[Feedback] Site Feedback: assembly converter error for wheat

Wed Jun 7 07:17:28 EDT 2017

URL         : http://ensembl.gramene.org/Triticum_aestivum/Info/Index

Subject     : assembly converter error for wheat

Name        : Marcela

Email       : mmonaco at cshl.edu

Organization: cshl

Comments    : 

On Wed, Jun 7, 2017 at 2:23 AM, Cornelia Hooper <cornelia.hooper at uwa.edu.au> wrote:

    Dear Marcela,

    Thank you for the email. I have linked up the maize data using the converter file. I have tried the converter tool with the maize and couldn’t get it to work using BED format. I also tried wheat data but no success. I have emailed the tech support while ago since the report indicated it was a code problem rather than input problem. I haven’t had a reply yet.

    We have our wheat data linked to the IWGSC1 and want to update ti to TGAC_v1. The data lists I entered into the converter tool are below. All failed. Can you let me know if there is a file similar to that one for maize also for wheat? I cannot see it in the wheat directory of the server.

    Thank you for your help.

    Kind regards,
    Conny

    chr4B 102718686 102720917
    chr4B 102730790 102736491
    chr4B 102845718 102849222
    chr4B 103137674 103140328
    chr4B 103162593 103166525
    chr4B 103221270 103228313
    chr4B 103411172 103417581

    chr4 103162593 103166525
    chr4 103221270 103228313
    chr4 103411172 103417581
    chr4 103419223 103424599
    chr4 103425750 103428816
    chr4 103429528 103431302
    chr4 103645420 103646038

    IWGSC_CSS_5BL_scaff_1082268 5 199
    IWGSC_CSS_6BL_scaff_430516 302 1741
    IWGSC_CSS_5AL_scaff_277801 1 200
    IWGSC_CSS_1DL_scaff_214882 798 1223
    IWGSC_CSS_1DL_scaff_59246 1 392
    IWGSC_CSS_7BS_scaff_31052 19 504
    IWGSC_CSS_7DL_scaff_2682 32 286
    IWGSC_CSS_7DS_scaff_38174 1 237
    IWGSC_CSS_7AS_scaff_423316 2 222

    Error message example:
    Error: Uncaught exception 'HiveException' with message '@ 2017-06-07 02:12:52: Read chain_file: /usr/local/ensembl-live/tools_data/assembly_converter/triticum_aestivum/IWGSC1_to_TGACv1.chain.gz ' Thrown by EnsEMBL::Web::RunnableDB::AssemblyConverter::run in module Bio::EnsEMBL::Hive::Process at /usr/local/ensembl-88/public-plugins/tools_hive/utils/../../../ensembl-hive//modules/Bio/EnsEMBL/Hive/Process.pm on line 140 Called by (eval) in module Bio::EnsEMBL::Hive::Process at /usr/local/ensembl-88/public-plugins/tools_hive/utils/../../../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-88/public-plugins/tools_hive/utils/../../../ensembl-hive//modules/Bio/EnsEMBL/Hive/Worker.pm on line 688 Called by (eval) in module Bio::EnsEMBL::Hive::Worker at /usr/local/ensembl-88/public-plugins/tools_hive/utils/../../../ensembl-hive//modules/Bio/EnsEMBL/Hive/Worker.p!
 m on line 674 Called by Bio::EnsEMBL::Hive::Worker::run_one_batch in module Bio::EnsEMBL::Hive::Worker at /usr/local/ensembl-88/public-plugins/tools_hive/utils/../../../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-88/public-plugins/tools_hive/utils/../../../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-88/public-plugins/tools_hive/utils/../../../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-88/public-plugins/tools_hive/utils/../../../ensembl-hive//scripts/runWorker.pl on line 140 Called by main::main in module main at /usr/local/ensembl-88/public-plugins/tools_hive/utils/../../../ensembl-hive//scripts/runWorker.pl on!
  line 24

    On 1 Jun 2017, at 4:39 am, Marcela K. Monaco <mmonaco at cshl.edu<mailto:mmonaco at cshl.edu>> wrote:

