Hi all, I'm starting with the "Analysis of Exome Data" using the manual "ulz_peter" posting in February 2010 and the passage "Variant recalibration quality score" that gives me leave sigueinte below.
Does anyone could help me?
Is there a version of this manual latest?.
Thank you very much.
M. Soriano.
"08:58:18,694 INFO RodBindingArgumentTypeDescriptor - Dynamically Determined type of / home / ibv / msoriano / software / data / Target_RefSeq.bed to be BED
------------------------------------------- 08:58:18,738 INFO HelpFormatter ---------------------------------------
08:58:18,738 INFO HelpFormatter - The Genome Analysis Toolkit (GATK) v1.4-37-g0b29d54, Compiled 2012/02/27 19:56:39
08:58:18,739 INFO HelpFormatter - Copyright (c) 2010 The Broad Institute
08:58:18,739 INFO HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
08:58:18,739 INFO HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
08:58:18,740 INFO HelpFormatter - Program Args:-R /-T home/ibv/msoriano/Sample03/hg19.fasta VariantRecalibrator - input / home/ibv/msoriano/Sample03/snpsSample3.vcf-resource: HapMap, VCF, known = false, training = true, truth = true, prior = 15.0 / home/ibv/msoriano/Sample03/hapmap_3.3.hg19.sites.vcf-resource: omni, VCF, known = false, training = true, truth = false, prior = 12.0 / home/ibv/msoriano/Sample03/1000G_omni2.5.hg19.sites.vcf-resource: dbSNP, VCF, known = true, training = false, truth = false, prior = 8.0 / home / ibv / QD-msoriano/Sample03/dbsnp_132.hg19.vcf-an-an n HaplotypeScore ReadPosRankSum MQRankSum-an-an FS-an MQ-recalFile / home/ibv/msoriano/Sample03/Sample3.marked.realigner.recal.bam-tranchesFile / home/ibv/msoriano/Sample03/Sample3.tranches-rscriptFile / home/ibv/msoriano/Sample03/Sample3.plots-L / home / ibv / msoriano / software / data / snp-mode Target_RefSeq.bed
08:58:18,740 INFO HelpFormatter - Date / Time: 2012/03/09 8:58:18
------------------------------------------- 08:58:18,740 INFO HelpFormatter ---------------------------------------
------------------------------------------- 08:58:18,740 INFO HelpFormatter ---------------------------------------
08:58:18,778 INFO RodBindingArgumentTypeDescriptor - Dynamically Determined type of / home/ibv/msoriano/Sample03/snpsSample3.vcf to be VCF
08:58:18,794 INFO GenomeAnalysisEngine - strictness is SILENT
08:58:18,943 INFO RMDTrackBuilder - Loading Tribble index from disk for file / home/ibv/msoriano/Sample03/snpsSample3.vcf
08:58:19,029 INFO RMDTrackBuilder - Loading Tribble index from disk for file / home/ibv/msoriano/Sample03/hapmap_3.3.hg19.sites.vcf
08:58:19,127 INFO RMDTrackBuilder - Loading Tribble index from disk for file / home/ibv/msoriano/Sample03/1000G_omni2.5.hg19.sites.vcf
08:58:19,235 INFO RMDTrackBuilder - Loading Tribble index from disk for file / home/ibv/msoriano/Sample03/dbsnp_132.hg19.vcf
08:58:23,454 WARN Utils - ****************************************** **************************************
08:58:23,455 WARN Utils - * WARNING:
08:58:23,455 WARN Utils - *
08:58:23,455 WARN Utils - * Rscript environment not found in path.
08:58:23,455 WARN Utils - * / will be generated home/ibv/msoriano/Sample03/Sample3.plots But PDF
08:58:23,455 WARN Utils - * plots will not.
