|
|
@@ -39,27 +39,54 @@ You should see output similar to the following:
|
|
|
|
|
|
::
|
|
|
|
|
|
- Tripal Job Launcher
|
|
|
- Running as user 'administrator'
|
|
|
- -------------------
|
|
|
- 2018-06-29 18:00:50: There are 1 jobs queued.
|
|
|
- 2018-06-29 18:00:50: Job ID 8.
|
|
|
- 2018-06-29 18:00:50: Calling: tripal_run_importer(12)
|
|
|
-
|
|
|
- Running 'Chado GFF3 File Loader' importer
|
|
|
- NOTE: Loading of file is performed using a database transaction.
|
|
|
- If it fails or is terminated prematurely then all insertions and
|
|
|
- updates are rolled back and will not be found in the database
|
|
|
-
|
|
|
- Opening /var/www/html/sites/default/files/tripal/users/1/Citrus_sinensis-orange1.1g015632m.g.gff3
|
|
|
- Percent complete: 100.00%. Memory: 32,211,360 bytes.
|
|
|
- Adding protein sequences if CDS exist and no proteins in GFF...
|
|
|
- Setting ranks of children...
|
|
|
-
|
|
|
- Done.
|
|
|
+ 2020-10-02 21:53:18
|
|
|
+ Tripal Job Launcher
|
|
|
+ Running as user 'admin'
|
|
|
+ -------------------
|
|
|
+ 2020-10-02 21:53:18: There are 1 jobs queued.
|
|
|
+ 2020-10-02 21:53:18: Job ID 1310.
|
|
|
+ 2020-10-02 21:53:18: Calling: tripal_run_importer(123)
|
|
|
+
|
|
|
+ Running 'Chado GFF3 File Loader' importer
|
|
|
+ NOTE: Loading of file is performed using a database transaction.
|
|
|
+ If it fails or is terminated prematurely then all insertions and
|
|
|
+ updates are rolled back and will not be found in the database
|
|
|
+
|
|
|
+ Opening /var/www/html/sites/default/files/tripal/users/1/Citrus_sinensis-orange1.1g015632m.g.gff3
|
|
|
+ Opening temporary cache file: /tmp/TripalGFF3Import_aUgoru
|
|
|
+ Step 1 of 26: Caching GFF3 file...
|
|
|
+ Step 2 of 26: Find existing landmarks...
|
|
|
+ Step 3 of 26: Insert new landmarks (if needed)...
|
|
|
+ Step 4 of 26: Find missing proteins...
|
|
|
+ Step 5 of 26: Add missing proteins to list of features...
|
|
|
+ Step 6 of 26: Find existing features...
|
|
|
+ Step 7 of 26: Clear attributes of existing features...
|
|
|
+ Step 8 of 26: Processing 135 features...
|
|
|
+ Step 9 of 26: Get new feature IDs...
|
|
|
+ Step 10 of 26: Insert locations...
|
|
|
+ Step 11 of 26: Associate parents and children...
|
|
|
+ Step 12 of 26: Calculate child ranks...
|
|
|
+ Step 13 of 26: Add child-parent relationships...
|
|
|
+ Step 14 of 26: Insert properties...
|
|
|
+ Step 15 of 26: Find synonyms (aliases)...
|
|
|
+ Step 16 of 26: Insert new synonyms (aliases)...
|
|
|
+ Step 17 of 26: Insert feature synonyms (aliases)...
|
|
|
+ Step 18 of 26: Find cross references...
|
|
|
+ Step 19 of 26: Insert new cross references...
|
|
|
+ Step 20 of 26: Get new cross references IDs...
|
|
|
+ Step 21 of 26: Insert feature cross references...
|
|
|
+ Step 22 of 26: Insert feature ontology terms...
|
|
|
+ Step 23 of 26: Insert 'derives_from' relationships...
|
|
|
+ Step 24 of 26: Insert Targets...
|
|
|
+ Step 25 of 26: Associate features with analysis....
|
|
|
+ Step 26 of 26: Adding sequences data (Skipped: none available)...
|
|
|
+
|
|
|
+ Done.
|
|
|
+ Committing Transaction...
|
|
|
+
|
|
|
+ Remapping Chado Controlled vocabularies to Tripal Terms...
|
|
|
+ Done.
|
|
|
|
|
|
- Remapping Chado Controlled vocabularies to Tripal Terms...
|
|
|
- Done.
|
|
|
|
|
|
.. note::
|
|
|
|
Stephen Ficklin