[Feedback] Site Feedback: Problem with converter tool B73 v2 to v4

[Marcela K. Monaco]

Dear Eva,

You just need to remove the "chr" prefix from your file (to match the
reference assembly) and it will work!

Like so:

INPUT
7 110755029 110755029
7 173495749 173495749

OUTPUT
7    113979322    113979322
7    177402711    177402711

Best,

Marcela


On Tue, Apr 4, 2017 at 9:45 AM, feedback at gramene.org <feedback at gramene.org>
wrote:

> URL         : 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=mkpgQs82XaCKIwNV8b32dmVOmERqJe
> 4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=da7y5bawH3XhRTnOwfOOV6fdikK48y
> MHWPvxE6iL-EI&s=2Ur_hpVTJcfOnZyYzCaIUtmFlFdWsvCWwQtAOl4jFYA&e=
>
> Subject     : Site Feedback: Problem with converter tool B73 v2 to v4
>
> Name        : Eva Bauer
>
> Email       : e.bauer at tum.de
>
> Organization: Technical University of Munich
>
> Comments    :
>
> Dear Helpdesk Team,
>
> 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.
>
> My input data are in the following format (bed):
>
> chr7 110755029 110755029
> chr7 173495749 173495749
>
> 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).
>
> I would be grateful for any help with this issue.
>
> Best regards
> Eva
>
>
> Error: Uncaught exception 'HiveException' with message 'Output file empty
> (zero bytes).' Thrown by EnsEMBL::Web::RunnableDB::AssemblyConverter::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
>
> 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=
>
>
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-- 

Marcela Karey Tello-Ruiz, PhD
Gramene Project Manager
Cold Spring Harbor Laboratory
One Bungtown Road, Williams #5
Cold Spring Harbor, NY 11724
Phone: 516-367-8808
Fax: 516-367-6851
E-mail: telloruiz at cshl.edu
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