More walnut genomes from Ebrahimi at Purdue

[mestato]

Publication and Data Information

Contact: Aziz Ebrahini at Purdue Awaiting:

• 12 fasta files of genomes
• 12 sets of genome annotation
• chloroplast and mitochondrial genomes

Not sure which species yet.

Additional Information

Checklist

See New Genome Documentation for detailed instructions.

• [ ] Create Organism
• [ ] Create Publication
• [ ] Create Reference Genome
• [ ] Create InterProScan Annotation
• [ ] Create BLAST Annotation
• [ ] Run Chado FASTA Loader for CDS
• [ ] Run Chado FASTA Loader for Polypeptides
• [ ] Publish Tripal content
• [ ] Create KEGG Annotation
• [ ] Run Chado KEGG Loader
• [ ] Run Chado BLAST XML results loader
• [ ] Run Chado InterProScan XML results loader
• [ ] Create Blast Database

[CaseyRichards92]

@mestato Have you heard back from the author so we can begin on this organism?

[CaseyRichards92]

Making files downloadable for each of the species.

[CaseyRichards92]

@mestato is there a publication I need to link to the Ebrahimi Reference genome?

[CaseyRichards92]

Not able to save Reference Genome

Could not save the TripalEntity: Unable to write fields to Chado: Array ( [field_number_of_scaffolds] => Array ( [0] => Array ( [value] => delete_me [chado-analysisprop__analysisprop_id] => [chado-analysisprop__analysis_id] => [chado-analysisprop__value] => [chado-analysisprop__type_id] => [chado-analysisprop__rank] => ) ) [field_assembly_size] => Array ( [0] => Array ( [value] => delete_me [chado-analysisprop__analysisprop_id] => [chado-analysisprop__analysis_id] => [chado-analysisprop__value] => [chado-analysisprop__type_id] => [chado-analysisprop__rank] => ) ) [sio__annotation] => Array ( [0] => Array ( [value] => delete_me [chado-analysis_cvterm__analysis_cvterm_id] => [chado-analysis_cvterm__cvterm_id] => [chado-analysis_cvterm__analysis_id] => [cv_id] => 0 [cvterm_name] => [chado-analysis_cvterm__is_not] => [chado-analysis_cvterm__rank] => [chado-analysis_cvterm_is_not] => ) ) [iao__version_number] => Array ( [0] => Array ( [value] => N/A ) ) [sbo__database_cross_reference] => Array ( [0] => Array ( [value] => delete_me [chado-analysis_dbxref__analysis_dbxref_id] => [chado-analysis_dbxref__analysis_id] => [chado-analysis_dbxref__dbxref_id] => [db_id] => 0 [accession] => ) ) [schema__publication] => Array ( [0] => Array ( [value] => [chado-analysis_pub__analysis_pub_id] => [chado-analysis_pub__analysis_id] => [chado-analysis_pub__pub_id] => [pub_title] => ) ) [schema__name] => Array ( [0] => Array ( [value] => Ebrahimi(Purdue) - Reference Genomes ) ) [obi__organism_linker] => Array ( [0] => Array ( [value] => 42 [chado-organism_analysis__organism_analysis_id] => [chado-organism_analysis__analysis_id] => [chado-organism_analysis__organism_id] => 42 ) [1] => Array ( [value] => 18 [chado-organism_analysis__organism_analysis_id] => [chado-organism_analysis__analysis_id] => [chado-organism_analysis__organism_id] => 18 ) ) [local__source_data] => Array ( [0] => Array ( [value] => [chado-analysis__sourcename] => [chado-analysis__sourceversion] => __NULL__ [chado-analysis__sourceuri] => __NULL__ [source_data] => Array ( [sourcename] => [sourceversion] => [sourceuri] => ) ) ) [field_number_of_annotated_genes] => Array ( [0] => Array ( [value] => delete_me [chado-analysisprop__analysisprop_id] => [chado-analysisprop__analysis_id] => [chado-analysisprop__value] => [chado-analysisprop__type_id] => [chado-analysisprop__rank] => ) ) [iao__algorithm] => Array ( ) [sbo__relationship] => Array ( [0] => Array ( [value] => [chado-analysis_relationship__analysis_relationship_id] => [chado-analysis_relationship__subject_id] => [chado-analysis_relationship__type_id] => [chado-analysis_relationship__object_id] => [chado-analysis_relationship__value] => [chado-analysis_relationship__rank] => [subject_name] => [vocabulary] => [type_name] => [object_name] => ) ) [schema__description] => Array ( ) [swo__software] => Array ( [0] => Array ( [value] => N/A ) ) [local__time_executed] => Array ( [0] => Array ( [value] => 2019-09-03 13:28:00 [show_todate] => 1 [timezone] => America/Halifax [offset] => -10800 [offset2] => -10800 [value2] => 2019-09-03 13:28:00 ) ) )
Cannot save entity

@almasaeed2010 this could be because I am trying to add a 2nd reference genome to some of the Juglans species. Is this not possible? I need to add the ebrahimi downloads to this reference genome and associate to correct organism.

[almasaeed2010]

This error is very vague. Were there any other messages?

[CaseyRichards92]

Nope, I tried twice and got same error.

[CaseyRichards92]

Reference genome https://www.hardwoodgenomics.org/Genome-assembly/3641871?tripal_pane=group_summary_tripalpane

Error was program and pipeline must be different

[CaseyRichards92]

Need to create organisms to associate downloads from reference genome with.

• [x] J.ailantifolia
• [x] J.cinera
• [x] J.intermedia
• [x] J.major
• [x] J.mandshurica
• [x] Jxbixbi
• [x] Jxquadrangulata

[CaseyRichards92]

Delete picture for quadrangulata, fix common names for both hybrids, and send email to Meg when finished.