[ensembl-dev] Problem with locator in LoadMembers.pm (ensembl-compara)
Francesco Lamanna
francesco.lamanna at gmail.com
Thu Jan 25 16:49:44 GMT 2018
Hi Mateus,
I am using release/91 of GenomeDB.pm (it misses
Bio::EnsEMBL::Compara::Utils::CoreDBAdaptor->pool_one_DBConnection($dba);
at line 184).
Anyway, if I comment lines 181 and 182 I get the following error:
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 | 2018-01-25 17:19:47 | 0 | WRITE_OUTPUT | Successfully
copied 1646504 'ncbi_taxa_node'
rows
| 0 |
| 3 | copy_table_from_master | 2 | 5 | 4
| 4 | 2018-01-25 17:23:03 | 0 | WRITE_OUTPUT | Successfully
copied 2504391 'ncbi_taxa_name'
rows
| 0 |
| 5 | load_genomedb | 3 | 9 | 7
| 7 | 2018-01-25 17:24:19 | 0 | RUN | Can't call
method "connected" on an undefined value at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm
line 186. | 1 |
| 5 | load_genomedb | 4 | 10 | 7
| 7 | 2018-01-25 17:24:21 | 0 | RUN | Can't call
method "connected" on an undefined value at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm
line 186. | 1 |
| 5 | load_genomedb | 5 | 9 | 6
| 6 | 2018-01-25 17:24:26 | 1 | RUN | Can't call
method "connected" on an undefined value at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm
line 186. | 1 |
| 5 | load_genomedb | 6 | 10 | 6
| 6 | 2018-01-25 17:24:27 | 1 | RUN | Can't call
method "connected" on an undefined value at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm
line 186. | 1 |
| 5 | load_genomedb | 7 | 9 | 8
| 8 | 2018-01-25 17:25:19 | 2 | RUN | Can't call
method "connected" on an undefined value at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm
line 186. | 1 |
| 5 | load_genomedb | 8 | 10 | 8
| 8 | 2018-01-25 17:25:20 | 2 | RUN | Can't call
method "connected" on an undefined value at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm
line 186. | 1 |
+-------------+------------------------+----------------+--------+---------+-----------+---------------------+-------+--------------+----------------------------------------------------------------------------------------------------------------------------------------------------------+----------+
It looks like GenomeDB is now missing something.
Additionally, if I run the analysis in debug mode, I get these two warnings:
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 10 ] Fatal : Can't call method
"connected" on an undefined value at
/home/hd/hd_hd/hd_cc141/EnsEMBL/ensembl-compara/modules/Bio/EnsEMBL/Compara/GenomeDB.pm
line 186.
Thanks,
Francesco.
2018-01-25 15:39 GMT+01:00 Mateus Patricio <mateus at ebi.ac.uk>:
> Hi Francesco,
>
> After discussing this issue with my colleagues.
>
> Could you please test something?
>
> In the file:
> modules/Bio/EnsEMBL/Compara/GenomeDB.pm
>
> Could you please comment lines 181, 182 and 184?
>
> Just like this:
>
> #assert_ref($dba, 'Bio::EnsEMBL::DBSQL::DBAdaptor', 'db_adaptor');
> #throw('$db_adaptor must refer to a Core database') unless $dba->group eq
> 'core';
> $self->{'_db_adaptor'} = $dba;
> #Bio::EnsEMBL::Compara::Utils::CoreDBAdaptor->pool_one_DBConnection($dba);
>
>
> I hope that helps.
>
> Cheers,
>
> Mateus.
>
>
>
> On 23 Jan 2018, at 15:39, Francesco Lamanna <francesco.lamanna at gmail.com>
> wrote:
>
> 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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