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ImputePipelinePlugin_fastq.log

bpoudel
Aug 5th, 2021 (edited)
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  1. Thu Aug 5 10:25:13 CDT 2021
  2. /tassel-5-standalone/lib/ahocorasick-0.2.4.jar:/tassel-5-standalone/lib/biojava-alignment-4.0.0.jar:/tassel-5-standalone/lib/biojava-core-4.0.0.jar:/tassel-5-standalone/lib/biojava-phylo-4.0.0.jar:/tassel-5-standalone/lib/colt-1.2.0.jar:/tassel-5-standalone/lib/commons-codec-1.10.jar:/tassel-5-standalone/lib/commons-math3-3.4.1.jar:/tassel-5-standalone/lib/ejml-0.23.jar:/tassel-5-standalone/lib/fastutil-8.2.2.jar:/tassel-5-standalone/lib/forester-1.038.jar:/tassel-5-standalone/lib/gs-core-1.3.jar:/tassel-5-standalone/lib/gs-ui-1.3.jar:/tassel-5-standalone/lib/guava-22.0.jar:/tassel-5-standalone/lib/htsjdk-2.23.0.jar:/tassel-5-standalone/lib/itextpdf-5.1.0.jar:/tassel-5-standalone/lib/javax.json-1.0.4.jar:/tassel-5-standalone/lib/jcommon-1.0.23.jar:/tassel-5-standalone/lib/jfreechart-1.0.19.jar:/tassel-5-standalone/lib/jfreesvg-3.2.jar:/tassel-5-standalone/lib/jhdf5-14.12.5.jar:/tassel-5-standalone/lib/json-simple-1.1.1.jar:/tassel-5-standalone/lib/junit-4.10.jar:/tassel-5-standalone/lib/kotlin-stdlib-1.3.50.jar:/tassel-5-standalone/lib/kotlin-stdlib-jdk7-1.3.50.jar:/tassel-5-standalone/lib/kotlin-stdlib-jdk8-1.3.50.jar:/tassel-5-standalone/lib/kotlinx-coroutines-core-1.3.0.jar:/tassel-5-standalone/lib/log4j-1.2.13.jar:/tassel-5-standalone/lib/mail-1.4.jar:/tassel-5-standalone/lib/phg.jar:/tassel-5-standalone/lib/postgresql-9.4-1201.jdbc41.jar:/tassel-5-standalone/lib/scala-library-2.10.1.jar:/tassel-5-standalone/lib/slf4j-api-1.7.10.jar:/tassel-5-standalone/lib/slf4j-simple-1.7.10.jar:/tassel-5-standalone/lib/snappy-java-1.1.1.6.jar:/tassel-5-standalone/lib/sqlite-jdbc-3.8.5-pre1.jar:/tassel-5-standalone/lib/trove-3.0.3.jar:/tassel-5-standalone/sTASSEL.jar
  3. Memory Settings: -Xms512m -Xmx215040m
  4. Tassel Pipeline Arguments: -debug -configParameters /phg/config_ImputePipelinePlugin_fastq.txt -ImputePipelinePlugin -imputeTarget pathToVCF -endPlugin
  5. [main] INFO net.maizegenetics.plugindef.ParameterCache - load: loading parameter cache with: /phg/config_ImputePipelinePlugin_fastq.txt
  6. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: DBtype value: sqlite
  7. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: maxSecondary value: 20
  8. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: host value: localHost
  9. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: minTransitionProb value: 0.001
  10. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: DB value: /phg/95HRSW_attempt4.db
  11. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: inputType value: fastq
  12. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: pangenomeDir value: /phg/outputDir/pangenome
  13. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: outputSecondaryStats value: false
  14. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: maxNodes value: 1000
  15. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: samDir value: /phg/inputDir/imputation/sam/
  16. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: fParameter value: f1000,5000
  17. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: minimapLocation value: minimap2
  18. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: numThreads value: 3
  19. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: pathMethod value: pathMethodwithnewdb_fq_GATK_PIPELINE
  20. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: probCorrect value: 0.99
  21. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: indexNumberBases value: 90G
  22. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: pangenomeHaplotypeMethod value: GATK_PIPELINE
  23. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: minTaxa value: 1
  24. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: indexKmerLength value: 21
  25. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: usebf value: false
  26. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: removeEqual value: true
  27. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: pathHaplotypeMethod value: GATK_PIPELINE
