How this output was created:
outrigger/commandline.py index --sj-out-tab ~/projects/tasic2016/sj_out_tab/*SJ.out.tab --gtf outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.subset.gtf --output $OUTPUT
Created
April 19, 2017 17:59
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Outrigger index UNIQUE id errors
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| 2017-04-19 10:50:01 Creating folder tasic2016_big_outrigger_output ... | |
| 2017-04-19 10:50:01 Done. | |
| 2017-04-19 10:50:01 Creating folder tasic2016_big_outrigger_output/index ... | |
| 2017-04-19 10:50:01 Done. | |
| 2017-04-19 10:50:01 Creating folder tasic2016_big_outrigger_output/index/gtf ... | |
| 2017-04-19 10:50:01 Done. | |
| 2017-04-19 10:50:01 Creating folder tasic2016_big_outrigger_output/junctions ... | |
| 2017-04-19 10:50:01 Done. | |
| 2017-04-19 10:50:01 Found compiled junction reads file in tasic2016_big_outrigger_output/junctions/reads.csv and reading it in ... | |
| 2017-04-19 10:50:03 Done. | |
| 2017-04-19 10:50:03 Filtering for only junctions with minimum 10 reads ... | |
| 2017-04-19 10:50:03 75379/108342 junctions remain after filtering out 32963 junctions with < 10 reads. | |
| 2017-04-19 10:50:03 Done. | |
| 2017-04-19 10:50:03 Creating splice junction metadata of merely where junctions start and stop | |
| 2017-04-19 10:50:03 Done. | |
| 2017-04-19 10:50:03 Found GTF file in outrigger/tests/data/tasic2016/unprocessed/gtf/gencode.vM10.annotation.subset.gtf | |
| 2017-04-19 10:50:03 Found existing built outrigger-built gffutils database file in tasic2016_big_outrigger_output/index/gtf/gencode.vM10.annotation.subset.gtf.db | |
| 2017-04-19 10:50:03 Looking up which exons are already defined ... | |
| 2017-04-19 10:50:03 Done. | |
| 2017-04-19 10:50:03 Detecting de novo exons based on gaps between junctions ... | |
| 2017-04-19 10:50:04 Finding all exons on chromosome GL456233.1 ... | |
| 2017-04-19 10:50:04 Done. | |
| 2017-04-19 10:50:04 Filtering for only novel exons on chromosome GL456233.1 ... | |
| 2017-04-19 10:50:04 Done. | |
| 2017-04-19 10:50:04 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:04 Done. | |
| 2017-04-19 10:50:04 Updating gffutils database with 4 novel exons on chromosome GL456233.1 ... | |
| 2017-04-19 10:50:04 Done. | |
| 2017-04-19 10:50:04 Finding all exons on chromosome GL456350.1 ... | |
| 2017-04-19 10:50:04 Done. | |
| 2017-04-19 10:50:04 Filtering for only novel exons on chromosome GL456350.1 ... | |
| 2017-04-19 10:50:04 Done. | |
| 2017-04-19 10:50:04 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:04 Done. | |
| 2017-04-19 10:50:04 Updating gffutils database with 1 novel exons on chromosome GL456350.1 ... | |
| 2017-04-19 10:50:05 Done. | |
| 2017-04-19 10:50:05 Finding all exons on chromosome GL456370.1 ... | |
| 2017-04-19 10:50:05 Done. | |
| 2017-04-19 10:50:05 Filtering for only novel exons on chromosome GL456370.1 ... | |
| 2017-04-19 10:50:05 Done. | |
| 2017-04-19 10:50:05 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:05 Done. | |
| 2017-04-19 10:50:05 Updating gffutils database with 0 novel exons on chromosome GL456370.1 ... | |
| 2017-04-19 10:50:05 No novel exons found on chromosome GL456370.1 | |
| 2017-04-19 10:50:05 Done. | |
| 2017-04-19 10:50:05 Finding all exons on chromosome JH584293.1 ... | |
| 2017-04-19 10:50:05 Done. | |
