Adding --offline option fixed the problem. But still wish you can add fission yeast to the list.<br>Best.<br><div class="gmail_quote"><div dir="ltr">2018年9月20日(木) 18:34 Yutze Li <<a href="mailto:liyutze.seikiri@gmail.com">liyutze.seikiri@gmail.com</a>>:<br></div><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex"><div dir="ltr"><span style="color:rgb(33,33,33);font-size:13px">I found the pre-built genome cache of fission yeast schizosaccharomyces pombe was on the ftp but not on the list when running the INSTALL.pl of VEP.</span><div style="color:rgb(33,33,33);font-size:13px">Also, adding the cache downloaded and uncompressed from the ftp to my ~/.vep/ did not work.<div>My command and the error message goes like:</div><div><br></div><div><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">$ </span>vep --cache --species schizosaccharomyces_pombe --cache_version 40 \</p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">>     --appris --biotype --pick --symbol --tsl --distance 100 \</p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo">>     -i $BASE.filter.vcf -o $BASE.ann.vcf</p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">-------------------- WARNING ----------------------</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">MSG: schizosaccharomyces_pombe is not a valid species name (check DB and API version)</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">FILE: Bio/EnsEMBL/Registry.pm LINE: 1334</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">CALLED BY: Bio/EnsEMBL/Registry.pm<span class="m_-8299105538417069902inbox-inbox-m_1665012408058006469inbox-inbox-Apple-converted-space"> <span class="m_-8299105538417069902inbox-inbox-Apple-converted-space"> </span></span>LINE: 1109</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Date (localtime)<span class="m_-8299105538417069902inbox-inbox-m_1665012408058006469inbox-inbox-Apple-converted-space">   <span class="m_-8299105538417069902inbox-inbox-Apple-converted-space"> </span></span>= Thu Sep 20 18:16:26 2018</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Ensembl API version = 93</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">---------------------------------------------------</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo;min-height:13px"><span style="font-variant-ligatures:no-common-ligatures"></span><br></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">-------------------- EXCEPTION --------------------</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">MSG: Can not find internal name for species 'schizosaccharomyces_pombe'</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">STACK Bio::EnsEMBL::Registry::get_adaptor /Users/lytzeseikiri/biotools/ensembl-vep/Bio/EnsEMBL/Registry.pm:1111</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">STACK Bio::EnsEMBL::VEP::BaseVEP::get_adaptor /Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:308</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">STACK Bio::EnsEMBL::VEP::BaseVEP::get_database_assembly /Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseVEP.pm:419</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">STACK Bio::EnsEMBL::VEP::BaseRunner::setup_db_connection /Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/BaseRunner.pm:123</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">STACK Bio::EnsEMBL::VEP::Runner::init /Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:118</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">STACK Bio::EnsEMBL::VEP::Runner::run /Users/lytzeseikiri/biotools/ensembl-vep/modules/Bio/EnsEMBL/VEP/Runner.pm:194</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">STACK toplevel /Users/lytzeseikiri/biotools/ensembl-vep/vep:224</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Date (localtime)<span class="m_-8299105538417069902inbox-inbox-m_1665012408058006469inbox-inbox-Apple-converted-space">   <span class="m_-8299105538417069902inbox-inbox-Apple-converted-space"> </span></span>= Thu Sep 20 18:16:26 2018</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">Ensembl API version = 93</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures">---------------------------------------------------</span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-variant-ligatures:no-common-ligatures"><br></span></p><p style="margin:0px;font-stretch:normal;font-size:11px;line-height:normal;font-family:Menlo"><span style="font-family:sans-serif;font-size:small">Thanks.</span></p></div></div></div>
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