  28. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: minReads value: 1
  29. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: keyFile value: /phg/readMapping_key_file_17C23-2fq.txt
  30. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: user value: sqlite
  31. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: lowMemMode value: false
  32. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: password value: sqlite
  33. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: splitNodes value: true
  34. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: outVcfFile value: 95HRSW_imputedwith17C23-2fastq_VCF
  35. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: maxReads value: 10000
  36. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: maxRefRangeErr value: 0.25
  37. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: indexWindowSize value: 11
  38. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: readMethodDescription value: readMethod+newdb_filetype
  39. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: minP value: 0.8
  40. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: splitProb value: 0.99
  41. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: fastqDir value: /phg/inputDir/imputation/fastq/
  42. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: pathMethodDescription value: pathMethod+newdb_filetype_HaplotypeMethod
  43. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: readMethod value: GATK_PIPELINE
  44. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: configFile value: /phg/config_ImputePipelinePlugin_fastq.txt
  45. [main] INFO net.maizegenetics.plugindef.ParameterCache - ParameterCache: key: liquibaseOutdir value: /phg/outputDir
  46. [main] INFO net.maizegenetics.tassel.TasselLogging - Tassel Version: 5.2.71 Date: March 26, 2021
  47. [main] INFO net.maizegenetics.tassel.TasselLogging - Max Available Memory Reported by JVM: 191147 MB
  48. [main] INFO net.maizegenetics.tassel.TasselLogging - Java Version: 1.8.0_242
  49. [main] INFO net.maizegenetics.tassel.TasselLogging - OS: Linux
  50. [main] INFO net.maizegenetics.tassel.TasselLogging - Number of Processors: 72
  51. [main] INFO net.maizegenetics.pipeline.TasselPipeline - Tassel Pipeline Arguments: [-fork1, -ImputePipelinePlugin, -imputeTarget, pathToVCF, -endPlugin, -runfork1]
  52. net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin
  53. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin: time: Aug 5, 2021 15:25:32
  54. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
  55. ImputePipelinePlugin Parameters
  56. imputeTarget: pathToVCF
  57. inputType: fastq
  58. configFile: /phg/config_ImputePipelinePlugin_fastq.txt
  59. pangenomeHaplotypeMethod: GATK_PIPELINE
  60. pathHaplotypeMethod: GATK_PIPELINE
  61. pangenomeDir: /phg/outputDir/pangenome
  62. pangenomeIndexName: null
  63. indexKmerLength: 21
  64. indexWindowSize: 11
  65. indexNumberBases: 90G
  66. minimapLocation: minimap2
  67. readMethod: GATK_PIPELINE
  68. readMethodDescription: readMethod+newdb_filetype
  69. outVcfFile: 95HRSW_imputedwith17C23-2fastq_VCF
  70. forceDBUpdate: false
  71. liquibaseOutdir: /phg/outputDir
  72. skipLiquibaseCheck: false
  73.  
  74. [pool-1-thread-1] INFO net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin - Checking if Liquibase can be run.
  75. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin: time: Aug 5, 2021 15:25:32
  76. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
  77. CheckDBVersionPlugin Parameters
  78. outputDir: /phg/outputDir
  79.  
  80. [pool-1-thread-1] INFO net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin - Deleting yesFile /phg/outputDir/run_yes.txt if it exists
  81. [pool-1-thread-1] INFO net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin - Deleting noFile /phg/outputDirrun_no.txt if it exists
  82. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - first connection: dbName from config file = /phg/95HRSW_attempt4.db host: localHost user: sqlite type: sqlite
  83. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Database URL: jdbc:sqlite:/phg/95HRSW_attempt4.db
  84. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Connected to database:
  85.  
