluster | 158958 | 2020-02-07 13:46:35.802482 +0100 GMT | | isolate oudated targets
node13.cluster | 158958 | 2020-02-07 13:46:35.806405 +0100 GMT | | construct priority queue
node13.cluster | 158958 | 2020-02-07 13:46:35.818980 +0100 GMT | run_check_imputation | trigger command
node13.cluster | 158958 | 2020-02-07 13:46:36.555254 +0100 GMT | | set common data
node13.cluster | 158958 | 2020-02-07 13:46:36.586333 +0100 GMT | | begin scheduling targets
node13.cluster | 158958 | 2020-02-07 13:46:38.547766 +0100 GMT | | sending common data
node13.cluster | 158958 | 2020-02-07 13:46:39.226349 +0100 GMT | run_check_imputation | trigger command
node13.cluster | 158958 | 2020-02-07 13:46:39.242576 +0100 GMT | run_check_imputation | target run_check_imputation
node15.cluster | 160213 | 2020-02-07 13:46:39.250836 +0100 GMT | run_check_imputation | build on an hpc worker
node13.cluster | 158958 | 2020-02-07 13:48:03.341091 +0100 GMT | | end make()
node13.cluster | 158958 | 2020-02-07 13:48:20.777226 +0100 GMT | | begin drake_config()
node13.cluster | 158958 | 2020-02-07 13:48:20.797756 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node13.cluster | 158958 | 2020-02-07 13:48:20.800723 +0100 GMT | | analyze environment
node13.cluster | 158958 | 2020-02-07 13:48:20.833758 +0100 GMT | | analyze imports
node13.cluster | 158958 | 2020-02-07 13:48:21.187625 +0100 GMT | | get knitr hash
node13.cluster | 158958 | 2020-02-07 13:48:21.193085 +0100 GMT | | analyze commands
node13.cluster | 158958 | 2020-02-07 13:48:21.219664 +0100 GMT | | set knitr files
node13.cluster | 158958 | 2020-02-07 13:48:21.234706 +0100 GMT | | create graph edges
node13.cluster | 158958 | 2020-02-07 13:48:21.241357 +0100 GMT | | connect output files
node13.cluster | 158958 | 2020-02-07 13:48:21.242566 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node13.cluster | 158958 | 2020-02-07 13:48:21.244977 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node13.cluster | 158958 | 2020-02-07 13:48:21.246338 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node13.cluster | 158958 | 2020-02-07 13:48:21.270486 +0100 GMT | | finalize graph edges
node13.cluster | 158958 | 2020-02-07 13:48:21.271690 +0100 GMT | | create igraph
node13.cluster | 158958 | 2020-02-07 13:48:21.273519 +0100 GMT | | trim neighborhoods
node13.cluster | 158958 | 2020-02-07 13:48:21.277900 +0100 GMT | | add igraph attributes
node13.cluster | 158958 | 2020-02-07 13:48:21.279893 +0100 GMT | | finalize igraph
node13.cluster | 158958 | 2020-02-07 13:48:21.302823 +0100 GMT | | end drake_config()
node13.cluster | 158958 | 2020-02-07 13:48:21.303901 +0100 GMT | | begin make()
node13.cluster | 158958 | 2020-02-07 13:48:21.514433 +0100 GMT | processx::run | import
node13.cluster | 158958 | 2020-02-07 13:48:21.535979 +0100 GMT | file code/check_imputation.sh | import
node13.cluster | 158958 | 2020-02-07 13:48:21.548011 +0100 GMT | file code/final_processing.sh | import
node13.cluster | 158958 | 2020-02-07 13:48:21.573898 +0100 GMT | file code/post_imputation_qc.sh | import
node13.cluster | 158958 | 2020-02-07 13:48:21.585190 +0100 GMT | file code/qc/maf_check.R | import
node13.cluster | 158958 | 2020-02-07 13:48:21.595715 +0100 GMT | file code/qc/ethnicity_check.R | import
node13.cluster | 158958 | 2020-02-07 13:48:21.606355 +0100 GMT | file code/qc/relatedness_filter.R | import
node13.cluster | 158958 | 2020-02-07 13:48:21.631630 +0100 GMT | file code/qc/update_pvar.R | import
node13.cluster | 158958 | 2020-02-07 13:48:21.646887 +0100 GMT | | begin outdated()
node13.cluster | 158958 | 2020-02-07 13:48:21.654516 +0100 GMT | | find more outdated targets
node13.cluster | 158958 | 2020-02-07 13:48:21.691338 +0100 GMT | run_check_imputation | trigger command
node13.cluster | 158958 | 2020-02-07 13:48:21.716216 +0100 GMT | run_post_imputation | trigger command
node13.cluster | 158958 | 2020-02-07 13:48:21.719075 +0100 GMT | cp_qc_report | trigger command
node13.cluster | 158958 | 2020-02-07 13:48:21.719939 +0100 GMT | | find downstream outdated targets
node13.cluster | 158958 | 2020-02-07 13:48:21.725370 +0100 GMT | | end outdated()
node13.cluster | 158958 | 2020-02-07 13:48:21.734818 +0100 GMT | | isolate oudated targets
node13.cluster | 158958 | 2020-02-07 13:48:21.737905 +0100 GMT | | construct priority queue
node13.cluster | 158958 | 2020-02-07 13:48:21.818039 +0100 GMT | run_check_imputation | trigger command
node13.cluster | 158958 | 2020-02-07 13:48:22.164335 +0100 GMT | | set common data
node13.cluster | 158958 | 2020-02-07 13:48:22.186686 +0100 GMT | | begin scheduling targets
node13.cluster | 158958 | 2020-02-07 13:48:24.073104 +0100 GMT | | sending common data
node13.cluster | 158958 | 2020-02-07 13:48:24.439053 +0100 GMT | run_check_imputation | trigger command
node13.cluster | 158958 | 2020-02-07 13:48:24.443054 +0100 GMT | run_check_imputation | target run_check_imputation
node15.cluster | 160275 | 2020-02-07 13:48:24.449054 +0100 GMT | run_check_imputation | build on an hpc worker
node13.cluster | 158958 | 2020-02-07 17:44:12.420954 +0100 GMT | run_check_imputation | store
node13.cluster | 158958 | 2020-02-07 17:44:16.964485 +0100 GMT | run_check_imputation | time 14133.602s (~3.93 hours) | 14152.547s (~3.93 hours) (exec | total)
node13.cluster | 158958 | 2020-02-07 17:44:17.313336 +0100 GMT | run_post_imputation | trigger command
node13.cluster | 158958 | 2020-02-07 17:44:17.318590 +0100 GMT | run_post_imputation | target run_post_imputation
node15.cluster | 160275 | 2020-02-07 17:44:17.329193 +0100 GMT | run_post_imputation | build on an hpc worker
node13.cluster | 158958 | 2020-02-08 04:01:41.353812 +0100 GMT | run_post_imputation | store
node13.cluster | 158958 | 2020-02-08 04:01:41.727360 +0100 GMT | run_post_imputation | time 37043.664s (~10.29 hours) | 37044.453s (~10.29 hours) (exec | total)
node13.cluster | 158958 | 2020-02-08 04:01:42.093618 +0100 GMT | cp_qc_report | build locally
node13.cluster | 158958 | 2020-02-08 04:01:42.157809 +0100 GMT | cp_qc_report | trigger command
node13.cluster | 158958 | 2020-02-08 04:01:42.164004 +0100 GMT | cp_qc_report | target cp_qc_report
node13.cluster | 158958 | 2020-02-08 04:01:42.701795 +0100 GMT | cp_qc_report | store
node13.cluster | 158958 | 2020-02-08 04:01:42.718706 +0100 GMT | cp_qc_report | time 0.525s | 0.619s (exec | total)
node13.cluster | 158958 | 2020-02-08 04:01:42.749816 +0100 GMT | cp_qc_check | build locally
node13.cluster | 158958 | 2020-02-08 04:01:44.743368 +0100 GMT | cp_qc_check | trigger command
node13.cluster | 158958 | 2020-02-08 04:01:44.747853 +0100 GMT | cp_qc_check | target cp_qc_check
node13.cluster | 158958 | 2020-02-08 04:01:45.077917 +0100 GMT | cp_qc_check | store
node13.cluster | 158958 | 2020-02-08 04:01:45.263805 +0100 GMT | cp_qc_check | time 0.325s | 2.508s (exec | total)
node13.cluster | 158958 | 2020-02-08 04:01:45.360494 +0100 GMT | run_final_processing | trigger command
node13.cluster | 158958 | 2020-02-08 04:01:45.368951 +0100 GMT | run_final_processing | target run_final_processing
node15.cluster | 160275 | 2020-02-08 04:01:45.415486 +0100 GMT | run_final_processing | build on an hpc worker
node13.cluster | 158958 | 2020-02-08 05:27:18.329291 +0100 GMT | run_final_processing | store
node13.cluster | 158958 | 2020-02-08 05:27:18.719765 +0100 GMT | run_final_processing | time 5132.37s (~1.43 hours) | 5133.411s (~1.43 hours) (exec | total)
node13.cluster | 158958 | 2020-02-08 05:27:26.996606 +0100 GMT | | end make()
node13.cluster | 162759 | 2020-02-08 18:37:28.882802 +0100 GMT | | begin drake_config()
node13.cluster | 162759 | 2020-02-08 18:37:28.937614 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node13.cluster | 162759 | 2020-02-08 18:37:28.940887 +0100 GMT | | analyze environment
node13.cluster | 162759 | 2020-02-08 18:37:29.011879 +0100 GMT | | get knitr hash
node13.cluster | 162759 | 2020-02-08 18:37:29.049446 +0100 GMT | | set knitr files
node13.cluster | 162759 | 2020-02-08 18:37:29.065372 +0100 GMT | | create graph edges
node13.cluster | 162759 | 2020-02-08 18:37:29.072796 +0100 GMT | | connect output files
node13.cluster | 162759 | 2020-02-08 18:37:29.083709 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node13.cluster | 162759 | 2020-02-08 18:37:29.086118 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node13.cluster | 162759 | 2020-02-08 18:37:29.087576 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node13.cluster | 162759 | 2020-02-08 18:37:29.151869 +0100 GMT | | end drake_config()
node13.cluster | 162759 | 2020-02-08 18:37:29.153236 +0100 GMT | | begin make()
node13.cluster | 162759 | 2020-02-08 18:37:29.496924 +0100 GMT | processx::run | import
node13.cluster | 162759 | 2020-02-08 18:37:29.552284 +0100 GMT | file code/check_imputation.sh | import
node13.cluster | 162759 | 2020-02-08 18:37:29.594157 +0100 GMT | file code/final_processing.sh | import
node13.cluster | 162759 | 2020-02-08 18:37:29.622797 +0100 GMT | file code/post_imputation_qc.sh | import
node13.cluster | 162759 | 2020-02-08 18:37:29.664554 +0100 GMT | file code/qc/maf_check.R | import
node13.cluster | 162759 | 2020-02-08 18:37:29.715102 +0100 GMT | file code/qc/ethnicity_check.R | import
node13.cluster | 162759 | 2020-02-08 18:37:29.806891 +0100 GMT | file code/qc/relatedness_filter.R | import
node13.cluster | 162759 | 2020-02-08 18:37:29.912843 +0100 GMT | file code/qc/update_pvar.R | import
node13.cluster | 162759 | 2020-02-08 18:37:29.950184 +0100 GMT | | begin outdated()
node13.cluster | 162759 | 2020-02-08 18:37:29.988336 +0100 GMT | | find more outdated targets
node13.cluster | 162759 | 2020-02-08 18:37:33.580181 +0100 GMT | run_check_imputation | skip
node13.cluster | 162759 | 2020-02-08 18:37:33.596516 +0100 GMT | run_post_imputation | trigger file
node13.cluster | 162759 | 2020-02-08 18:37:33.618074 +0100 GMT | cp_qc_report | skip
node13.cluster | 162759 | 2020-02-08 18:37:33.619802 +0100 GMT | | find more outdated targets
node13.cluster | 162759 | 2020-02-08 18:37:37.119783 +0100 GMT | cp_qc_check | skip
node13.cluster | 162759 | 2020-02-08 18:37:37.121644 +0100 GMT | | find more outdated targets
node13.cluster | 162759 | 2020-02-08 18:37:37.124522 +0100 GMT | | find downstream outdated targets
node13.cluster | 162759 | 2020-02-08 18:37:37.131866 +0100 GMT | | end outdated()
node13.cluster | 162759 | 2020-02-08 18:37:37.132885 +0100 GMT | | isolate oudated targets
node13.cluster | 162759 | 2020-02-08 18:37:37.136419 +0100 GMT | | construct priority queue
node13.cluster | 162759 | 2020-02-08 18:37:37.171887 +0100 GMT | run_post_imputation | trigger file
node13.cluster | 162759 | 2020-02-08 18:37:37.566853 +0100 GMT | | set common data
node13.cluster | 162759 | 2020-02-08 18:37:37.597979 +0100 GMT | | begin scheduling targets
node13.cluster | 162759 | 2020-02-08 18:37:40.333857 +0100 GMT | | sending common data
node13.cluster | 162759 | 2020-02-08 18:37:40.666060 +0100 GMT | run_post_imputation | trigger file
node13.cluster | 162759 | 2020-02-08 18:37:40.670154 +0100 GMT | run_post_imputation | target run_post_imputation
