[Feedback] Site Feedback: VCF sample did not work on assembly converter, costum track, and VEP

[feedback at gramene.org]

URL         : http://dev.gramene.org/Oryza_sativa/Tools/AssemblyConverter?db=core

Subject     : Site Feedback: VCF sample did not work on assembly converter, costum track, and VEP

Name        : Marcela

Email       : mmonaco at cshl.edu

Organization: CSHL

Comments    : 

We have used this VCF sample before but now it is not working:

##fileformat=VCFv4.0
##fileDate=20120328
##source=MaizeHapMap2
##reference=B73RefGenV2
##phasing=no
##INFO=<ID=MQ,Number=.,Type=Float,Description="RMS mapping quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  B73:MZ  B97:MZ   BKN009:MZ       BKN010:MZ       BKN011:MZ
1       71      PZE0100000071   T       C       .       PASS    MQ=92   GT      0/0     0/0     0/0     0/0     0/0
1       203     PZE0100000203   G       A       .       PASS    MQ=91   GT      0/0     0/0     0/0     0/0     0/0


Errors I get:

Upload data on custom track error =

There was a problem uploading your data: File did not validate as format vcf.
Please try again.

VEP error =

Error: Uncaught exception 'HiveException' with message 'ERROR: Cache assembly version (AGPv3) and database or selected assembly version (AGPv4) do not match' Thrown by EnsEMBL::Web::RunnableDB::VEP::run in module Bio::EnsEMBL::Hive::Process at /usr/local/ensembl-86/ensembl-hive/modules/Bio/EnsEMBL/Hive/Process.pm on line 140 Called by (eval) in module Bio::EnsEMBL::Hive::Process at /usr/local/ensembl-86/ensembl-hive/modules/Bio/EnsEMBL/Hive/Process.pm on line 127 Called by Bio::EnsEMBL::Hive::Process::life_cycle in module Bio::EnsEMBL::Hive::Worker at /usr/local/ensembl-86/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm on line 688 Called by (eval) in module Bio::EnsEMBL::Hive::Worker at /usr/local/ensembl-86/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm on line 674 Called by Bio::EnsEMBL::Hive::Worker::run_one_batch in module Bio::EnsEMBL::Hive::Worker at /usr/local/ensembl-86/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm on line 526 Called by Bio::EnsEMBL::Hive::Worker::run in module Bio::EnsEMBL::Hive::Scripts::RunWorker at /usr/local/ensembl-86/ensembl-hive/modules/Bio/EnsEMBL/Hive/Scripts/RunWorker.pm on line 85 Called by (eval) in module Bio::EnsEMBL::Hive::Scripts::RunWorker at /usr/local/ensembl-86/ensembl-hive/modules/Bio/EnsEMBL/Hive/Scripts/RunWorker.pm on line 94 Called by Bio::EnsEMBL::Hive::Scripts::RunWorker::runWorker in module main at /usr/local/ensembl-86/ensembl-hive/scripts/runWorker.pl on line 135 Called by main::main in module main at /usr/local/ensembl-86/ensembl-hive/scripts/runWorker.pl on line 23

Plants Ensembl site runs it (assembly converter) but then the actual coordinates are missing from the output:

##fileformat=VCFv4.0
##fileDate=20120328
##source=MaizeHapMap2
##reference=B73RefGenV2
##phasing=no
##INFO=<ID=MQ,Number=.,Type=Float,Description="RMS mapping quality">
##FORMAT=<ID=GT,Number=1,Type=String,Description="Genotype">
##liftOverProgram=CrossMap(https://sourceforge.net/projects/crossmap/)
##liftOverFile=/nfs/public/rw/ensembl/ensembl-genomes/eg_data/release-33/assembly_converter/zea_mays/AGPv4_to_AGPv3.chain.gz
##new_reference_genome=/nfs/public/rw/ensembl/ensembl-genomes/eg_data/release-33/assembly_converter/zea_mays/Zea_mays.AGPv3.dna.toplevel.fa
##liftOverTime=November11,2016
#CHROM  POS     ID      REF     ALT     QUAL    FILTER  INFO    FORMAT  B73:MZ  B97:MZ   BKN009:MZ       BKN010:MZ       BKN011:MZ


http://www.warelab.org/bugs/view.php?id=5508