  86. [pool-1-thread-1] INFO net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin - queueHaplotypeNodesByRange: query: select name FROM sqlite_master where type='table' and name='variants';
  87. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin: time: Aug 5, 2021 15:25:32
  88. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - net.maizegenetics.pangenome.liquibase.CheckDBVersionPlugin Citation: Bradbury PJ, Zhang Z, Kroon DE, Casstevens TM, Ramdoss Y, Buckler ES. (2007) TASSEL: Software for association mapping of complex traits in diverse samples. Bioinformatics 23:2633-2635.
  89. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin: time: Aug 5, 2021 15:25:32
  90. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
  91. LiquibaseUpdatePlugin Parameters
  92. outputDir: /phg/outputDir
  93. command: status
  94.  
  95. [pool-1-thread-1] INFO net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin - Please wait, begin Command:liquibase --driver=org.sqlite.JDBC --url=jdbc:sqlite:/phg/95HRSW_attempt4.db --username=sqlite --password=sqlite --changeLogFile=/liquibase/changelogs/db.changelog-master.xml status --verbose
  96. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.pangenome.liquibase.LiquibaseUpdatePlugin: time: Aug 5, 2021 15:25:34
  97. [pool-1-thread-1] INFO net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin - PHG DB is up to date. Proceeding with Populating the PHG DB.
  98. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: time: Aug 5, 2021 15:25:34
  99. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
  100. HaplotypeGraphBuilderPlugin Parameters
  101. configFile: /phg/config_ImputePipelinePlugin_fastq.txt
  102. methods: GATK_PIPELINE
  103. includeSequences: true
  104. includeVariantContexts: false
  105. haplotypeIds: null
  106. chromosomes: null
  107. taxa: null
  108.  
  109. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - first connection: dbName from config file = /phg/95HRSW_attempt4.db host: localHost user: sqlite type: sqlite
  110. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Database URL: jdbc:sqlite:/phg/95HRSW_attempt4.db
  111. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Connected to database:
  112.  
  113. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: query statement: select reference_ranges.ref_range_id, chrom, range_start, range_end, methods.name from reference_ranges INNER JOIN ref_range_ref_range_method on ref_range_ref_range_method.ref_range_id=reference_ranges.ref_range_id INNER JOIN methods on ref_range_ref_range_method.method_id = methods.method_id AND methods.method_type = 7 ORDER BY reference_ranges.ref_range_id
  114. methods size: 1
  115. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: number of reference ranges: 94229
  116. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: time: 0.624981529 secs.
  117. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: query statement: SELECT gamete_haplotypes.gamete_grp_id, genotypes.line_name FROM gamete_haplotypes INNER JOIN gametes ON gamete_haplotypes.gameteid = gametes.gameteid INNER JOIN genotypes on gametes.genoid = genotypes.genoid ORDER BY gamete_haplotypes.gamete_grp_id;
  118. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: number of taxa lists: 136337
  119. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: time: 6.726373845 secs.
  120. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: haplotype method: GATK_PIPELINE range group method: null
  121. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: query statement: SELECT haplotypes_id, gamete_grp_id, haplotypes.ref_range_id, asm_contig, asm_start_coordinate, asm_end_coordinate, genome_file_id, sequence, seq_hash, seq_len FROM haplotypes WHERE method_id = 3;
  122. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - addNodes: number of nodes: 8857526
  123. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - addNodes: number of reference ranges: 94229
  124. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: time: 440.934323876 secs.