node14.cluster | 111696 | 2020-02-08 18:37:40.677292 +0100 GMT | run_post_imputation | build on an hpc worker
node13.cluster | 162759 | 2020-02-08 18:38:02.385926 +0100 GMT | | end make()
node13.cluster | 162759 | 2020-02-08 18:39:12.967501 +0100 GMT | | begin drake_config()
node13.cluster | 162759 | 2020-02-08 18:39:12.990824 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node13.cluster | 162759 | 2020-02-08 18:39:12.993415 +0100 GMT | | analyze environment
node13.cluster | 162759 | 2020-02-08 18:39:13.026454 +0100 GMT | | analyze imports
node13.cluster | 162759 | 2020-02-08 18:39:13.348739 +0100 GMT | | get knitr hash
node13.cluster | 162759 | 2020-02-08 18:39:13.363199 +0100 GMT | | analyze commands
node13.cluster | 162759 | 2020-02-08 18:39:13.423545 +0100 GMT | | set knitr files
node13.cluster | 162759 | 2020-02-08 18:39:13.438393 +0100 GMT | | create graph edges
node13.cluster | 162759 | 2020-02-08 18:39:13.445123 +0100 GMT | | connect output files
node13.cluster | 162759 | 2020-02-08 18:39:13.455801 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node13.cluster | 162759 | 2020-02-08 18:39:13.457597 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node13.cluster | 162759 | 2020-02-08 18:39:13.459033 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node13.cluster | 162759 | 2020-02-08 18:39:13.474467 +0100 GMT | | end drake_config()
node13.cluster | 162759 | 2020-02-08 18:39:13.475448 +0100 GMT | | begin make()
node13.cluster | 162759 | 2020-02-08 18:39:13.698287 +0100 GMT | processx::run | import
node13.cluster | 162759 | 2020-02-08 18:39:13.720560 +0100 GMT | file code/check_imputation.sh | import
node13.cluster | 162759 | 2020-02-08 18:39:13.768115 +0100 GMT | file code/final_processing.sh | import
node13.cluster | 162759 | 2020-02-08 18:39:13.800944 +0100 GMT | file code/post_imputation_qc.sh | import
node13.cluster | 162759 | 2020-02-08 18:39:13.829665 +0100 GMT | file code/qc/maf_check.R | import
node13.cluster | 162759 | 2020-02-08 18:39:13.886873 +0100 GMT | file code/qc/ethnicity_check.R | import
node13.cluster | 162759 | 2020-02-08 18:39:13.935704 +0100 GMT | file code/qc/relatedness_filter.R | import
node13.cluster | 162759 | 2020-02-08 18:39:13.989274 +0100 GMT | file code/qc/update_pvar.R | import
node13.cluster | 162759 | 2020-02-08 18:39:14.012993 +0100 GMT | | begin outdated()
node13.cluster | 162759 | 2020-02-08 18:39:14.020870 +0100 GMT | | find more outdated targets
node13.cluster | 162759 | 2020-02-08 18:39:17.497093 +0100 GMT | run_check_imputation | skip
node13.cluster | 162759 | 2020-02-08 18:39:17.510008 +0100 GMT | run_post_imputation | trigger file
node13.cluster | 162759 | 2020-02-08 18:39:17.523720 +0100 GMT | cp_qc_report | skip
node13.cluster | 162759 | 2020-02-08 18:39:17.525334 +0100 GMT | | find more outdated targets
node13.cluster | 162759 | 2020-02-08 18:39:21.004733 +0100 GMT | cp_qc_check | skip
node13.cluster | 162759 | 2020-02-08 18:39:21.006967 +0100 GMT | | find more outdated targets
node13.cluster | 162759 | 2020-02-08 18:39:21.009316 +0100 GMT | | find downstream outdated targets
node13.cluster | 162759 | 2020-02-08 18:39:21.013305 +0100 GMT | | end outdated()
node13.cluster | 162759 | 2020-02-08 18:39:21.014463 +0100 GMT | | isolate oudated targets
node13.cluster | 162759 | 2020-02-08 18:39:21.017054 +0100 GMT | | construct priority queue
node13.cluster | 162759 | 2020-02-08 18:39:21.093092 +0100 GMT | run_post_imputation | trigger file
node13.cluster | 162759 | 2020-02-08 18:39:21.410258 +0100 GMT | | set common data
node13.cluster | 162759 | 2020-02-08 18:39:21.441829 +0100 GMT | | begin scheduling targets
node13.cluster | 162759 | 2020-02-08 18:39:23.331008 +0100 GMT | | sending common data
node13.cluster | 162759 | 2020-02-08 18:39:23.654040 +0100 GMT | run_post_imputation | trigger file
node13.cluster | 162759 | 2020-02-08 18:39:23.658106 +0100 GMT | run_post_imputation | target run_post_imputation
node14.cluster | 111757 | 2020-02-08 18:39:23.665747 +0100 GMT | run_post_imputation | build on an hpc worker
node13.cluster | 162759 | 2020-02-09 04:05:49.538071 +0100 GMT | run_post_imputation | store
node13.cluster | 162759 | 2020-02-09 04:05:50.179269 +0100 GMT | run_post_imputation | time 33982.278s (~9.44 hours) | 33986.521s (~9.44 hours) (exec | total)
node13.cluster | 162759 | 2020-02-09 04:05:51.018496 +0100 GMT | run_final_processing | trigger change
node13.cluster | 162759 | 2020-02-09 04:05:51.049033 +0100 GMT | run_final_processing | target run_final_processing
node14.cluster | 111757 | 2020-02-09 04:05:51.169302 +0100 GMT | run_final_processing | build on an hpc worker
node13.cluster | 162759 | 2020-02-09 05:58:42.591855 +0100 GMT | run_final_processing | store
node13.cluster | 162759 | 2020-02-09 05:58:43.051822 +0100 GMT | run_final_processing | time 6771.16s (~1.88 hours) | 6772.209s (~1.88 hours) (exec | total)
node13.cluster | 162759 | 2020-02-09 05:58:45.851274 +0100 GMT | | end make()
node13.cluster | 162759 | 2020-02-10 13:30:53.453259 +0100 GMT | | begin drake_config()
node13.cluster | 162759 | 2020-02-10 13:30:53.485603 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node13.cluster | 162759 | 2020-02-10 13:30:53.488826 +0100 GMT | | analyze environment
node13.cluster | 162759 | 2020-02-10 13:30:53.553257 +0100 GMT | | get knitr hash
node13.cluster | 162759 | 2020-02-10 13:30:53.613944 +0100 GMT | | set knitr files
node13.cluster | 162759 | 2020-02-10 13:30:53.656156 +0100 GMT | | create graph edges
node13.cluster | 162759 | 2020-02-10 13:30:53.682880 +0100 GMT | | connect output files
node13.cluster | 162759 | 2020-02-10 13:30:53.683885 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node13.cluster | 162759 | 2020-02-10 13:30:53.685424 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node13.cluster | 162759 | 2020-02-10 13:30:53.686700 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node13.cluster | 162759 | 2020-02-10 13:30:53.693772 +0100 GMT | | end drake_config()
node13.cluster | 162759 | 2020-02-10 13:30:53.694557 +0100 GMT | | begin make()
node13.cluster | 162759 | 2020-02-10 13:31:01.887914 +0100 GMT | processx::run | import
node13.cluster | 162759 | 2020-02-10 13:31:01.902593 +0100 GMT | file code/check_imputation.sh | import
node13.cluster | 162759 | 2020-02-10 13:31:01.916792 +0100 GMT | file code/final_processing.sh | import
node13.cluster | 162759 | 2020-02-10 13:31:01.940404 +0100 GMT | file code/post_imputation_qc.sh | import
node13.cluster | 162759 | 2020-02-10 13:31:01.953332 +0100 GMT | file code/qc/maf_check.R | import
node13.cluster | 162759 | 2020-02-10 13:31:01.965595 +0100 GMT | file code/qc/ethnicity_check.R | import
node13.cluster | 162759 | 2020-02-10 13:31:02.071824 +0100 GMT | file code/qc/relatedness_filter.R | import
node13.cluster | 162759 | 2020-02-10 13:31:02.083984 +0100 GMT | file code/qc/update_pvar.R | import
node13.cluster | 162759 | 2020-02-10 13:31:02.097043 +0100 GMT | | begin outdated()
node13.cluster | 162759 | 2020-02-10 13:31:02.107513 +0100 GMT | | find more outdated targets
node13.cluster | 162759 | 2020-02-10 13:31:02.119933 +0100 GMT | run_check_imputation | trigger file
node13.cluster | 162759 | 2020-02-10 13:31:02.137534 +0100 GMT | run_post_imputation | trigger change
node13.cluster | 162759 | 2020-02-10 13:31:02.141868 +0100 GMT | cp_qc_report | trigger change
node13.cluster | 162759 | 2020-02-10 13:31:02.142814 +0100 GMT | | find downstream outdated targets
node13.cluster | 162759 | 2020-02-10 13:31:02.149394 +0100 GMT | | end outdated()
node13.cluster | 162759 | 2020-02-10 13:31:02.150297 +0100 GMT | | isolate oudated targets
node13.cluster | 162759 | 2020-02-10 13:31:02.152945 +0100 GMT | | construct priority queue
node13.cluster | 162759 | 2020-02-10 13:31:02.162971 +0100 GMT | run_check_imputation | trigger file
node13.cluster | 162759 | 2020-02-10 13:31:02.440555 +0100 GMT | | set common data
node13.cluster | 162759 | 2020-02-10 13:31:02.543508 +0100 GMT | | begin scheduling targets
node13.cluster | 162759 | 2020-02-10 13:31:17.920720 +0100 GMT | | sending common data
node13.cluster | 162759 | 2020-02-10 13:31:23.384869 +0100 GMT | run_check_imputation | trigger file
node13.cluster | 162759 | 2020-02-10 13:31:23.389308 +0100 GMT | run_check_imputation | target run_check_imputation
node14.cluster | 119713 | 2020-02-10 13:31:23.420671 +0100 GMT | run_check_imputation | build on an hpc worker
node13.cluster | 162759 | 2020-02-10 13:32:07.506032 +0100 GMT | | end make()
node13.cluster | 162759 | 2020-02-10 13:33:21.170984 +0100 GMT | | begin drake_config()
node13.cluster | 162759 | 2020-02-10 13:33:21.196049 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node13.cluster | 162759 | 2020-02-10 13:33:21.200226 +0100 GMT | | analyze environment
node13.cluster | 162759 | 2020-02-10 13:33:21.271525 +0100 GMT | | analyze imports
node13.cluster | 162759 | 2020-02-10 13:33:21.471731 +0100 GMT | | get knitr hash
node13.cluster | 162759 | 2020-02-10 13:33:21.509269 +0100 GMT | | analyze commands
node13.cluster | 162759 | 2020-02-10 13:33:21.532185 +0100 GMT | | set knitr files
node13.cluster | 162759 | 2020-02-10 13:33:21.538621 +0100 GMT | | create graph edges
node13.cluster | 162759 | 2020-02-10 13:33:21.546969 +0100 GMT | | connect output files
node13.cluster | 162759 | 2020-02-10 13:33:21.547856 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node13.cluster | 162759 | 2020-02-10 13:33:21.549273 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node13.cluster | 162759 | 2020-02-10 13:33:21.550400 +0100 GMT | file analysis/QC/15_final_processing | file_out
node13.cluster | 162759 | 2020-02-10 13:33:21.551448 +0100 GMT | file analysis/QC/09_extract_typed | file_out
node13.cluster | 162759 | 2020-02-10 13:33:21.552490 +0100 GMT | file analysis/QC/08_plink_convert | file_out
node13.cluster | 162759 | 2020-02-10 13:33:21.553472 +0100 GMT | file analysis/QC/14_mafcheck | file_out
node13.cluster | 162759 | 2020-02-10 13:33:21.554468 +0100 GMT | file analysis/QC/12_ethnicity_admixture | file_out
node13.cluster | 162759 | 2020-02-10 13:33:21.555450 +0100 GMT | file analysis/QC/10_merge_imputed | file_out
node13.cluster | 162759 | 2020-02-10 13:33:21.556529 +0100 GMT | file analysis/QC/13_hwecheck | file_out
node13.cluster | 162759 | 2020-02-10 13:33:21.557825 +0100 GMT | file analysis/QC/11_relatedness | file_out
node13.cluster | 162759 | 2020-02-10 13:33:21.558886 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node13.cluster | 162759 | 2020-02-10 13:33:21.564086 +0100 GMT | | finalize graph edges
node13.cluster | 162759 | 2020-02-10 13:33:21.564959 +0100 GMT | | create igraph
node13.cluster | 162759 | 2020-02-10 13:33:21.566511 +0100 GMT | | trim neighborhoods
node13.cluster | 162759 | 2020-02-10 13:33:21.571096 +0100 GMT | | add igraph attributes
node13.cluster | 162759 | 2020-02-10 13:33:21.572969 +0100 GMT | | finalize igraph
node13.cluster | 162759 | 2020-02-10 13:33:21.587402 +0100 GMT | | end drake_config()
node13.cluster | 162759 | 2020-02-10 13:33:21.588106 +0100 GMT | | begin make()
node13.cluster | 162759 | 2020-02-10 13:33:21.779097 +0100 GMT | processx::run | import