08:58:23,456 WARN Utils - ****************************************** **************************************
08:58:23,464 INFO TrainingSet - Found HapMap track: Known Training = true = false = true Truth Prior = Q15.0
08:58:23,465 INFO TrainingSet - omni Found track: Known Training = true = false = false Prior Truth = Q12.0
08:58:23,465 INFO TrainingSet - Found dbSNP track: Training Known = true = false = Truth = false Prior Q8.0
08:58:23,585 INFO TraversalEngine - [INITIALIZATION COMPLETE; traversal STARTING]
08:58:23,585 INFO TraversalEngine - Location processed.sites per.1M.sites completed total.runtime Remaining runtime
08:58:53,822 INFO TraversalEngine - ChR2: 27728656 1.06E +05 30.4 s 4.8 m 4.8 m 10.5% 4.3 m
08:59:23,970 INFO TraversalEngine - chr3: 186503873 2.15e +05 60.5 s 4.7 m 4.6 m 21.9% 3.6 m
08:59:54,256 INFO TraversalEngine - chr6: 87972970 s 3.42e +05 90.8 33.7% 4.4 m 4.5 m 3.0 m
09:00:24,505 INFO TraversalEngine - CHR9: 74863763 4.54e +05 2.0 m 4.4 m 4.5 m 45.1% 2.5 m
09:00:54,547 INFO TraversalEngine - chr11: 124959175 5.74e +05 2.5 m 4.4 m 4.4 m 56.8% 114.9 s
09:01:24,862 INFO TraversalEngine - chr15: 62361735 6.92e +05 3.0 m 4.4 m 4.4 m 68.7% 82.7 s
09:01:54,999 INFO TraversalEngine - chr18: 47802329 8.17e +05 3.5 m 4.3 m 4.4 m 80.5% 51.1 s
09:02:25,000 INFO TraversalEngine - CHRX: 38180348 9.52e +05 4.0 m 4.2 m 4.3 m 92.9% 18.4 s
09:02:31,527 INFO VariantDataManager - QD: mean = standard deviation = NaN NaN
09:02:33,196 INFO GATKRunReport - Uploaded run statistics report to AWS S3
# # # # # ERROR -------------------------------------------- ----------------------------------------------
# # # # # ERROR USER ERROR has occurred (version 1.4-37-g0b29d54):
# # # # # ERROR The arguments invalid inputs or Must Be Corrected Before The GATK can proceed
# # # # # ERROR Please do not mistake Post this GATK to the forum
# # # # # ERROR
# # # # # ERROR See the documentation (rerun with-h) for this tool to view command-line arguments allowable.
# # # # # ERROR Visit our wiki for documentation EXTENSIVE http://www.broadinstitute.org/gsa/wiki
# # # # # ERROR Visit our forum to view answers to Commonly asked questions http://getsatisfaction.com/gsa
# # # # # ERROR
# # # # # ERROR MESSAGE: Bad input: Values for QD annotation for ANY training not detected in the input callset variant. VariantAnnotator may be Used to add these annotations. See http://www.broadinstitute.org/gsa/wi...riantAnnotator
# # # # # ERROR -------------------------------------------- ----------------------------------------------
Does anyone could help me?
Is there a version of this manual latest?.
Thank you very much.
M. Soriano.
"08:58:18,694 INFO RodBindingArgumentTypeDescriptor - Dynamically Determined type of / home / ibv / msoriano / software / data / Target_RefSeq.bed to be BED
------------------------------------------- 08:58:18,738 INFO HelpFormatter ---------------------------------------
08:58:18,738 INFO HelpFormatter - The Genome Analysis Toolkit (GATK) v1.4-37-g0b29d54, Compiled 2012/02/27 19:56:39
08:58:18,739 INFO HelpFormatter - Copyright (c) 2010 The Broad Institute
08:58:18,739 INFO HelpFormatter - Please view our documentation at http://www.broadinstitute.org/gsa/wiki
08:58:18,739 INFO HelpFormatter - For support, please view our support site at http://getsatisfaction.com/gsa
08:58:18,740 INFO HelpFormatter - Program Args:-R /-T home/ibv/msoriano/Sample03/hg19.fasta VariantRecalibrator - input / home/ibv/msoriano/Sample03/snpsSample3.vcf-resource: HapMap, VCF, known = false, training = true, truth = true, prior = 15.0 / home/ibv/msoriano/Sample03/hapmap_3.3.hg19.sites.vcf-resource: omni, VCF, known = false, training = true, truth = false, prior = 12.0 / home/ibv/msoriano/Sample03/1000G_omni2.5.hg19.sites.vcf-resource: dbSNP, VCF, known = true, training = false, truth = false, prior = 8.0 / home / ibv / QD-msoriano/Sample03/dbsnp_132.hg19.vcf-an-an n HaplotypeScore ReadPosRankSum MQRankSum-an-an FS-an MQ-recalFile / home/ibv/msoriano/Sample03/Sample3.marked.realigner.recal.bam-tranchesFile / home/ibv/msoriano/Sample03/Sample3.tranches-rscriptFile / home/ibv/msoriano/Sample03/Sample3.plots-L / home / ibv / msoriano / software / data / snp-mode Target_RefSeq.bed
08:58:18,740 INFO HelpFormatter - Date / Time: 2012/03/09 8:58:18
------------------------------------------- 08:58:18,740 INFO HelpFormatter ---------------------------------------
------------------------------------------- 08:58:18,740 INFO HelpFormatter ---------------------------------------
08:58:18,778 INFO RodBindingArgumentTypeDescriptor - Dynamically Determined type of / home/ibv/msoriano/Sample03/snpsSample3.vcf to be VCF
08:58:18,794 INFO GenomeAnalysisEngine - strictness is SILENT
08:58:18,943 INFO RMDTrackBuilder - Loading Tribble index from disk for file / home/ibv/msoriano/Sample03/snpsSample3.vcf
08:58:19,029 INFO RMDTrackBuilder - Loading Tribble index from disk for file / home/ibv/msoriano/Sample03/hapmap_3.3.hg19.sites.vcf
08:58:19,127 INFO RMDTrackBuilder - Loading Tribble index from disk for file / home/ibv/msoriano/Sample03/1000G_omni2.5.hg19.sites.vcf
08:58:19,235 INFO RMDTrackBuilder - Loading Tribble index from disk for file / home/ibv/msoriano/Sample03/dbsnp_132.hg19.vcf
08:58:23,454 WARN Utils - ****************************************** **************************************
08:58:23,455 WARN Utils - * WARNING:
08:58:23,455 WARN Utils - *
08:58:23,455 WARN Utils - * Rscript environment not found in path.