  125. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.HaplotypeGraph - Created graph edges: created when requested number of nodes: 8857526 number of reference ranges: 94229
  126. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: time: Aug 5, 2021 15:33:9
  127. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin: time: Aug 5, 2021 15:33:9
  128. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
  129. FastqToMappingPlugin Parameters
  130. minimap2IndexFile: /phg/outputDir/pangenome/pangenome_GATK_PIPELINE_k21w11I90G.mmi
  131. keyFile: /phg/readMapping_key_file_17C23-2fq.txt
  132. fastqDir: /phg/inputDir/imputation/fastq/
  133. maxRefRangeErr: 0.25
  134. lowMemMode: false
  135. maxSecondary: 20
  136. fParameter: f1000,5000
  137. minimapLocation: minimap2
  138. methodName: GATK_PIPELINE
  139. methodDescription: readMethod+newdb_filetype
  140. debugDir:
  141. outputSecondaryStats: false
  142.  
  143. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - first connection: dbName from config file = /phg/95HRSW_attempt4.db host: localHost user: sqlite type: sqlite
  144. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Database URL: jdbc:sqlite:/phg/95HRSW_attempt4.db
  145. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Connected to database:
  146.  
  147. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - PHGdbAccess - db is setup, init prepared statements, load hash table
  148. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess -
  149. beginning - isSqlite is true
  150. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all geneotypes in genotype table=95
  151. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - refRangeRefRangeIDMap is null, creating new one with size : 94229
  152. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - loadAnchorHash: at end, size of refRangeRefRangeIDMap: 94229, number of rs.next processed: 94229
  153. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all methods in method table=10
  154. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all groups in taxa_groups table=0
  155. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all groups in gamete_groups table=136337
  156. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all gametes in gametes table=95
  157. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading readMappingHash, size of all read_mappings in read_mapping table=1
  158. [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapCalling.Minimap2Utils - Skipping Keyfile entry: cultivar 17C23-2, flowcell_lane wgs has already been processed and loaded into the DB.
  159. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - Closing DB
  160. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.pangenome.hapCalling.FastqToMappingPlugin: time: Aug 5, 2021 15:33:13
  161. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: time: Aug 5, 2021 15:33:13
  162. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
  163. HaplotypeGraphBuilderPlugin Parameters
  164. configFile: /phg/config_ImputePipelinePlugin_fastq.txt
  165. methods: GATK_PIPELINE
  166. includeSequences: false
  167. includeVariantContexts: false
  168. haplotypeIds: null
  169. chromosomes: null
  170. taxa: null
  171.  
  172. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - first connection: dbName from config file = /phg/95HRSW_attempt4.db host: localHost user: sqlite type: sqlite
  173. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Database URL: jdbc:sqlite:/phg/95HRSW_attempt4.db
  174. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Connected to database:
  175.  
  176. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: query statement: select reference_ranges.ref_range_id, chrom, range_start, range_end, methods.name from reference_ranges INNER JOIN ref_range_ref_range_method on ref_range_ref_range_method.ref_range_id=reference_ranges.ref_range_id INNER JOIN methods on ref_range_ref_range_method.method_id = methods.method_id AND methods.method_type = 7 ORDER BY reference_ranges.ref_range_id
  177. methods size: 1
  178. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: number of reference ranges: 94229
  179. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: time: 0.421060762 secs.
  180. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: query statement: SELECT gamete_haplotypes.gamete_grp_id, genotypes.line_name FROM gamete_haplotypes INNER JOIN gametes ON gamete_haplotypes.gameteid = gametes.gameteid INNER JOIN genotypes on gametes.genoid = genotypes.genoid ORDER BY gamete_haplotypes.gamete_grp_id;
  181. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: number of taxa lists: 136337
  182. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: time: 4.490692238 secs.
  183. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: haplotype method: GATK_PIPELINE range group method: null
  184. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: query statement: SELECT haplotypes_id, gamete_grp_id, haplotypes.ref_range_id, asm_contig, asm_start_coordinate, asm_end_coordinate, genome_file_id, seq_hash, seq_len FROM haplotypes WHERE method_id = 3;
  185. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - addNodes: number of nodes: 8857526
  186. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - addNodes: number of reference ranges: 94229
  187. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: time: 117.803670678 secs.