node13.cluster | 162759 | 2020-02-10 13:33:21.816061 +0100 GMT | file code/final_processing.sh | import
node13.cluster | 162759 | 2020-02-10 13:33:21.827402 +0100 GMT | file code/post_imputation_qc.sh | import
node13.cluster | 162759 | 2020-02-10 13:33:21.843694 +0100 GMT | file code/qc/maf_check.R | import
node13.cluster | 162759 | 2020-02-10 13:33:21.854479 +0100 GMT | file code/qc/ethnicity_check.R | import
node13.cluster | 162759 | 2020-02-10 13:33:21.864501 +0100 GMT | file code/qc/relatedness_filter.R | import
node13.cluster | 162759 | 2020-02-10 13:33:21.874565 +0100 GMT | file code/qc/update_pvar.R | import
node13.cluster | 162759 | 2020-02-10 13:33:22.001546 +0100 GMT | file code/check_imputation.sh | import
node13.cluster | 162759 | 2020-02-10 13:33:22.015666 +0100 GMT | | begin outdated()
node13.cluster | 162759 | 2020-02-10 13:33:22.061425 +0100 GMT | | find more outdated targets
node01.cluster | 219199 | 2020-02-10 18:04:44.440355 +0100 GMT | | begin drake_config()
node01.cluster | 219199 | 2020-02-10 18:04:44.468596 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node01.cluster | 219199 | 2020-02-10 18:04:44.472388 +0100 GMT | | analyze environment
node01.cluster | 219199 | 2020-02-10 18:04:44.505706 +0100 GMT | | get knitr hash
node01.cluster | 219199 | 2020-02-10 18:04:44.513465 +0100 GMT | | set knitr files
node01.cluster | 219199 | 2020-02-10 18:04:44.522848 +0100 GMT | | create graph edges
node01.cluster | 219199 | 2020-02-10 18:04:44.532162 +0100 GMT | | connect output files
node01.cluster | 219199 | 2020-02-10 18:04:44.533462 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node01.cluster | 219199 | 2020-02-10 18:04:44.535505 +0100 GMT | file analysis/QC/15_final_processing | file_out
node01.cluster | 219199 | 2020-02-10 18:04:44.536964 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node01.cluster | 219199 | 2020-02-10 18:04:44.538451 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node01.cluster | 219199 | 2020-02-10 18:04:44.548005 +0100 GMT | | end drake_config()
node01.cluster | 219199 | 2020-02-10 18:04:44.549420 +0100 GMT | | begin make()
node01.cluster | 219199 | 2020-02-10 18:04:49.831159 +0100 GMT | processx::run | import
node01.cluster | 219199 | 2020-02-10 18:04:49.865676 +0100 GMT | file code/post_imputation_qc.sh | import
node01.cluster | 219199 | 2020-02-10 18:04:49.885811 +0100 GMT | file code/qc/maf_check.R | import
node01.cluster | 219199 | 2020-02-10 18:04:49.906416 +0100 GMT | file code/qc/ethnicity_check.R | import
node01.cluster | 219199 | 2020-02-10 18:04:49.934005 +0100 GMT | file code/qc/relatedness_filter.R | import
node01.cluster | 219199 | 2020-02-10 18:04:49.969295 +0100 GMT | file code/qc/update_pvar.R | import
node01.cluster | 219199 | 2020-02-10 18:04:49.988862 +0100 GMT | file code/check_imputation.sh | import
node01.cluster | 219199 | 2020-02-10 18:04:50.007286 +0100 GMT | file code/final_processing.sh | import
node01.cluster | 219199 | 2020-02-10 18:04:50.024751 +0100 GMT | | begin outdated()
node01.cluster | 219199 | 2020-02-10 18:04:50.036751 +0100 GMT | | find more outdated targets
node01.cluster | 219199 | 2020-02-10 18:04:50.056269 +0100 GMT | run_check_imputation | trigger file
node01.cluster | 219199 | 2020-02-10 18:04:50.077177 +0100 GMT | run_post_imputation | trigger change
node01.cluster | 219199 | 2020-02-10 18:04:50.082311 +0100 GMT | cp_qc_report | trigger change
node01.cluster | 219199 | 2020-02-10 18:04:50.083618 +0100 GMT | | find downstream outdated targets
node01.cluster | 219199 | 2020-02-10 18:04:50.091253 +0100 GMT | | end outdated()
node01.cluster | 219199 | 2020-02-10 18:04:50.092306 +0100 GMT | | isolate oudated targets
node01.cluster | 219199 | 2020-02-10 18:04:50.096104 +0100 GMT | | construct priority queue
node01.cluster | 219199 | 2020-02-10 18:04:50.113749 +0100 GMT | run_check_imputation | trigger file
node01.cluster | 219199 | 2020-02-10 18:04:50.901144 +0100 GMT | | set common data
node01.cluster | 219199 | 2020-02-10 18:04:50.945495 +0100 GMT | | begin scheduling targets
node01.cluster | 219199 | 2020-02-10 18:05:12.107266 +0100 GMT | | sending common data
node01.cluster | 219199 | 2020-02-10 18:05:14.152582 +0100 GMT | run_check_imputation | trigger file
node01.cluster | 219199 | 2020-02-10 18:05:14.159627 +0100 GMT | run_check_imputation | target run_check_imputation
node15.cluster | 172698 | 2020-02-10 18:05:14.184064 +0100 GMT | run_check_imputation | build on an hpc worker
node01.cluster | 219199 | 2020-02-10 18:06:04.566211 +0100 GMT | | end make()
node01.cluster | 219199 | 2020-02-10 18:06:16.265177 +0100 GMT | | begin drake_config()
node01.cluster | 219199 | 2020-02-10 18:06:16.287025 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node01.cluster | 219199 | 2020-02-10 18:06:16.291560 +0100 GMT | | analyze environment
node01.cluster | 219199 | 2020-02-10 18:06:16.328107 +0100 GMT | | get knitr hash
node01.cluster | 219199 | 2020-02-10 18:06:16.335901 +0100 GMT | | set knitr files
node01.cluster | 219199 | 2020-02-10 18:06:16.360177 +0100 GMT | | end drake_config()
node01.cluster | 219199 | 2020-02-10 18:06:16.361348 +0100 GMT | | begin make()
node01.cluster | 219199 | 2020-02-10 18:06:16.525270 +0100 GMT | processx::run | import
node01.cluster | 219199 | 2020-02-10 18:06:16.550881 +0100 GMT | file code/post_imputation_qc.sh | import
node01.cluster | 219199 | 2020-02-10 18:06:16.564803 +0100 GMT | file code/qc/maf_check.R | import
node01.cluster | 219199 | 2020-02-10 18:06:16.580492 +0100 GMT | file code/qc/ethnicity_check.R | import
node01.cluster | 219199 | 2020-02-10 18:06:16.593276 +0100 GMT | file code/qc/relatedness_filter.R | import
node01.cluster | 219199 | 2020-02-10 18:06:16.615917 +0100 GMT | file code/qc/update_pvar.R | import
node01.cluster | 219199 | 2020-02-10 18:06:16.630037 +0100 GMT | file code/check_imputation.sh | import
node01.cluster | 219199 | 2020-02-10 18:06:16.644365 +0100 GMT | file code/final_processing.sh | import
node01.cluster | 219199 | 2020-02-10 18:06:16.826978 +0100 GMT | | begin outdated()
node01.cluster | 219199 | 2020-02-10 18:06:16.843203 +0100 GMT | | find more outdated targets
node01.cluster | 219199 | 2020-02-10 18:06:16.862151 +0100 GMT | run_check_imputation | trigger file
node01.cluster | 219199 | 2020-02-10 18:06:16.886414 +0100 GMT | run_post_imputation | trigger change
node01.cluster | 219199 | 2020-02-10 18:06:16.892607 +0100 GMT | cp_qc_report | trigger change
node01.cluster | 219199 | 2020-02-10 18:06:16.894048 +0100 GMT | | find downstream outdated targets
node01.cluster | 219199 | 2020-02-10 18:06:16.902806 +0100 GMT | | end outdated()
node01.cluster | 219199 | 2020-02-10 18:06:16.904035 +0100 GMT | | isolate oudated targets
node01.cluster | 219199 | 2020-02-10 18:06:16.907589 +0100 GMT | | construct priority queue
node01.cluster | 219199 | 2020-02-10 18:06:16.964300 +0100 GMT | run_check_imputation | trigger file
node01.cluster | 219199 | 2020-02-10 18:06:17.123537 +0100 GMT | | set common data
node01.cluster | 219199 | 2020-02-10 18:06:17.139911 +0100 GMT | | begin scheduling targets
node01.cluster | 219199 | 2020-02-10 18:06:19.084052 +0100 GMT | | sending common data
node01.cluster | 219199 | 2020-02-10 18:06:19.439755 +0100 GMT | run_check_imputation | trigger file
node01.cluster | 219199 | 2020-02-10 18:06:19.446230 +0100 GMT | run_check_imputation | target run_check_imputation
node15.cluster | 172758 | 2020-02-10 18:06:19.455909 +0100 GMT | run_check_imputation | build on an hpc worker
node01.cluster | 219199 | 2020-02-10 22:03:41.442521 +0100 GMT | run_check_imputation | store
node01.cluster | 219199 | 2020-02-10 22:03:45.325528 +0100 GMT | run_check_imputation | time 14231.493s (~3.95 hours) | 14245.893s (~3.96 hours) (exec | total)
node01.cluster | 219199 | 2020-02-10 22:03:45.695335 +0100 GMT | run_post_imputation | trigger change
node01.cluster | 219199 | 2020-02-10 22:03:45.701437 +0100 GMT | run_post_imputation | target run_post_imputation
node15.cluster | 172758 | 2020-02-10 22:03:45.733448 +0100 GMT | run_post_imputation | build on an hpc worker
node01.cluster | 219199 | 2020-02-11 07:52:35.812523 +0100 GMT | run_post_imputation | store
node01.cluster | 219199 | 2020-02-11 07:52:36.222255 +0100 GMT | run_post_imputation | time 35329.645s (~9.81 hours) | 35330.701s (~9.81 hours) (exec | total)
node01.cluster | 219199 | 2020-02-11 07:52:36.761224 +0100 GMT | cp_qc_report | build locally
node01.cluster | 219199 | 2020-02-11 07:52:36.836987 +0100 GMT | cp_qc_report | trigger change
node01.cluster | 219199 | 2020-02-11 07:52:36.843526 +0100 GMT | cp_qc_report | target cp_qc_report
node01.cluster | 219199 | 2020-02-11 07:52:37.238189 +0100 GMT | cp_qc_report | store
node01.cluster | 219199 | 2020-02-11 07:52:37.283582 +0100 GMT | cp_qc_report | time 0.384s | 0.516s (exec | total)
node01.cluster | 219199 | 2020-02-11 07:52:37.387170 +0100 GMT | cp_qc_check | build locally
node01.cluster | 219199 | 2020-02-11 07:52:40.743002 +0100 GMT | cp_qc_check | trigger file
node01.cluster | 219199 | 2020-02-11 07:52:40.749573 +0100 GMT | cp_qc_check | target cp_qc_check
node01.cluster | 219199 | 2020-02-11 07:52:40.902057 +0100 GMT | cp_qc_check | store
node01.cluster | 219199 | 2020-02-11 07:52:41.216186 +0100 GMT | cp_qc_check | time 0.144s | 3.824s (exec | total)
node01.cluster | 219199 | 2020-02-11 09:12:00.945497 +0100 GMT | run_final_processing | trigger command
node01.cluster | 219199 | 2020-02-11 09:12:01.413790 +0100 GMT | run_final_processing | target run_final_processing
node01.cluster | 219199 | 2020-02-11 11:13:24.699287 +0100 GMT | | end make()
node01.cluster | 219199 | 2020-02-11 11:13:54.690274 +0100 GMT | | begin drake_config()
node01.cluster | 219199 | 2020-02-11 11:13:54.703256 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node01.cluster | 219199 | 2020-02-11 11:13:54.705910 +0100 GMT | | analyze environment
node01.cluster | 219199 | 2020-02-11 11:13:54.729971 +0100 GMT | | get knitr hash
node01.cluster | 219199 | 2020-02-11 11:13:54.736937 +0100 GMT | | set knitr files
node01.cluster | 219199 | 2020-02-11 11:13:54.744120 +0100 GMT | | create graph edges
node01.cluster | 219199 | 2020-02-11 11:13:54.752458 +0100 GMT | | connect output files
node01.cluster | 219199 | 2020-02-11 11:13:54.753738 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node01.cluster | 219199 | 2020-02-11 11:13:54.755425 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node01.cluster | 219199 | 2020-02-11 11:13:54.756962 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node01.cluster | 219199 | 2020-02-11 11:13:54.765947 +0100 GMT | | end drake_config()
node01.cluster | 219199 | 2020-02-11 11:13:54.766839 +0100 GMT | | begin make()
node01.cluster | 219199 | 2020-02-11 11:13:55.590187 +0100 GMT | processx::run | import
node01.cluster | 219199 | 2020-02-11 11:13:55.602902 +0100 GMT | file code/post_imputation_qc.sh | import
node01.cluster | 219199 | 2020-02-11 11:13:55.616722 +0100 GMT | file code/qc/maf_check.R | import
node01.cluster | 219199 | 2020-02-11 11:13:55.670197 +0100 GMT | file code/qc/ethnicity_check.R | import
