perform UnifiedGenotyper for empty vcf file

livefallflylivefallfly Posts: 23Member
edited November 2012 in Ask the GATK team

Hi, I use bowtie to do the mapping. And then use samtools to convert the sam to bam file, then use Picard to add RG info, then use the GATK local indel tool, then use the GATK UnifiedGenotyper to call SNP.

java -Xmx4g -jar ~/fly/GenomeAnalysisTK-2.2-3/GenomeAnalysisTK.jar -T UnifiedGenotyper -I read_target.bam --dbsnp ../human_chr.vcf -R ~/fly/GenomeAnalysisTK-2.2-3/ucsc.hg19.fasta -o read.vcf -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 1000

And all the progress, there is no error. But I just got a vcf file as following.

##fileformat=VCFv4.1
##FILTER=<ID=LowQual,Description="Low quality">
##FORMAT=<ID=AD,Number=.,Type=Integer,Description="Allelic depths for the ref and alt alleles in the order listed">
##FORMAT=<ID=DP,Number=1,Type=Integer,Description="Approximate read depth (reads with MQ=255 or with bad mates are filtered)">
##FORMAT=<ID=GQ,Number=1,Type=Integer,Description="Genotype Quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##FORMAT=<ID=PL,Number=G,Type=Integer,Description="Normalized, Phred-scaled likelihoods for genotypes as defined in the VCF specification">
##INFO=<ID=AC,Number=A,Type=Integer,Description="Allele count in genotypes, for each ALT allele, in the same order as listed">
##INFO=<ID=AF,Number=A,Type=Float,Description="Allele Frequency, for each ALT allele, in the same order as listed">
##INFO=<ID=AN,Number=1,Type=Integer,Description="Total number of alleles in called genotypes">
##INFO=<ID=BaseQRankSum,Number=1,Type=Float,Description="Z-score from Wilcoxon rank sum test of Alt Vs. Ref base qualities">
##INFO=<ID=DB,Number=0,Type=Flag,Description="dbSNP Membership">
...
action_per_sample=0.25 indel_heterozygosity=1.25E-4 indelGapContinuationPenalty=10 indelGapOpenPenalty=45 indelHaplotypeSize=80 noBandedIndel=false indelDebug=false ignoreSNPAlleles=false allReadsSP=false ignoreLaneInfo=false reference_sample_calls=(RodBinding name= source=UNBOUND) reference_sample_name=null sample_ploidy=2 min_quality_score=1 max_quality_score=40 site_quality_prior=20 min_power_threshold_for_calling=0.95 min_reference_depth=100 exclude_filtered_reference_sites=false heterozygosity=0.001 genotyping_mode=DISCOVERY output_mode=EMIT_VARIANTS_ONLY standard_min_confidence_threshold_for_calling=50.0 standard_min_confidence_threshold_for_emitting=10.0 alleles=(RodBinding name= source=UNBOUND) max_alternate_alleles=3 dbsnp=(RodBinding name=dbsnp source=exampleSNP.vcf) comp=[] out=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub no_cmdline_in_header=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub sites_only=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub bcf=org.broadinstitute.sting.gatk.io.stubs.VariantContextWriterStub debug_file=null metrics_file=null annotation=[] excludeAnnotation=[] filter_mismatching_base_and_quals=false"
##contig=<ID=chr1,length=100000>
##reference=file:///home/fly//GenomeAnalysisTK-2.2-3/ucsc.hg19.fasta
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  read.bam

I don't know why, but I am sure it can't be right with no SNPs. Through the samtools pileup method, I can get about 100 thousand SNPs.

Hope to get your answer, thanks.

Post edited by Geraldine_VdAuwera on

Answers

  • Geraldine_VdAuweraGeraldine_VdAuwera Posts: 6,466Administrator, GATK Developer admin

    Can you also post the output of the console from the UG run?