  188. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.HaplotypeGraph - Created graph edges: created when requested number of nodes: 8857526 number of reference ranges: 94229
  189. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: time: Aug 5, 2021 15:35:20
  190. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin: time: Aug 5, 2021 15:35:20
  191. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
  192. BestHaplotypePathPlugin Parameters
  193. keyFile: /phg/readMapping_key_file_17C23-2fq_pathKeyFile.txt
  194. readFile: null
  195. readDir: null
  196. outDir: null
  197. readMethod: GATK_PIPELINE
  198. pathMethod: pathMethodwithnewdb_fq_GATK_PIPELINE
  199. pathMethodDescription: pathMethod+newdb_filetype_HaplotypeMethod
  200. overwrite: false
  201. minTaxa: 1
  202. minReads: 1
  203. maxReads: 10000
  204. maxNodes: 1000
  205. minTransitionProb: 0.001
  206. probCorrect: 0.99
  207. splitNodes: true
  208. splitProb: 0.99
  209. usebf: false
  210. minP: 0.8
  211. bfInfoFile: null
  212. removeEqual: true
  213. numThreads: 3
  214. requiredTaxa: null
  215. algorithmType: classic
  216.  
  217. [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin - Classic filter found 0 ranges missing one of the required taxa, 0 ranges with too many nodes, and 0 with too few taxa}
  218. [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin - Classic filter removed 0 ranges
  219. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createEdges: creating edges from nodes.
  220. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createEdges: time: 6.264702469 secs.
  221. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.HaplotypeGraph - Created graph number of edges: 8855552 number of nodes: 8857526 number of reference ranges: 94229
  222. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createEdgesFullyConnected: creating edges from nodes.
  223. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createEdgesFullyConnected: time: 1473.881245856 secs.
  224. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.HaplotypeGraph - Created graph number of edges: 832421888 number of nodes: 8857526 number of reference ranges: 94229
  225. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - first connection: dbName from config file = /phg/95HRSW_attempt4.db host: localHost user: sqlite type: sqlite
  226. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Database URL: jdbc:sqlite:/phg/95HRSW_attempt4.db
  227. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Connected to database:
  228.  
  229. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - PHGdbAccess - db is setup, init prepared statements, load hash table
  230. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess -
  231. beginning - isSqlite is true
  232. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all geneotypes in genotype table=95
  233. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - refRangeRefRangeIDMap is null, creating new one with size : 94229
  234. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - loadAnchorHash: at end, size of refRangeRefRangeIDMap: 94229, number of rs.next processed: 94229
  235. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all methods in method table=10
  236. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all groups in taxa_groups table=0
  237. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all groups in gamete_groups table=136337
  238. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all gametes in gametes table=95
  239. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading readMappingHash, size of all read_mappings in read_mapping table=1
  240. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - first connection: dbName from config file = /phg/95HRSW_attempt4.db host: localHost user: sqlite type: sqlite
  241. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Database URL: jdbc:sqlite:/phg/95HRSW_attempt4.db
  242. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Connected to database:
  243.  
  244. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - PHGdbAccess - db is setup, init prepared statements, load hash table
  245. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess -
  246. beginning - isSqlite is true
  247. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all geneotypes in genotype table=95
  248. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - refRangeRefRangeIDMap is null, creating new one with size : 94229
  249. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - loadAnchorHash: at end, size of refRangeRefRangeIDMap: 94229, number of rs.next processed: 94229
  250. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all methods in method table=10
  251. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all groups in taxa_groups table=0
  252. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all groups in gamete_groups table=136337
  253. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading hash, size of all gametes in gametes table=95
  254. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - before loading readMappingHash, size of all read_mappings in read_mapping table=1
  255. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - Closing DB
  256. [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin - The pathKeyFile has 1 rows. Paths will be found for 0. The others already have paths in the db.