node01.cluster | 219199 | 2020-02-11 11:13:55.718162 +0100 GMT | file code/qc/relatedness_filter.R | import
node01.cluster | 219199 | 2020-02-11 11:13:55.931679 +0100 GMT | file code/qc/update_pvar.R | import
node01.cluster | 219199 | 2020-02-11 11:13:55.974312 +0100 GMT | file code/check_imputation.sh | import
node01.cluster | 219199 | 2020-02-11 11:13:56.013479 +0100 GMT | file code/final_processing.sh | import
node01.cluster | 219199 | 2020-02-11 11:13:56.037197 +0100 GMT | | begin outdated()
node01.cluster | 219199 | 2020-02-11 11:13:56.046216 +0100 GMT | | find more outdated targets
node01.cluster | 219199 | 2020-02-11 11:13:57.852941 +0100 GMT | run_check_imputation | skip
node01.cluster | 219199 | 2020-02-11 11:13:57.869831 +0100 GMT | run_post_imputation | skip
node01.cluster | 219199 | 2020-02-11 11:13:57.874089 +0100 GMT | cp_qc_report | skip
node01.cluster | 219199 | 2020-02-11 11:13:57.875574 +0100 GMT | | find more outdated targets
node01.cluster | 219199 | 2020-02-11 11:13:59.660212 +0100 GMT | cp_qc_check | skip
node01.cluster | 219199 | 2020-02-11 11:13:59.669189 +0100 GMT | run_final_processing | trigger change
node01.cluster | 219199 | 2020-02-11 11:13:59.670700 +0100 GMT | | find more outdated targets
node01.cluster | 219199 | 2020-02-11 11:13:59.672994 +0100 GMT | | find downstream outdated targets
node01.cluster | 219199 | 2020-02-11 11:13:59.675654 +0100 GMT | | end outdated()
node01.cluster | 219199 | 2020-02-11 11:13:59.676693 +0100 GMT | | isolate oudated targets
node01.cluster | 219199 | 2020-02-11 11:13:59.679215 +0100 GMT | | construct priority queue
node01.cluster | 219199 | 2020-02-11 11:13:59.688242 +0100 GMT | run_final_processing | trigger change
node01.cluster | 219199 | 2020-02-11 11:13:59.854969 +0100 GMT | | set common data
node01.cluster | 219199 | 2020-02-11 11:13:59.869707 +0100 GMT | | begin scheduling targets
node01.cluster | 219199 | 2020-02-11 11:14:06.740359 +0100 GMT | | sending common data
node01.cluster | 219199 | 2020-02-11 11:14:07.757828 +0100 GMT | run_final_processing | trigger change
node01.cluster | 219199 | 2020-02-11 11:14:07.761862 +0100 GMT | run_final_processing | target run_final_processing
node01.cluster | 219199 | 2020-02-11 11:14:07.766015 +0100 GMT | | load run_post_imputation
node15.cluster | 179702 | 2020-02-11 11:14:07.779479 +0100 GMT | run_final_processing | build on an hpc worker
node01.cluster | 219199 | 2020-02-11 13:34:57.348500 +0100 GMT | run_final_processing | store
node01.cluster | 219199 | 2020-02-11 13:34:57.687357 +0100 GMT | run_final_processing | time 8440.96s (~2.34 hours) | 8449.933s (~2.35 hours) (exec | total)
node01.cluster | 219199 | 2020-02-11 13:35:07.450065 +0100 GMT | | end make()
master.cluster | 91607 | 2020-02-13 14:52:20.925765 +0100 GMT | | begin drake_config()
master.cluster | 91607 | 2020-02-13 14:52:21.001545 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
master.cluster | 91607 | 2020-02-13 14:52:21.008600 +0100 GMT | | analyze environment
master.cluster | 91607 | 2020-02-13 14:52:21.063310 +0100 GMT | | analyze imports
master.cluster | 91607 | 2020-02-13 14:52:21.301632 +0100 GMT | | get knitr hash
master.cluster | 91607 | 2020-02-13 14:52:21.308776 +0100 GMT | | analyze commands
master.cluster | 91607 | 2020-02-13 14:52:21.328882 +0100 GMT | | set knitr files
master.cluster | 91607 | 2020-02-13 14:52:21.337582 +0100 GMT | | create graph edges
master.cluster | 91607 | 2020-02-13 14:52:21.346998 +0100 GMT | | connect output files
master.cluster | 91607 | 2020-02-13 14:52:21.348802 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
master.cluster | 91607 | 2020-02-13 14:52:21.351427 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
master.cluster | 91607 | 2020-02-13 14:52:21.353656 +0100 GMT | file analysis/QC/07_imputation_check | file_out
master.cluster | 91607 | 2020-02-13 14:52:21.362537 +0100 GMT | | finalize graph edges
master.cluster | 91607 | 2020-02-13 14:52:21.364531 +0100 GMT | | create igraph
master.cluster | 91607 | 2020-02-13 14:52:21.367067 +0100 GMT | | trim neighborhoods
master.cluster | 91607 | 2020-02-13 14:52:21.566662 +0100 GMT | | add igraph attributes
master.cluster | 91607 | 2020-02-13 14:52:21.573539 +0100 GMT | | finalize igraph
master.cluster | 91607 | 2020-02-13 14:52:21.585199 +0100 GMT | | end drake_config()
master.cluster | 91607 | 2020-02-13 14:52:21.587315 +0100 GMT | | begin make()
master.cluster | 91607 | 2020-02-13 14:52:25.831222 +0100 GMT | dplyr::select | import
master.cluster | 91607 | 2020-02-13 14:52:25.851851 +0100 GMT | processx::run | import
master.cluster | 91607 | 2020-02-13 14:52:25.872406 +0100 GMT | file code/post_imputation_qc.sh | import
master.cluster | 91607 | 2020-02-13 14:52:25.892910 +0100 GMT | file code/qc/maf_check.R | import
master.cluster | 91607 | 2020-02-13 14:52:25.912017 +0100 GMT | file code/qc/ethnicity_check.R | import
master.cluster | 91607 | 2020-02-13 14:52:25.930526 +0100 GMT | file code/qc/relatedness_filter.R | import
master.cluster | 91607 | 2020-02-13 14:52:25.949840 +0100 GMT | file code/qc/update_pvar.R | import
master.cluster | 91607 | 2020-02-13 14:52:25.967935 +0100 GMT | file code/final_processing.sh | import
master.cluster | 91607 | 2020-02-13 14:52:25.988880 +0100 GMT | file analysis/QC/12_ethnicity_admixture/snpweights | import
master.cluster | 91607 | 2020-02-13 14:52:26.008611 +0100 GMT | file .NA.predpc | missing missing
master.cluster | 91607 | 2020-02-13 14:52:26.021032 +0100 GMT | file PSYMETAB_GWAS | missing missing
master.cluster | 91607 | 2020-02-13 14:52:26.032037 +0100 GMT | file code/check_imputation.sh | import
master.cluster | 91607 | 2020-02-13 14:52:26.071614 +0100 GMT | munge_snp_weights | import
master.cluster | 91607 | 2020-02-13 14:52:26.084405 +0100 GMT | | begin outdated()
master.cluster | 91607 | 2020-02-13 14:52:26.096590 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-13 14:52:26.127402 +0100 GMT | run_post_imputation | skip
master.cluster | 91607 | 2020-02-13 14:52:28.320258 +0100 GMT | run_check_imputation | skip
master.cluster | 91607 | 2020-02-13 14:52:28.326714 +0100 GMT | cp_qc_report | skip
master.cluster | 91607 | 2020-02-13 14:52:28.329147 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-13 14:52:30.432667 +0100 GMT | cp_qc_check | skip
master.cluster | 91607 | 2020-02-13 14:52:30.445711 +0100 GMT | run_final_processing | skip
master.cluster | 91607 | 2020-02-13 14:52:30.448153 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-13 14:52:30.451813 +0100 GMT | | find downstream outdated targets
master.cluster | 91607 | 2020-02-13 14:52:30.459737 +0100 GMT | | end outdated()
master.cluster | 91607 | 2020-02-13 14:52:30.461526 +0100 GMT | | isolate oudated targets
master.cluster | 91607 | 2020-02-13 14:52:30.466488 +0100 GMT | | construct priority queue
master.cluster | 91607 | 2020-02-13 14:52:30.475960 +0100 GMT | snp_weights | build locally
master.cluster | 91607 | 2020-02-13 14:52:30.488063 +0100 GMT | snp_weights | trigger missing
master.cluster | 91607 | 2020-02-13 14:52:30.493052 +0100 GMT | snp_weights | target snp_weights
master.cluster | 91607 | 2020-02-13 14:52:30.499075 +0100 GMT | | load run_post_imputation
master.cluster | 91607 | 2020-02-13 14:52:30.529553 +0100 GMT | snp_weights | Warning: cannot open file 'analysis/QC/12_ethnicity_admixture/snpweightsPSYMETAB_GWAS.NA.predpc': No such file or directory
master.cluster | 91607 | 2020-02-13 14:52:30.534051 +0100 GMT | snp_weights | fail snp_weights
master.cluster | 91607 | 2020-02-13 14:52:30.547574 +0100 GMT | | Target `snp_weights` failed. Call `diagnose(snp_weights)` for details. Error message:
cannot open the connection
master.cluster | 91607 | 2020-02-13 14:52:30.550548 +0100 GMT | | end make()
master.cluster | 91607 | 2020-02-13 14:52:55.115198 +0100 GMT | | begin drake_config()
master.cluster | 91607 | 2020-02-13 14:52:55.130792 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
master.cluster | 91607 | 2020-02-13 14:52:55.135033 +0100 GMT | | analyze environment
master.cluster | 91607 | 2020-02-13 14:52:55.160137 +0100 GMT | | analyze imports
master.cluster | 91607 | 2020-02-13 14:52:55.396951 +0100 GMT | | get knitr hash
master.cluster | 91607 | 2020-02-13 14:52:55.403950 +0100 GMT | | analyze commands
master.cluster | 91607 | 2020-02-13 14:52:55.424587 +0100 GMT | | set knitr files
master.cluster | 91607 | 2020-02-13 14:52:55.485654 +0100 GMT | | create graph edges
master.cluster | 91607 | 2020-02-13 14:52:55.498469 +0100 GMT | | connect output files
master.cluster | 91607 | 2020-02-13 14:52:55.501011 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
master.cluster | 91607 | 2020-02-13 14:52:55.503979 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
master.cluster | 91607 | 2020-02-13 14:52:55.506639 +0100 GMT | file analysis/QC/07_imputation_check | file_out
master.cluster | 91607 | 2020-02-13 14:52:55.517826 +0100 GMT | | finalize graph edges
master.cluster | 91607 | 2020-02-13 14:52:55.520147 +0100 GMT | | create igraph
master.cluster | 91607 | 2020-02-13 14:52:55.523256 +0100 GMT | | trim neighborhoods
master.cluster | 91607 | 2020-02-13 14:52:55.532523 +0100 GMT | | add igraph attributes
master.cluster | 91607 | 2020-02-13 14:52:55.535964 +0100 GMT | | finalize igraph
master.cluster | 91607 | 2020-02-13 14:52:55.546309 +0100 GMT | | end drake_config()
master.cluster | 91607 | 2020-02-13 14:52:55.548204 +0100 GMT | | begin make()
master.cluster | 91607 | 2020-02-13 14:52:55.753792 +0100 GMT | dplyr::select | import
master.cluster | 91607 | 2020-02-13 14:52:55.770105 +0100 GMT | processx::run | import
master.cluster | 91607 | 2020-02-13 14:52:55.795067 +0100 GMT | file code/post_imputation_qc.sh | import
master.cluster | 91607 | 2020-02-13 14:52:55.813873 +0100 GMT | file code/qc/maf_check.R | import
master.cluster | 91607 | 2020-02-13 14:52:55.832048 +0100 GMT | file code/qc/ethnicity_check.R | import
master.cluster | 91607 | 2020-02-13 14:52:55.849017 +0100 GMT | file code/qc/relatedness_filter.R | import
master.cluster | 91607 | 2020-02-13 14:52:55.866428 +0100 GMT | file code/qc/update_pvar.R | import
master.cluster | 91607 | 2020-02-13 14:52:55.882449 +0100 GMT | file code/final_processing.sh | import
master.cluster | 91607 | 2020-02-13 14:52:55.903486 +0100 GMT | file analysis/QC/12_ethnicity_admixture/snpweights/ | import
master.cluster | 91607 | 2020-02-13 14:52:56.245591 +0100 GMT | file .NA.predpc | missing missing
master.cluster | 91607 | 2020-02-13 14:52:56.446889 +0100 GMT | file PSYMETAB_GWAS | missing missing
master.cluster | 91607 | 2020-02-13 14:52:56.467451 +0100 GMT | file code/check_imputation.sh | import
master.cluster | 91607 | 2020-02-13 14:52:56.497082 +0100 GMT | munge_snp_weights | import
master.cluster | 91607 | 2020-02-13 14:52:56.513091 +0100 GMT | | begin outdated()
master.cluster | 91607 | 2020-02-13 14:52:56.528233 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-13 14:52:56.566084 +0100 GMT | run_post_imputation | skip
master.cluster | 91607 | 2020-02-13 14:52:58.653739 +0100 GMT | run_check_imputation | skip