    Geraldine Van der Auwera, PhD

  • livefallflylivefallfly Posts: 23Member

    Sorry for delay. The console info is like following. INFO 21:44:54,446 HelpFormatter - -------------------------------------------------------------------------------- INFO 21:44:54,448 HelpFormatter - The Genome Analysis Toolkit (GATK) v2.1-5-gf3daab0, Compiled 2012/08/27 17:19:33 INFO 21:44:54,448 HelpFormatter - Copyright (c) 2010 The Broad Institute INFO 21:44:54,448 HelpFormatter - For support and documentation go to http://www.broadinstitute.org/gatk INFO 21:44:54,448 HelpFormatter - Program Args: -T UnifiedGenotyper -I read_target.bam --dbsnp ../human_chr.vcf -R /home/fly/GenomeAnalysisTK-2.2-3/ucsc.hg19.fasta -o read.vcf -stand_call_conf 50.0 -stand_emit_conf 10.0 -dcov 1000 INFO 21:44:54,448 HelpFormatter - Date/Time: 2012/11/27 21:44:54 INFO 21:44:54,448 HelpFormatter - -------------------------------------------------------------------------------- INFO 21:44:54,449 HelpFormatter - -------------------------------------------------------------------------------- INFO 21:44:54,481 ArgumentTypeDescriptor - Dynamically determined type of ../human_chr.vcf to be VCF INFO 21:44:54,487 GenomeAnalysisEngine - Strictness is SILENT INFO 21:44:54,592 SAMDataSource$SAMReaders - Initializing SAMRecords in serial INFO 21:44:54,634 SAMDataSource$SAMReaders - Done initializing BAM readers: total time 0.04 INFO 21:44:54,670 RMDTrackBuilder - Loading Tribble index from disk for file ../human_chr.vcf INFO 21:44:55,780 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTING] INFO 21:44:55,781 TraversalEngine - Location processed.sites runtime per.1M.sites completed total.runtime remaining INFO 21:45:25,454 TraversalEngine - chr1:10533430 1.06e+07 30.0 s 2.8 s 0.3% 2.5 h 2.5 h INFO 21:45:55,456 TraversalEngine - chr1:21228430 2.12e+07 60.0 s 2.8 s 0.7% 2.5 h 2.4 h INFO 21:46:25,456 TraversalEngine - chr1:31976430 3.20e+07 90.0 s 2.8 s 1.0% 2.5 h 2.4 h INFO 21:46:55,466 TraversalEngine - chr1:42713430 4.27e+07 2.0 m 2.8 s 1.4% 2.4 h 2.4 h INFO 21:47:25,467 TraversalEngine - chr1:53220430 5.32e+07 2.5 m 2.8 s 1.7% 2.5 h 2.4 h INFO 21:47:55,470 TraversalEngine - chr1:64172430 6.42e+07 3.0 m 2.8 s 2.0% 2.4 h 2.4 h INFO 21:48:25,472 TraversalEngine - chr1:75270430 7.53e+07 3.5 m 2.8 s 2.4% 2.4 h 2.4 h INFO 21:48:55,473 TraversalEngine - chr1:86197430 8.62e+07 4.0 m 2.8 s 2.7% 2.4 h 2.4 h INFO 21:49:25,476 TraversalEngine - chr1:96955430 9.70e+07 4.5 m 2.8 s 3.1% 2.4 h 2.4 h INFO 21:49:55,479 TraversalEngine - chr1:107618430 1.08e+08 5.0 m 2.8 s 3.4% 2.4 h 2.3 h INFO 21:50:25,480 TraversalEngine - chr1:118660430 1.19e+08 5.5 m 2.8 s 3.8% 2.4 h 2.3 h INFO 21:50:57,104 TraversalEngine - chr1:144179430 1.44e+08 6.0 m 2.5 s 4.6% 2.2 h 2.1 h INFO 21:51:28,231 TraversalEngine - chr1:148275430 1.48e+08 6.5 m 2.6 s 4.7% 2.3 h 2.2 h INFO 21:51:58,234 TraversalEngine - chr1:157422430 1.57e+08 7.0 m 2.7 s 5.0% 2.3 h 2.2 h INFO 21:52:28,236 TraversalEngine - chr1:168372430 1.68e+08 7.5 m 2.7 s 5.4% 2.3 h 2.2 h INFO 21:52:58,238 TraversalEngine - chr1:179451430 1.79e+08 8.0 m 2.7 s 5.7% 2.3 h 2.2 h INFO 21:53:28,239 TraversalEngine - chr1:190619430 1.91e+08 8.5 m 2.7 s 6.1% 2.3 h 2.2 h INFO 21:53:58,243 TraversalEngine - chr1:202113430 2.02e+08 9.0 m 2.7 s 6.4% 2.3 h 2.2 h INFO 21:54:28,244 TraversalEngine - chr1:213677430 2.14e+08 9.5 m 2.7 s 6.8% 2.3 h 2.2 h INFO 21:54:58,246 TraversalEngine - chr1:225013430 2.25e+08 10.0 m 2.7 s 7.2% 2.3 h 2.2 h INFO 21:55:28,248 TraversalEngine - chr1:236340430 2.36e+08 10.5 m 2.7 s 7.5% 2.3 h 2.2 h INFO 21:55:58,249 TraversalEngine - chr1:247477430 2.47e+08 11.0 m 2.7 s 7.9% 2.3 h 2.1 h INFO 21:56:28,251 TraversalEngine - chr2:9418809 2.59e+08 11.5 m 2.7 s 8.2% 2.3 h 2.1 h INFO 21:56:58,254 TraversalEngine - chr2:20701809 2.70e+08 12.0 m 2.7 s 8.6% 2.3 h 2.1 h INFO 21:57:28,257 TraversalEngine - chr2:31861809 2.81e+08 12.5 m 2.7 s 9.0% 2.3 h 2.1 h INFO 21:57:58,257 TraversalEngine - chr2:42757809 2.92e+08 13.0 m 2.7 s 9.3% 2.3 h 2.1 h INFO 