  257. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.PHGdbAccess - Closing DB
  258. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.pangenome.hapCalling.BestHaplotypePathPlugin: time: Aug 5, 2021 16:31:23
  259. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: time: Aug 5, 2021 16:31:23
  260. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
  261. HaplotypeGraphBuilderPlugin Parameters
  262. configFile: /phg/config_ImputePipelinePlugin_fastq.txt
  263. methods: GATK_PIPELINE
  264. includeSequences: false
  265. includeVariantContexts: true
  266. haplotypeIds: null
  267. chromosomes: null
  268. taxa: null
  269.  
  270. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - first connection: dbName from config file = /phg/95HRSW_attempt4.db host: localHost user: sqlite type: sqlite
  271. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Database URL: jdbc:sqlite:/phg/95HRSW_attempt4.db
  272. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Connected to database:
  273.  
  274. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: query statement: select reference_ranges.ref_range_id, chrom, range_start, range_end, methods.name from reference_ranges INNER JOIN ref_range_ref_range_method on ref_range_ref_range_method.ref_range_id=reference_ranges.ref_range_id INNER JOIN methods on ref_range_ref_range_method.method_id = methods.method_id AND methods.method_type = 7 ORDER BY reference_ranges.ref_range_id
  275. methods size: 1
  276. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: number of reference ranges: 94229
  277. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - referenceRangesAsMap: time: 0.403850626 secs.
  278. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: query statement: SELECT gamete_haplotypes.gamete_grp_id, genotypes.line_name FROM gamete_haplotypes INNER JOIN gametes ON gamete_haplotypes.gameteid = gametes.gameteid INNER JOIN genotypes on gametes.genoid = genotypes.genoid ORDER BY gamete_haplotypes.gamete_grp_id;
  279. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: number of taxa lists: 136337
  280. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - taxaListMap: time: 4.734796851 secs.
  281. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.VariantUtils - variantIdsToVariantMap: query statement: SELECT variant_id, chrom, position, ref_allele_id, alt_allele_id FROM variants;
  282. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: haplotype method: GATK_PIPELINE range group method: null
  283. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: query statement: SELECT haplotypes_id, gamete_grp_id, haplotypes.ref_range_id, asm_contig, asm_start_coordinate, asm_end_coordinate, genome_file_id, seq_hash, seq_len, variant_list FROM haplotypes WHERE method_id = 3;
  284. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - addNodes: number of nodes: 8857526
  285. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - addNodes: number of reference ranges: 94229
  286. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.CreateGraphUtils - createHaplotypeNodes: time: 202.517586763 secs.
  287. [pool-1-thread-1] INFO net.maizegenetics.pangenome.api.HaplotypeGraph - Created graph edges: created when requested number of nodes: 8857526 number of reference ranges: 94229
  288. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.pangenome.api.HaplotypeGraphBuilderPlugin: time: Aug 5, 2021 16:34:56
  289. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin: time: Aug 5, 2021 16:34:56
  290. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
  291. ImportDiploidPathPlugin Parameters
  292. pathMethodName: pathMethodwithnewdb_fq_GATK_PIPELINE
  293.  
  294. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - first connection: dbName from config file = /phg/95HRSW_attempt4.db host: localHost user: sqlite type: sqlite
  295. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Database URL: jdbc:sqlite:/phg/95HRSW_attempt4.db
  296. [pool-1-thread-1] INFO net.maizegenetics.pangenome.db_loading.DBLoadingUtils - Connected to database:
  297.  
  298. [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin - importPathsFromDB: query: SELECT line_name, paths_data FROM paths, genotypes, methods WHERE paths.genoid=genotypes.genoid AND methods.method_id=paths.method_id AND methods.name='pathMethodwithnewdb_fq_GATK_PIPELINE'
  299. [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin - importPathsFromDB: number of path list: 1
  300. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.pangenome.hapCalling.ImportDiploidPathPlugin: time: Aug 5, 2021 16:34:57
  301. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Starting net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin: time: Aug 5, 2021 16:34:57
  302. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
  303. PathsToVCFPlugin Parameters
  304. outputFile: 95HRSW_imputedwith17C23-2fastq_VCF.vcf
  305. refRangeFileVCF: null
  306. referenceFasta: null
  307. makeDiploid: true
  308. positions: null
  309.  
