scottdaniel
commented
4 years ago I got a similar error when running creat_local_taxonomy_db.py
What seemed to fix it was installing brocc under python 2.7
Open Sofie8 opened 5 years ago
scottdaniel
commented
4 years ago I got a similar error when running creat_local_taxonomy_db.py
What seemed to fix it was installing brocc under python 2.7
Hello,
I am setting up the local database using create_local_taxonomy_db.py. It created a database of around 5 Gb (5,541,363,712), but I also received an error (below), so not sure if it worked... I have a Tb of space left, and the error says database full? I don't understand the error. Can you suggest me a solution?
2019-04-23 06:05:11 (16.4 MB/s) - “/ddn1/vol1/site_scratch/leuven/314/vsc31426/db/brocc/tmpoykqldgv/taxdump.tar.gz” saved [48094496]
citations.dmp delnodes.dmp division.dmp gencode.dmp merged.dmp names.dmp nodes.dmp gc.prt readme.txt Error: near line 14: database or disk is full Error: near line 15: database or disk is full Traceback (most recent call last): File "create_local_taxonomy_db.py", line 5, in
brocclib.taxonomy_db.main()
File "/vsc-hard-mounts/leuven-data/314/vsc31426/miniconda3/envs/brocc/lib/python3.6/site-packages/brocclib/taxonomy_db.py", line 92, in main
init_db(database_fp, download_dir, accessions, nodes)
File "/vsc-hard-mounts/leuven-data/314/vsc31426/miniconda3/envs/brocc/lib/python3.6/site-packages/brocclib/taxonomy_db.py", line 187, in init_db
subprocess.check_call(["sqlite3", db], stdin=f, cwd=temp_dir)
File "/vsc-hard-mounts/leuven-data/314/vsc31426/miniconda3/envs/brocc/lib/python3.6/subprocess.py", line 291, in check_call
raise CalledProcessError(retcode, cmd)
subprocess.CalledProcessError: Command '['sqlite3', '/ddn1/vol1/site_scratch/leuven/314/vsc31426/db/brocc/.brocc/taxonomy.db']' returned non-zero exit status 1.
Thank you! Sofie