master.cluster | 91607 | 2020-02-13 14:52:58.660319 +0100 GMT | cp_qc_report | skip
master.cluster | 91607 | 2020-02-13 14:52:58.662770 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-13 14:53:00.747688 +0100 GMT | cp_qc_check | skip
master.cluster | 91607 | 2020-02-13 14:53:00.759946 +0100 GMT | run_final_processing | skip
master.cluster | 91607 | 2020-02-13 14:53:00.762355 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-13 14:53:00.765682 +0100 GMT | | find downstream outdated targets
master.cluster | 91607 | 2020-02-13 14:53:00.772980 +0100 GMT | | end outdated()
master.cluster | 91607 | 2020-02-13 14:53:00.774762 +0100 GMT | | isolate oudated targets
master.cluster | 91607 | 2020-02-13 14:53:00.778400 +0100 GMT | | construct priority queue
master.cluster | 91607 | 2020-02-13 14:53:00.821114 +0100 GMT | snp_weights | build locally
master.cluster | 91607 | 2020-02-13 14:53:01.121618 +0100 GMT | snp_weights | trigger missing
master.cluster | 91607 | 2020-02-13 14:53:01.144691 +0100 GMT | snp_weights | target snp_weights
master.cluster | 91607 | 2020-02-13 14:53:01.150555 +0100 GMT | | load run_post_imputation
master.cluster | 91607 | 2020-02-13 14:53:01.309360 +0100 GMT | snp_weights | store
master.cluster | 91607 | 2020-02-13 14:53:01.348900 +0100 GMT | snp_weights | time 0.153s | 0.521s (exec | total)
master.cluster | 91607 | 2020-02-13 14:53:01.419323 +0100 GMT | snp_weights_munge | build locally
master.cluster | 91607 | 2020-02-13 14:53:01.426701 +0100 GMT | snp_weights_munge | trigger missing
master.cluster | 91607 | 2020-02-13 14:53:01.431708 +0100 GMT | snp_weights_munge | target snp_weights_munge
master.cluster | 91607 | 2020-02-13 14:53:01.472209 +0100 GMT | snp_weights_munge | store
master.cluster | 91607 | 2020-02-13 14:53:01.506734 +0100 GMT | snp_weights_munge | time 0.034s | 0.084s (exec | total)
master.cluster | 91607 | 2020-02-13 14:53:01.529100 +0100 GMT | snp_weights_out | build locally
master.cluster | 91607 | 2020-02-13 14:53:01.557932 +0100 GMT | snp_weights_out | trigger missing
master.cluster | 91607 | 2020-02-13 14:53:01.562184 +0100 GMT | snp_weights_out | target snp_weights_out
master.cluster | 91607 | 2020-02-13 14:53:02.504385 +0100 GMT | snp_weights_out | store
master.cluster | 91607 | 2020-02-13 14:53:02.529478 +0100 GMT | snp_weights_out | time 0.936s | 0.971s (exec | total)
master.cluster | 91607 | 2020-02-13 14:53:06.009341 +0100 GMT | | end make()
master.cluster | 91607 | 2020-02-13 14:54:22.663864 +0100 GMT | | begin drake_config()
master.cluster | 91607 | 2020-02-13 14:54:22.690031 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
master.cluster | 91607 | 2020-02-13 14:54:22.696154 +0100 GMT | | analyze environment
master.cluster | 91607 | 2020-02-13 14:54:22.730345 +0100 GMT | | analyze imports
master.cluster | 91607 | 2020-02-13 14:54:22.935493 +0100 GMT | | get knitr hash
master.cluster | 91607 | 2020-02-13 14:54:22.941688 +0100 GMT | | analyze commands
master.cluster | 91607 | 2020-02-13 14:54:22.961376 +0100 GMT | | set knitr files
master.cluster | 91607 | 2020-02-13 14:54:22.970563 +0100 GMT | | create graph edges
master.cluster | 91607 | 2020-02-13 14:54:22.980089 +0100 GMT | | connect output files
master.cluster | 91607 | 2020-02-13 14:54:22.982052 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
master.cluster | 91607 | 2020-02-13 14:54:22.984521 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
master.cluster | 91607 | 2020-02-13 14:54:22.986645 +0100 GMT | file analysis/QC/07_imputation_check | file_out
master.cluster | 91607 | 2020-02-13 14:54:22.995398 +0100 GMT | | finalize graph edges
master.cluster | 91607 | 2020-02-13 14:54:22.997323 +0100 GMT | | create igraph
master.cluster | 91607 | 2020-02-13 14:54:22.999768 +0100 GMT | | trim neighborhoods
master.cluster | 91607 | 2020-02-13 14:54:23.007227 +0100 GMT | | add igraph attributes
master.cluster | 91607 | 2020-02-13 14:54:23.009924 +0100 GMT | | finalize igraph
master.cluster | 91607 | 2020-02-13 14:54:23.025309 +0100 GMT | | end drake_config()
master.cluster | 91607 | 2020-02-13 14:54:23.027038 +0100 GMT | | begin make()
master.cluster | 91607 | 2020-02-13 14:54:23.255458 +0100 GMT | dplyr::select | import
master.cluster | 91607 | 2020-02-13 14:54:23.273520 +0100 GMT | processx::run | import
master.cluster | 91607 | 2020-02-13 14:54:23.291915 +0100 GMT | file code/post_imputation_qc.sh | import
master.cluster | 91607 | 2020-02-13 14:54:23.313321 +0100 GMT | file code/qc/maf_check.R | import
master.cluster | 91607 | 2020-02-13 14:54:23.333344 +0100 GMT | file code/qc/ethnicity_check.R | import
master.cluster | 91607 | 2020-02-13 14:54:23.353559 +0100 GMT | file code/qc/relatedness_filter.R | import
master.cluster | 91607 | 2020-02-13 14:54:23.374024 +0100 GMT | file code/qc/update_pvar.R | import
master.cluster | 91607 | 2020-02-13 14:54:23.393298 +0100 GMT | file code/final_processing.sh | import
master.cluster | 91607 | 2020-02-13 14:54:23.413223 +0100 GMT | file analysis/QC/12_ethnicity_admixture/snpweights/PSYMETAB_GWAS.NA.predpc | import
master.cluster | 91607 | 2020-02-13 14:54:23.530713 +0100 GMT | file code/check_imputation.sh | import
master.cluster | 91607 | 2020-02-13 14:54:23.560747 +0100 GMT | munge_snp_weights | import
master.cluster | 91607 | 2020-02-13 14:54:23.589342 +0100 GMT | | begin outdated()
master.cluster | 91607 | 2020-02-13 14:54:23.603960 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-13 14:54:23.649876 +0100 GMT | run_post_imputation | skip
master.cluster | 91607 | 2020-02-13 14:54:25.805170 +0100 GMT | run_check_imputation | skip
master.cluster | 91607 | 2020-02-13 14:54:25.812756 +0100 GMT | cp_qc_report | skip
master.cluster | 91607 | 2020-02-13 14:54:25.815320 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-13 14:54:25.827155 +0100 GMT | snp_weights | trigger command
master.cluster | 91607 | 2020-02-13 14:54:27.909867 +0100 GMT | cp_qc_check | skip
master.cluster | 91607 | 2020-02-13 14:54:27.921400 +0100 GMT | run_final_processing | skip
master.cluster | 91607 | 2020-02-13 14:54:27.923941 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-13 14:54:27.927040 +0100 GMT | | find downstream outdated targets
master.cluster | 91607 | 2020-02-13 14:54:27.934157 +0100 GMT | | end outdated()
master.cluster | 91607 | 2020-02-13 14:54:27.935921 +0100 GMT | | isolate oudated targets
master.cluster | 91607 | 2020-02-13 14:54:27.939693 +0100 GMT | | construct priority queue
master.cluster | 91607 | 2020-02-13 14:54:27.945320 +0100 GMT | snp_weights | build locally
master.cluster | 91607 | 2020-02-13 14:54:27.951285 +0100 GMT | snp_weights | trigger command
master.cluster | 91607 | 2020-02-13 14:54:27.955116 +0100 GMT | snp_weights | target snp_weights
master.cluster | 91607 | 2020-02-13 14:54:27.959257 +0100 GMT | | load run_post_imputation
master.cluster | 91607 | 2020-02-13 14:54:28.001890 +0100 GMT | snp_weights | store
master.cluster | 91607 | 2020-02-13 14:54:28.010132 +0100 GMT | snp_weights | time 0.039s | 0.061s (exec | total)
master.cluster | 91607 | 2020-02-13 14:54:28.026990 +0100 GMT | snp_weights_munge | build locally
master.cluster | 91607 | 2020-02-13 14:54:28.033532 +0100 GMT | snp_weights_munge | skip
master.cluster | 91607 | 2020-02-13 14:54:28.038519 +0100 GMT | snp_weights_out | build locally
master.cluster | 91607 | 2020-02-13 14:54:28.043772 +0100 GMT | snp_weights_out | trigger command
master.cluster | 91607 | 2020-02-13 14:54:28.047060 +0100 GMT | snp_weights_out | target snp_weights_out
master.cluster | 91607 | 2020-02-13 14:54:28.051118 +0100 GMT | | load snp_weights_munge
master.cluster | 91607 | 2020-02-13 14:54:28.102406 +0100 GMT | snp_weights_out | store
master.cluster | 91607 | 2020-02-13 14:54:28.110019 +0100 GMT | snp_weights_out | time 0.043s | 0.068s (exec | total)
master.cluster | 91607 | 2020-02-13 14:54:28.889962 +0100 GMT | | end make()
master.cluster | 91607 | 2020-02-19 16:43:28.971260 +0100 GMT | | begin drake_config()
master.cluster | 91607 | 2020-02-19 16:43:29.015552 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
master.cluster | 91607 | 2020-02-19 16:43:29.075364 +0100 GMT | | analyze environment
master.cluster|91607|2020-02-19 16:43:29.079369 +0100 GMT||unloadtargets from environment:
snp_weights_munge
snp_weights
related_inds
master.cluster | 91607 | 2020-02-19 16:43:29.204002 +0100 GMT | | analyze imports
master.cluster | 91607 | 2020-02-19 16:43:29.849575 +0100 GMT | | get knitr hash
master.cluster | 91607 | 2020-02-19 16:43:29.881978 +0100 GMT | | analyze commands
master.cluster | 91607 | 2020-02-19 16:43:29.930211 +0100 GMT | | set knitr files
master.cluster | 91607 | 2020-02-19 16:43:29.957984 +0100 GMT | | create graph edges
master.cluster | 91607 | 2020-02-19 16:43:29.967652 +0100 GMT | | connect output files
master.cluster | 91607 | 2020-02-19 16:43:29.969624 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
master.cluster | 91607 | 2020-02-19 16:43:29.971998 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
master.cluster | 91607 | 2020-02-19 16:43:30.049380 +0100 GMT | file analysis/QC/07_imputation_check | file_out
master.cluster | 91607 | 2020-02-19 16:43:30.086418 +0100 GMT | | finalize graph edges
master.cluster | 91607 | 2020-02-19 16:43:30.088241 +0100 GMT | | create igraph
master.cluster | 91607 | 2020-02-19 16:43:30.171112 +0100 GMT | | trim neighborhoods
master.cluster | 91607 | 2020-02-19 16:43:30.200673 +0100 GMT | | add igraph attributes
master.cluster | 91607 | 2020-02-19 16:43:30.203401 +0100 GMT | | finalize igraph
master.cluster | 91607 | 2020-02-19 16:43:30.225160 +0100 GMT | | end drake_config()
master.cluster | 91607 | 2020-02-19 16:43:30.226718 +0100 GMT | | begin make()
master.cluster | 91607 | 2020-02-19 16:43:37.740991 +0100 GMT | processx::run | import
master.cluster | 91607 | 2020-02-19 16:43:37.790482 +0100 GMT | dplyr::select | import
master.cluster | 91607 | 2020-02-19 16:43:37.891549 +0100 GMT | file analysis/QC/11_relatedness/PSYMETAB_GWAS_related_ids.txt | import
master.cluster | 91607 | 2020-02-19 16:43:37.931701 +0100 GMT | file code/final_processing.sh | import
master.cluster | 91607 | 2020-02-19 16:43:38.033636 +0100 GMT | file analysis/QC/12_ethnicity_admixture/snpweights/PSYMETAB_GWAS.NA.predpc | import
master.cluster | 91607 | 2020-02-19 16:43:38.165647 +0100 GMT | file code/check_imputation.sh | import
master.cluster | 91607 | 2020-02-19 16:43:38.228691 +0100 GMT | file code/post_imputation_qc.sh | import
master.cluster | 91607 | 2020-02-19 16:43:38.298039 +0100 GMT | file code/qc/maf_check.R | import
master.cluster | 91607 | 2020-02-19 16:43:38.358335 +0100 GMT | file code/qc/ethnicity_check.R | import
master.cluster | 91607 | 2020-02-19 16:43:38.426124 +0100 GMT | file code/qc/relatedness_filter.R | import
master.cluster | 91607 | 2020-02-19 16:43:38.493579 +0100 GMT | file code/qc/update_pvar.R | import
master.cluster | 91607 | 2020-02-19 16:43:38.573107 +0100 GMT | munge_snp_weights | import
master.cluster | 91607 | 2020-02-19 16:43:38.599395 +0100 GMT | | begin outdated()