21:58:28,261 TraversalEngine - chr2:53746809 3.03e+08 13.5 m 2.7 s 9.7% 2.3 h 2.1 h INFO 21:58:58,264 TraversalEngine - chr2:64867809 3.14e+08 14.0 m 2.7 s 10.0% 2.3 h 2.1 h INFO 21:59:28,266 TraversalEngine - chr2:75954809 3.25e+08 14.5 m 2.7 s 10.4% 2.3 h 2.1 h INFO 21:59:58,367 TraversalEngine - chr2:87195809 3.36e+08 15.0 m 2.7 s 10.7% 2.3 h 2.1 h INFO 22:00:28,370 TraversalEngine - chr2:100881809 3.50e+08 15.5 m 2.7 s 11.2% 2.3 h 2.1 h INFO 22:00:58,511 TraversalEngine - chr2:110887809 3.60e+08 16.1 m 2.7 s 11.5% 2.3 h 2.1 h INFO 22:01:28,703 TraversalEngine - chr2:116900809 3.66e+08 16.6 m 2.7 s 11.7% 2.4 h 2.1 h INFO 22:01:58,712 TraversalEngine - chr2:124321809 3.74e+08 17.1 m 2.7 s 11.9% 2.4 h 2.1 h INFO 22:02:28,714 TraversalEngine - chr2:133966809 3.83e+08 17.6 m 2.7 s 12.2% 2.4 h 2.1 h INFO 22:02:58,715 TraversalEngine - chr2:144380809 3.94e+08 18.1 m 2.8 s 12.5% 2.4 h 2.1 h INFO 22:03:28,716 TraversalEngine - chr2:155265809 4.05e+08 18.6 m 2.8 s 12.9% 2.4 h 2.1 h INFO 22:03:58,717 TraversalEngine - chr2:165599809 4.15e+08 19.1 m 2.8 s 13.2% 2.4 h 2.1 h INFO 22:04:28,720 TraversalEngine - chr2:175871809 4.25e+08 19.6 m 2.8 s 13.6% 2.4 h 2.1 h INFO 22:04:58,721 TraversalEngine - chr2:186061809 4.35e+08 20.1 m 2.8 s 13.9% 2.4 h 2.1 h INFO 22:05:28,723 TraversalEngine - chr2:196755809 4.46e+08 20.6 m 2.8 s 14.2% 2.4 h 2.1 h INFO 22:05:58,726 TraversalEngine - chr2:207448809 4.57e+08 21.1 m 2.8 s 14.6% 2.4 h 2.1 h INFO 22:06:28,727 TraversalEngine - chr2:217899809 4.67e+08 21.6 m 2.8 s 14.9% 2.4 h 2.1 h INFO 22:06:58,730 TraversalEngine - chr2:228468809 4.78e+08 22.1 m 2.8 s 15.2% 2.4 h 2.0 h INFO 22:07:28,730 TraversalEngine - chr2:238837809 4.88e+08 22.6 m 2.8 s 15.6% 2.4 h 2.0 h INFO 22:07:58,732 TraversalEngine - chr3:5883436 4.98e+08 23.1 m 2.8 s 15.9% 2.4 h 2.0 h INFO 22:08:28,732 TraversalEngine - chr3:16293436 5.09e+08 23.6 m 2.8 s 16.2% 2.4 h 2.0 h INFO 22:08:58,735 TraversalEngine - chr3:27285436 5.20e+08 24.1 m 2.8 s 16.6% 2.4 h 2.0 h INFO 22:09:28,737 TraversalEngine - chr3:38000436 5.30e+08 24.6 m 2.8 s 16.9% 2.4 h 2.0 h INFO 22:09:58,740 TraversalEngine - chr3:48611436 5.41e+08 25.1 m 2.8 s 17.2% 2.4 h 2.0 h INFO 22:10:28,741 TraversalEngine - chr3:59370436 5.52e+08 25.6 m 2.8 s 17.6% 2.4 h 119.7 m INFO 22:10:58,745 TraversalEngine - chr3:70030436 5.62e+08 26.1 m 2.8 s 17.9% 2.4 h 119.3 m INFO 22:11:28,746 TraversalEngine - chr3:80961436 5.73e+08 26.6 m 2.8 s 18.3% 2.4 h 118.7 m INFO 22:11:58,747 TraversalEngine - chr3:93699436 5.86e+08 27.1 m 2.8 s 18.7% 2.4 h 117.7 m INFO 22:12:28,750 TraversalEngine - chr3:103705436 5.96e+08 27.6 m 2.8 s 19.0% 2.4 h 117.4 m INFO 22:12:58,752 TraversalEngine - chr3:114250436 6.07e+08 28.1 m 2.8 s 19.3% 2.4 h 117.0 m INFO 22:13:28,756 TraversalEngine - chr3:124966436 6.17e+08 28.6 m 2.8 s 19.7% 2.4 h 116.5 m INFO 22:13:58,758 TraversalEngine - chr3:135244436 6.28e+08 29.1 m 2.8 s 20.0% 2.4 h 116.2 m INFO 22:14:28,760 TraversalEngine - chr3:145932436 6.38e+08 29.6 m 2.8 s 20.3% 2.4 h 115.7 m INFO 22:14:58,760 TraversalEngine - chr3:156489436 6.49e+08 30.1 m 2.8 s 20.7% 2.4 h 115.2 m INFO 22:15:28,761 TraversalEngine - chr3:167311436 6.60e+08 30.6 m 2.8 s 21.0% 2.4 h 114.7 m INFO 22:15:58,763 TraversalEngine - chr3:178354436 6.71e+08 31.1 m 2.8 s 21.4% 2.4 h 114.2 m INFO 22:16:28,763 TraversalEngine - chr3:189432436 6.82e+08 31.6 m 2.8 s 21.7% 2.4 h 113.6 m INFO 22:16:58,764 TraversalEngine - chr4:2269006 6.93e+08 32.1 m 2.8 s 22.1% 2.4 h 113.1 m INFO 22:17:28,767 TraversalEngine - chr4:11802006 7.02e+08 32.6 m 2.8 s 22.4% 2.4 h 112.9 m INFO 22:17:58,787 TraversalEngine - chr4:22430006 7.13e+08 33.1 m 2.8 s 22.7% 2.4 h 112.4 m INFO 22:18:28,789 TraversalEngine - chr4:33202006 7.24e+08 33.6 m 2.8 s 23.1% 2.4 h 111.9 m INFO 22:18:58,792 TraversalEngine - chr4:43943006 7.34e+08 34.1 m 2.8 s 23.4% 2.4 h 111.4 m INFO 22:19:28,793 TraversalEngine - chr4:56159006 7.47e+08 34.6 m 2.8 s 23.8% 2.4 h 110.6 m INFO 22:19:58,817 TraversalEngine - chr4:66667006 7.57e+08 35.1 m 2.8 s 24.1% 2.4 h 