    Dear Cornelia,

    I noticed that you have been using our old maize v4 site.  You may a fully functional assembly conversion tool for the V2, V3 and V4 assemblies of maize in the Gramene browser at ensembl.gramene.org/Zea_mays/Tools/AssemblyConverter?db=core<https://urldefense.proofpoint.com/v2/url?u=http-3A__ensembl.gramene.org_Zea-5Fmays_Tools_AssemblyConverter-3Fdb-3Dcore&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=-IMtSpZQdrx6-bZpQ_1JPbCs1SWSq0fMA49dWw6auYs&s=3E4jurFF9Jvqx_y1uh6mJcJ4u51ng25F1kxP0S3U5Z8&e=>

    Also, in the maize species page<https://urldefense.proofpoint.com/v2/url?u=http-3A__ensembl.gramene.org_Zea-5Fmays_Info_Index&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=-IMtSpZQdrx6-bZpQ_1JPbCs1SWSq0fMA49dWw6auYs&s=O8ezOyeOOlvSCx7WL6zGstz0TtH61u0qv9CpIkYulJs&e=>, we provide a mapping table for gene IDs: Maize B73 V3 <=> V4 gene ID mapping<https://urldefense.proofpoint.com/v2/url?u=ftp-3A__ftp.gramene.org_pub_gramene_CURRENT-5FRELEASE_data_gff3_zea-5Fmays_gene-5Fid-5Fmapping-5Fv3-5Fto-5Fv4_&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=-IMtSpZQdrx6-bZpQ_1JPbCs1SWSq0fMA49dWw6auYs&s=yCSuaLwRePYcnhHPn12rT82X8oroVUsKPPdj86IeqrU&e=>

    Hope this is useful!  Best regards,

    Marcela

    On Wed, May 31, 2017 at 8:08 AM, Ware, Doreen <ware at cshl.edu<mailto:ware at cshl.edu>> wrote:
    Andrew and Joe,

    Can you please work with Cornelia.

    Doreen

    From: Cornelia Hooper <cornelia.hooper at uwa.edu.au<mailto:cornelia.hooper at uwa.edu.au><mailto:cornelia.hooper at uwa.edu.au<mailto:cornelia.hooper at uwa.edu.au>>>
    Date: Wednesday, May 31, 2017 at 1:46 AM
    To: Doreen Ware <ware at cshl.edu<mailto:ware at cshl.edu><mailto:ware at cshl.edu<mailto:ware at cshl.edu>>>
    Cc: \"Tello-Ruiz, Marcela\" <telloruiz at cshl.edu<mailto:telloruiz at cshl.edu><mailto:telloruiz at cshl.edu<mailto:telloruiz at cshl.edu>>>, \"Mulvaney, Joseph\" <jmulvane at cshl.edu<mailto:jmulvane at cshl.edu><mailto:jmulvane at cshl.edu<mailto:jmulvane at cshl.edu>>>, \"Olson, Andrew\" <olson at cshl.edu<mailto:olson at cshl.edu><mailto:olson at cshl.edu<mailto:olson at cshl.edu>>>
    Subject: Re: SUBA & CROPPAL

    Dear Doreen,

    I haven’t heard back from you since my last email. It is almost time for the next conference in Hawaii already!

    I can see you have been very busy with new releases. Well done on the efforts! It looks good! We are currently updating our cropPAL data resources (http://crop-pal.org/<https://urldefense.proofpoint.com/v2/url?u=http-3A__crop-2Dpal.org_&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=-IMtSpZQdrx6-bZpQ_1JPbCs1SWSq0fMA49dWw6auYs&s=NSNlIw0LBT1SMCqBpYhcy-42exHEIqYxRHlnVC2G898&e=><https://urldefense.proofpoint.com/v2/url?u=http-3A__crop-2Dpal.org_&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=o9bHzY93KcMdckSgeLYlVQ&m=eTAFHeoaZFN9lZgA03HnTLnIKmjqnsVfCJN29_JS6zE&s=-dVbpZ9uau7a-EeTZ7oS0pm6y1IIUsq7l8S0HMZUHjM&e=>) for subcellular protein data to match the new Gramene version and the zea mays and wheat have changed a lot. I have tried to download any sort of conversion table for our bulk data set to convert old IDs to new IDs but have had no luck so far.

