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Old 03-09-2012, 03:28 AM   #1
msorianoc
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Location: Spain

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Default Bad input: Values ​​for QD annotation for ANY training not detected in the input call

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 -------------------------------------------- ----------------------------------------------
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Old 03-22-2012, 03:10 AM   #2
aituka
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Hi,
I have the same problem and would be interested if you found something to solve that issue. I think the problem may lie in a bad alignment (well i am still junior in this field .. so it is more a guess).
In this thread http://seqanswers.com/forums/showthr...t=hapmap+exome i show the result I got after applying the flagstat and idxstats method from samtools on the bam file. Do you have similar results for your bam?
bests,tuka.
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Old 04-05-2012, 10:01 AM   #3
caddymob
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I had this same error and it was because a bug in my script had the wrong path to dbSNP135.vcf. Your log seems to show that dbSNP, hapmap and omni were loaded OK, but I noticed some weird chromosome names like ChR2, CHR9 with others like chr11. I am using b37 so no chr prefix, but not sure what the hg19 version you are using looks like. Do the reference vcfs and your fa have the same chr prefix?
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Old 09-18-2012, 10:19 AM   #4
yeppomonkey
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Hi, I am having a similar problem with VariantRecalibrator, did you find a solution? below is my error:
Quote:
INFO 13:13:03,317 ArgumentTypeDescriptor - Dynamically determined type of /dbsnp_135.hg19.vcf to be VCF
INFO 13:13:03,345 GenomeAnalysisEngine - Strictness is SILENT
INFO 13:13:03,718 RMDTrackBuilder - Loading Tribble index from disk for file 17 1.n80.raw.snps.indels.vcf
INFO 13:13:04,018 RMDTrackBuilder - Loading Tribble index from disk for file /hapmap_3.3.hg19.sites.vcf
INFO 13:13:04,315 RMDTrackBuilder - Loading Tribble index from disk for file /1000G_omni2.5.hg19.sites.vcf
INFO 13:13:06,108 RMDTrackBuilder - Loading Tribble index from disk for file /Mills_and_1000G_gold_standard.indels.hg19.sites.vcf
WARN 13:13:07,159 VCFStandardHeaderLines$Standards - Repairing standard header line for field GQ because -- type disagree; header has Float but standard is Int eger
INFO 13:13:07,170 RMDTrackBuilder - Loading Tribble index from disk for file /dbsnp_135.hg19.vcf
WARN 13:13:07,609 VCFStandardHeaderLines$Standards - Repairing standard header line for field AF because -- count types disagree; header has UNBOUNDED but stan dard is A
INFO 13:13:07,985 TrainingSet - Found hapmap track: Known = false Training = true Truth = true Prior = Q15.0
INFO 13:13:07,987 TrainingSet - Found omni track: Known = false Training = true Truth = false Prior = Q12.0
INFO 13:13:07,988 TrainingSet - Found mills track: Known = true Training = true Truth = true Prior = Q12.0
INFO 13:13:07,989 TrainingSet - Found dbsnp track: Known = true Training = false Truth = false Prior = Q6.0
INFO 13:13:08,317 TraversalEngine - [INITIALIZATION COMPLETE; TRAVERSAL STARTIN G]
INFO 13:13:08,318 TraversalEngine - Location processed.sites runtime pe r.1M.sites completed total.runtime remaining
INFO 13:13:38,070 TraversalEngine - chr1:108536799 2.02e+06 30.0 s 14.8 s 43.5% 68.9 s 38.9 s
INFO 13:14:08,078 TraversalEngine - chr1:246989336 4.22e+06 60.0 s 14.2 s 99.1% 60.6 s 0.5 s
INFO 13:14:08,906 VariantDataManager - QD < 2.0: mean = NaN standard deviation = NaN
INFO 13:14:11,552 GATKRunReport - Uploaded run statistics report to AWS S3
##### ERROR ------------------------------------------------------------------------------------------
##### ERROR A USER ERROR has occurred (version 2.1-8-g5efb575):
##### ERROR The invalid arguments or inputs must be corrected before the GATK can proceed
##### ERROR Please do not post this error to the GATK forum
##### ERROR
##### ERROR See the documentation (rerun with -h) for this tool to view allowable command-line arguments.
##### ERROR Visit our website and forum for extensive documentation and answers to
##### ERROR commonly asked questions http://www.broadinstitute.org/gatk
##### ERROR
##### ERROR MESSAGE: Bad input: Values for QD < 2.0 annotation not detected for ANY training variant in the input callset. VariantAnnotator may be used to add these annotations. See http://www.broadinstitute.org/gsa/wi...riantAnnotator
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Old 09-18-2012, 10:20 PM   #5
msorianoc
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Hi, my problem was in the script that transformed the CSFASTA and QUAL into FASTQ. I could not tell exactly what was the problem because I solved using a script that gave me a colleague.

regards
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