110.2 m INFO 22:20:28,818 TraversalEngine - chr4:77286006 7.68e+08 35.6 m 2.8 s 24.5% 2.4 h 109.7 m INFO 22:20:58,819 TraversalEngine - chr4:88194006 7.79e+08 36.1 m 2.8 s 24.8% 2.4 h 109.2 m INFO 22:21:28,824 TraversalEngine - chr4:98763006 7.89e+08 36.6 m 2.8 s 25.2% 2.4 h 108.7 m INFO 22:21:58,825 TraversalEngine - chr4:108978006 7.99e+08 37.1 m 2.8 s 25.5% 2.4 h 108.4 m INFO 22:22:28,827 TraversalEngine - chr4:119573006 8.10e+08 37.6 m 2.8 s 25.8% 2.4 h 107.9 m INFO 22:22:58,831 TraversalEngine - chr4:129894006 8.20e+08 38.1 m 2.8 s 26.2% 2.4 h 107.5 m INFO 22:23:28,833 TraversalEngine - chr4:140674006 8.31e+08 38.6 m 2.8 s 26.5% 2.4 h 107.0 m INFO 22:23:58,835 TraversalEngine - chr4:151269006 8.42e+08 39.1 m 2.8 s 26.8% 2.4 h 106.5 m INFO 22:24:28,836 TraversalEngine - chr4:161696006 8.52e+08 39.6 m 2.8 s 27.2% 2.4 h 106.1 m INFO 22:24:58,837 TraversalEngine - chr4:172052006 8.63e+08 40.1 m 2.8 s 27.5% 2.4 h 105.6 m INFO 22:25:28,840 TraversalEngine - chr4:182831006 8.73e+08 40.6 m 2.8 s 27.8% 2.4 h 105.1 m INFO 22:25:58,842 TraversalEngine - chr5:2521730 8.84e+08 41.1 m 2.8 s 28.2% 2.4 h 104.6 m INFO 22:26:28,843 TraversalEngine - chr5:13450730 8.95e+08 41.6 m 2.8 s 28.5% 2.4 h 104.1 m INFO 22:26:58,847 TraversalEngine - chr5:24281730 9.06e+08 42.1 m 2.8 s 28.9% 2.4 h 103.6 m INFO 22:27:28,850 TraversalEngine - chr5:34910730 9.17e+08 42.6 m 2.8 s 29.2% 2.4 h 103.1 m INFO 22:27:58,853 TraversalEngine - chr5:45058730 9.27e+08 43.1 m 2.8 s 29.5% 2.4 h 102.7 m INFO 22:28:28,854 TraversalEngine - chr5:57669730 9.39e+08 43.6 m 2.8 s 29.9% 2.4 h 101.9 m INFO 22:28:58,856 TraversalEngine - chr5:68139730 9.50e+08 44.1 m 2.8 s 30.3% 2.4 h 101.5 m INFO 22:29:28,858 TraversalEngine - chr5:77893730 9.60e+08 44.6 m 2.8 s 30.6% 2.4 h 101.1 m INFO 22:29:58,859 TraversalEngine - chr5:88636730 9.70e+08 45.1 m 2.8 s 30.9% 2.4 h 100.6 m INFO 22:30:28,862 TraversalEngine - chr5:99475730 9.81e+08 45.6 m 2.8 s 31.3% 2.4 h 100.1 m INFO 22:30:58,892 TraversalEngine - chr5:109953730 9.92e+08 46.1 m 2.8 s 31.6% 2.4 h 99.7 m INFO 22:31:28,901 TraversalEngine - chr5:120537730 1.00e+09 46.6 m 2.8 s 31.9% 2.4 h 99.2 m INFO 22:31:58,902 TraversalEngine - chr5:131097730 1.01e+09 47.1 m 2.8 s 32.3% 2.4 h 98.7 m INFO 22:32:28,904 TraversalEngine - chr5:141713730 1.02e+09 47.6 m 2.8 s 32.6% 2.4 h 98.2 m INFO 22:32:58,905 TraversalEngine - chr5:152524730 1.03e+09 48.1 m 2.8 s 33.0% 2.4 h 97.7 m INFO 22:33:28,908 TraversalEngine - chr5:163086730 1.04e+09 48.6 m 2.8 s 33.3% 2.4 h 97.3 m INFO 22:33:58,911 TraversalEngine - chr5:173539730 1.06e+09 49.1 m 2.8 s 33.6% 2.4 h 96.8 m INFO 22:34:28,912 TraversalEngine - chr6:3487470 1.07e+09 49.6 m 2.8 s 34.0% 2.4 h 96.3 m INFO 22:34:58,913 TraversalEngine - chr6:14334470 1.08e+09 50.1 m 2.8 s 34.3% 2.4 h 95.8 m INFO 22:35:28,915 TraversalEngine - chr6:25224470 1.09e+09 50.6 m 2.8 s 34.7% 2.4 h 95.3 m INFO 22:35:58,918 TraversalEngine - chr6:35820470 1.10e+09 51.1 m 2.8 s 35.0% 2.4 h 94.8 m INFO 22:36:28,919 TraversalEngine - chr6:46560470 1.11e+09 51.6 m 2.8 s 35.4% 2.4 h 94.3 m INFO 22:36:58,921 TraversalEngine - chr6:57356470 1.12e+09 52.1 m 2.8 s 35.7% 2.4 h 93.8 m INFO 22:37:28,923 TraversalEngine - chr6:70367470 1.13e+09 52.6 m 2.8 s 36.1% 2.4 h 93.0 m INFO 22:37:58,926 TraversalEngine - chr6:80706470 1.14e+09 53.1 m 2.8 s 36.4% 2.4 h 92.5 m INFO 22:38:28,926 TraversalEngine - chr6:90478470 1.15e+09 53.6 m 2.8 s 36.8% 2.4 h 92.2 m INFO 22:38:58,928 TraversalEngine - chr6:101326470 1.16e+09 54.1 m 2.8 s 37.1% 2.4 h 91.7 m INFO 22:39:28,929 TraversalEngine - chr6:112146470 1.17e+09 54.6 m 2.8 s 37.4% 2.4 h 91.1 m INFO 22:39:58,931 TraversalEngine - chr6:122995470 1.19e+09 55.1 m 2.8 s 37.8% 2.4 h 90.6 m INFO 22:40:28,931 TraversalEngine - chr6:133869470 1.20e+09 55.6 m 2.8 s 38.1% 2.4 h 90.1 m INFO 22:40:58,933 TraversalEngine - chr6:144815470 1.21e+09 56.1 m 2.8 s 38.5% 2.4 h 89.6 m INFO 22:41:28,934 TraversalEngine - chr6:155638470 1.22e+09 56.6 m 2.8 s 38.8% 2.4 h 89.1 m INFO 22:41:58,936 TraversalEngine - chr6:166126470 