search

openvax / pyensembl

Python interface to access reference genome features (such as genes, transcripts, and exons) from Ensembl
Apache License 2.0
365 stars 66 forks source link

$ pyensembl install --species mouse --release 93 error #218

Closed AhmedArslan closed 4 years ago

AhmedArslan commented 5 years ago

Trying to install pyensembl database (mouse) on my ssh server (python3) and need help with the following error:

2019-02-04 11:50:44,821 - datacache.database_helpers - WARNING - Failed to create tables ['start_codon', 'exon', 'gene', 'stop_codon', 'CDS', 'transcript'] in database /home/aarslan/.cache/pyensembl/GRCm38/ensembl93/Mus_musculus.GRCm38.93.gtf.db Traceback (most recent call last): File "/usr/bin/pyensembl", line 11, in load_entry_point('pyensembl==1.7.3', 'console_scripts', 'pyensembl')() File "/usr/lib/python3.4/site-packages/pyensembl/shell.py", line 261, in run genome.index(overwrite=args.overwrite) File "/usr/lib/python3.4/site-packages/pyensembl/genome.py", line 280, in index self.db.connect_or_create(overwrite=overwrite) File "/usr/lib/python3.4/site-packages/pyensembl/database.py", line 293, in connect_or_create return self.create(overwrite=overwrite) File "/usr/lib/python3.4/site-packages/pyensembl/database.py", line 253, in create version=DATABASE_SCHEMA_VERSION) File "/usr/lib/python3.4/site-packages/datacache/database_helpers.py", line 183, in db_from_dataframes_with_absolute_path version=version) File "/usr/lib/python3.4/site-packages/datacache/database_helpers.py", line 102, in _create_cached_db db.create(tables, version) File "/usr/lib/python3.4/site-packages/datacache/database.py", line 183, in create self._fill_table(table.name, table.rows) File "/usr/lib/python3.4/site-packages/datacache/database.py", line 164, in _fill_table self.connection.executemany(sql, rows) sqlite3.OperationalError: disk I/O error

fabianegli commented 4 years ago

From the distance, looking at sqlite3.OperationalError: disk I/O error it looks like there might not be enough disk space available in /home/aarslan/.cache/pyensembl/GRCm38/ensembl93/ where the Mus_musculus.GRCm38.93.gtf.db is written - or there are permission problems, e.g. Backup/Sync processes or "Do not use SQLite with a networked file system." (because sqlite locks dbs - only one process can access it at a time), that can arise from a multitude of sources and would require more information from your side to troubleshoot.

iskandr commented 4 years ago

Agree with @fabianegli -- going to close this issue but will reopen if @AhmedArslan can add more info.