Hello! I'm new to start with outrigger. After finishing the installation using conda(and -h working well), i ran with my data:
outrigger index -j SJ.out.tab --ignore-multimapping --gtf GRCh38.p13_genomic.sorted.gff
The issue came out:
INFO:gffutils.create:Populating features
Traceback (most recent call last):t-order relations: 98000 features
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 540, in maybe_make_db
db = gffutils.FeatureDB(db_filename)
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/gffutils/interface.py", line 185, in __init__
version, dialect = c.fetchone()
TypeError: 'NoneType' object is not iterable
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/gffutils/create.py", line 589, in _populate_from_lines
self._insert(f, c)
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/gffutils/create.py", line 530, in _insert
cursor.execute(constants._INSERT, feature.astuple())
sqlite3.IntegrityError: UNIQUE constraint failed: features.id
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/miniconda2/envs/outrigger-env/bin/outrigger", line 10, in <module>
sys.exit(main())
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 1071, in main
cl = CommandLine(sys.argv[1:])
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 344, in __init__
self.args.func()
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 348, in index
index.execute()
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 752, in execute
db = self.maybe_make_db()
_make_db
db = gtf.create_db(self.gtf_filename, db_filename)
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/io/gtf.py", line 60, in create_db
force_merge_fields=['source'])
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/gffutils/create.py", line 1292, in create_db
c.create()
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/gffutils/create.py", line 507, in create
self._populate_from_lines(self.iterator)
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/gffutils/create.py", line 598, in _populate_from_lines
fixed.id))
sqlite3.OperationalError: disk I/O error
and i had another try with the same command:
INFO:gffutils.create:Populating features
Traceback (most recent call last):t-order relations: 98000 features
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 540, in maybe_make_db
db = gffutils.FeatureDB(db_filename)
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/gffutils/interface.py", line 185, in __init__
version, dialect = c.fetchone()
TypeError: 'NoneType' object is not iterable
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/home/miniconda2/envs/outrigger-env/bin/outrigger", line 10, in <module>
sys.exit(main())
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 1071, in main
cl = CommandLine(sys.argv[1:])
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 344, in __init__
self.args.func()
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 348, in index
index.execute()
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 752, in execute
db = self.maybe_make_db()
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/commandline.py", line 548, in maybe_make_db
db = gtf.create_db(self.gtf_filename, db_filename)
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/outrigger/io/gtf.py", line 60, in create_db
force_merge_fields=['source'])
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/gffutils/create.py", line 1292, in create_db
c.create()
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/gffutils/create.py", line 507, in create
self._populate_from_lines(self.iterator)
File "/home/miniconda2/envs/outrigger-env/lib/python3.6/site-packages/gffutils/create.py", line 627, in _populate_from_lines
''', (parent, f.id))
sqlite3.OperationalError: disk I/O error
Although different lines where errors lie, the final error is sqlite3.OperationalError: disk I/O error.
I am not familiar with sqlite3 module. So any idea about this issue?
Thanks a lot for Any help.
Hello! I'm new to start with outrigger. After finishing the installation using conda(and -h working well), i ran with my data:
The issue came out:
and i had another try with the same command:
Although different lines where errors lie, the final error is
sqlite3.OperationalError: disk I/O error.I am not familiar with sqlite3 module. So any idea about this issue?
Thanks a lot for Any help.