| 2017-04-19 10:50:05 Filtering for only novel exons on chromosome JH584293.1 ... | |
| 2017-04-19 10:50:05 Done. | |
| 2017-04-19 10:50:05 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:05 Done. | |
| 2017-04-19 10:50:05 Updating gffutils database with 3 novel exons on chromosome JH584293.1 ... | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Finding all exons on chromosome JH584294.1 ... | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Filtering for only novel exons on chromosome JH584294.1 ... | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Updating gffutils database with 2 novel exons on chromosome JH584294.1 ... | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Finding all exons on chromosome JH584304.1 ... | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Filtering for only novel exons on chromosome JH584304.1 ... | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Updating gffutils database with 0 novel exons on chromosome JH584304.1 ... | |
| 2017-04-19 10:50:06 No novel exons found on chromosome JH584304.1 | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Finding all exons on chromosome JH792828.1 ... | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Filtering for only novel exons on chromosome JH792828.1 ... | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Updating gffutils database with 0 novel exons on chromosome JH792828.1 ... | |
| 2017-04-19 10:50:06 No novel exons found on chromosome JH792828.1 | |
| 2017-04-19 10:50:06 Done. | |
| 2017-04-19 10:50:06 Finding all exons on chromosome JH792830.1 ... | |
| 2017-04-19 10:50:07 Done. | |
| 2017-04-19 10:50:07 Filtering for only novel exons on chromosome JH792830.1 ... | |
| 2017-04-19 10:50:07 Done. | |
| 2017-04-19 10:50:07 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:07 Done. | |
| 2017-04-19 10:50:07 Updating gffutils database with 1 novel exons on chromosome JH792830.1 ... | |
| 2017-04-19 10:50:07 Done. | |
| 2017-04-19 10:50:07 Finding all exons on chromosome KB469738.1 ... | |
| 2017-04-19 10:50:07 Done. | |
| 2017-04-19 10:50:07 Filtering for only novel exons on chromosome KB469738.1 ... | |
| 2017-04-19 10:50:07 Done. | |
| 2017-04-19 10:50:07 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:07 Done. | |
| 2017-04-19 10:50:07 Updating gffutils database with 2 novel exons on chromosome KB469738.1 ... | |
| 2017-04-19 10:50:07 Done. | |
| 2017-04-19 10:50:07 Finding all exons on chromosome KB469740.1 ... | |
| 2017-04-19 10:50:08 Done. | |
| 2017-04-19 10:50:08 Filtering for only novel exons on chromosome KB469740.1 ... | |
| 2017-04-19 10:50:08 Done. | |
| 2017-04-19 10:50:08 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:08 Done. | |
| 2017-04-19 10:50:08 Updating gffutils database with 3 novel exons on chromosome KB469740.1 ... | |
| 2017-04-19 10:50:08 Done. | |
| 2017-04-19 10:50:08 Finding all exons on chromosome KB469741.1 ... | |
| 2017-04-19 10:50:08 Done. | |
| 2017-04-19 10:50:08 Filtering for only novel exons on chromosome KB469741.1 ... | |
| 2017-04-19 10:50:08 Done. | |
| 2017-04-19 10:50:08 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:08 Done. | |
| 2017-04-19 10:50:08 Updating gffutils database with 1 novel exons on chromosome KB469741.1 ... | |
| 2017-04-19 10:50:09 Done. | |
| 2017-04-19 10:50:09 Finding all exons on chromosome chr1 ... | |
| 2017-04-19 10:50:38 Done. | |
