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Feb 24th, 2020
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  1. job.txt:
  2.  
  3. 20/02/24 14:05:03 Executing Job installation....
  4. 20/02/24 14:05:03 Preparing Application 'Genotype Imputation (Minimac4)'...
  5. 20/02/24 14:05:03 Application 'Genotype Imputation (Minimac4)'is already installed.
  6. 20/02/24 14:05:03 Preparing Application 'HapMap 2'...
  7. 20/02/24 14:05:03 Application 'HapMap 2'is already installed.
  8. 20/02/24 14:05:03 Executing Job setups....
  9. 20/02/24 14:05:03 Planner: WDL evaluated.
  10. 20/02/24 14:05:03 Planner: DAG created.
  11. 20/02/24 14:05:03 Nodes: 3
  12. 20/02/24 14:05:03 Input Validation
  13. 20/02/24 14:05:03 Inputs:
  14. 20/02/24 14:05:03 Outputs:
  15. 20/02/24 14:05:03 Quality Control
  16. 20/02/24 14:05:03 Inputs:
  17. 20/02/24 14:05:03 Outputs: mafFile chunkFileDir statisticDir
  18. 20/02/24 14:05:03 Quality Control (Report)
  19. 20/02/24 14:05:03 Inputs: mafFile r2Filter myseparator
  20. 20/02/24 14:05:03 Outputs: qcreport
  21. 20/02/24 14:05:03 Dipendencies: 2
  22. 20/02/24 14:05:03 Input Validation->Quality Control
  23. 20/02/24 14:05:03 Quality Control->Quality Control (Report)
  24. 20/02/24 14:05:03 Executor: execute DAG...
  25. 20/02/24 14:05:03 ------------------------------------------------------
  26. 20/02/24 14:05:03 Input Validation
  27. 20/02/24 14:05:03 ------------------------------------------------------
  28. 20/02/24 14:05:03 Configuration file '/data/apps/imputationserver/1.2.4/job.config' not available. Use default values.
  29. 20/02/24 14:05:03 Input Validation [0 sec]
  30. 20/02/24 14:05:03 ------------------------------------------------------
  31. 20/02/24 14:05:03 Quality Control
  32. 20/02/24 14:05:03 ------------------------------------------------------
  33. 20/02/24 14:05:03 Configuration file '/data/apps/imputationserver/1.2.4/job.config' not available. Use default values.
  34. 20/02/24 14:05:04 Quality Control [0 sec]
  35. 20/02/24 14:05:04 Exporting parameter statisticDir...
  36. 20/02/24 14:05:04 ------------------------------------------------------
  37. 20/02/24 14:05:04 Quality Control (Report)
  38. 20/02/24 14:05:04 ------------------------------------------------------
  39. 20/02/24 14:05:04 Running script /data/apps/imputationserver/1.2.4/qc-report.Rmd...
  40. 20/02/24 14:05:04 Working Directory: /data/apps/imputationserver/1.2.4
  41. 20/02/24 14:05:04 Output: /data/jobs/job-20200224-140503-181/qcreport/qcreport.html
  42. 20/02/24 14:05:04 Parameters:
  43. 20/02/24 14:05:04 /data/jobs/job-20200224-140503-181/temp/mafFile/mafFile
  44. 20/02/24 14:05:04 Creating RMarkdown report from /data/apps/imputationserver/1.2.4/qc-report.Rmd...
  45. 20/02/24 14:05:09 Quality Control (Report) [5 sec]
  46. 20/02/24 14:05:09 Exporting parameter qcreport...
  47. 20/02/24 14:05:09 Planner: WDL evaluated.
  48. 20/02/24 14:05:14 Planner: WDL evaluated.
