[Feedback] Site Feedback: assembly conversion works selectively* with same maize v4 data in BED but not GFF

[feedback at gramene.org]

URL         : http://ensembl.gramene.org/Oryza_sativa/Tools/AssemblyConverter/View?db=core;tl=XQqol9QFKD4TsAmt-25205

Subject     : Site Feedback: assembly conversion works selectively* with same maize v4 data in BED but not GFF 

Name        : Marcela

Email       : mmonaco at cshl.edu

Organization: CSHL

Comments    : 

When converting maize v4 coordinates into v3 coordinates (test file included neighboring genes: Zm00001d023210 and Zm00001d023211), we got identical results (i.e., v3 coordinates) for Zm00001d023210 whether we used BED or GFF formatted data.  However, we got NO Results from the GFF formatted file for Zm00001d023211 coordinates, only got results (i.e., three v3 segments) from the BED formatted file.

Sample files:

Input BED-

10	218781	220384	gene:Zm00001d023210	.	-	gramene	gene	.	ID=gene:Zm00001d023210
10	265243	271813	gene:Zm00001d023211	.	-	gramene	gene	.	ID=gene:Zm00001d023211

Output BED-

10	717402	719005	gene:Zm00001d023210	.	-	gramene	gene	.	ID=gene:Zm00001d023210
10	761516	762553	gene:Zm00001d023211	.	-	gramene	gene	.	ID=gene:Zm00001d023211
10	762554	764318	gene:Zm00001d023211	.	-	gramene	gene	.	ID=gene:Zm00001d023211
10	764319	768088	gene:Zm00001d023211	.	-	gramene	gene	.	ID=gene:Zm00001d023211

Input GFF-

10	gramene	gene	218781	220384	.	-	.	ID=gene:Zm00001d023210
10	gramene	gene	265243	271813	.	-	.	ID=gene:Zm00001d023211

Output GFF-

10	gramene	gene	717402	719005	.	-	.	ID=gene:Zm00001d023210


When I tried pasting a single line of data (the one that did not work):

10	gramene	gene	265243	271813	.	-	.	ID=gene:Zm00001d023211

The job failed with the following error:

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

http://www.warelab.org/bugs/view.php?id=5528