1.23e+09 57.1 m 2.8 s 39.2% 2.4 h 88.6 m INFO 22:42:28,940 TraversalEngine - chr7:6003403 1.24e+09 57.6 m 2.8 s 39.5% 2.4 h 88.1 m INFO 22:42:58,942 TraversalEngine - chr7:16481403 1.25e+09 58.1 m 2.8 s 39.8% 2.4 h 87.6 m INFO 22:43:28,944 TraversalEngine - chr7:26918403 1.26e+09 58.6 m 2.8 s 40.2% 2.4 h 87.2 m INFO 22:43:58,948 TraversalEngine - chr7:37519403 1.27e+09 59.1 m 2.8 s 40.5% 2.4 h 86.7 m INFO 22:44:28,979 TraversalEngine - chr7:47972403 1.28e+09 59.6 m 2.8 s 40.9% 2.4 h 86.2 m INFO 22:44:58,979 TraversalEngine - chr7:57482403 1.29e+09 60.1 m 2.8 s 41.2% 2.4 h 85.9 m INFO 22:45:28,988 TraversalEngine - chr7:69059403 1.30e+09 60.6 m 2.8 s 41.5% 2.4 h 85.3 m INFO 22:45:58,990 TraversalEngine - chr7:78534403 1.31e+09 61.1 m 2.8 s 41.8% 2.4 h 84.9 m INFO 22:46:28,992 TraversalEngine - chr7:89037403 1.32e+09 61.6 m 2.8 s 42.2% 2.4 h 84.4 m INFO 22:46:58,996 TraversalEngine - chr7:99586403 1.33e+09 62.1 m 2.8 s 42.5% 2.4 h 84.0 m INFO 22:47:28,996 TraversalEngine - chr7:109488403 1.34e+09 62.6 m 2.8 s 42.8% 2.4 h 83.6 m INFO 22:47:58,999 TraversalEngine - chr7:120144403 1.35e+09 63.1 m 2.8 s 43.2% 2.4 h 83.1 m INFO 22:48:29,001 TraversalEngine - chr7:130894403 1.36e+09 63.6 m 2.8 s 43.5% 2.4 h 82.6 m INFO 22:48:59,003 TraversalEngine - chr7:141234403 1.37e+09 64.1 m 2.8 s 43.8% 2.4 h 82.1 m INFO 22:49:29,004 TraversalEngine - chr7:151589403 1.39e+09 64.6 m 2.8 s 44.2% 2.4 h 81.6 m INFO 22:49:59,005 TraversalEngine - chr8:3053740 1.40e+09 65.1 m 2.8 s 44.5% 2.4 h 81.2 m INFO 22:50:29,007 TraversalEngine - chr8:12774740 1.41e+09 65.6 m 2.8 s 44.8% 2.4 h 80.8 m INFO 22:50:59,009 TraversalEngine - chr8:22779740 1.42e+09 66.1 m 2.8 s 45.1% 2.4 h 80.3 m INFO 22:51:29,011 TraversalEngine - chr8:33628740 1.43e+09 66.6 m 2.8 s 45.5% 2.4 h 79.8 m INFO 22:51:59,013 TraversalEngine - chr8:44153740 1.44e+09 67.1 m 2.8 s 45.8% 2.4 h 79.3 m INFO 22:52:29,014 TraversalEngine - chr8:56625740 1.45e+09 67.6 m 2.8 s 46.2% 2.4 h 78.7 m INFO 22:52:59,018 TraversalEngine - chr8:67412740 1.46e+09 68.1 m 2.8 s 46.5% 2.4 h 78.2 m INFO 22:53:29,019 TraversalEngine - chr8:77935740 1.47e+09 68.6 m 2.8 s 46.9% 2.4 h 77.7 m INFO 22:53:59,020 TraversalEngine - chr8:88555740 1.48e+09 69.1 m 2.8 s 47.2% 2.4 h 77.2 m INFO 22:54:29,021 TraversalEngine - chr8:98573740 1.49e+09 69.6 m 2.8 s 47.5% 2.4 h 76.8 m INFO 22:54:59,046 TraversalEngine - chr8:109265740 1.50e+09 70.1 m 2.8 s 47.9% 2.4 h 76.3 m INFO 22:55:29,063 TraversalEngine - chr8:120062740 1.51e+09 70.6 m 2.8 s 48.2% 2.4 h 75.8 m INFO 22:55:59,065 TraversalEngine - chr8:130782740 1.52e+09 71.1 m 2.8 s 48.6% 2.4 h 75.3 m INFO 22:56:29,067 TraversalEngine - chr8:140341740 1.53e+09 71.6 m 2.8 s 48.9% 2.4 h 74.9 m INFO 22:56:59,073 TraversalEngine - chr9:3522718 1.54e+09 72.1 m 2.8 s 49.2% 2.4 h 74.5 m INFO 22:57:29,077 TraversalEngine - chr9:13451718 1.55e+09 72.6 m 2.8 s 49.5% 2.4 h 74.1 m INFO 22:57:59,080 TraversalEngine - chr9:23460718 1.56e+09 73.1 m 2.8 s 49.8% 2.4 h 73.6 m INFO 22:58:29,082 TraversalEngine - chr9:34075718 1.57e+09 73.6 m 2.8 s 50.1% 2.4 h 73.1 m INFO 22:58:59,083 TraversalEngine - chr9:44676718 1.58e+09 74.1 m 2.8 s 50.5% 2.4 h 72.6 m INFO 22:59:29,085 TraversalEngine - chr9:69693718 1.61e+09 74.6 m 2.8 s 51.3% 2.4 h 70.8 m INFO 22:59:59,087 TraversalEngine - chr9:80633718 1.62e+09 75.1 m 2.8 s 51.6% 2.4 h 70.3 m INFO 23:00:29,088 TraversalEngine - chr9:91539718 1.63e+09 75.6 m 2.8 s 52.0% 2.4 h 69.8 m INFO 23:00:59,090 TraversalEngine - chr9:102291718 1.64e+09 76.1 m 2.8 s 52.3% 2.4 h 69.3 m INFO 23:01:29,097 TraversalEngine - chr9:112754718 1.65e+09 76.6 m 2.8 s 52.7% 2.4 h 68.8 m INFO 23:01:59,097 TraversalEngine - chr9:123532718 1.66e+09 77.1 m 2.8 s 53.0% 2.4 h 68.3 m INFO 23:02:29,098 TraversalEngine - chr9:134308718 1.67e+09 77.6 m 2.8 s 53.3% 2.4 h 67.8 m INFO 23:02:59,099 TraversalEngine - chr10:3863287 1.68e+09 78.1 m 2.8 s 53.7% 2.4 h 67.3 m INFO 23:03:29,102 TraversalEngine - chr10:14354287 1.69e+09 78.6 m 2.8 s 54.0% 2.4 h 66.9 m INFO 23:03:59,105 TraversalEngine - chr10:23893287 