I encounter this error when running HaplotypeCaller on picard-validated bam files using the b37 reference in the GATK resource bundle with GATK v2.3-4-g57ea19f. My commands are : -R resources/BroadInstitute/bundle_1.5/b37/human_g1k_v37.fasta \ -T HaplotypeCaller \ -L 1:233766919-233767204 \ -debug \ -allowPotentiallyMisencodedQuals \ -I sample1.recal.bam -I sample2.recal.bam [...] -I sample36.recal.bam \ -dcov 1200 \ -o samples.3:60800001-60830896.raw.snps.indels.vcf
There was no problem running UnifiedGenotyper on the same data. The stack trace (with debug info) is pasted below.
Any help would be greatly appreciated.
Thanks,
Paige
INFO 14:33:33,576 HelpFormatter - -------------------------------------------------------------------------------- INFO 14:33:33,579 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.3-4-g57ea19f, Compiled 2012/12/20 15:09:50 INFO 14:33:33,579 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 14:33:33,579 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 14:33:33,584 HelpFormatter - Program Args: -allowPotentiallyMisencodedQuals -R /scratch1/tmp/tpaige/resources/BroadInstitute/bundle_1.5/b37/human_g1k_v37.fasta -T HaplotypeCaller -L 1:233766919-233767204 -debug -I /scratch0/tmp/tpaige/projects/SRP/6-recal/112_25.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/128_26.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/133_6.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R01_013A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R06_303A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R97_375.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/L01_362.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/L10_440A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R00_113A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R00_294A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R00_421A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R01_210A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R01_489A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R02_217A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R02_363A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R02_449A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R05_304A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R05_449C.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R06_527A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R08_045A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R08_134A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R08_273A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R08_553A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R09_101A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R09_524A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R09_588A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R10_483A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R10_640A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R10_711D.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R96_010A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R97_030B.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R97_051B.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R97_145A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R98_219A.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R98_463E.markdup.realigned.recalibrated.bam -I /scratch0/tmp/tpaige/projects/SRP/6-recal/R98_468D.markdup.realigned.recalibrated.bam -dcov 1200 -o /scratch0/tmp/tpaige/projects/SRP/7-rawVariants/haplotypeCaller/byChr_v3/troubleshoot/SRP.markdup.realigned.recalibrated.haplotypeCaller.1:233766919-233767204.raw.snps.indels.vcf INFO 14:33:33,585 HelpFormatter - Date/Time: 2013/01/02 14:33:33 INFO 14:33:33,585 HelpFormatter - -------------------------------------------------------------------------------- INFO 14:33:33,585 HelpFormatter - -------------------------------------------------------------------------------- INFO 14:33:33,607 GenomeAnalysisEngine - Strictness is SILENT WARN 14:33:33,616 FSLockWithShared - WARNING: Unable to lock file /scratch1/tmp/tpaige/resources/BroadInstitute/bundle_1.5/b37/human_g1k_v37.dict: Function not implemented. INFO 14:33:33,617 ReferenceDataSource - Unable to create a lock on dictionary file: Function not implemented INFO 14:33:33,617 ReferenceDataSource - Treating existing dictionary file as complete. WARN 14:33:33,617 FSLockWithShared - WARNING: Unable to lock file /scratch1/tmp/tpaige/resources/BroadInstitute/bundle_1.5/b37/human_g1k_v37.fasta.fai: Function not implemented. INFO 14:33:33,618 ReferenceDataSource - Unable to create a lock on index file: Function not implemented INFO 14:33:33,618 ReferenceDataSource - Treating existing index file as complete. INFO 14:33:33,815 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1200, Using the new downsampling implementation INFO 14:33:33,823 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 14:33:34,449 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.63 INFO 14:33:34,535 GenomeAnalysisEngine - Processing 286 bp from intervals INFO 14:33:34,544 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 14:33:34,544 ProgressMeter - Location processed.active regions runtime per.1M.active regions completed total.runtime remaining