| 2017-04-19 10:50:38 Filtering for only novel exons on chromosome chr1 ... | |
| 2017-04-19 10:50:38 Done. | |
| 2017-04-19 10:50:38 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:39 Done. | |
| 2017-04-19 10:50:39 Updating gffutils database with 1277 novel exons on chromosome chr1 ... | |
| 2017-04-19 10:50:41 Done. | |
| 2017-04-19 10:50:41 Finding all exons on chromosome chr10 ... | |
| 2017-04-19 10:50:54 Done. | |
| 2017-04-19 10:50:54 Filtering for only novel exons on chromosome chr10 ... | |
| 2017-04-19 10:50:54 Done. | |
| 2017-04-19 10:50:54 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:50:54 Done. | |
| 2017-04-19 10:50:54 Updating gffutils database with 1000 novel exons on chromosome chr10 ... | |
| 2017-04-19 10:50:56 Done. | |
| 2017-04-19 10:50:56 Finding all exons on chromosome chr11 ... | |
| 2017-04-19 10:51:45 Done. | |
| 2017-04-19 10:51:45 Filtering for only novel exons on chromosome chr11 ... | |
| 2017-04-19 10:51:45 Done. | |
| 2017-04-19 10:51:45 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:51:46 Done. | |
| 2017-04-19 10:51:46 Updating gffutils database with 1663 novel exons on chromosome chr11 ... | |
| 2017-04-19 10:51:49 Done. | |
| 2017-04-19 10:51:50 Finding all exons on chromosome chr12 ... | |
| 2017-04-19 10:52:01 Done. | |
| 2017-04-19 10:52:01 Filtering for only novel exons on chromosome chr12 ... | |
| 2017-04-19 10:52:01 Done. | |
| 2017-04-19 10:52:01 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:52:02 Done. | |
| 2017-04-19 10:52:02 Updating gffutils database with 1026 novel exons on chromosome chr12 ... | |
| 2017-04-19 10:52:04 Done. | |
| 2017-04-19 10:52:04 Finding all exons on chromosome chr13 ... | |
| 2017-04-19 10:52:11 Done. | |
| 2017-04-19 10:52:11 Filtering for only novel exons on chromosome chr13 ... | |
| 2017-04-19 10:52:11 Done. | |
| 2017-04-19 10:52:11 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:52:12 Done. | |
| 2017-04-19 10:52:12 Updating gffutils database with 860 novel exons on chromosome chr13 ... | |
| 2017-04-19 10:52:14 Done. | |
| 2017-04-19 10:52:14 Finding all exons on chromosome chr14 ... | |
| 2017-04-19 10:52:20 Done. | |
| 2017-04-19 10:52:20 Filtering for only novel exons on chromosome chr14 ... | |
| 2017-04-19 10:52:20 Done. | |
| 2017-04-19 10:52:20 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:52:21 Done. | |
| 2017-04-19 10:52:21 Updating gffutils database with 848 novel exons on chromosome chr14 ... | |
| 2017-04-19 10:52:22 Done. | |
| 2017-04-19 10:52:22 Finding all exons on chromosome chr15 ... | |
| 2017-04-19 10:52:30 Done. | |
| 2017-04-19 10:52:30 Filtering for only novel exons on chromosome chr15 ... | |
| 2017-04-19 10:52:30 Done. | |
| 2017-04-19 10:52:30 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:52:30 Done. | |
| 2017-04-19 10:52:30 Updating gffutils database with 794 novel exons on chromosome chr15 ... | |
| 2017-04-19 10:52:30 Done. | |
| 2017-04-19 10:52:30 Finding all exons on chromosome chr16 ... | |
| 2017-04-19 10:52:37 Done. | |
| 2017-04-19 10:52:37 Filtering for only novel exons on chromosome chr16 ... | |
| 2017-04-19 10:52:37 Done. | |
| 2017-04-19 10:52:37 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:52:37 Done. | |
| 2017-04-19 10:52:37 Updating gffutils database with 784 novel exons on chromosome chr16 ... | |
| 2017-04-19 10:52:38 Done. | |