1.70e+09 79.1 m 2.8 s 54.3% 2.4 h 66.5 m INFO 23:04:29,121 TraversalEngine - chr10:31032287 1.71e+09 79.6 m 2.8 s 54.6% 2.4 h 66.3 m INFO 23:04:59,122 TraversalEngine - chr10:42640287 1.72e+09 80.1 m 2.8 s 54.9% 2.4 h 65.7 m INFO 23:05:29,124 TraversalEngine - chr10:53153287 1.73e+09 80.6 m 2.8 s 55.3% 2.4 h 65.2 m INFO 23:05:59,125 TraversalEngine - chr10:64098287 1.74e+09 81.1 m 2.8 s 55.6% 2.4 h 64.7 m INFO 23:06:29,128 TraversalEngine - chr10:74541287 1.76e+09 81.6 m 2.8 s 55.9% 2.4 h 64.2 m INFO 23:06:59,131 TraversalEngine - chr10:85225287 1.77e+09 82.1 m 2.8 s 56.3% 2.4 h 63.7 m INFO 23:07:29,132 TraversalEngine - chr10:95753287 1.78e+09 82.6 m 2.8 s 56.6% 2.4 h 63.3 m INFO 23:07:59,134 TraversalEngine - chr10:106184287 1.79e+09 83.1 m 2.8 s 56.9% 2.4 h 62.8 m INFO 23:08:29,138 TraversalEngine - chr10:116852287 1.80e+09 83.6 m 2.8 s 57.3% 2.4 h 62.3 m INFO 23:08:59,140 TraversalEngine - chr10:127371287 1.81e+09 84.1 m 2.8 s 57.6% 2.4 h 61.8 m INFO 23:09:29,143 TraversalEngine - chr11:2855540 1.82e+09 84.6 m 2.8 s 58.0% 2.4 h 61.3 m INFO 23:09:59,146 TraversalEngine - chr11:13149540 1.83e+09 85.1 m 2.8 s 58.3% 2.4 h 60.8 m INFO 23:10:29,149 TraversalEngine - chr11:23833540 1.84e+09 85.6 m 2.8 s 58.6% 2.4 h 60.3 m INFO 23:10:59,150 TraversalEngine - chr11:34514540 1.85e+09 86.1 m 2.8 s 59.0% 2.4 h 59.8 m INFO 23:11:29,151 TraversalEngine - chr11:44796540 1.86e+09 86.6 m 2.8 s 59.3% 2.4 h 59.4 m INFO 23:11:59,155 TraversalEngine - chr11:56832540 1.87e+09 87.1 m 2.8 s 59.7% 2.4 h 58.8 m INFO 23:12:29,158 TraversalEngine - chr11:66954540 1.88e+09 87.6 m 2.8 s 60.0% 2.4 h 58.3 m INFO 23:12:59,160 TraversalEngine - chr11:77608540 1.89e+09 88.1 m 2.8 s 60.4% 2.4 h 57.8 m INFO 23:13:29,163 TraversalEngine - chr11:88155540 1.90e+09 88.6 m 2.8 s 60.7% 2.4 h 57.4 m INFO 23:13:59,164 TraversalEngine - chr11:98798540 1.91e+09 89.1 m 2.8 s 61.0% 2.4 h 56.9 m INFO 23:14:29,165 TraversalEngine - chr11:109601540 1.93e+09 89.6 m 2.8 s 61.4% 2.4 h 56.4 m INFO 23:14:59,166 TraversalEngine - chr11:120553540 1.94e+09 90.1 m 2.8 s 61.7% 2.4 h 55.8 m INFO 23:15:29,168 TraversalEngine - chr11:131246540 1.95e+09 90.6 m 2.8 s 62.1% 2.4 h 55.3 m INFO 23:15:59,171 TraversalEngine - chr12:7635024 1.96e+09 91.1 m 2.8 s 62.4% 2.4 h 54.8 m INFO 23:16:29,173 TraversalEngine - chr12:18640024 1.97e+09 91.6 m 2.8 s 62.8% 2.4 h 54.3 m INFO 23:16:59,174 TraversalEngine - chr12:30029024 1.98e+09 92.1 m 2.8 s 63.1% 2.4 h 53.7 m INFO 23:17:29,176 TraversalEngine - chr12:43200024 1.99e+09 92.6 m 2.8 s 63.6% 2.4 h 53.1 m INFO 23:17:59,177 TraversalEngine - chr12:54273024 2.01e+09 93.1 m 2.8 s 63.9% 2.4 h 52.5 m INFO 23:18:29,178 TraversalEngine - chr12:65348024 2.02e+09 93.6 m 2.8 s 64.3% 2.4 h 52.0 m INFO 23:18:59,181 TraversalEngine - chr12:76545024 2.03e+09 94.1 m 2.8 s 64.6% 2.4 h 51.5 m INFO 23:19:29,210 TraversalEngine - chr12:88130024 2.04e+09 94.6 m 2.8 s 65.0% 2.4 h 50.9 m INFO 23:19:59,212 TraversalEngine - chr12:99446024 2.05e+09 95.1 m 2.8 s 65.4% 2.4 h 50.4 m INFO 23:20:29,212 TraversalEngine - chr12:110658024 2.06e+09 95.6 m 2.8 s 65.7% 2.4 h 49.9 m INFO 23:20:59,213 TraversalEngine - chr12:121915024 2.07e+09 96.1 m 2.8 s 66.1% 2.4 h 49.3 m INFO 23:21:29,214 TraversalEngine - chr12:133475024 2.08e+09 96.6 m 2.8 s 66.4% 2.4 h 48.8 m INFO 23:21:59,217 TraversalEngine - chr13:23582129 2.11e+09 97.1 m 2.8 s 67.2% 2.4 h 47.4 m INFO 23:22:29,218 TraversalEngine - chr13:34977129 2.12e+09 97.6 m 2.8 s 67.6% 2.4 h 46.8 m INFO 23:22:59,221 TraversalEngine - chr13:46382129 2.13e+09 98.1 m 2.8 s 67.9% 2.4 h 46.3 m INFO 23:23:29,223 TraversalEngine - chr13:57749129 2.14e+09 98.6 m 2.8 s 68.3% 2.4 h 45.8 m INFO 23:23:59,225 TraversalEngine - chr13:69524425 2.15e+09 99.1 m 2.8 s 68.7% 2.4 h 45.2 m INFO 23:24:29,227 TraversalEngine - chr13:81138425 2.17e+09 99.6 m 2.8 s 69.0% 2.4 h 44.6 m INFO 23:24:59,229 TraversalEngine - chr13:93014425 2.18e+09 100.1 m 2.8 s 69.4% 2.4 h 44.1 m INFO 23:25:29,231 TraversalEngine - chr13:104729425 2.19e+09 100.6 m 2.8 s 69.8% 2.4 h 