    I found a link to a conversion tool http://maizev4.gramene.org/Zea_mays/Tools/IDMapper?db=core<https://urldefense.proofpoint.com/v2/url?u=http-3A__maizev4.gramene.org_Zea-5Fmays_Tools_IDMapper-3Fdb-3Dcore&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=-IMtSpZQdrx6-bZpQ_1JPbCs1SWSq0fMA49dWw6auYs&s=rskm2xEdfqes1M9kLGdsl7a98krHLPo5yhQ80GMgoPc&e=><https://urldefense.proofpoint.com/v2/url?u=http-3A__maizev4.gramene.org_Zea-5Fmays_Tools_IDMapper-3Fdb-3Dcore&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=o9bHzY93KcMdckSgeLYlVQ&m=eTAFHeoaZFN9lZgA03HnTLnIKmjqnsVfCJN29_JS6zE&s=QDdOOX72NzOOQnenjD_EDhzFXU22b1_h8aoY0TM93MA&e=> but it seems not connected. We are hoping to get the new data out and about soon and if you already have a conversion table we could use to more simply relink the previous data that would be so helpful. I am happy with sql, csv or a link to the tool. If you or one of your technical staff could help out it would be mu!
 ch appreciated.

    Best regards,
    Conny

    Dr. Cornelia M Hooper (née Bertram)
    Research Fellow
    Computational Biologist

    Plant Energy Biology
    ARC Centre of Excellence
    The University of Western Australia
    M316, 35 Stirling Highway, Crawley WA 6009 Australia

    Tel. +61 8 6488 4411<tel:%2B61%208%206488%204411>
    Email: Cornelia.Hooper at uwa.edu.au<mailto:Cornelia.Hooper at uwa.edu.au><mailto:Cornelia.Bertram at uwa.edu.au<mailto:Cornelia.Bertram at uwa.edu.au>>
    www.uwa.edu.au<https://urldefense.proofpoint.com/v2/url?u=http-3A__www.uwa.edu.au_&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=-IMtSpZQdrx6-bZpQ_1JPbCs1SWSq0fMA49dWw6auYs&s=pwPtmwvpxYB-60SsA8pzU6wh2DIKOKFMH5sWMJzB69I&e=><https://urldefense.proofpoint.com/v2/url?u=http-3A__www.uwa.edu.au&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=o9bHzY93KcMdckSgeLYlVQ&m=eTAFHeoaZFN9lZgA03HnTLnIKmjqnsVfCJN29_JS6zE&s=bUZwjmeNL7MKSzp685V0dHJEyXB5QlIjUQhKIKDJT2w&e=>

    Visit our subcellular resources:
    Arabidopsis: http://SUBA.live<https://urldefense.proofpoint.com/v2/url?u=http-3A__suba.live_&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=-IMtSpZQdrx6-bZpQ_1JPbCs1SWSq0fMA49dWw6auYs&s=UrpcfZiswdBdUJ_ReUSTU1LhgUs780Dy1EeMM8Bibdk&e=><https://urldefense.proofpoint.com/v2/url?u=http-3A__SUBA.live&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=o9bHzY93KcMdckSgeLYlVQ&m=eTAFHeoaZFN9lZgA03HnTLnIKmjqnsVfCJN29_JS6zE&s=aHVoXU8lJrpKrYFA8SdwV2uLYdKoI2M4glJ90fFvRFI&e=>
    Crops: http://crop-PAL.org<https://urldefense.proofpoint.com/v2/url?u=http-3A__crop-2Dpal.org_&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=_Zc33CcBZfVwbQ1K4e-3NQ&m=-IMtSpZQdrx6-bZpQ_1JPbCs1SWSq0fMA49dWw6auYs&s=NSNlIw0LBT1SMCqBpYhcy-42exHEIqYxRHlnVC2G898&e=><https://urldefense.proofpoint.com/v2/url?u=http-3A__crop-2DPAL.org&d=DwMGaQ&c=mkpgQs82XaCKIwNV8b32dmVOmERqJe4bBOtF0CetP9Y&r=o9bHzY93KcMdckSgeLYlVQ&m=eTAFHeoaZFN9lZgA03HnTLnIKmjqnsVfCJN29_JS6zE&s=8Tz956-pJokdejUY8Z4dZFQjZAd25I453fJuCDFMcwc&e=>

http://www.warelab.org/bugs/view.php?id=5630