<div dir="ltr"><div><div><div>Dear Eva,<br><br></div>You just need to remove the "chr" prefix from your file (to match the reference assembly) and it will work! <br><br></div>Like so:<br><br></div>INPUT<br><div>7 110755029 110755029<br>7 173495749 173495749<br><br></div><div>OUTPUT<br>7 113979322 113979322<br>7 177402711 177402711<br><br></div><div>Best,<br><br></div><div>Marcela<br></div><div><br></div></div><div class="gmail_extra"><br><div class="gmail_quote">On Tue, Apr 4, 2017 at 9:45 AM, <a href="mailto:feedback@gramene.org">feedback@gramene.org</a> <span dir="ltr"><<a href="mailto:feedback@gramene.org" target="_blank">feedback@gramene.org</a>></span> wrote:<br><blockquote class="gmail_quote" style="margin:0 0 0 .8ex;border-left:1px #ccc solid;padding-left:1ex">URL : <a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__ensembl.gramene.org_Oryza-5Fsativa_Tools_AssemblyConverter_View-3Fdb-3Dcore-3Btl-3DwzKMlPA6rvLL19eA-2D128496&d=DwICAg&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=da7y5bawH3XhRTnOwfOOV6fdikK48yMHWPvxE6iL-EI&s=2Ur_hpVTJcfOnZyYzCaIUtmFlFdWsvCWwQtAOl4jFYA&e=" rel="noreferrer" target="_blank">https://urldefense.proofpoint.<wbr>com/v2/url?u=http-3A__ensembl.<wbr>gramene.org_Oryza-5Fsativa_<wbr>Tools_AssemblyConverter_View-<wbr>3Fdb-3Dcore-3Btl-<wbr>3DwzKMlPA6rvLL19eA-2D128496&d=<wbr>DwICAg&c=<wbr>mkpgQs82XaCKIwNV8b32dmVOmERqJe<wbr>4bBOtF0CetP9Y&r=_<wbr>Zc33CcBZfVwbQ1K4e-3NQ&m=<wbr>da7y5bawH3XhRTnOwfOOV6fdikK48y<wbr>MHWPvxE6iL-EI&s=2Ur_<wbr>hpVTJcfOnZyYzCaIUtmFlFdWsvCWwQ<wbr>tAOl4jFYA&e=</a><br>
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Subject : Site Feedback: Problem with converter tool B73 v2 to v4<br>
<br>
Name : Eva Bauer<br>
<br>
Email : <a href="mailto:e.bauer@tum.de">e.bauer@tum.de</a><br>
<br>
Organization: Technical University of Munich<br>
<br>
Comments :<br>
<br>
Dear Helpdesk Team,<br>
<br>
I have a problem with conversion of B73 v2 to v4 positions. The same problem occurred some weeks ago and I think I used the "report to helpdesk" tool, but the error persists.<br>
<br>
My input data are in the following format (bed):<br>
<br>
chr7 110755029 110755029<br>
chr7 173495749 173495749<br>
<br>
Is it a problem with the file format? I also tried with different start/stop positions (just added +1 to the stop position). But it still fails and gives an error message (copied below).<br>
<br>
I would be grateful for any help with this issue.<br>
<br>
Best regards<br>
Eva<br>
<br>
<br>
Error: Uncaught exception 'HiveException' with message 'Output file empty (zero bytes).' Thrown by EnsEMBL::Web::RunnableDB::<wbr>AssemblyConverter::run in module Bio::EnsEMBL::Hive::Process at /usr/local/ensembl-86/ensembl-<wbr>hive/modules/Bio/EnsEMBL/Hive/<wbr>Process.pm on line 140 Called by (eval) in module Bio::EnsEMBL::Hive::Process at /usr/local/ensembl-86/ensembl-<wbr>hive/modules/Bio/EnsEMBL/Hive/<wbr>Process.pm on line 127 Called by Bio::EnsEMBL::Hive::Process::<wbr>life_cycle in module Bio::EnsEMBL::Hive::Worker at /usr/local/ensembl-86/ensembl-<wbr>hive/modules/Bio/EnsEMBL/Hive/<wbr>Worker.pm