[ensembl-dev] Problem with locator in LoadMembers.pm (ensembl-compara)
Francesco Lamanna
francesco.lamanna at gmail.com
Tue Jan 23 15:39:49 GMT 2018
Hi Mateus,
I have changed the order of some entries in the json file, it looks now
like this:
[
{
"production_name" : "branchiostoma_floridae",
"taxonomy_id" : "7739",
"cds_fasta" :
"/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/amphioxus_longest_CDS.fa",
"prot_fasta" :
"/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/amphioxus_longest_proteins.fa",
"gene_coord_gff" :
"/home/hd/hd_hd/hd_cc141/Genomes/amphioxus/NCBI/GCF_000003815.1_Version_2_genomic.gff",
"source" : "refseq",
},
{
"production_name" : "petromyzon_marinus",
"taxonomy_id" : "7757",
"cds_fasta" :
"/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/sea_lamprey_CDS_no_monoexon.fa",
"prot_fasta" :
"/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/sea_lamprey_proteins_no_monoexon.fa",
"gene_coord_gff" :
"/home/hd/hd_hd/hd_cc141/Lamprey_annotation/germ_final/PMZ_v3.1_final/PMZ_v3.1_genes.gtf",
"source" : "augustus_maker",
},
]
but I get a different error message:
Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] -> FETCH_INPUT
Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] -> RUN
ParamWarning: value for param('genome_component') is used before having
been initialized!
ParamWarning: value for param('master_genome_db') is used before having
been initialized!
Worker 10 [ Role 10 , load_genomedb(5), Job 9 ] Fatal :
-------------------- EXCEPTION --------------------
MSG: db_adaptor's type 'Bio::EnsEMBL::Compara::GenomeMF' is not an ISA of
'Bio::EnsEMBL::DBSQL::DBAdaptor'
STACK Bio::EnsEMBL::Utils::Scalar::assert_ref_pp
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl/modules/Bio/EnsEMBL/Utils/Scalar.pm:231
STACK Bio::EnsEMBL::Compara::GenomeDB::db_adaptor
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm:181
STACK Bio::EnsEMBL::Compara::GenomeDB::new_from_DBAdaptor
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm:146
STACK Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB::create_genome_db
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/LoadOneGenomeDB.pm:204
STACK Bio::EnsEMBL::Compara::RunnableDB::LoadOneGenomeDB::run
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/RunnableDB/LoadOneGenomeDB.pm:186
STACK (eval)
/beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Process.pm:140
STACK Bio::EnsEMBL::Hive::Process::life_cycle
/beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Process.pm:127
STACK (eval)
/beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:688
STACK Bio::EnsEMBL::Hive::Worker::run_one_batch
/beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:674
STACK Bio::EnsEMBL::Hive::Worker::run
/beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Worker.pm:486
STACK (eval)
/beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Scripts/RunWorker.pm:88
STACK Bio::EnsEMBL::Hive::Scripts::RunWorker::runWorker
/beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/modules/Bio/EnsEMBL/Hive/Scripts/RunWorker.pm:94
STACK main::main
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/scripts/runWorker.pl:140
STACK toplevel
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/scripts/runWorker.pl:24
Date (localtime) = Tue Jan 23 16:29:39 2018
Ensembl API version = 91
---------------------------------------------------
Do you have any idea?
Cheers,
Francesco
2018-01-23 13:43 GMT+01:00 Mateus Patricio <mateus at ebi.ac.uk>:
> Hi Francesco,
>
> Could you please, check if your non_ensembl_species.json file is formatted
> like the one bellow:
>
> [
> {
> "production_name" : "species_1",
> "taxonomy_id" : "1234",
> "cds_fasta" : "species_1.cds.fa",
> "prot_fasta" : "species_1.prot.fa",
> "gene_coord_gff" : "species_1.gff",
> "source" : "your_source",
> },
> {
> "production_name" : "species_2",
> "taxonomy_id" : "4321",
> "cds_fasta" : "species_2.cds.fa",
> "prot_fasta" : "species_2.prot.fa",
> "gene_coord_gff" : "species_2.gff",
> "source" : "your_source",
> },
> ]
>
> Cheers,
>
> Mateus.