Assembling 1:233766919-233767204 with 14701 reads: (with overlap region = 1:233766854-233767269) Found 27 candidate haplotypes to evaluate every read against. TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT
Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAAGATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACGGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGATCGGAAGAGCACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 248M9I168M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGAGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCCTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGGTGGCAAAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 245M7I171M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTAGATCACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 244M1D3M1I168M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGACCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTACCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCTCTTCCGATCTGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 117M11I299M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGATCTATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATCTTTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 119M3I297M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACAATGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 238M2I178M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACAGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATCTGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 110M5D301M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGAGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGACCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGATTCTGACAACATCAGGATATGAAAGGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGATTCTGACAACATCAGGATATGAAAGGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACGGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGAGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGATTCTGACAACATCAGGATATGAAAGGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGAGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGATTCTGACAACATCAGGATATGAAAGGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACGGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGATTCTGACAACATCAGGATATGAAATGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGATTCTGACAACATCAGGATATGAAATGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACGGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAGGATATGAAATGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAGGATATGAAATGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACGGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAATGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M INFO 14:34:04,547 ProgressMeter - 1:233767204 0.00e+00 30.0 s 49.6 w 99.7% 30.1 s 0.1 s INFO 14:34:34,549 ProgressMeter - 1:233767204 0.00e+00 60.0 s 99.2 w 99.7% 60.2 s 0.2 s INFO 14:35:04,553 ProgressMeter - 1:233767204 0.00e+00 90.0 s 148.8 w 99.7% 90.3 s 0.3 s INFO 14:35:34,558 ProgressMeter - 1:233767204 0.00e+00 2.0 m 198.4 w 99.7% 2.0 m 0.4 s INFO 14:36:04,563 ProgressMeter - 1:233767204 0.00e+00 2.5 m 248.0 w 99.7% 2.5 m 0.5 s INFO 14:36:34,568 ProgressMeter - 1:233767204 0.00e+00 3.0 m 297.7 w 99.7% 3.0 m 0.6 s Chose haplotypes 18 and 7 with diploid likelihood = 0.0 Chose haplotypes 18 and 8 with diploid likelihood = -533.747309737968 Chose haplotypes 18 and 0 with diploid likelihood = -777.1108623066011 Chose haplotypes 18 and 1 with diploid likelihood = -1310.8581720445072 Chose haplotypes 7 and 3 with diploid likelihood = -1451.1726611647882 Chose haplotypes 19 and 7 with diploid likelihood = -1501.7146670729999 Chose haplotypes 7 and 4 with diploid likelihood = -1695.1134320870115 Chose haplotypes 17 and 7 with diploid likelihood = -1713.464772552341 Chose haplotypes 8 and 3 with diploid likelihood = -1984.9199709026507 Chose haplotypes 8 and 4 with diploid likelihood = -2228.860741824894 Chose haplotypes 19 and 0 with diploid likelihood = -2278.8255293794828 Chose haplotypes 17 and 0 with diploid likelihood = -2490.5756348588693 Chose haplotypes 20 and 7 with diploid likelihood = -2585.3380487913055 Chose haplotypes 20 and 0 with diploid likelihood = -3362.448911097821 Chose haplotypes 21 and 7 with diploid likelihood = -3483.4850108307965 Chose haplotypes 15 and 7 with diploid likelihood = -3568.629541037797 Chose haplotypes 16 and 7 with diploid likelihood = -3777.6186484047903 Chose 12 alternate haplotypes to genotype in all samples. === Best Haplotypes === TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M Left and right breaks = (0 , 0)