43.5 m INFO 23:25:59,232 TraversalEngine - chr14:5290547 2.21e+09 101.1 m 2.7 s 70.3% 2.4 h 42.7 m INFO 23:26:29,235 TraversalEngine - chr14:25833547 2.23e+09 101.6 m 2.7 s 70.9% 2.4 h 41.6 m INFO 23:26:59,237 TraversalEngine - chr14:37522547 2.24e+09 102.1 m 2.7 s 71.3% 2.4 h 41.0 m INFO 23:27:29,238 TraversalEngine - chr14:48800547 2.25e+09 102.6 m 2.7 s 71.7% 2.4 h 40.5 m INFO 23:27:59,240 TraversalEngine - chr14:60191547 2.26e+09 103.1 m 2.7 s 72.0% 2.4 h 40.0 m INFO 23:28:29,243 TraversalEngine - chr14:71698547 2.27e+09 103.6 m 2.7 s 72.4% 2.4 h 39.5 m INFO 23:28:59,244 TraversalEngine - chr14:83344547 2.28e+09 104.1 m 2.7 s 72.8% 2.4 h 38.9 m INFO 23:29:29,247 TraversalEngine - chr14:94990547 2.30e+09 104.6 m 2.7 s 73.2% 2.4 h 38.4 m INFO 23:29:59,248 TraversalEngine - chr14:106993547 2.31e+09 105.1 m 2.7 s 73.5% 2.4 h 37.8 m INFO 23:30:29,249 TraversalEngine - chr15:24952007 2.33e+09 105.6 m 2.7 s 74.3% 2.4 h 36.4 m INFO 23:30:59,252 TraversalEngine - chr15:36267007 2.34e+09 106.1 m 2.7 s 74.7% 2.4 h 35.9 m INFO 23:31:29,254 TraversalEngine - chr15:47800007 2.36e+09 106.6 m 2.7 s 75.1% 2.4 h 35.4 m INFO 23:31:59,255 TraversalEngine - chr15:59057007 2.37e+09 107.1 m 2.7 s 75.4% 2.4 h 34.9 m INFO 23:32:29,257 TraversalEngine - chr15:70666007 2.38e+09 107.6 m 2.7 s 75.8% 2.4 h 34.3 m INFO 23:32:59,258 TraversalEngine - chr15:82220007 2.39e+09 108.1 m 2.7 s 76.2% 2.4 h 33.8 m INFO 23:33:29,259 TraversalEngine - chr15:93623007 2.40e+09 108.6 m 2.7 s 76.5% 2.4 h 33.3 m INFO 23:33:59,261 TraversalEngine - chr16:2803615 2.41e+09 109.1 m 2.7 s 76.9% 2.4 h 32.8 m INFO 23:34:29,263 TraversalEngine - chr16:13772615 2.42e+09 109.6 m 2.7 s 77.3% 2.4 h 32.3 m INFO 23:34:59,265 TraversalEngine - chr16:24003615 2.43e+09 110.1 m 2.7 s 77.6% 2.4 h 31.8 m INFO 23:35:29,268 TraversalEngine - chr16:34662615 2.44e+09 110.6 m 2.7 s 77.9% 2.4 h 31.3 m INFO 23:35:59,270 TraversalEngine - chr16:53726615 2.46e+09 111.1 m 2.7 s 78.5% 2.4 h 30.4 m INFO 23:36:29,271 TraversalEngine - chr16:65235615 2.48e+09 111.6 m 2.7 s 78.9% 2.4 h 29.8 m INFO 23:36:59,287 TraversalEngine - chr16:76628615 2.49e+09 112.1 m 2.7 s 79.3% 2.4 h 29.3 m INFO 23:37:29,288 TraversalEngine - chr16:87879615 2.50e+09 112.6 m 2.7 s 79.6% 2.4 h 28.8 m INFO 23:37:59,289 TraversalEngine - chr17:9078862 2.51e+09 113.1 m 2.7 s 80.0% 2.4 h 28.3 m INFO 23:38:29,291 TraversalEngine - chr17:20330862 2.52e+09 113.6 m 2.7 s 80.3% 2.4 h 27.8 m INFO 23:38:59,291 TraversalEngine - chr17:34206862 2.53e+09 114.1 m 2.7 s 80.8% 2.4 h 27.1 m INFO 23:39:29,293 TraversalEngine - chr17:45599862 2.55e+09 114.6 m 2.7 s 81.1% 2.4 h 26.6 m INFO 23:39:59,296 TraversalEngine - chr17:57418862 2.56e+09 115.1 m 2.7 s 81.5% 2.4 h 26.1 m INFO 23:40:29,296 TraversalEngine - chr17:68931862 2.57e+09 115.6 m 2.7 s 81.9% 2.4 h 25.6 m INFO 23:40:59,299 TraversalEngine - chr17:80868862 2.58e+09 116.1 m 2.7 s 82.3% 2.4 h 25.0 m INFO 23:41:29,321 TraversalEngine - chr18:11010652 2.59e+09 116.6 m 2.7 s 82.6% 2.4 h 24.5 m INFO 23:41:59,322 TraversalEngine - chr18:24790652 2.61e+09 117.1 m 2.7 s 83.1% 2.3 h 23.9 m INFO 23:42:29,324 TraversalEngine - chr18:36582652 2.62e+09 117.6 m 2.7 s 83.5% 2.3 h 23.3 m INFO 23:42:59,326 TraversalEngine - chr18:48081652 2.63e+09 118.1 m 2.7 s 83.8% 2.3 h 22.8 m INFO 23:43:29,327 TraversalEngine - chr18:59879652 2.64e+09 118.6 m 2.7 s 84.2% 2.3 h 22.3 m INFO 23:43:59,329 TraversalEngine - chr18:71357652 2.65e+09 119.1 m 2.7 s 84.6% 2.3 h 21.7 m INFO 23:44:29,330 TraversalEngine - chr19:5235404 2.66e+09 119.6 m 2.7 s 84.9% 2.3 h 21.2 m INFO 23:44:59,345 TraversalEngine - chr19:16400404 2.68e+09 2.0 h 2.7 s 85.3% 2.3 h 20.7 m INFO 23:45:29,346 TraversalEngine - chr19:29317404 2.69e+09 2.0 h 2.7 s 85.7% 2.3 h 20.1 m INFO 23:45:59,347 TraversalEngine - chr19:40730404 2.70e+09 2.0 h 2.7 s 86.1% 2.3 h 19.6 m INFO 23:46:29,351 TraversalEngine - chr19:51642404 2.71e+09 2.0 h 2.7 s 86.4% 2.3 h 19.1 m INFO 23:46:59,354 TraversalEngine - chr20:3551421 2.72e+09 2.0 h 2.7 s 86.8% 2.3 h 18.6 m INFO 23:47:29,356 