>
>
> On 23 Jan 2018, at 10:03, Francesco Lamanna <francesco.lamanna at gmail.com>
> wrote:
>
> Hi all,
>
> I am trying to build a members db using a set of core and custom genome
> assemblies. I have set up the locator column for both the core and custom
> databases in the genome_db table of the master database. However, when I
> run the LoadMembers pipeline, the load_genomedb analysis fails to load the
> custom genomes:
>
> mysql> SELECT * FROM msg;
> +-------------+------------------------+----------------+---
> -----+---------+-----------+---------------------+-------+--
> ------------+-----------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------+----------+
> | analysis_id | logic_name | log_message_id | job_id | role_id
> | worker_id | when_logged | retry | status |
> msg
>
>
>
> |
> is_error |
> +-------------+------------------------+----------------+---
> -----+---------+-----------+---------------------+-------+--
> ------------+-----------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------+----------+
> | 3 | copy_table_from_master | 1 | 4 | 3
> | 3 | 2018-01-22 18:00:51 | 0 | WRITE_OUTPUT | Successfully
> copied 1646504 'ncbi_taxa_node' rows
>
>
>
> | 0 |
> | 3 | copy_table_from_master | 2 | 5 | 4
> | 4 | 2018-01-22 18:03:12 | 0 | WRITE_OUTPUT | Successfully
> copied 2504391 'ncbi_taxa_name' rows
>
>
>
> | 0 |
> | 5 | load_genomedb | 3 | 10 | 7
> | 7 | 2018-01-22 18:05:17 | 0 | FETCH_INPUT | Sorry, could not
> figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::
> GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_
> project/Ensembl_compara/non_ensembl_species.json;index=2' at
> /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/
> modules/Bio/EnsEMBL/Hive/Utils.pm line 366. | 1 |
> | 5 | load_genomedb | 4 | 10 | 7
> | 7 | 2018-01-22 18:05:18 | 1 | FETCH_INPUT | Sorry, could not
> figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::
> GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_
> project/Ensembl_compara/non_ensembl_species.json;index=2' at
> /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/
> modules/Bio/EnsEMBL/Hive/Utils.pm line 366. | 1 |
> | 5 | load_genomedb | 5 | 9 | 6
> | 6 | 2018-01-22 18:05:19 | 0 | FETCH_INPUT | Sorry, could not
> figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::
> GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_
> project/Ensembl_compara/non_ensembl_species.json;index=1' at
> /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/
> modules/Bio/EnsEMBL/Hive/Utils.pm line 366. | 1 |
> | 5 | load_genomedb | 6 | 9 | 6
> | 6 | 2018-01-22 18:05:20 | 1 | FETCH_INPUT | Sorry, could not
> figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::
> GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_
> project/Ensembl_compara/non_ensembl_species.json;index=1' at
> /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/
> modules/Bio/EnsEMBL/Hive/Utils.pm line 366. | 1 |
> | 5 | load_genomedb | 7 | 9 | 8
> | 8 | 2018-01-22 18:06:08 | 2 | FETCH_INPUT | Sorry, could not
> figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::
> GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_
> project/Ensembl_compara/non_ensembl_species.json;index=1' at
> /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/
> modules/Bio/EnsEMBL/Hive/Utils.pm line 366. | 1 |
> | 5 | load_genomedb | 8 | 10 | 8
> | 8 | 2018-01-22 18:06:08 | 2 | FETCH_INPUT | Sorry, could not
> figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::
> GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_
> project/Ensembl_compara/non_ensembl_species.json;index=2' at
> /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/
> modules/Bio/EnsEMBL/Hive/Utils.pm line 366. | 1 |
> | 5 | load_genomedb | 9 | 9 | 10
> | 10 | 2018-01-22 18:08:49 | 1 | FETCH_INPUT | Sorry, could not
> figure out how to make a DBConnection object out of 'Bio::EnsEMBL::Compara::
> GenomeMF/filename=/home/hd/hd_hd/hd_cc141/Vertebrates_
> project/Ensembl_compara/non_ensembl_species.json;index=1' at
> /beegfs/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-hive/
> modules/Bio/EnsEMBL/Hive/Utils.pm line 366. | 1 |
> +-------------+------------------------+----------------+---
> -----+---------+-----------+---------------------+-------+--
> ------------+-----------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------------------------------------------------
> ------------------+----------+
> 9 rows in set (0.00 sec)
>
> Any suggestion would be highly appreciated.
>
> Cheers,
> Francesco
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