master.cluster | 91607 | 2020-02-19 16:43:38.624679 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-19 16:43:38.755181 +0100 GMT | run_post_imputation | skip
master.cluster | 91607 | 2020-02-19 16:44:14.763808 +0100 GMT | run_check_imputation | skip
master.cluster | 91607 | 2020-02-19 16:44:14.811773 +0100 GMT | cp_qc_report | skip
master.cluster | 91607 | 2020-02-19 16:44:14.814343 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-19 16:44:18.012956 +0100 GMT | cp_qc_check | skip
master.cluster | 91607 | 2020-02-19 16:44:18.029495 +0100 GMT | snp_weights | skip
master.cluster | 91607 | 2020-02-19 16:44:18.083781 +0100 GMT | run_final_processing | skip
master.cluster | 91607 | 2020-02-19 16:44:18.087337 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-19 16:44:18.091901 +0100 GMT | | find downstream outdated targets
master.cluster | 91607 | 2020-02-19 16:44:18.101128 +0100 GMT | | end outdated()
master.cluster | 91607 | 2020-02-19 16:44:18.103125 +0100 GMT | | isolate oudated targets
master.cluster | 91607 | 2020-02-19 16:44:18.107838 +0100 GMT | | construct priority queue
master.cluster | 91607 | 2020-02-19 16:44:18.114652 +0100 GMT | related_inds | build locally
master.cluster | 91607 | 2020-02-19 16:44:18.120138 +0100 GMT | related_inds | trigger missing
master.cluster | 91607 | 2020-02-19 16:44:18.125410 +0100 GMT | related_inds | target related_inds
master.cluster | 91607 | 2020-02-19 16:44:18.130527 +0100 GMT | | load run_post_imputation
master.cluster | 91607 | 2020-02-19 16:44:18.194575 +0100 GMT | related_inds | store
master.cluster | 91607 | 2020-02-19 16:44:18.212876 +0100 GMT | related_inds | time 0.048s | 0.093s (exec | total)
master.cluster | 91607 | 2020-02-19 16:44:18.276297 +0100 GMT | snp_weights_munge | build locally
master.cluster | 91607 | 2020-02-19 16:44:18.294587 +0100 GMT | snp_weights_munge | trigger command
master.cluster | 91607 | 2020-02-19 16:44:18.299942 +0100 GMT | snp_weights_munge | target snp_weights_munge
master.cluster | 91607 | 2020-02-19 16:44:18.305393 +0100 GMT | | load snp_weights
master.cluster | 91607 | 2020-02-19 16:44:18.317942 +0100 GMT | snp_weights_munge | fail snp_weights_munge
master.cluster | 91607 | 2020-02-19 16:44:18.357742 +0100 GMT | | Target `snp_weights_munge` failed. Call `diagnose(snp_weights_munge)` for details. Error message:
unused argument (related_inds)
master.cluster | 91607 | 2020-02-19 16:44:18.360485 +0100 GMT | | end make()
master.cluster | 91607 | 2020-02-19 16:45:07.263493 +0100 GMT | | begin drake_config()
master.cluster | 91607 | 2020-02-19 16:45:07.278054 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
master.cluster | 91607 | 2020-02-19 16:45:07.281571 +0100 GMT | | analyze environment
master.cluster | 91607 | 2020-02-19 16:45:07.334878 +0100 GMT | | analyze imports
master.cluster | 91607 | 2020-02-19 16:45:07.519276 +0100 GMT | | get knitr hash
master.cluster | 91607 | 2020-02-19 16:45:07.527849 +0100 GMT | | analyze commands
master.cluster | 91607 | 2020-02-19 16:45:07.559223 +0100 GMT | | set knitr files
master.cluster | 91607 | 2020-02-19 16:45:07.575149 +0100 GMT | | end drake_config()
master.cluster | 91607 | 2020-02-19 16:45:07.576712 +0100 GMT | | begin make()
master.cluster | 91607 | 2020-02-19 16:45:07.730431 +0100 GMT | processx::run | import
master.cluster | 91607 | 2020-02-19 16:45:07.743475 +0100 GMT | dplyr::select | import
master.cluster | 91607 | 2020-02-19 16:45:07.754923 +0100 GMT | file analysis/QC/11_relatedness/PSYMETAB_GWAS_related_ids.txt | import
master.cluster | 91607 | 2020-02-19 16:45:07.769078 +0100 GMT | file code/final_processing.sh | import
master.cluster | 91607 | 2020-02-19 16:45:07.782311 +0100 GMT | file analysis/QC/12_ethnicity_admixture/snpweights/PSYMETAB_GWAS.NA.predpc | import
master.cluster | 91607 | 2020-02-19 16:45:07.796269 +0100 GMT | file code/check_imputation.sh | import
master.cluster | 91607 | 2020-02-19 16:45:07.809806 +0100 GMT | file code/post_imputation_qc.sh | import
master.cluster | 91607 | 2020-02-19 16:45:07.823698 +0100 GMT | file code/qc/maf_check.R | import
master.cluster | 91607 | 2020-02-19 16:45:07.837072 +0100 GMT | file code/qc/ethnicity_check.R | import
master.cluster | 91607 | 2020-02-19 16:45:07.850467 +0100 GMT | file code/qc/relatedness_filter.R | import
master.cluster | 91607 | 2020-02-19 16:45:07.865145 +0100 GMT | file code/qc/update_pvar.R | import
master.cluster | 91607 | 2020-02-19 16:45:07.895309 +0100 GMT | munge_snp_weights | import
master.cluster | 91607 | 2020-02-19 16:45:07.909448 +0100 GMT | | begin outdated()
master.cluster | 91607 | 2020-02-19 16:45:07.919067 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-19 16:45:07.972762 +0100 GMT | run_post_imputation | skip
master.cluster | 91607 | 2020-02-19 16:45:10.476664 +0100 GMT | run_check_imputation | skip
master.cluster | 91607 | 2020-02-19 16:45:10.482657 +0100 GMT | cp_qc_report | skip
master.cluster | 91607 | 2020-02-19 16:45:10.484837 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-19 16:45:13.548395 +0100 GMT | cp_qc_check | skip
master.cluster | 91607 | 2020-02-19 16:45:13.560666 +0100 GMT | snp_weights | skip
master.cluster | 91607 | 2020-02-19 16:45:13.570683 +0100 GMT | related_inds | skip
master.cluster | 91607 | 2020-02-19 16:45:13.581802 +0100 GMT | run_final_processing | skip
master.cluster | 91607 | 2020-02-19 16:45:13.584939 +0100 GMT | | find more outdated targets
master.cluster | 91607 | 2020-02-19 16:45:13.594945 +0100 GMT | snp_weights_munge | trigger command
master.cluster | 91607 | 2020-02-19 16:45:13.596757 +0100 GMT | | find downstream outdated targets
master.cluster | 91607 | 2020-02-19 16:45:13.603985 +0100 GMT | | end outdated()
master.cluster | 91607 | 2020-02-19 16:45:13.605631 +0100 GMT | | isolate oudated targets
master.cluster | 91607 | 2020-02-19 16:45:13.610893 +0100 GMT | | construct priority queue
master.cluster | 91607 | 2020-02-19 16:45:13.619876 +0100 GMT | snp_weights_munge | build locally
master.cluster | 91607 | 2020-02-19 16:45:13.627013 +0100 GMT | snp_weights_munge | trigger command
master.cluster | 91607 | 2020-02-19 16:45:13.633034 +0100 GMT | snp_weights_munge | target snp_weights_munge
master.cluster | 91607 | 2020-02-19 16:45:13.640923 +0100 GMT | | load snp_weights
master.cluster | 91607 | 2020-02-19 16:45:13.640923 +0100 GMT | | load related_inds
master.cluster | 91607 | 2020-02-19 16:45:13.711697 +0100 GMT | snp_weights_munge | store
master.cluster | 91607 | 2020-02-19 16:45:13.744856 +0100 GMT | snp_weights_munge | time 0.057s | 0.12s (exec | total)
master.cluster | 91607 | 2020-02-19 16:45:13.767046 +0100 GMT | snp_weights_out | build locally
master.cluster | 91607 | 2020-02-19 16:45:13.788133 +0100 GMT | snp_weights_out | trigger depend
master.cluster | 91607 | 2020-02-19 16:45:13.792381 +0100 GMT | snp_weights_out | target snp_weights_out
master.cluster | 91607 | 2020-02-19 16:45:13.927392 +0100 GMT | snp_weights_out | store
master.cluster | 91607 | 2020-02-19 16:45:13.936038 +0100 GMT | snp_weights_out | time 0.129s | 0.165s (exec | total)
master.cluster | 91607 | 2020-02-19 16:45:21.753247 +0100 GMT | | end make()
node14.cluster | 240503 | 2020-03-12 11:26:01.708512 +0100 GMT | | begin drake_config()
node14.cluster | 240503 | 2020-03-12 11:26:01.949661 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node14.cluster | 240503 | 2020-03-12 11:26:01.957753 +0100 GMT | | analyze environment
node14.cluster | 240503 | 2020-03-12 11:26:02.060475 +0100 GMT | | analyze imports
node14.cluster | 240503 | 2020-03-12 11:26:02.351527 +0100 GMT | | get knitr hash
node14.cluster | 240503 | 2020-03-12 11:26:02.392462 +0100 GMT | | analyze commands
node14.cluster | 240503 | 2020-03-12 11:26:02.455569 +0100 GMT | | set knitr files
node14.cluster | 240503 | 2020-03-12 11:26:02.497241 +0100 GMT | | create graph edges
node14.cluster | 240503 | 2020-03-12 11:26:02.519737 +0100 GMT | | connect output files
node14.cluster | 240503 | 2020-03-12 11:26:02.521135 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node14.cluster | 240503 | 2020-03-12 11:26:02.523308 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node14.cluster | 240503 | 2020-03-12 11:26:02.524657 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node14.cluster | 240503 | 2020-03-12 11:26:02.525990 +0100 GMT | file docs/generated_reports/qcreport.html | file_out
node14.cluster | 240503 | 2020-03-12 11:26:02.546383 +0100 GMT | | finalize graph edges
node14.cluster | 240503 | 2020-03-12 11:26:02.547622 +0100 GMT | | create igraph
node14.cluster | 240503 | 2020-03-12 11:26:02.549502 +0100 GMT | | trim neighborhoods
node14.cluster | 240503 | 2020-03-12 11:26:02.555089 +0100 GMT | | add igraph attributes
node14.cluster | 240503 | 2020-03-12 11:26:02.557790 +0100 GMT | | finalize igraph
node14.cluster | 240503 | 2020-03-12 11:26:02.587941 +0100 GMT | | end drake_config()
node14.cluster | 240503 | 2020-03-12 11:26:02.588928 +0100 GMT | | begin make()
node14.cluster | 240503 | 2020-03-12 11:26:07.671868 +0100 GMT | file analysis/QC/11_relatedness/PSYMETAB_GWAS_related_ids.txt | missing missing
node14.cluster | 240503 | 2020-03-12 11:26:07.751310 +0100 GMT | processx::run | import
node14.cluster | 240503 | 2020-03-12 11:26:07.777747 +0100 GMT | file code/check_imputation.sh | import
node14.cluster | 240503 | 2020-03-12 11:26:07.851945 +0100 GMT | file analysis/QC/12_ethnicity_admixture/snpweights/PSYMETAB_GWAS.NA.predpc | missing missing
node14.cluster | 240503 | 2020-03-12 11:26:07.950134 +0100 GMT | file code/post_imputation_qc.sh | import
node14.cluster | 240503 | 2020-03-12 11:26:07.986002 +0100 GMT | file code/qc/maf_check.R | import
node14.cluster | 240503 | 2020-03-12 11:26:08.003577 +0100 GMT | file code/qc/ethnicity_check.R | import
node14.cluster | 240503 | 2020-03-12 11:26:08.029136 +0100 GMT | file code/qc/relatedness_filter.R | import
node14.cluster | 240503 | 2020-03-12 11:26:08.048184 +0100 GMT | file code/qc/update_pvar.R | import
node14.cluster | 240503 | 2020-03-12 11:26:08.186016 +0100 GMT | file code/final_processing.sh | import
node14.cluster | 240503 | 2020-03-12 11:26:08.223094 +0100 GMT | file analysis/QC/06_imputation_get/qcreport.html | import
node14.cluster | 240503 | 2020-03-12 11:26:08.373186 +0100 GMT | | begin outdated()
node14.cluster | 240503 | 2020-03-12 11:26:09.151769 +0100 GMT | | find more outdated targets
node14.cluster | 240503 | 2020-03-12 11:26:09.181268 +0100 GMT | run_post_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 11:26:11.183609 +0100 GMT | run_check_imputation | skip
node14.cluster | 240503 | 2020-03-12 11:26:11.230602 +0100 GMT | cp_qc_report | trigger command
node14.cluster | 240503 | 2020-03-12 11:26:11.231925 +0100 GMT | | find more outdated targets
node14.cluster | 240503 | 2020-03-12 11:26:16.275652 +0100 GMT | cp_qc_check | skip
node14.cluster | 240503 | 2020-03-12 11:26:16.279421 +0100 GMT | | find more outdated targets
node14.cluster | 240503 | 2020-03-12 11:26:16.284887 +0100 GMT | | find downstream outdated targets
node14.cluster | 240503 | 2020-03-12 11:26:16.302792 +0100 GMT | | end outdated()
