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warning: The sequences in variant file are not sorted according to the reference.

Open netwon123 opened this issue 1 year ago • 0 comments

Sorry authors, I got so many many many error when I use ReSeq tool, one was listed follow:

!!! bool reseq::InsertLengthSpline::GetSamplePositions(const reseq::Vect&) [/opt/conda/conda-bld/reseq_1607076765868/work/reseq/FragmentDistributionStats.cpp:1686]: error: Sampling insert lengths did not find at least two usable lengths. !!! bool reseq::Simulator::Simulate(const char*, const char*, reseq::Reference&, reseq::DataStats&, const reseq::ProbabilityEstimates&, reseq::uintNumThreads, reseq::uintSeed, reseq::uintFragCount, double, reseq::RefSeqBiasSimulation, const string&, const string&, const string&, const string&, const string&) [/opt/conda/conda-bld/reseq_1607076765868/work/reseq/Simulator.cpp:2844]: error: An error occurred in the process: Terminating simulation

25-10-23 20:40:29: info: Generated 0 read pairs (0%). ??? void reseq::Reference::CloseVcfFile() [/opt/conda/conda-bld/reseq_1607076765868/work/reseq/Reference.cpp:430]: warning: The sequences in variant file are not sorted according to the reference. The following variation record and all after it have been ignored during simulation: 2 2216421 . C T 146308 . AC=656;AF=0.315;AN=2082;BaseQRankSum=3.520;DP=13406;Dels=0.00;ExcessHet=-0.0000;FS=2.597;HaplotypeScore=5.9402;InbreedingCoeff=0.4487;MLEAC=638;MLEAF=0.306;MQ=58.99;MQ0=227;MQRankSum=11.863;QD=25.91;ReadPosRankSum=1.672;SOR=0.867;ANNOVAR_DATE=2017-06-01;Func.refGene=intronic;Gene.refGene=gene:ENSSSCG00000034390;GeneDetail.refGene=.;ExonicFunc.refGene=.;AAChange.refGene=.;ALLELE_END GT:AD:DP:GQ:PL 1/1:0,8:8:24:318,24,0

I check my vcf format with test.vcf in github, there was no differents I found, Could u tell me how to solve this error? Thanks!

netwon123 avatar Oct 25 '23 16:10 netwon123