johnomics
commented
5 years ago Hi Sasha,
Thank you very much for trying Tapestry - I'm sorry you're having difficulties. This is a problem with my database code, not your data. I'm trying to load too many reads at once, and will need to rewrite the code to load reads in batches. Unfortunately I'm away this week and it will take me some time to get this fixed - apologies - but I will get to it soon.
In the meantime, I would try reducing the depth to 10 and/or increasing the read length to 2000 or 5000. Tapestry may complain that you don't have enough coverage but it should still run and produce a report (if it doesn't, let me know). If you include 1000bp reads, you will be including a lot of reads from repeat regions that won't map uniquely, and they often don't tell you very much about the quality of the assembly. So you'll probably learn about the same amount from your report if you throw out these reads and just stick to the longer reads, even if your overall coverage is low.
Thanks John
aleksandrabliznina
Hi John,
Thank you for your tool! I am very excited about using it for my assembly, but always run into this problem:
Processing contigs: 0%| | 0/41 [00:00<?, ? contig/s]multiprocessing.pool.RemoteTraceback: """ Traceback (most recent call last): File "/home/a/aleksandrabliznina/.local/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1244, in _execute_context cursor, statement, parameters, context File "/home/a/aleksandrabliznina/.local/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 550, in do_execute cursor.execute(statement, parameters) sqlite3.OperationalError: too many SQL variables
The above exception was the direct cause of the following exception:
Traceback (most recent call last): File "/apps/unit/LuscombeU/python/3.7.3/lib/python3.7/multiprocessing/pool.py", line 121, in worker result = (True, func(*args, **kwds)) File "/work/.apps/unit/LuscombeU/tapestry/0.9/tapestry/contig.py", line 48, in process_contig contig.process() File "/work/.apps/unit/LuscombeU/tapestry/0.9/tapestry/contig.py", line 138, in process self.left_connectors, self.right_connectors = self.get_connectors() File "/work/.apps/unit/LuscombeU/tapestry/0.9/tapestry/contig.py", line 307, in get_connectors left_connectors = self.get_region_connectors(0, 10000) File "/work/.apps/unit/LuscombeU/tapestry/0.9/tapestry/contig.py", line 282, in get_region_connectors for aln in self.alignments.connectors(self.name, region_start, region_end): File "/work/.apps/unit/LuscombeU/tapestry/0.9/tapestry/alignments.py", line 452, in connectors read_results = self.engine.connect().execute(stmt).fetchall() File "/home/a/aleksandrabliznina/.local/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 988, in execute return meth(self, multiparams, params) File "/home/a/aleksandrabliznina/.local/lib/python3.7/site-packages/sqlalchemy/sql/elements.py", line 287, in _execute_on_connection return connection._execute_clauseelement(self, multiparams, params) File "/home/a/aleksandrabliznina/.local/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1107, in _execute_clauseelement distilled_params, File "/home/a/aleksandrabliznina/.local/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1248, in _execute_context e, statement, parameters, cursor, context File "/home/a/aleksandrabliznina/.local/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1466, in _handle_dbapi_exception util.raise_from_cause(sqlalchemy_exception, exc_info) File "/home/a/aleksandrabliznina/.local/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 383, in raise_from_cause reraise(type(exception), exception, tb=exc_tb, cause=cause) File "/home/a/aleksandrabliznina/.local/lib/python3.7/site-packages/sqlalchemy/util/compat.py", line 128, in reraise raise value.with_traceback(tb) File "/home/a/aleksandrabliznina/.local/lib/python3.7/site-packages/sqlalchemy/engine/base.py", line 1244, in _execute_context cursor, statement, parameters, context File "/home/a/aleksandrabliznina/.local/lib/python3.7/site-packages/sqlalchemy/engine/default.py", line 550, in do_execute cursor.execute(statement, parameters) sqlalchemy.exc.OperationalError: (sqlite3.OperationalError) too many SQL variables [SQL: SELECT alignments.contig, alignments.ref_start, alignments.ref_end FROM alignments WHERE alignments."query" IN (?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?, ?) AND alignments.contig != ? AND (alignments.alntype = ? OR alignments.alntype = ?)]
Please, see the attached file for more details!
slurm-5725678.out.txt
I do not clearly understand the problem. Is something wrong with my data? Genome size is around 65 Mb and I had to significantly reduce the read length (down to 1000) and depth (down to 30) parameters because the majority of my nanopore reads are much shorter.
Thanks! Looking forward to your reply!
Best regards, Sasha