Outrigger index dying

outrigger index --sj-out-tab ../ep-cj-n2-ndiff-hs_S1_R1_001.polyATrim.adapterTrim.rmRep.bamSJ.out.tab --gtf /projeyeolab/genomes/hg19/gencode_v19/gencode.v19.annotation.gtf
2017-04-13 16:51:57     Creating folder ./outrigger_output ...
2017-04-13 16:51:57             Done.
2017-04-13 16:51:57     Creating folder ./outrigger_output/index ...
2017-04-13 16:51:57             Done.
2017-04-13 16:51:57     Creating folder ./outrigger_output/index/gtf ...
2017-04-13 16:51:57             Done.
2017-04-13 16:51:57     Creating folder ./outrigger_output/junctions ...
2017-04-13 16:51:57             Done.
2017-04-13 16:51:57     Found compiled junction reads file in ./outrigger_output/junctions/reads.csv and reading it in ...
2017-04-13 16:51:58             Done.
2017-04-13 16:51:58     Filtering for only junctions with minimum 10 reads ...
2017-04-13 16:52:06             126971/250927 junctions remain after filtering out 123956 junctions with < 10 reads.
2017-04-13 16:52:06             Done.
2017-04-13 16:52:06     Creating splice junction metadata of merely where junctions start and stop
2017-04-13 16:52:06             Done.
2017-04-13 16:52:06     Found GTF file in /projects/ps-yeolab/genomes/hg19/gencode_v19/gencode.v19.annotation.gtf
2017-04-13 16:52:07     Found existing built outrigger-built gffutils database file in ./outrigger_output/index/gtf/gencode.v19.annotation.gtf.db
2017-04-13 16:52:08             Looking up which exons are already defined ...
2017-04-13 16:52:12                     Done.
2017-04-13 16:52:12     Detecting de novo exons based on gaps between junctions ...
2017-04-13 16:52:13             Finding all exons on chromosome chr1 ...
2017-04-13 17:17:39                     Done.
2017-04-13 17:17:39                     Filtering for only novel exons on chromosome chr1 ...
2017-04-13 17:17:39                             Done.
2017-04-13 17:17:39                     Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene
2017-04-13 17:27:00                             Done.
2017-04-13 17:27:00                     Updating gffutils database with 71 novel exons on chromosome chr1 ...
Traceback (most recent call last):
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/gffutils/create.py", line 981, in _update_relations
    self._insert(f, c)
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/gffutils/create.py", line 510, 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 "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/bin/outrigger", line 11, in <module>
    sys.exit(main())
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/outrigger/commandline.py", line 1072, in main
    cl = CommandLine(sys.argv[1:])
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/outrigger/commandline.py", line 344, in __init__
    self.args.func()
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/outrigger/commandline.py", line 348, in index
    index.execute()
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/outrigger/commandline.py", line 755, in execute
    metadata, db)
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/outrigger/commandline.py", line 619, in make_exon_junction_adjacencies
    exon_junction_adjacencies.detect_exons_from_junctions()
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/outrigger/index/adjacencies.py", line 221, in detect_exons_from_junctions
    transform=transform)
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/gffutils/interface.py", line 827, in update
    db._update_relations()
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/gffutils/create.py", line 983, in _update_relations
    fixed, final_strategy = self._do_merge(f, 'merge')
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/gffutils/create.py", line 288, in _do_merge
    self._add_duplicate(orig_id, uniqued_feature.id)
  File "/projects/ps-yeolab/software/eclipconda/envs/outrigger-1.0.0/lib/python3.5/site-packages/gffutils/create.py", line 360, in _add_duplicate
    (idspecid, newid))
sqlite3.IntegrityError: UNIQUE constraint failed: duplicates.newid