08:58:23,455 WARN Utils - * / will be generated home/ibv/msoriano/Sample03/Sample3.plots But PDF
08:58:23,455 WARN Utils - * plots will not.
08:58:23,456 WARN Utils - ****************************************** **************************************
08:58:23,464 INFO TrainingSet - Found HapMap track: Known Training = true = false = true Truth Prior = Q15.0
08:58:23,465 INFO TrainingSet - omni Found track: Known Training = true = false = false Prior Truth = Q12.0
08:58:23,465 INFO TrainingSet - Found dbSNP track: Training Known = true = false = Truth = false Prior Q8.0
08:58:23,585 INFO TraversalEngine - [INITIALIZATION COMPLETE; traversal STARTING]
08:58:23,585 INFO TraversalEngine - Location processed.sites per.1M.sites completed total.runtime Remaining runtime
08:58:53,822 INFO TraversalEngine - ChR2: 27728656 1.06E +05 30.4 s 4.8 m 4.8 m 10.5% 4.3 m
08:59:23,970 INFO TraversalEngine - chr3: 186503873 2.15e +05 60.5 s 4.7 m 4.6 m 21.9% 3.6 m
08:59:54,256 INFO TraversalEngine - chr6: 87972970 s 3.42e +05 90.8 33.7% 4.4 m 4.5 m 3.0 m
09:00:24,505 INFO TraversalEngine - CHR9: 74863763 4.54e +05 2.0 m 4.4 m 4.5 m 45.1% 2.5 m
09:00:54,547 INFO TraversalEngine - chr11: 124959175 5.74e +05 2.5 m 4.4 m 4.4 m 56.8% 114.9 s
09:01:24,862 INFO TraversalEngine - chr15: 62361735 6.92e +05 3.0 m 4.4 m 4.4 m 68.7% 82.7 s
09:01:54,999 INFO TraversalEngine - chr18: 47802329 8.17e +05 3.5 m 4.3 m 4.4 m 80.5% 51.1 s
09:02:25,000 INFO TraversalEngine - CHRX: 38180348 9.52e +05 4.0 m 4.2 m 4.3 m 92.9% 18.4 s
09:02:31,527 INFO VariantDataManager - QD: mean = standard deviation = NaN NaN
09:02:33,196 INFO GATKRunReport - Uploaded run statistics report to AWS S3
# # # # # ERROR -------------------------------------------- ----------------------------------------------
# # # # # ERROR USER ERROR has occurred (version 1.4-37-g0b29d54):
# # # # # ERROR The arguments invalid inputs or Must Be Corrected Before The GATK can proceed
# # # # # ERROR Please do not mistake Post this GATK to the forum
# # # # # ERROR
# # # # # ERROR See the documentation (rerun with-h) for this tool to view command-line arguments allowable.
# # # # # ERROR Visit our wiki for documentation EXTENSIVE http://www.broadinstitute.org/gsa/wiki
# # # # # ERROR Visit our forum to view answers to Commonly asked questions http://getsatisfaction.com/gsa
# # # # # ERROR
# # # # # ERROR MESSAGE: Bad input: Values for QD annotation for ANY training not detected in the input callset variant. VariantAnnotator may be Used to add these annotations. See http://www.broadinstitute.org/gsa/wi...riantAnnotator
# # # # # ERROR -------------------------------------------- ----------------------------------------------
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