TraversalEngine - chr20:15256421 2.73e+09 2.0 h 2.7 s 87.1% 2.3 h 18.1 m INFO 23:47:59,357 TraversalEngine - chr20:28445421 2.75e+09 2.1 h 2.7 s 87.6% 2.3 h 17.5 m INFO 23:48:29,360 TraversalEngine - chr20:40850421 2.76e+09 2.1 h 2.7 s 88.0% 2.3 h 16.9 m INFO 23:48:59,363 TraversalEngine - chr20:52451421 2.77e+09 2.1 h 2.7 s 88.3% 2.3 h 16.4 m INFO 23:49:29,364 TraversalEngine - chr21:4200901 2.79e+09 2.1 h 2.7 s 88.8% 2.3 h 15.7 m INFO 23:49:59,366 TraversalEngine - chr21:21565901 2.80e+09 2.1 h 2.7 s 89.4% 2.3 h 14.9 m INFO 23:50:29,368 TraversalEngine - chr21:33311901 2.82e+09 2.1 h 2.7 s 89.7% 2.3 h 14.4 m INFO 23:50:59,373 TraversalEngine - chr21:45088901 2.83e+09 2.1 h 2.7 s 90.1% 2.3 h 13.8 m INFO 23:51:29,375 TraversalEngine - chr22:19409006 2.85e+09 2.1 h 2.7 s 90.8% 2.3 h 12.8 m INFO 23:51:59,379 TraversalEngine - chr22:30950006 2.86e+09 2.1 h 2.7 s 91.2% 2.3 h 12.3 m INFO 23:52:29,381 TraversalEngine - chr22:42315006 2.87e+09 2.1 h 2.7 s 91.5% 2.3 h 11.8 m INFO 23:52:59,382 TraversalEngine - chrX:3334440 2.88e+09 2.1 h 2.7 s 91.9% 2.3 h 11.2 m INFO 23:53:29,385 TraversalEngine - chrX:15064440 2.90e+09 2.1 h 2.7 s 92.3% 2.3 h 10.7 m INFO 23:53:59,387 TraversalEngine - chrX:26683440 2.91e+09 2.2 h 2.7 s 92.7% 2.3 h 10.2 m INFO 23:54:29,389 TraversalEngine - chrX:38470440 2.92e+09 2.2 h 2.7 s 93.1% 2.3 h 9.7 m INFO 23:54:59,389 TraversalEngine - chrX:49396440 2.93e+09 2.2 h 2.7 s 93.4% 2.3 h 9.2 m INFO 23:55:29,391 TraversalEngine - chrX:62420440 2.94e+09 2.2 h 2.7 s 93.8% 2.3 h 8.6 m INFO 23:55:59,392 TraversalEngine - chrX:73260440 2.95e+09 2.2 h 2.7 s 94.2% 2.3 h 8.1 m INFO 23:56:29,395 TraversalEngine - chrX:84200440 2.97e+09 2.2 h 2.7 s 94.5% 2.3 h 7.6 m INFO 23:56:59,396 TraversalEngine - chrX:95723440 2.98e+09 2.2 h 2.7 s 94.9% 2.3 h 7.1 m INFO 23:57:29,402 TraversalEngine - chrX:106857440 2.99e+09 2.2 h 2.7 s 95.2% 2.3 h 6.6 m INFO 23:57:59,405 TraversalEngine - chrX:118289440 3.00e+09 2.2 h 2.7 s 95.6% 2.3 h 6.1 m INFO 23:58:29,408 TraversalEngine - chrX:129570440 3.01e+09 2.2 h 2.7 s 96.0% 2.3 h 5.6 m INFO 23:58:59,410 TraversalEngine - chrX:141011440 3.02e+09 2.2 h 2.7 s 96.3% 2.3 h 5.1 m INFO 23:59:29,440 TraversalEngine - chrX:152601440 3.03e+09 2.2 h 2.7 s 96.7% 2.3 h 4.6 m INFO 23:59:59,443 TraversalEngine - chrY:9928880 3.05e+09 2.3 h 2.7 s 97.1% 2.3 h 4.0 m INFO 00:00:29,445 TraversalEngine - chrY:24583880 3.06e+09 2.3 h 2.7 s 97.6% 2.3 h 3.4 m INFO 00:00:59,445 TraversalEngine - chrY:56178880 3.09e+09 2.3 h 2.6 s 98.6% 2.3 h 117.9 s INFO 00:01:29,447 TraversalEngine - chr6_dbb_hap3:2569040 3.13e+09 2.3 h 2.6 s 99.1% 2.3 h 73.4 s INFO 00:01:59,450 TraversalEngine - chr6_qbl_hap6:3745983 3.21e+09 2.3 h 2.6 s 99.6% 2.3 h 33.0 s INFO 00:02:25,479 TraversalEngine - Total runtime 8250.03 secs, 137.50 min, 2.29 hours INFO 00:02:25,480 TraversalEngine - 321726458 reads were filtered out during traversal out of 321726458 total (100.00%) INFO 00:02:25,481 TraversalEngine - -> 321726458 reads (100.00% of total) failing MappingQualityUnavailableFilter INFO 00:02:29,029 GATKRunReport - Uploaded run statistics report to AWS S3

  • ebanksebanks Posts: 683GATK Developer mod

    Look at the last 2 lines of the output you posted. All of your reads are getting filtered out because they have undefined mapping quality.

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • livefallflylivefallfly Posts: 23Member

    Thanks very much. I think it is the problem. Could you tell me how I can solve it?

  • ebanksebanks Posts: 683GATK Developer mod

    You'll need to contact the developers of Bowtie and ask them since they are generating alignments with no mapping quality. Or maybe this is fixed in a newer version of the tool?

    Eric Banks, PhD -- Senior Group Leader, MPG Analysis, Broad Institute of Harvard and MIT

  • livefallflylivefallfly Posts: 23Member

    Thanks, I reviewed the format of the bam file. And I found the situation, the bowtie couldn't be used in GATK.

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