  49. 20/02/24 14:05:14 Details:
  50. 20/02/24 14:05:14 Name: test3
  51. 20/02/24 14:05:14 Job-Id: job-20200224-140503-181
  52. 20/02/24 14:05:14 Submitted On: Mon Feb 24 14:05:03 UTC 2020
  53. 20/02/24 14:05:14 Completed On: Thu Jan 01 00:00:00 UTC 1970
  54. 20/02/24 14:05:14 Inputs:
  55. 20/02/24 14:05:14 Reference Panel (<a href="https://imputationserver.sph.umich.edu/start.html#!pages/refpanels" target="_blank">Details</a>): apps@hapmap-2@2.0.0
  56. 20/02/24 14:05:14 Input Files (<a href="http://www.1000genomes.org/wiki/Analysis/Variant%20Call%20Format/vcf-variant-call-format-version-41" target="_blank">VCF</a>): /data/jobs/job-20200224-140503-181/input/files
  57. 20/02/24 14:05:14 Array Build: hg19
  58. 20/02/24 14:05:14 rsq Filter: 0
  59. 20/02/24 14:05:14 Phasing: eagle
  60. 20/02/24 14:05:14 Population: eur
  61. 20/02/24 14:05:14 Mode: imputation
  62. 20/02/24 14:05:14 AES 256 encryption: no
  63. 20/02/24 14:05:14 null:
  64. 20/02/24 14:05:14 Password set by user.: auto
  65. 20/02/24 14:05:14 I will not attempt to re-identify or contact research participants.: accepted
  66. 20/02/24 14:05:14 I will report any inadvertent data release, security breach or other data management incident of which I become aware.: accepted
  67. 20/02/24 14:05:14 Outputs:
  68. 20/02/24 14:05:14 Quality-Control Report: /data/jobs/job-20200224-140503-181/qcreport/qcreport
  69. 20/02/24 14:05:14 QC Statistics: /data/jobs/job-20200224-140503-181/statisticDir
  70. 20/02/24 14:05:14 Imputation Results: /data/jobs/job-20200224-140503-181/local
  71. 20/02/24 14:05:14 Logs: /data/jobs/job-20200224-140503-181/logfile
  72. 20/02/24 14:05:14 Hadoop Task Logs: /data/jobs/job-20200224-140503-181/hadooplogs
  73. 20/02/24 14:05:14 Preparing Job....
  74. 20/02/24 14:05:14 Executing Job....
  75. 20/02/24 14:05:14 Planner: WDL evaluated.
  76. 20/02/24 14:05:14 Planner: DAG created.
  77. 20/02/24 14:05:14 Nodes: 2
  78. 20/02/24 14:05:14 Pre-phasing and Imputation
  79. 20/02/24 14:05:14 Inputs:
  80. 20/02/24 14:05:14 Outputs: outputimputation local logfile hadooplogs
  81. 20/02/24 14:05:14 Data Compression and Encryption
  82. 20/02/24 14:05:14 Inputs:
  83. 20/02/24 14:05:14 Outputs:
  84. 20/02/24 14:05:14 Dipendencies: 1
  85. 20/02/24 14:05:14 Pre-phasing and Imputation->Data Compression and Encryption
  86. 20/02/24 14:05:14 Executor: execute DAG...
  87. 20/02/24 14:05:14 ------------------------------------------------------
  88. 20/02/24 14:05:14 Pre-phasing and Imputation
  89. 20/02/24 14:05:14 ------------------------------------------------------
  90. 20/02/24 14:15:42 Pre-phasing and Imputation [ERROR]
  91. 20/02/24 14:15:42 Exporting parameter hadooplogs...
  92. 20/02/24 14:15:42 Executing onFailure...
  93. 20/02/24 14:15:42 ------------------------------------------------------
  94. 20/02/24 14:15:42 Send Notification on Failure
  95. 20/02/24 14:15:42 ------------------------------------------------------
  96. 20/02/24 14:15:42 Configuration file '/data/apps/imputationserver/1.2.4/job.config' not available. Use default values.
  97. 20/02/24 14:15:42 Send Notification on Failure [ERROR]
  98. 20/02/24 14:15:42 onFailure execution failed.
  99. 20/02/24 14:15:42 Job Execution failed: Job Execution failed.
  100. 20/02/24 14:15:42 Cleaning up...
  101. 20/02/24 14:15:42 Cleaning up uploaded local files...
  102. 20/02/24 14:15:42 Cleaning up temporary local files...
  103. 20/02/24 14:15:42 Cleaning up temporary hdfs files...
