INFO 10:00:37,163 HelpFormatter - -------------------------------------------------------------------------------- INFO 10:00:37,165 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.7-2-g6bda569, Compiled 2013/08/28 16:30:29 INFO 10:00:37,165 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 10:00:37,165 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 10:00:37,169 HelpFormatter - Program Args: -T HaplotypeCaller -R ReferenceFiles\human_g1k_v37.fasta -I ReferenceFiles\reduced_reads.bam --genotyping_mode DISCOVERY --dbsnp ReferenceFiles\dbsnp_137.b37.excluding_sites_after_129.vcf -L 20 -L 21 -stand_emit_conf 10 -stand_call_conf 30 -o ReferenceFiles\raw_variants.vcf INFO 10:00:37,169 HelpFormatter - Date/Time: 2013/12/04 10:00:37 INFO 10:00:37,169 HelpFormatter - -------------------------------------------------------------------------------- INFO 10:00:37,169 HelpFormatter - -------------------------------------------------------------------------------- INFO 10:00:37,216 ArgumentTypeDescriptor - Dynamically determined type of ReferenceFiles\dbsnp_137.b37.excluding_sites_after_129.vcf to be VCF Class class org.broadinstitute.sting.gatk.phonehome.GATKRunReport Class class org.broadinstitute.sting.gatk.phonehome.GATKRunReport INFO 10:00:37,542 GenomeAnalysisEngine - Strictness is SILENT INFO 10:00:37,768 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 250 INFO 10:00:37,775 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 10:00:37,830 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.05 INFO 10:00:37,858 HCMappingQualityFilter - Filtering out reads with MAPQ < 20 INFO 10:00:37,966 RMDTrackBuilder - Loading Tribble index from disk for file ReferenceFiles\dbsnp_137.b37.excluding_sites_after_129.vcf INFO 10:00:38,320 IntervalUtils - Processing 111155415 bp from intervals INFO 10:00:38,684 GenomeAnalysisEngine - Preparing for traversal over 1 BAM files INFO 10:00:38,827 GenomeAnalysisEngine - Done preparing for traversal INFO 10:00:38,827 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] INFO 10:00:38,827 ProgressMeter - Location processed.active regions runtime per.1M.active regions completed total.runtime remaining INFO 10:00:38,913 HaplotypeCaller - Using global mismapping rate of 45 => -4.5 in log10 likelihood units INFO 10:01:08,832 ProgressMeter - 20:28910030 0.00e+00 30.0 s 49.6 w 26.0% 115.0 s 85.0 s INFO 10:01:38,835 ProgressMeter - 20:60633414 0.00e+00 60.0 s 99.2 w 54.5% 109.0 s 49.0 s INFO 10:02:08,838 ProgressMeter - 21:28017385 6.30e+07 90.0 s 1.0 s 81.9% 109.0 s 19.0 s INFO 10:02:32,691 HaplotypeCaller - Ran local assembly on 0 active regions INFO 10:02:32,697 ProgressMeter - done 1.11e+08 113.0 s 1.0 s 100.0% 113.0 s 0.0 s INFO 10:02:32,697 ProgressMeter - Total runtime 113.86 secs, 1.90 min, 0.03 hours INFO 10:02:32,698 MicroScheduler - 2584 reads were filtered out during the traversal out of approximately 5401 total reads (47.84%) INFO 10:02:32,698 MicroScheduler - -> 0 reads (0.00% of total) failing DuplicateReadFilter INFO 10:02:32,698 MicroScheduler - -> 0 reads (0.00% of total) failing FailsVendorQualityCheckFilter INFO 10:02:32,698 MicroScheduler - -> 2584 reads (47.84% of total) failing HCMappingQualityFilter INFO 10:02:32,698 MicroScheduler - -> 0 reads (0.00% of total) failing MalformedReadFilter INFO 10:02:32,698 MicroScheduler - -> 0 reads (0.00% of total) failing MappingQualityUnavailableFilter INFO 10:02:32,698 MicroScheduler - -> 0 reads (0.00% of total) failing NotPrimaryAlignmentFilter INFO 10:02:32,698 MicroScheduler - -> 0 reads (0.00% of total) failing UnmappedReadFilter Class class org.broadinstitute.sting.gatk.phonehome.GATKRunReport Class class org.broadinstitute.sting.gatk.phonehome.GATKRunReport INFO 10:02:34,228 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection refused: connect INFO 10:02:34,229 HttpMethodDirector - Retrying request INFO 10:02:35,240 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection refused: connect INFO 10:02:35,240 HttpMethodDirector - Retrying request INFO 10:02:36,251 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection refused: connect INFO 10:02:36,251 HttpMethodDirector - Retrying request INFO 10:02:37,272 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection refused: connect INFO 10:02:37,272 HttpMethodDirector - Retrying request INFO 10:02:38,305 HttpMethodDirector - I/O exception (java.net.ConnectException) caught when processing request: Connection refused: connect INFO 10:02:38,305 HttpMethodDirector - Retrying request