node14.cluster | 240503 | 2020-03-12 11:26:16.304393 +0100 GMT | | isolate oudated targets
node14.cluster | 240503 | 2020-03-12 11:26:16.309561 +0100 GMT | | construct priority queue
node14.cluster | 240503 | 2020-03-12 11:26:16.387898 +0100 GMT | run_post_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 11:26:16.631028 +0100 GMT | | set common data
node14.cluster | 240503 | 2020-03-12 11:26:16.651072 +0100 GMT | | begin scheduling targets
node14.cluster | 240503 | 2020-03-12 11:26:31.478889 +0100 GMT | | sending common data
node14.cluster | 240503 | 2020-03-12 11:26:33.803555 +0100 GMT | run_post_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 11:26:33.810460 +0100 GMT | run_post_imputation | target run_post_imputation
node16.cluster | 3441 | 2020-03-12 11:26:33.821161 +0100 GMT | run_post_imputation | build on an hpc worker
node14.cluster | 240503 | 2020-03-12 11:50:26.179495 +0100 GMT | | end make()
node14.cluster | 240503 | 2020-03-12 11:52:55.911852 +0100 GMT | | begin drake_config()
node14.cluster | 240503 | 2020-03-12 11:52:55.941879 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node14.cluster | 240503 | 2020-03-12 11:52:55.947641 +0100 GMT | | analyze environment
node14.cluster | 240503 | 2020-03-12 11:52:56.029237 +0100 GMT | | get knitr hash
node14.cluster | 240503 | 2020-03-12 11:52:56.134524 +0100 GMT | | set knitr files
node14.cluster | 240503 | 2020-03-12 11:52:56.178845 +0100 GMT | | create graph edges
node14.cluster | 240503 | 2020-03-12 11:52:56.195213 +0100 GMT | | connect output files
node14.cluster | 240503 | 2020-03-12 11:52:56.197262 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node14.cluster | 240503 | 2020-03-12 11:52:56.200010 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node14.cluster | 240503 | 2020-03-12 11:52:56.202393 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node14.cluster | 240503 | 2020-03-12 11:52:56.204623 +0100 GMT | file docs/generated_reports/qcreport.html | file_out
node14.cluster | 240503 | 2020-03-12 11:52:56.255672 +0100 GMT | | end drake_config()
node14.cluster | 240503 | 2020-03-12 11:52:56.257439 +0100 GMT | | begin make()
node14.cluster | 240503 | 2020-03-12 11:52:56.489953 +0100 GMT | file analysis/QC/11_relatedness/PSYMETAB_GWAS_related_ids.txt | missing missing
node14.cluster | 240503 | 2020-03-12 11:52:56.568056 +0100 GMT | processx::run | import
node14.cluster | 240503 | 2020-03-12 11:52:56.623746 +0100 GMT | file code/check_imputation.sh | import
node14.cluster | 240503 | 2020-03-12 11:52:56.674511 +0100 GMT | file analysis/QC/12_ethnicity_admixture/snpweights/PSYMETAB_GWAS.NA.predpc | missing missing
node14.cluster | 240503 | 2020-03-12 11:52:56.711386 +0100 GMT | file code/post_imputation_qc.sh | import
node14.cluster | 240503 | 2020-03-12 11:52:56.737500 +0100 GMT | file code/qc/maf_check.R | import
node14.cluster | 240503 | 2020-03-12 11:52:56.812678 +0100 GMT | file code/qc/ethnicity_check.R | import
node14.cluster | 240503 | 2020-03-12 11:52:56.835087 +0100 GMT | file code/qc/relatedness_filter.R | import
node14.cluster | 240503 | 2020-03-12 11:52:56.907601 +0100 GMT | file code/qc/update_pvar.R | import
node14.cluster | 240503 | 2020-03-12 11:52:56.949378 +0100 GMT | file code/final_processing.sh | import
node14.cluster | 240503 | 2020-03-12 11:52:56.977837 +0100 GMT | file analysis/QC/06_imputation_get/qcreport.html | import
node14.cluster | 240503 | 2020-03-12 11:52:57.013345 +0100 GMT | | begin outdated()
node14.cluster | 240503 | 2020-03-12 11:52:57.030858 +0100 GMT | | find more outdated targets
node14.cluster | 240503 | 2020-03-12 11:52:57.065629 +0100 GMT | run_post_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 11:52:57.091998 +0100 GMT | run_check_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 11:52:57.105637 +0100 GMT | cp_qc_report | trigger command
node14.cluster | 240503 | 2020-03-12 11:52:57.107427 +0100 GMT | | find downstream outdated targets
node14.cluster | 240503 | 2020-03-12 11:52:57.120042 +0100 GMT | | end outdated()
node14.cluster | 240503 | 2020-03-12 11:52:57.121672 +0100 GMT | | isolate oudated targets
node14.cluster | 240503 | 2020-03-12 11:52:57.126060 +0100 GMT | | construct priority queue
node14.cluster | 240503 | 2020-03-12 11:52:57.148514 +0100 GMT | run_post_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 11:52:57.326346 +0100 GMT | | set common data
node14.cluster | 240503 | 2020-03-12 11:52:57.345567 +0100 GMT | | begin scheduling targets
node14.cluster | 240503 | 2020-03-12 11:53:18.847385 +0100 GMT | | sending common data
node14.cluster | 240503 | 2020-03-12 11:53:19.174009 +0100 GMT | run_post_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 11:53:19.180441 +0100 GMT | run_post_imputation | target run_post_imputation
node16.cluster | 3636 | 2020-03-12 11:53:19.190154 +0100 GMT | run_post_imputation | build on an hpc worker
node14.cluster | 240503 | 2020-03-12 11:53:55.295987 +0100 GMT | | end make()
node14.cluster | 240503 | 2020-03-12 11:54:36.815329 +0100 GMT | | begin drake_config()
node14.cluster | 240503 | 2020-03-12 11:54:36.839604 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node14.cluster | 240503 | 2020-03-12 11:54:36.844440 +0100 GMT | | analyze environment
node14.cluster | 240503 | 2020-03-12 11:54:36.890824 +0100 GMT | | analyze imports
node14.cluster | 240503 | 2020-03-12 11:54:37.207192 +0100 GMT | | get knitr hash
node14.cluster | 240503 | 2020-03-12 11:54:37.216984 +0100 GMT | | analyze commands
node14.cluster | 240503 | 2020-03-12 11:54:37.250965 +0100 GMT | | set knitr files
node14.cluster | 240503 | 2020-03-12 11:54:37.258162 +0100 GMT | | create graph edges
node14.cluster | 240503 | 2020-03-12 11:54:37.267530 +0100 GMT | | connect output files
node14.cluster | 240503 | 2020-03-12 11:54:37.269510 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node14.cluster | 240503 | 2020-03-12 11:54:37.280715 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node14.cluster | 240503 | 2020-03-12 11:54:37.283018 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node14.cluster | 240503 | 2020-03-12 11:54:37.284722 +0100 GMT | file data/processed/extractions/PSYMETAB_GWAS.snpweights | file_out
node14.cluster | 240503 | 2020-03-12 11:54:37.285952 +0100 GMT | file docs/generated_reports/qcreport.html | file_out
node14.cluster | 240503 | 2020-03-12 11:54:37.307490 +0100 GMT | | finalize graph edges
node14.cluster | 240503 | 2020-03-12 11:54:37.308656 +0100 GMT | | create igraph
node14.cluster | 240503 | 2020-03-12 11:54:37.310327 +0100 GMT | | trim neighborhoods
node14.cluster | 240503 | 2020-03-12 11:54:37.315702 +0100 GMT | | add igraph attributes
node14.cluster | 240503 | 2020-03-12 11:54:37.319200 +0100 GMT | | finalize igraph
node14.cluster | 240503 | 2020-03-12 11:54:37.330533 +0100 GMT | | end drake_config()
node14.cluster | 240503 | 2020-03-12 11:54:37.331989 +0100 GMT | | begin make()
node14.cluster | 240503 | 2020-03-12 11:54:37.569680 +0100 GMT | processx::run | import
node14.cluster | 240503 | 2020-03-12 11:54:37.592908 +0100 GMT | file code/check_imputation.sh | import
node14.cluster | 240503 | 2020-03-12 11:54:37.634186 +0100 GMT | file code/post_imputation_qc.sh | import
node14.cluster | 240503 | 2020-03-12 11:54:37.653601 +0100 GMT | file code/qc/maf_check.R | import
node14.cluster | 240503 | 2020-03-12 11:54:37.674206 +0100 GMT | file code/qc/ethnicity_check.R | import
node14.cluster | 240503 | 2020-03-12 11:54:37.694889 +0100 GMT | file code/qc/relatedness_filter.R | import
node14.cluster | 240503 | 2020-03-12 11:54:37.711464 +0100 GMT | file code/qc/update_pvar.R | import
node14.cluster | 240503 | 2020-03-12 11:54:37.725216 +0100 GMT | file code/final_processing.sh | import
node14.cluster | 240503 | 2020-03-12 11:54:37.739866 +0100 GMT | file analysis/QC/06_imputation_get/qcreport.html | import
node14.cluster | 240503 | 2020-03-12 11:54:37.768511 +0100 GMT | | begin outdated()
node14.cluster | 240503 | 2020-03-12 11:54:37.781983 +0100 GMT | | find more outdated targets
node14.cluster | 240503 | 2020-03-12 11:54:37.800924 +0100 GMT | run_post_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 11:54:37.808341 +0100 GMT | run_check_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 11:54:37.818555 +0100 GMT | cp_qc_report | trigger command
node14.cluster | 240503 | 2020-03-12 11:54:37.819739 +0100 GMT | | find downstream outdated targets
node14.cluster | 240503 | 2020-03-12 11:54:37.831990 +0100 GMT | | end outdated()
node14.cluster | 240503 | 2020-03-12 11:54:37.832745 +0100 GMT | | isolate oudated targets
node14.cluster | 240503 | 2020-03-12 11:54:37.834905 +0100 GMT | | construct priority queue
node14.cluster | 240503 | 2020-03-12 11:54:37.855932 +0100 GMT | run_post_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 11:54:38.014513 +0100 GMT | | set common data
node14.cluster | 240503 | 2020-03-12 11:54:38.030890 +0100 GMT | | begin scheduling targets
node14.cluster | 240503 | 2020-03-12 11:54:48.957810 +0100 GMT | | sending common data
node14.cluster | 240503 | 2020-03-12 11:54:49.410070 +0100 GMT | run_post_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 11:54:49.414642 +0100 GMT | run_post_imputation | target run_post_imputation
node16.cluster | 3694 | 2020-03-12 11:54:49.421968 +0100 GMT | run_post_imputation | build on an hpc worker
node14.cluster | 240503 | 2020-03-12 17:29:00.672324 +0100 GMT | run_post_imputation | store
node14.cluster | 240503 | 2020-03-12 17:29:01.019438 +0100 GMT | run_post_imputation | time 20047.888s (~5.57 hours) | 20051.611s (~5.57 hours) (exec | total)
node14.cluster | 240503 | 2020-03-12 17:29:01.255861 +0100 GMT | run_check_imputation | trigger file
node14.cluster | 240503 | 2020-03-12 17:29:01.259496 +0100 GMT | run_check_imputation | target run_check_imputation
node16.cluster | 3694 | 2020-03-12 17:29:01.288869 +0100 GMT | run_check_imputation | build on an hpc worker
node14.cluster | 240503 | 2020-03-12 21:26:41.541281 +0100 GMT | run_check_imputation | store
node14.cluster | 240503 | 2020-03-12 21:26:45.785115 +0100 GMT | run_check_imputation | time 14252.408s (~3.96 hours) | 14264.578s (~3.96 hours) (exec | total)
node14.cluster | 240503 | 2020-03-12 21:26:45.894342 +0100 GMT | cp_qc_report | build locally
node14.cluster | 240503 | 2020-03-12 21:26:46.175010 +0100 GMT | cp_qc_report | trigger command
node14.cluster | 240503 | 2020-03-12 21:26:46.181489 +0100 GMT | cp_qc_report | target cp_qc_report
node14.cluster | 240503 | 2020-03-12 21:26:46.509949 +0100 GMT | cp_qc_report | store
node14.cluster | 240503 | 2020-03-12 21:26:46.545464 +0100 GMT | cp_qc_report | time 0.317s | 0.646s (exec | total)
node14.cluster | 240503 | 2020-03-12 21:26:46.575267 +0100 GMT | snp_weights | build locally
node14.cluster | 240503 | 2020-03-12 21:26:46.623392 +0100 GMT | snp_weights | trigger command
node14.cluster | 240503 | 2020-03-12 21:26:46.690527 +0100 GMT | snp_weights | target snp_weights
node14.cluster | 240503 | 2020-03-12 21:26:46.855891 +0100 GMT | snp_weights | store
node14.cluster | 240503 | 2020-03-12 21:26:46.903293 +0100 GMT | snp_weights | time 0.156s | 0.324s (exec | total)