  104. 20/02/24 14:15:42 Cleaning up hdfs files...
  105. 20/02/24 14:15:42 Cleanup successful.
  106.  
  107.  
  108. std.out:
  109.  
  110. Version: null (Built by null on null)
  111. Export parameter 'statisticDir'...
  112.  
  113.  
  114. processing file: qc-report.Rmd
  115. output file: qc-report.knit.md
  116.  
  117.  
  118. Output created: /data/jobs/job-20200224-140503-181/qcreport/qcreport.html
  119.  
  120.  
  121. |
  122. | | 0%
  123. |
  124. |......... | 14%
  125. ordinary text without R code
  126.  
  127.  
  128. |
  129. |................... | 29%
  130. label: unnamed-chunk-1 (with options)
  131. List of 1
  132. $ echo: logi FALSE
  133.  
  134.  
  135. |
  136. |............................ | 43%
  137. ordinary text without R code
  138.  
  139.  
  140. |
  141. |..................................... | 57%
  142. label: unnamed-chunk-2 (with options)
  143. List of 1
  144. $ echo: logi FALSE
  145.  
  146.  
  147. |
  148. |.............................................. | 71%
  149. ordinary text without R code
  150.  
  151.  
  152. |
  153. |........................................................ | 86%
  154. label: unnamed-chunk-3 (with options)
  155. List of 1
  156. $ echo: logi FALSE
  157.  
  158.  
  159. |
  160. |.................................................................| 100%
  161. ordinary text without R code
  162.  
  163.  
  164. /usr/bin/pandoc +RTS -K512m -RTS qc-report.utf8.md --to html4 --from markdown+autolink_bare_uris+ascii_identifiers+tex_math_single_backslash --output /data/jobs/job-20200224-140503-181/qcreport/qcreport.html --smart --email-obfuscation none --self-contained --standalone --section-divs --template /usr/local/lib/R/site-library/rmarkdown/rmd/h/default.html --no-highlight --variable highlightjs=1 --variable 'theme:bootstrap' --include-in-header /tmp/RtmpNYD8If/rmarkdown-strf141b520c9c.html --mathjax --variable 'mathjax-url:https://mathjax.rstudio.com/latest/MathJax.js?config=TeX-AMS-MML_HTMLorMML'
  165.  
  166. Export parameter 'qcreport'...
  167. Reference Panel:
  168. Name: apps@hapmap-2@2.0.0
  169. ID: hapmap2
  170. Build: hg19
  171. Location: cloudgene/apps/hapmap-2@2.0.0/2.0.0/m3vcfs/hapmap_r22.chr$chr.CEU.hg19.recode.m3vcf.gz
  172. Legend: /data/apps/hapmap-2/2.0.0/legends/hapmap_r22.chr$chr.CEU.hg19_impute.legend.gz
  173. Version: ??
  174. Eagle Map: cloudgene/apps/hapmap-2@2.0.0/2.0.0/map/genetic_map_hg19_withX.txt.gz
  175. Eagle BCFs: cloudgene/apps/hapmap-2@2.0.0/2.0.0/bcfs/hapmap_r22.chr$chr.CEU.hg19.recode.bcf
  176. Minimac Map: null
  177. Populations:
  178. eur/EUR
  179. mixed/Mixed
  180. Samples:
  181. eur/60
  182. mixed/-1
  183. Reference panel has no minimac map file.
  184. Input data is unphased.
  185. Setting up eagle reference and map files...
  186. Running job chr_4....
  187. [INFO] Configuration file '/data/apps/imputationserver/1.2.4/job.config' not available. Use default values
  188. [INFO] minimac.command: --refHaps ${ref} --haps ${vcf} --start ${start} --end ${end} --window ${window} --prefix ${prefix} --chr ${chr} --cpus 1 --noPhoneHome --format GT,DS,GP --allTypedSites --meta --minRatio 0.00001 ${chr =='MT' ? '--myChromosome ' + chr : ''} ${unphased ? '--unphasedOutput' : ''} ${mapMinimac != null ? '--referenceEstimates --map ' + mapMinimac : ''}
  189. [INFO] minimac.window: 500000
  190. [INFO] chunksize: 20000000
  191. [INFO] minimac.tmp: /tmp
  192. [INFO] hg19Tohg38: chains/hg19ToHg38.over.chain.gz
  193. [INFO] hg38Tohg19: chains/hg38ToHg19.over.chain.gz
  194. [INFO] server.url: https://imputationserver.sph.umich.edu
  195. [INFO] minimac.sendmail: no
  196. [INFO] phasing.window: 5000000
  197. [INFO] ref.fasta: v37
  198. [INFO] Setting up Distributed Cache...