Events = {} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGATTCTGACAACATCAGGATATGAAAGGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M Left and right breaks = (0 , 0) Events = {233767008=[VC HC1 @ 1:233767008 Q. of type=SNP alleles=[T*, A] attr={} GT=[], 233767023=[VC HC1 @ 1:233767023 Q. of type=SNP alleles=[A*, G] attr={} GT=[], 233767059=[VC HC1 @ 1:233767059 Q. of type=SNP alleles=[T*, C] attr={} GT=[]} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGATTCTGACAACATCAGGATATGAAAGGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACGGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M Left and right breaks = (0 , 274) Events = {233767008=[VC HC2 @ 1:233767008 Q. of type=SNP alleles=[T*, A] attr={} GT=[], 233767023=[VC HC2 @ 1:233767023 Q. of type=SNP alleles=[A*, G] attr={} GT=[], 233767059=[VC HC2 @ 1:233767059 Q. of type=SNP alleles=[T*, C] attr={} GT=[], 233767105=[VC HC2 @ 1:233767105 Q. of type=SNP alleles=[A*, G] attr={} GT=[]} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGAGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGATTCTGACAACATCAGGATATGAAAGGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M Left and right breaks = (104 , 0) Events = {233767008=[VC HC3 @ 1:233767008 Q. of type=SNP alleles=[T*, A] attr={} GT=[], 233767023=[VC HC3 @ 1:233767023 Q. of type=SNP alleles=[A*, G] attr={} GT=[], 233767059=[VC HC3 @ 1:233767059 Q. of type=SNP alleles=[T*, C] attr={} GT=[], 233766958=[VC HC3 @ 1:233766958 Q. of type=SNP alleles=[C*, A] attr={} GT=[]} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGAGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGATTCTGACAACATCAGGATATGAAAGGTTGTCACTCACTGAACCCCTAATGCGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACGGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M Left and right breaks = (104 , 274) Events = {233767008=[VC HC4 @ 1:233767008 Q. of type=SNP alleles=[T*, A] attr={} GT=[], 233767023=[VC HC4 @ 1:233767023 Q. of type=SNP alleles=[A*, G] attr={} GT=[], 233767059=[VC HC4 @ 1:233767059 Q. of type=SNP alleles=[T*, C] attr={} GT=[], 233767105=[VC HC4 @ 1:233767105 Q. of type=SNP alleles=[A*, G] attr={} GT=[], 233766958=[VC HC4 @ 1:233766958 Q. of type=SNP alleles=[C*, A] attr={} GT=[]} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGAGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M Left and right breaks = (104 , 0) Events = {233766958=[VC HC5 @ 1:233766958 Q. of type=SNP alleles=[C*, A] attr={} GT=[]} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACGGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M Left and right breaks = (0 , 0) Events = {233767105=[VC HC6 @ 1:233767105 Q. of type=SNP alleles=[A*, G] attr={} GT=[]} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCCTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M Left and right breaks = (105 , 0) Events = {233766959=[VC HC7 @ 1:233766959 Q. of type=SNP alleles=[G*, C] attr={} GT=[]} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGACACAAGATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M Left and right breaks = (0 , 256) Events = {233767107=[VC HC8 @ 1:233767107 Q. of type=SNP alleles=[A*, G] attr={} GT=[], 233767106=[VC HC8 @ 1:233767106 Q. of type=SNP alleles=[G*, A] attr={} GT=[]} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGAGATCGGAAGAGCACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 248M9I168M Left and right breaks = (0 , 258) Events = {233767101=[VC HC9 @ 1:233767101 Q. of type=SYMBOLIC alleles=[A*,
] attr={} GT=[]} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTGGTGGCAAAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 245M7I171M Left and right breaks = (0 , 253) Events = {233767098=[VC HC10 @ 1:233767098 Q. of type=SYMBOLIC alleles=[G*, ] attr={} GT=[]} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGACCTGAGACACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 416M Left and right breaks = (0 , 241) Events = {233767094=[VC HC11 @ 1:233767094 Q. of type=SNP alleles=[C*, A] attr={} GT=[]} TTCTGACAAGGAAAAGACCGTGCCTCATCTCTGGCTCTCAGAATTGTCCATCATCCACAGTCTATTTTATTTATACCTACGTGGTAACTGCTAACTCAAATAGGCGTGATGGTGACCGATTATCATTGTGTTTCCCTTTGCCACCAGGTGCGGGTTTCTGACAACATCAAGATATGAAAGGTTGTCACTCACTGAACCCCTAATGTGTGTTTAACTGTTGGGGAAGAATGGGAATCACTGCCCTAGATCACAGAATTTAATTAGGCCTGCTTCTTTGTGTTTCTCTTTAATGATAGGATTTTAAGCTCAACGGTTATCAGCTCAAAAGCAGAAAATGTTCATTCCCGTTTGTGCCCTGGTATCTTGAAGAATGTGCAATAGGTGAGCTTGCCATTAATCTAACTGAATTTCTCCCT Cigar = 244M1D3M1I168M Left and right breaks = (0 , 249) Events = {233767097=[VC HC12 @ 1:233767097-233767098 Q. of type=INDEL alleles=[TG*, T] attr={} GT=[], 