node14.cluster | 240503 | 2020-03-12 21:26:46.936124 +0100 GMT | related_inds | build locally
node14.cluster | 240503 | 2020-03-12 21:26:46.947894 +0100 GMT | related_inds | trigger command
node14.cluster | 240503 | 2020-03-12 21:26:46.952499 +0100 GMT | related_inds | target related_inds
node14.cluster | 240503 | 2020-03-12 21:26:46.969764 +0100 GMT | related_inds | Warning: cannot open file 'analysis/QC/11_relatedness/PSYMETAB_GWAS_related_ids.txt': No such file or directory
node14.cluster | 240503 | 2020-03-12 21:26:46.973497 +0100 GMT | related_inds | fail related_inds
node14.cluster | 240503 | 2020-03-12 21:26:47.001397 +0100 GMT | | Target `related_inds` failed. Call `diagnose(related_inds)` for details. Error message:
cannot open the connection
node14.cluster | 240503 | 2020-03-12 21:26:47.016357 +0100 GMT | | end make()
node15.cluster | 36191 | 2020-03-13 11:01:41.044292 +0100 GMT | | begin drake_config()
node15.cluster | 36191 | 2020-03-13 11:01:41.458482 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node15.cluster | 36191 | 2020-03-13 11:01:41.523559 +0100 GMT | | analyze environment
node15.cluster | 36191 | 2020-03-13 11:01:41.580884 +0100 GMT | | analyze imports
node15.cluster | 36191 | 2020-03-13 11:01:41.950627 +0100 GMT | | get knitr hash
node15.cluster | 36191 | 2020-03-13 11:01:41.974119 +0100 GMT | | analyze commands
node15.cluster | 36191 | 2020-03-13 11:01:42.057984 +0100 GMT | | set knitr files
node15.cluster | 36191 | 2020-03-13 11:01:42.082477 +0100 GMT | | create graph edges
node15.cluster | 36191 | 2020-03-13 11:01:42.089908 +0100 GMT | | connect output files
node15.cluster | 36191 | 2020-03-13 11:01:42.102046 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node15.cluster | 36191 | 2020-03-13 11:01:42.104609 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node15.cluster | 36191 | 2020-03-13 11:01:42.105955 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node15.cluster | 36191 | 2020-03-13 11:01:42.107395 +0100 GMT | file data/processed/extractions/PSYMETAB_GWAS.snpweights | file_out
node15.cluster | 36191 | 2020-03-13 11:01:42.108795 +0100 GMT | file docs/generated_reports/qcreport.html | file_out
node15.cluster | 36191 | 2020-03-13 11:01:42.153705 +0100 GMT | | end drake_config()
node15.cluster | 36191 | 2020-03-13 11:01:42.154787 +0100 GMT | | begin make()
node15.cluster | 36191 | 2020-03-13 11:01:42.518952 +0100 GMT | processx::run | import
node15.cluster | 36191 | 2020-03-13 11:01:42.544015 +0100 GMT | file code/check_imputation.sh | import
node15.cluster | 36191 | 2020-03-13 11:01:42.556919 +0100 GMT | file code/post_imputation_qc.sh | import
node15.cluster | 36191 | 2020-03-13 11:01:42.570068 +0100 GMT | file code/qc/maf_check.R | import
node15.cluster | 36191 | 2020-03-13 11:01:42.603017 +0100 GMT | file code/qc/ethnicity_check.R | import
node15.cluster | 36191 | 2020-03-13 11:01:42.635292 +0100 GMT | file code/qc/relatedness_filter.R | import
node15.cluster | 36191 | 2020-03-13 11:01:42.648695 +0100 GMT | file code/qc/update_pvar.R | import
node15.cluster | 36191 | 2020-03-13 11:01:42.669330 +0100 GMT | file code/final_processing.sh | import
node15.cluster | 36191 | 2020-03-13 11:01:42.727885 +0100 GMT | file analysis/QC/06_imputation_get/qcreport.html | import
node15.cluster | 36191 | 2020-03-13 11:01:42.839122 +0100 GMT | | begin outdated()
node15.cluster | 36191 | 2020-03-13 11:01:42.848027 +0100 GMT | | find more outdated targets
node15.cluster | 36191 | 2020-03-13 11:01:42.887751 +0100 GMT | run_post_imputation | trigger file
node15.cluster | 36191 | 2020-03-13 11:01:47.897233 +0100 GMT | run_check_imputation | skip
node15.cluster | 36191 | 2020-03-13 11:01:48.004374 +0100 GMT | cp_qc_report | skip
node15.cluster | 36191 | 2020-03-13 11:01:48.014914 +0100 GMT | | find more outdated targets
node15.cluster | 36191 | 2020-03-13 11:01:51.745620 +0100 GMT | cp_qc_check | trigger file
node15.cluster | 36191 | 2020-03-13 11:01:51.746967 +0100 GMT | | find downstream outdated targets
node15.cluster | 36191 | 2020-03-13 11:01:51.756754 +0100 GMT | | end outdated()
node15.cluster | 36191 | 2020-03-13 11:01:51.757859 +0100 GMT | | isolate oudated targets
node15.cluster | 36191 | 2020-03-13 11:01:51.761741 +0100 GMT | | construct priority queue
node15.cluster | 36191 | 2020-03-13 11:01:51.792609 +0100 GMT | run_post_imputation | trigger file
node15.cluster | 36191 | 2020-03-13 11:01:52.288535 +0100 GMT | | set common data
node15.cluster | 36191 | 2020-03-13 11:01:52.305123 +0100 GMT | | begin scheduling targets
node15.cluster | 36191 | 2020-03-13 11:01:56.813006 +0100 GMT | | sending common data
node15.cluster | 36191 | 2020-03-13 11:01:57.536586 +0100 GMT | run_post_imputation | trigger file
node15.cluster | 36191 | 2020-03-13 11:01:57.541253 +0100 GMT | run_post_imputation | target run_post_imputation
node16.cluster | 9721 | 2020-03-13 11:01:57.552382 +0100 GMT | run_post_imputation | build on an hpc worker
node15.cluster | 36191 | 2020-03-13 18:09:03.596009 +0100 GMT | run_post_imputation | store
node15.cluster | 36191 | 2020-03-13 18:09:04.069508 +0100 GMT | run_post_imputation | time 25621.187s (~7.12 hours) | 25626.527s (~7.12 hours) (exec | total)
node15.cluster | 36191 | 2020-03-13 18:09:04.416351 +0100 GMT | cp_qc_check | build locally
node15.cluster | 36191 | 2020-03-13 18:09:06.631017 +0100 GMT | cp_qc_check | trigger file
node15.cluster | 36191 | 2020-03-13 18:09:06.636858 +0100 GMT | cp_qc_check | target cp_qc_check
node15.cluster | 36191 | 2020-03-13 18:09:07.142282 +0100 GMT | cp_qc_check | store
node15.cluster | 36191 | 2020-03-13 18:09:07.248699 +0100 GMT | cp_qc_check | time 0.495s | 2.827s (exec | total)
node15.cluster | 36191 | 2020-03-13 18:09:07.271738 +0100 GMT | snp_weights | build locally
node15.cluster | 36191 | 2020-03-13 18:09:07.297290 +0100 GMT | snp_weights | trigger depend
node15.cluster | 36191 | 2020-03-13 18:09:07.343428 +0100 GMT | snp_weights | target snp_weights
node15.cluster | 36191 | 2020-03-13 18:09:07.463984 +0100 GMT | snp_weights | store
node15.cluster | 36191 | 2020-03-13 18:09:07.484408 +0100 GMT | snp_weights | time 0.111s | 0.209s (exec | total)
node15.cluster | 36191 | 2020-03-13 18:09:07.516593 +0100 GMT | related_inds | build locally
node15.cluster | 36191 | 2020-03-13 18:09:07.539564 +0100 GMT | related_inds | trigger command
node15.cluster | 36191 | 2020-03-13 18:09:07.543476 +0100 GMT | related_inds | target related_inds
node15.cluster | 36191 | 2020-03-13 18:09:07.565960 +0100 GMT | related_inds | store
node15.cluster | 36191 | 2020-03-13 18:09:07.582201 +0100 GMT | related_inds | time 0.016s | 0.062s (exec | total)
node15.cluster | 36191 | 2020-03-13 18:09:07.696653 +0100 GMT | run_final_processing | trigger file
node15.cluster | 36191 | 2020-03-13 18:09:07.701253 +0100 GMT | run_final_processing | target run_final_processing
node16.cluster | 9721 | 2020-03-13 18:09:07.814729 +0100 GMT | run_final_processing | build on an hpc worker
node15.cluster | 36191 | 2020-03-13 19:07:04.134380 +0100 GMT | run_final_processing | store
node15.cluster | 36191 | 2020-03-13 19:07:04.498939 +0100 GMT | run_final_processing | time 3476.078s (~57.93 minutes) | 3476.892s (~57.95 minutes) (exec | total)
node15.cluster | 36191 | 2020-03-13 19:07:04.795866 +0100 GMT | snp_weights_munge | build locally
node15.cluster | 36191 | 2020-03-13 19:07:04.870210 +0100 GMT | snp_weights_munge | trigger depend
node15.cluster | 36191 | 2020-03-13 19:07:05.014330 +0100 GMT | snp_weights_munge | target snp_weights_munge
node15.cluster | 36191 | 2020-03-13 19:07:05.025663 +0100 GMT | snp_weights_munge | fail snp_weights_munge
node15.cluster | 36191 | 2020-03-13 19:07:05.162077 +0100 GMT | | Target `snp_weights_munge` failed. Call `diagnose(snp_weights_munge)` for details. Error message:
could not find function "munge_snp_weights"
node15.cluster | 36191 | 2020-03-13 19:07:05.271492 +0100 GMT | | end make()
node14.cluster | 7153 | 2020-03-16 13:20:05.787686 +0100 GMT | | begin drake_config()
node14.cluster | 7153 | 2020-03-16 13:20:07.389614 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node14.cluster | 7153 | 2020-03-16 13:20:07.398123 +0100 GMT | | analyze environment
node14.cluster | 7153 | 2020-03-16 13:20:07.434965 +0100 GMT | | get knitr hash
node14.cluster | 7153 | 2020-03-16 13:20:07.446269 +0100 GMT | | set knitr files
node14.cluster | 7153 | 2020-03-16 13:20:07.478902 +0100 GMT | | create graph edges
node14.cluster | 7153 | 2020-03-16 13:20:07.496351 +0100 GMT | | connect output files
node14.cluster | 7153 | 2020-03-16 13:20:07.524227 +0100 GMT | file docs/generated_reports/CrossCohortReport.html | file_out
node14.cluster | 7153 | 2020-03-16 13:20:07.531882 +0100 GMT | file docs/generated_reports/07_imputation_check.html | file_out
node14.cluster | 7153 | 2020-03-16 13:20:07.543965 +0100 GMT | file data/processed/extractions/PSYMETAB_GWAS.snpweights | file_out
node14.cluster | 7153 | 2020-03-16 13:20:07.600843 +0100 GMT | file docs/generated_reports/qcreport.html | file_out
node14.cluster | 7153 | 2020-03-16 13:20:07.608126 +0100 GMT | file analysis/QC/07_imputation_check | file_out
node14.cluster | 7153 | 2020-03-16 13:20:07.630299 +0100 GMT | | end drake_config()
node14.cluster | 7153 | 2020-03-16 13:20:07.635621 +0100 GMT | | begin make()
node14.cluster | 7153 | 2020-03-16 13:20:07.659118 +0100 GMT | | end make()
node14.cluster | 7153 | 2020-03-16 14:34:13.380016 +0100 GMT | | begin drake_config()
node14.cluster | 7153 | 2020-03-16 14:34:13.409410 +0100 GMT | | cache /data/sgg2/jenny/projects/PSYMETAB/.drake
node14.cluster | 7153 | 2020-03-16 14:34:13.415895 +0100 GMT | | analyze environment
node14.cluster | 7153 | 2020-03-16 14:34:13.461451 +0100 GMT | | get knitr hash
node14.cluster | 7153 | 2020-03-16 14:34:13.485162 +0100 GMT | | set knitr files
node14.cluster | 7153 | 2020-03-16 14:34:13.506256 +0100 GMT | | end drake_config()
node14.cluster | 7153 | 2020-03-16 14:34:13.507727 +0100 GMT | | begin make()
node14.cluster | 7153 | 2020-03-16 14:34:14.060657 +0100 GMT | dplyr::select | import
node14.cluster | 7153 | 2020-03-16 14:34:14.107235 +0100 GMT | processx::run | import
node14.cluster | 7153 | 2020-03-16 14:34:14.134581 +0100 GMT | file analysis/QC/06_imputation_get/qcreport.html | import
node14.cluster | 7153 | 2020-03-16 14:34:14.153418 +0100 GMT | file code/post_imputation_qc.sh | import
node14.cluster | 7153 | 2020-03-16 14:34:14.169964 +0100 GMT | file code/qc/maf_check.R | import
node14.cluster | 7153 | 2020-03-16 14:34:14.191947 +0100 GMT | file code/qc/ethnicity_check.R | import
node14.cluster | 7153 | 2020-03-16 14:34:14.209175 +0100 GMT | file code/qc/relatedness_filter.R | import
node14.cluster | 7153 | 2020-03-16 14:34:14.393419 +0100 GMT | file code/qc/update_pvar.R | import
node14.cluster | 7153 | 2020-03-16 14:34:14.582397 +0100 GMT | file code/final_processing.sh | import
node14.cluster | 7153 | 2020-03-16 14:34:14.702856 +0100 GMT | file code/check_imputation.sh | import
node14.cluster | 7153 | 2020-03-16 14:34:14.800904 +0100 GMT | munge_snp_weights | import