  199. [INFO] Distribute binaries cloudgene/apps/imputationserver@1.2.4/1.2.4/bin to distributed cache...
  200. [INFO] Add Minimac reference panel cloudgene/apps/hapmap-2@2.0.0/2.0.0/m3vcfs/hapmap_r22.chr4.CEU.hg19.recode.m3vcf.gz to distributed cache...
  201. [INFO] Add Eagle map cloudgene/apps/hapmap-2@2.0.0/2.0.0/map/genetic_map_hg19_withX.txt.gz to distributed cache...
  202. [INFO] Add Eagle reference cloudgene/apps/hapmap-2@2.0.0/2.0.0/bcfs/hapmap_r22.chr4.CEU.hg19.recode.bcf do distributed cache...
  203. [INFO] Add Eagle reference index cloudgene/apps/hapmap-2@2.0.0/2.0.0/bcfs/hapmap_r22.chr4.CEU.hg19.recode.bcf.csi to distributed cache...
  204. [INFO] Running Preprocessing...
  205. [INFO] Creating Job job-20200224-140503-181-chr-4...
  206. [INFO] Input Path: hdfs:///user/root/cloudgene/data/job-20200224-140503-181/temp/4
  207. [INFO] Output Path: hdfs:///user/root/cloudgene/data/job-20200224-140503-181/temp/outputimputation/4/temp
  208. [INFO] Driver jar: /data/apps/imputationserver/1.2.4/imputationserver.jar
  209. [INFO] Running Job...
  210. [INFO] Execution failed.
  211. [INFO] Cleanup executed.
  212. Job chr_4 (job_202002241319_0004) failed.
  213. Kill all running jobs...
  214. All jobs terminated.
  215. Imputation on chromosome 4 failed. Imputation was stopped.
  216. Summary:
  217. [INFO] Downloading events...
  218. [INFO] Downloaded 6 events.
  219. [INFO] Downloading 12 log files...
  220. [INFO] Downloading http://a2b9b38184f9:50060/tasklog?attemptid=attempt_202002241319_0004_m_000000_0&plaintext=true&filter=stdout...
  221. [INFO] Downloading http://a2b9b38184f9:50060/tasklog?attemptid=attempt_202002241319_0004_m_000000_0&plaintext=true&filter=stderr...
  222. [INFO] Downloading http://a2b9b38184f9:50060/tasklog?attemptid=attempt_202002241319_0004_m_000000_1&plaintext=true&filter=stdout...
  223. [INFO] Downloading http://a2b9b38184f9:50060/tasklog?attemptid=attempt_202002241319_0004_m_000000_1&plaintext=true&filter=stderr...
  224. [INFO] Downloading http://a2b9b38184f9:50060/tasklog?attemptid=attempt_202002241319_0004_m_000000_2&plaintext=true&filter=stdout...
  225. [INFO] Downloading http://a2b9b38184f9:50060/tasklog?attemptid=attempt_202002241319_0004_m_000000_2&plaintext=true&filter=stderr...
  226. [INFO] Downloading http://a2b9b38184f9:50060/tasklog?attemptid=attempt_202002241319_0004_m_000000_3&plaintext=true&filter=stdout...
  227. [INFO] Downloading http://a2b9b38184f9:50060/tasklog?attemptid=attempt_202002241319_0004_m_000000_3&plaintext=true&filter=stderr...
  228. [INFO] Downloading log files successful.
  229. [FAIL] Chr 4 (job_202002241319_0004)
  230. Export parameter 'hadooplogs'...
  231. No action required. Email notification has been disabled in job.config
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