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PhaseByTransmission does not phase any genotype

Dear GATK development team:
Hi, I'm trying to use GATK to phase trio data. Below is the log that I copied, I filtered my PED file and VCF file so that both files contains the exactly same set of samples as well as strictly matched trio relationship.

However, the result I got is always the same as the input file, none of the genotype is phased. Could anyone help me out here?

Thanks a million!

INFO  19:39:01,840 HelpFormatter - ---------------------------------------------------------------------------------- 
INFO  19:39:01,842 HelpFormatter - The Genome Analysis Toolkit (GATK) v3.8-0-ge9d806836, Compiled 2017/07/28 21:26:50 
INFO  19:39:01,843 HelpFormatter - Copyright (c) 2010-2016 The Broad Institute 
INFO  19:39:01,843 HelpFormatter - For support and documentation go to https://software.broadinstitute.org/gatk 
INFO  19:39:01,843 HelpFormatter - [Thu Dec 14 19:39:01 EST 2017] Executing on Linux 3.13.0-135-generic amd64 
INFO  19:39:01,843 HelpFormatter - Java HotSpot(TM) 64-Bit Server VM 1.8.0_151-b12 
INFO  19:39:01,848 HelpFormatter - Program Args: -T PhaseByTransmission -R resource/hs37d5.fa -V ALL.chr20.pass.minDP0.gtonly.genotypes.bcf.HRC.10k.site.sorted.vcf.gz.has.ped.recode.vcf.gz -ped ./no.problem.trio.family.list.ped -o output.vcf 
INFO  19:39:01,854 HelpFormatter - Executing as [email protected] on Linux 3.13.0-135-generic amd64; Java HotSpot(TM) 64-Bit Server VM 1.8.0_151-b12. 
INFO  19:39:01,855 HelpFormatter - Date/Time: 2017/12/14 19:39:01 
INFO  19:39:01,855 HelpFormatter - ---------------------------------------------------------------------------------- 
INFO  19:39:01,855 HelpFormatter - ---------------------------------------------------------------------------------- 
ERROR StatusLogger Unable to create class org.apache.logging.log4j.core.impl.Log4jContextFactory specified in jar:file:/net/wonderland/home/fanzhang/WorkingSpace/install-packages/gatk/GenomeAnalysisTK-3.8-0-ge9d806836/GenomeAnalysisTK.jar!/META-INF/log4j-provider.prope
ERROR StatusLogger Log4j2 could not find a logging implementation. Please add log4j-core to the classpath. Using SimpleLogger to log to the console...
INFO  19:39:02,010 GenomeAnalysisEngine - Deflater: JdkDeflater 
INFO  19:39:02,010 GenomeAnalysisEngine - Inflater: JdkInflater 
INFO  19:39:02,011 GenomeAnalysisEngine - Strictness is SILENT 
INFO  19:39:02,139 GenomeAnalysisEngine - Downsampling Settings: Method: BY_SAMPLE, Target Coverage: 1000 
WARN  19:39:02,210 IndexDictionaryUtils - Track variant doesn't have a sequence dictionary built in, skipping dictionary validation 
INFO  19:39:02,219 PedReader - Reading PED file ./no.problem.trio.family.list.ped with missing fields: [] 
INFO  19:39:02,273 PedReader - Phenotype is other? false 
INFO  19:39:02,375 GenomeAnalysisEngine - Preparing for traversal 
INFO  19:39:02,381 GenomeAnalysisEngine - Done preparing for traversal 
INFO  19:39:02,381 ProgressMeter - [INITIALIZATION COMPLETE; STARTING PROCESSING] 
INFO  19:39:02,382 ProgressMeter -                 | processed |    time |    per 1M |           |   total | remaining 
INFO  19:39:02,382 ProgressMeter -        Location |     sites | elapsed |     sites | completed | runtime |   runtime 
INFO  19:39:32,388 ProgressMeter -       20:158114         0.0    30.0 s      49.6 w       86.7%    34.0 s       4.0 s 
INFO  19:40:02,392 ProgressMeter -       20:228889         0.0    60.0 s      99.2 w       86.7%    69.0 s       9.0 s 
INFO  19:40:32,397 ProgressMeter -       20:303259         0.0    90.0 s     148.8 w       86.7%   103.0 s      13.0 s 
INFO  19:41:02,399 ProgressMeter -       20:381399         0.0   120.0 s     198.4 w       86.7%     2.3 m      18.0 s 
INFO  19:41:32,401 ProgressMeter -       20:484650         0.0     2.5 m     248.0 w       86.7%     2.9 m      23.0 s 
INFO  19:42:02,402 ProgressMeter -       20:578423         0.0     3.0 m     297.7 w       86.7%     3.5 m      27.0 s 
INFO  19:42:32,404 ProgressMeter -       20:678727         0.0     3.5 m     347.3 w       86.7%     4.0 m      32.0 s 
INFO  19:42:34,827 PhaseByTransmission - Number of complete trio-genotypes: 9920280 
INFO  19:42:34,827 PhaseByTransmission - Number of trio-genotypes containing no call(s): 0 
INFO  19:42:34,828 PhaseByTransmission - Number of trio-genotypes phased: 0 
INFO  19:42:34,828 PhaseByTransmission - Number of resulting Het/Het/Het trios: 108196 
INFO  19:42:34,828 PhaseByTransmission - Number of remaining single mendelian violations in trios: 0 
INFO  19:42:34,828 PhaseByTransmission - Number of remaining double mendelian violations in trios: 0 
INFO  19:42:34,828 PhaseByTransmission - Number of complete pair-genotypes: 0 
INFO  19:42:34,828 PhaseByTransmission - Number of pair-genotypes containing no call(s): 0 
INFO  19:42:34,829 PhaseByTransmission - Number of pair-genotypes phased: 0 
INFO  19:42:34,829 PhaseByTransmission - Number of resulting Het/Het pairs: 0 
INFO  19:42:34,829 PhaseByTransmission - Number of remaining mendelian violations in pairs: 0 
INFO  19:42:34,829 PhaseByTransmission - Number of genotypes updated: 0 
INFO  19:42:34,847 ProgressMeter -            done     10427.0     3.5 m       5.7 h       86.7%     4.1 m      32.0 s 
INFO  19:42:34,848 ProgressMeter - Total runtime 212.47 secs, 3.54 min, 0.06 hours 
------------------------------------------------------------------------------------------
Done. —————————————————————————————————————————————

Issue · Github
by Sheila

Issue Number
2785
State
closed
Last Updated
Assignee
Array
Closed By
vdauwera

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