[ensembl-dev] Error using Web Assembly Converter

Fin Swimmer ensembl at need-login.de
Mon Oct 15 11:53:15 BST 2018


Hello,

I'm trying to convert a vcf file from GRCh38 to GRCh37 using Assembly 
Converter 
(http://www.ensembl.org/Homo_sapiens/Tools/AssemblyConverter/). The job 
failed with this information:

Error with message: pysam.utils.SamtoolsError: 'samtools returned with 
error 1: stdout=, stderr=Could not build fai index 
/nfs/public/release/ensweb-data/latest/tools/www/e94/assembly_converter/homo_sapiens/Homo_sapiens.GRCh37.dna.toplevel.fa.fai\n'
Thrown by EnsEMBL::Web::RunnableDB::AssemblyConverter::run at 
Bio::EnsEMBL::Hive::Process (140)
Thrown by (eval) at Bio::EnsEMBL::Hive::Process (127) Thrown by 
Bio::EnsEMBL::Hive::Process::life_cycle at Bio::EnsEMBL::Hive::Worker 
(681)
Thrown by (eval) at Bio::EnsEMBL::Hive::Worker (652) Thrown by 
Bio::EnsEMBL::Hive::Worker::run_one_batch at Bio::EnsEMBL::Hive::Worker 
(500)
Thrown by Bio::EnsEMBL::Hive::Worker::run at main (141) Thrown by 
main::main at main (22)

It doesn't matter whether I uploaded my whole vcf file or just paste in 
a part of it.

fin swimmer



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