233767101=[VC HC12 @ 1:233767101 Q. of type=INDEL alleles=[A*, AT] attr={} GT=[]} Found consecutive biallelic events with R^2 = 0.0303 -- [VC HC3 @ 1:233766958 Q. of type=SNP alleles=[C*, A] attr={} GT=[] -- [VC HC7 @ 1:233766959 Q. of type=SNP alleles=[G*, C] attr={} GT=[] Found consecutive biallelic events with R^2 = 0.0083 -- [VC HC11 @ 1:233767094 Q. of type=SNP alleles=[C*, A] attr={} GT=[] -- [VC HC12 @ 1:233767097-233767098 Q. of type=INDEL alleles=[TG*, T] attr={} GT=[] Found consecutive biallelic events with R^2 = 1.0000 -- [VC HC12 @ 1:233767097-233767098 Q. of type=INDEL alleles=[TG*, T] attr={} GT=[] -- [VC HC12 @ 1:233767101 Q. of type=INDEL alleles=[A*, AT] attr={} GT=[] ====> [VC merged @ 1:233767098-233767101 Q. of type=MNP alleles=[GAGA*, AGAT] attr={} GT=[] Found consecutive biallelic events with R^2 = 0.0303 -- [VC HC3 @ 1:233766958 Q. of type=SNP alleles=[C*, A] attr={} GT=[] -- [VC HC7 @ 1:233766959 Q. of type=SNP alleles=[G*, C] attr={} GT=[] Found consecutive biallelic events with R^2 = 0.0182 -- [VC HC11 @ 1:233767094 Q. of type=SNP alleles=[C*, A] attr={} GT=[] -- [VC merged @ 1:233767098-233767101 Q. of type=MNP alleles=[GAGA*, AGAT] attr={} GT=[] Found consecutive biallelic events with R^2 = 0.0667 -- [VC merged @ 1:233767098-233767101 Q. of type=MNP alleles=[GAGA*, AGAT] attr={} GT=[] -- [VC HC2 @ 1:233767105 Q. of type=SNP alleles=[A*, G] attr={} GT=[] Found consecutive biallelic events with R^2 = 0.0303 -- [VC HC2 @ 1:233767105 Q. of type=SNP alleles=[A*, G] attr={} GT=[] -- [VC HC8 @ 1:233767106 Q. of type=SNP alleles=[G*, A] attr={} GT=[] Found consecutive biallelic events with R^2 = 1.0000 -- [VC HC8 @ 1:233767106 Q. of type=SNP alleles=[G*, A] attr={} GT=[] -- [VC HC8 @ 1:233767107 Q. of type=SNP alleles=[A*, G] attr={} GT=[] ====> [VC merged @ 1:233767106-233767107 Q. of type=MNP alleles=[GA*, AG] attr={} GT=[] Found consecutive biallelic events with R^2 = 0.0303 -- [VC HC3 @ 1:233766958 Q. of type=SNP alleles=[C*, A] attr={} GT=[] -- [VC HC7 @ 1:233766959 Q. of type=SNP alleles=[G*, C] attr={} GT=[] Found consecutive biallelic events with R^2 = 0.0182 -- [VC HC11 @ 1:233767094 Q. of type=SNP alleles=[C*, A] attr={} GT=[] -- [VC merged @ 1:233767098-233767101 Q. of type=MNP alleles=[GAGA*, AGAT] attr={} GT=[] Found consecutive biallelic events with R^2 = 0.0667 -- [VC merged @ 1:233767098-233767101 Q. of type=MNP alleles=[GAGA*, AGAT] attr={} GT=[] -- [VC HC2 @ 1:233767105 Q. of type=SNP alleles=[A*, G] attr={} GT=[] Found consecutive biallelic events with R^2 = 0.0303 -- [VC HC2 @ 1:233767105 Q. of type=SNP alleles=[A*, G] attr={} GT=[] -- [VC merged @ 1:233767106-233767107 Q. of type=MNP alleles=[GA*, AG] attr={} GT=[] Genotyping event at 233766958 with alleles = [C*, A] Genotyping event at 233766959 with alleles = [G*, C] Genotyping event at 233767008 with alleles = [T*, A] Genotyping event at 233767023 with alleles = [A*, G] Genotyping event at 233767059 with alleles = [T*, C] Genotyping event at 233767094 with alleles = [C*, A] INFO 14:36:57,341 GATKRunReport - Uploaded run statistics report to AWS S3
java.lang.IllegalArgumentException: Cannot extend a symbolic allele at org.broadinstitute.sting.utils.variantcontext.Allele.extend(Allele.java:182) at org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.resolveIncompatibleAlleles(VariantContextUtils.java:842) at org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.simpleMerge(VariantContextUtils.java:545) at org.broadinstitute.sting.utils.variantcontext.VariantContextUtils.simpleMerge(VariantContextUtils.java:452) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.GenotypingEngine.assignGenotypeLikelihoodsAndCallIndependentEvents(GenotypingEngine.java:159) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:411) at org.broadinstitute.sting.gatk.walkers.haplotypecaller.HaplotypeCaller.map(HaplotypeCaller.java:107) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegion(TraverseActiveRegions.java:285) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.callWalkerMapOnActiveRegions(TraverseActiveRegions.java:230) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.processActiveRegions(TraverseActiveRegions.java:205) at org.broadinstitute.sting.gatk.traversals.TraverseActiveRegions.endTraversal(TraverseActiveRegions.java:294) at org.broadinstitute.sting.gatk.executive.LinearMicroScheduler.execute(LinearMicroScheduler.java:93) at org.broadinstitute.sting.gatk.GenomeAnalysisEngine.execute(GenomeAnalysisEngine.java:281) at org.broadinstitute.sting.gatk.CommandLineExecutable.execute(CommandLineExecutable.java:113) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:237) at org.broadinstitute.sting.commandline.CommandLineProgram.start(CommandLineProgram.java:147) at org.broadinstitute.sting.gatk.CommandLineGATK.main(CommandLineGATK.java:94)
