jianxinwang
commented
4 years ago It may be an issue of missing some steps during database setup. Can you double check that you followed the instructions in our documentation ( https://github.com/ubccr/genesysv/blob/master/docs/source/index.rst) step by step?
Jason
On Mon, Apr 27, 2020 at 9:14 PM Matthew J. Oldach notifications@github.com wrote:
I'm getting an error trying to install/run genesysv. After following the installation examples the following code is partially working. I'm able to open but something in the error isn't loading the example data in properly.
(genesysv) mtg@mtg-ThinkPad-P53:~/bin/GenESysV$ python manage.py runserver 0.0.0.0:8000 Performing system checks...
System check identified no issues (0 silenced). April 27, 2020 - 21:03:38 Django version 2.0.5, using settings 'genesysv.settings' Starting development server at http://0.0.0.0:8000/ Quit the server with CONTROL-C.
I'm able to open local host and login:
[image: Screenshot from 2020-04-27 19-12-42] https://user-images.githubusercontent.com/5749465/80435961-30f75980-88bb-11ea-99b3-f81c0100a653.png
but cannot click on anything (pretty sure the example is the next part). Trying the example
(genesysv) mtg@mtg-ThinkPad-P53:~/bin/GenESysV$ python utils/load_vcf.py --vcf test_data/test_4families_annovar.vcf.gz --tmp_dir /tmp --annot annovar --hostname 127.0.0.1 --port 9200 --index test_4families_annovar --study_name test_4families_annovar --dataset_name test_4families_annovar --num_cores 4 --assembly hg19 --ped test_data/test_4families.ped --cleanup Pid 25941: processed 5000 variants Pid 25942: processed 5000 variants Pid 25944: processed 5000 variants Pid 25943: processed 5000 variants Pid 25941: processed 10000 variants Pid 25944: processed 10000 variants Pid 25942: processed 10000 variants Pid 25943: processed 10000 variants Pid 25941: processed 12501 variants Process 25941 finished ... Pid 25942: processed 12501 variants Pid 25944: processed 12498 variants Process 25942 finished ... Pid 25943: processed 12501 variants Process 25943 finished ... Process 25944 finished ... Finished parsing vcf file in 11.873375177383423 seconds, now creating ElasticSearch index ... deleting 'test_4families_annovar' index... response: '{'acknowledged': True}' creating 'test_4families_annovar' index... % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 590 100 98 100 492 1689 8482 --:--:-- --:--:-- --:--:-- 10000 % Total % Received % Xferd Average Speed Time Time Time Current Dload Upload Total Spent Left Speed 100 25391 100 28 100 25363 1750 1548k --:--:-- --:--:-- --:--:-- 1549k Response: '{ "acknowledged" : true, "shards_acknowledged" : true, "index" : "test_4families_annovar" } { "acknowledged" : true } ' Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_0.json Took: 3.564603328704834 seconds Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_1.json Took: 3.5286946296691895 seconds Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_2.json Took: 3.4319169521331787 seconds Indexing file /tmp/test_4families_annovar.vcf.gz.chunk_3.json Took: 3.6023032665252686 seconds Finished creating ES index, parsing time: 11.873375177383423 seconds, indexing time: 14.294233560562134 seconds, vcf: test_data/test_4families_annovar.vcf.gz
Creating Web user interface, please wait ... Unmapped GUI CLNVAR_nested Unmapped GUI COSMIC_nested Unmapped GUI GTEx_nested Unmapped GUI ICGC_nested Unmapped GUI RGQ Unmapped GUI mendelian_diseases Unmapped GUI RGQ Unmapped GUI mendelian_diseases
Study Name: test_4families_annovar Dataset Name: test_4families_annovar_hg19 Dataset ES Index Name: test_4families_annovar Dataset ES Type Name: test_4familiesannovar Dataset ES Host: 127.0.0.1 Dataset ES Port: 9200 Traceback (most recent call last): File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 85, in _execute return self.cursor.execute(sql, params) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/sqlite3/base.py", line 303, in execute return Database.Cursor.execute(self, query, params) sqlite3.OperationalError: no such table: main.core_analysistype__old
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "utils/load_vcf.py", line 1715, in
make_gui(es, hostname, port, index_name, study, dataset_name, type_name, gui_mapping) File "/home/mtg/bin/GenESysV/utils/make_gui.py", line 961, in make_gui dataset_obj.analysis_type.add(a) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/fields/related_descriptors.py", line 898, in add self._add_items(self.source_field_name, self.target_field_name, objs) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/fields/related_descriptors.py", line 1065, in _add_items for obj_id in new_ids File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/query.py", line 466, in bulk_create ids = self._batched_insert(objs_without_pk, fields, batch_size) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/query.py", line 1148, in _batched_insert self._insert(item, fields=fields, using=self.db) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/query.py", line 1125, in _insert return query.get_compiler(using=using).execute_sql(return_id) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/models/sql/compiler.py", line 1283, in execute_sql cursor.execute(sql, params) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 100, in execute return super().execute(sql, params) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 68, in execute return self._execute_with_wrappers(sql, params, many=False, executor=self._execute) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 77, in _execute_with_wrappers return executor(sql, params, many, context) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 85, in _execute return self.cursor.execute(sql, params) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/utils.py", line 89, in exit raise dj_exc_value.with_traceback(traceback) from exc_value File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/utils.py", line 85, in _execute return self.cursor.execute(sql, params) File "/home/mtg/bin/genesysv/lib/python3.7/site-packages/django/db/backends/sqlite3/base.py", line 303, in execute return Database.Cursor.execute(self, query, params) django.db.utils.OperationalError: no such table: main.core_analysistype__old Not sure what I'm missing.
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moldach
linnil1
I'm getting an error trying to install/run
genesysv. After following the installation examples the following code is partially working. I'm able to open but something in the error isn't loading the example data in properly.I'm able to open local host and login:
but cannot click on anything (pretty sure the example is the next part).
Trying the example
Not sure what I'm missing.