on line 688 Called by (eval) in module Bio::EnsEMBL::Hive::Worker at /usr/local/ensembl-86/ensembl-<wbr>hive/modules/Bio/EnsEMBL/Hive/<wbr>Worker.pm on line 674 Called by Bio::EnsEMBL::Hive::Worker::<wbr>run_one_batch in module Bio::EnsEMBL::Hive::Worker at /usr/local/ensembl-86/ensembl-<wbr>hive/modules/Bio/EnsEMBL/Hive/<wbr>Worker.pm on line 526 Called by Bio::EnsEMBL::Hive::Worker::<wbr>run in module Bio::EnsEMBL::Hive::Scripts::<wbr>RunWorker !<br>
at /usr/local/ensembl-86/ensembl-<wbr>hive/modules/Bio/EnsEMBL/Hive/<wbr>Scripts/RunWorker.pm on line 85 Called by (eval) in module Bio::EnsEMBL::Hive::Scripts::<wbr>RunWorker at /usr/local/ensembl-86/ensembl-<wbr>hive/modules/Bio/EnsEMBL/Hive/<wbr>Scripts/RunWorker.pm on line 94 Called by Bio::EnsEMBL::Hive::Scripts::<wbr>RunWorker::runWorker in module main at /usr/local/ensembl-86/ensembl-<wbr>hive/scripts/runWorker.pl on line 135 Called by main::main in module main at /usr/local/ensembl-86/ensembl-<wbr>hive/scripts/runWorker.pl on line 23<br>
<br>
<a href="https://urldefense.proofpoint.com/v2/url?u=http-3A__www.warelab.org_bugs_view.php-3Fid-3D5580&d=DwICAg&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=da7y5bawH3XhRTnOwfOOV6fdikK48yMHWPvxE6iL-EI&s=tzlGeiGcNaSzlZt0UjUWQbGXNi6KujWWH4q2fTCOzoY&e=" rel="noreferrer" target="_blank">https://urldefense.proofpoint.<wbr>com/v2/url?u=http-3A__www.<wbr>warelab.org_bugs_view.php-<wbr>3Fid-3D5580&d=DwICAg&c=<wbr>mkpgQs82XaCKIwNV8b32dmVOmERqJe<wbr>4bBOtF0CetP9Y&r=_<wbr>Zc33CcBZfVwbQ1K4e-3NQ&m=<wbr>da7y5bawH3XhRTnOwfOOV6fdikK48y<wbr>MHWPvxE6iL-EI&s=<wbr>tzlGeiGcNaSzlZt0UjUWQbGXNi6Kuj<wbr>WWH4q2fTCOzoY&e=</a><br>
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<br>
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</font></span></blockquote></div><br><br clear="all"><br>-- <br><div class="gmail_signature" data-smartmail="gmail_signature"><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><div dir="ltr"><div><span style="border-collapse:collapse;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px"><font size="1"><br>Marcela Karey Tello-Ruiz, PhD</font> <font size="1"><br>Gramene Project Manager<br>Cold Spring Harbor Laboratory<br>One Bungtown Road, Williams #5<br>Cold Spring Harbor, NY 11724<br></font></span><span style="border-collapse:collapse;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px"><font size="1">Phone: <span style="background-color:rgb(255,255,255)">516-<span>367</span>-<span><span style="background-image:initial;color:rgb(34,34,34)"><span><font size="1">8808</font></span></span></span><a value="+15163676998" style="color:rgb(17,85,204)"><span></span></a></span><br>
Fax: <span>516</span>-<span>367</span>-6851</font></span></div><div><span style="border-collapse:collapse;color:rgb(34,34,34);font-family:arial,sans-serif;font-size:13px"><font size="1">E-mail: <a href="mailto:telloruiz@cshl.edu" target="_blank">telloruiz@cshl.edu</a></font></span></div></div></div></div></div></div></div></div></div></div></div>
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