I've use both sj.out.tab and bam from STAR along with their GTF files. My bam is sorted and indexed also.
Still only junctions files are only created with 0 kb gtf.db file and program is ending abruptly with following error.
2017-11-23 13:57:40 Done.
2017-11-23 13:57:40 Filtering for only junctions with minimum 10 reads ...
2017-11-23 13:57:41 28883/75449 junctions remain after filtering out 46566 junctions with < 10 reads.
2017-11-23 13:57:41 Done.
2017-11-23 13:57:41 Creating splice junction metadata of merely where junctions start and stop
2017-11-23 13:57:41 Done.
2017-11-23 13:57:41 Writing metadata of junctions to ./outrigger_output/junctions/metadata.csv ...
2017-11-23 13:57:42 Found GTF file in IVYsorted.gtf
2017-11-23 13:57:42 Creating a "gffutils" database ./outrigger_output/index/gtf/IVYsorted.gtf.db ...
Traceback (most recent call last):
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 540, in maybe_make_db
db = gffutils.FeatureDB(db_filename)
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/gffutils/interface.py", line 111, in init
raise ValueError("Database file %s does not exist" % dbfn)
ValueError: Database file ./outrigger_output/index/gtf/IVYsorted.gtf.db does not exist
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/root/miniconda3/envs/outrigger-env/bin/outrigger", line 6, in
sys.exit(outrigger.commandline.main())
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 1071, in main
cl = CommandLine(sys.argv[1:])
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 344, in init
self.args.func()
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 348, in index
index.execute()
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 752, in execute
db = self.maybe_make_db()
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 548, in maybe_make_db
db = gtf.create_db(self.gtf_filename, db_filename)
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/io/gtf.py", line 60, in create_db
force_merge_fields=['source'])
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/gffutils/create.py", line 1293, in create_db
c.create()
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/gffutils/create.py", line 508, in create
self._init_tables()
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/gffutils/create.py", line 440, in _init_tables
self.set_pragmas(self.pragmas)
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/gffutils/create.py", line 426, in set_pragmas
c.execute('PRAGMA journal_mode=wal')
sqlite3.OperationalError: database is locked
Description
I've use both sj.out.tab and bam from STAR along with their GTF files. My bam is sorted and indexed also. Still only junctions files are only created with 0 kb gtf.db file and program is ending abruptly with following error.
Expected behavior: [What you expected to happen]
Create gtf.db in outrigger_output=>gtf folder
Actual behavior: [What actually happened] (outrigger-env) root@MSM:/media/neuro/proteoGenomics/STAR_test# outrigger index -b Aligned.out.bam -g IVYsorted.gtf 2017-11-23 12:55:08 Creating folder ./outrigger_output ... 2017-11-23 12:55:08 Done. 2017-11-23 12:55:08 Creating folder ./outrigger_output/index ... 2017-11-23 12:55:08 Done. 2017-11-23 12:55:08 Creating folder ./outrigger_output/index/gtf ... 2017-11-23 12:55:08 Done. 2017-11-23 12:55:08 Creating folder ./outrigger_output/junctions ... 2017-11-23 12:55:08 Done. 2017-11-23 12:55:08 Reading bam files and creating a big splice junction table of reads spanning exon-exon junctions 2017-11-23 13:57:38 Writing ./outrigger_output/junctions/reads.csv ...
2017-11-23 13:57:40 Done. 2017-11-23 13:57:40 Filtering for only junctions with minimum 10 reads ... 2017-11-23 13:57:41 28883/75449 junctions remain after filtering out 46566 junctions with < 10 reads. 2017-11-23 13:57:41 Done. 2017-11-23 13:57:41 Creating splice junction metadata of merely where junctions start and stop 2017-11-23 13:57:41 Done. 2017-11-23 13:57:41 Writing metadata of junctions to ./outrigger_output/junctions/metadata.csv ... 2017-11-23 13:57:42 Found GTF file in IVYsorted.gtf 2017-11-23 13:57:42 Creating a "gffutils" database ./outrigger_output/index/gtf/IVYsorted.gtf.db ... Traceback (most recent call last): File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 540, in maybe_make_db db = gffutils.FeatureDB(db_filename) File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/gffutils/interface.py", line 111, in init raise ValueError("Database file %s does not exist" % dbfn) ValueError: Database file ./outrigger_output/index/gtf/IVYsorted.gtf.db does not exist
During handling of the above exception, another exception occurred:
Traceback (most recent call last): File "/root/miniconda3/envs/outrigger-env/bin/outrigger", line 6, in
sys.exit(outrigger.commandline.main())
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 1071, in main
cl = CommandLine(sys.argv[1:])
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 344, in init
self.args.func()
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 348, in index
index.execute()
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 752, in execute
db = self.maybe_make_db()
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/commandline.py", line 548, in maybe_make_db
db = gtf.create_db(self.gtf_filename, db_filename)
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/outrigger/io/gtf.py", line 60, in create_db
force_merge_fields=['source'])
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/gffutils/create.py", line 1293, in create_db
c.create()
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/gffutils/create.py", line 508, in create
self._init_tables()
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/gffutils/create.py", line 440, in _init_tables
self.set_pragmas(self.pragmas)
File "/root/miniconda3/envs/outrigger-env/lib/python3.5/site-packages/gffutils/create.py", line 426, in set_pragmas
c.execute('PRAGMA journal_mode=wal')
sqlite3.OperationalError: database is locked
Versions
outrigger 1.1.1