  310. [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin - PathsToVCFPlugin: processData: number of ranges: 94229
  311. [pool-1-thread-1] INFO net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin - PathsToVCFPlugin: processData: number of taxa: 1
  312. [pool-1-thread-1] DEBUG net.maizegenetics.plugindef.AbstractPlugin - Parent job is Cancelling
  313. kotlinx.coroutines.JobCancellationException: Parent job is Cancelling; job=UndispatchedCoroutine{Cancelled}@7dbcd962
  314. Caused by: java.lang.IllegalStateException: Allele in genotype C not in the variant context [C, C]
  315. at htsjdk.variant.variantcontext.VariantContext$Validation.validateGenotypes(VariantContext.java:382)
  316. at htsjdk.variant.variantcontext.VariantContext$Validation.access$200(VariantContext.java:323)
  317. at htsjdk.variant.variantcontext.VariantContext$Validation$2.validate(VariantContext.java:331)
  318. at htsjdk.variant.variantcontext.VariantContext.lambda$validate$0(VariantContext.java:1384)
  319. at java.lang.Iterable.forEach(Iterable.java:75)
  320. at htsjdk.variant.variantcontext.VariantContext.validate(VariantContext.java:1384)
  321. at htsjdk.variant.variantcontext.VariantContext.<init>(VariantContext.java:489)
  322. at htsjdk.variant.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:647)
  323. at htsjdk.variant.variantcontext.VariantContextBuilder.make(VariantContextBuilder.java:638)
  324. at net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin.createVariantContext(PathsToVCFPlugin.kt:342)
  325. at net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin.variantContexts(PathsToVCFPlugin.kt:475)
  326. at net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin.access$variantContexts(PathsToVCFPlugin.kt:53)
  327. at net.maizegenetics.pangenome.hapCalling.PathsToVCFPlugin$infosByRange$2$invokeSuspend$$inlined$forEach$lambda$1.invokeSuspend(PathsToVCFPlugin.kt:216)
  328. at kotlin.coroutines.jvm.internal.BaseContinuationImpl.resumeWith(ContinuationImpl.kt:33)
  329. at kotlinx.coroutines.DispatchedTask.run(Dispatched.kt:241)
  330. at kotlinx.coroutines.scheduling.CoroutineScheduler.runSafely(CoroutineScheduler.kt:594)
  331. at kotlinx.coroutines.scheduling.CoroutineScheduler.access$runSafely(CoroutineScheduler.kt:60)
  332. at kotlinx.coroutines.scheduling.CoroutineScheduler$Worker.run(CoroutineScheduler.kt:740)
  333. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin -
  334. Usage:
  335. PathsToVCFPlugin <options>
  336. -outputFile <Output VCF File Name> : Output file name (required)
  337. -refRangeFileVCF <Reference Range File> : Reference Range file used to subset the paths for only specified regions of the genome.
  338. -referenceFasta <Reference Genome> : Reference Genome.
  339. -makeDiploid <true | false> : Whether to report haploid paths as homozygousdiploid (Default: true)
  340. -positions <Position List> : Positions to include in VCF. Can be specified by Genotype file (i.e. VCF, Hapmap, etc.), bed file, or json file containing the requested positions.
  341.  
  342. [pool-1-thread-1] ERROR net.maizegenetics.plugindef.AbstractPlugin - Parent job is Cancelling
  343. [pool-1-thread-1] INFO net.maizegenetics.plugindef.AbstractPlugin - Finished net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin: time: Aug 5, 2021 16:34:58
  344. [pool-1-thread-1] INFO net.maizegenetics.pipeline.TasselPipeline - net.maizegenetics.pangenome.pipeline.ImputePipelinePlugin: time: Aug 5, 2021 16:34:58: progress: 100%
  345.  
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