| 2017-04-19 10:52:38 Finding all exons on chromosome chr17 ... | |
| 2017-04-19 10:52:50 Done. | |
| 2017-04-19 10:52:50 Filtering for only novel exons on chromosome chr17 ... | |
| 2017-04-19 10:52:50 Done. | |
| 2017-04-19 10:52:50 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:52:50 Done. | |
| 2017-04-19 10:52:50 Updating gffutils database with 934 novel exons on chromosome chr17 ... | |
| 2017-04-19 10:52:51 Done. | |
| 2017-04-19 10:52:51 Finding all exons on chromosome chr18 ... | |
| 2017-04-19 10:52:53 Done. | |
| 2017-04-19 10:52:53 Filtering for only novel exons on chromosome chr18 ... | |
| 2017-04-19 10:52:53 Done. | |
| 2017-04-19 10:52:53 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:52:53 Done. | |
| 2017-04-19 10:52:53 Updating gffutils database with 657 novel exons on chromosome chr18 ... | |
| 2017-04-19 10:52:54 Done. | |
| 2017-04-19 10:52:54 Finding all exons on chromosome chr19 ... | |
| 2017-04-19 10:52:58 Done. | |
| 2017-04-19 10:52:58 Filtering for only novel exons on chromosome chr19 ... | |
| 2017-04-19 10:52:58 Done. | |
| 2017-04-19 10:52:58 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:52:58 Done. | |
| 2017-04-19 10:52:58 Updating gffutils database with 660 novel exons on chromosome chr19 ... | |
| 2017-04-19 10:52:59 Done. | |
| 2017-04-19 10:52:59 Finding all exons on chromosome chr2 ... | |
| 2017-04-19 10:53:58 Done. | |
| 2017-04-19 10:53:58 Filtering for only novel exons on chromosome chr2 ... | |
| 2017-04-19 10:53:58 Done. | |
| 2017-04-19 10:53:58 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:53:58 Done. | |
| 2017-04-19 10:53:58 Updating gffutils database with 1903 novel exons on chromosome chr2 ... | |
| 2017-04-19 10:53:59 Done. | |
| 2017-04-19 10:53:59 Finding all exons on chromosome chr3 ... | |
| 2017-04-19 10:54:12 Done. | |
| 2017-04-19 10:54:12 Filtering for only novel exons on chromosome chr3 ... | |
| 2017-04-19 10:54:12 Done. | |
| 2017-04-19 10:54:12 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:54:12 Done. | |
| 2017-04-19 10:54:12 Updating gffutils database with 980 novel exons on chromosome chr3 ... | |
| 2017-04-19 10:54:13 Done. | |
| 2017-04-19 10:54:13 Finding all exons on chromosome chr4 ... | |
| 2017-04-19 10:54:31 Done. | |
| 2017-04-19 10:54:31 Filtering for only novel exons on chromosome chr4 ... | |
| 2017-04-19 10:54:31 Done. | |
| 2017-04-19 10:54:31 Creating gffutils.Feature objects for each novel exon, plus potentially its overlapping gene | |
| 2017-04-19 10:54:31 Done. | |
| 2017-04-19 10:54:31 Updating gffutils database with 1300 novel exons on chromosome chr4 ... | |
| Traceback (most recent call last): | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py", line 991, in _update_relations | |
| self._insert(f, c) | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py", line 520, 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 "/Users/olga/anaconda3/envs/outrigger/bin/outrigger", line 9, in <module> | |
| load_entry_point('outrigger', 'console_scripts', 'outrigger')() | |
| File "/Users/olga/workspace-git/outrigger/outrigger/commandline.py", line 1071, in main | |
| cl = CommandLine(sys.argv[1:]) | |
| File "/Users/olga/workspace-git/outrigger/outrigger/commandline.py", line 344, in __init__ | |
| self.args.func() | |
| File "/Users/olga/workspace-git/outrigger/outrigger/commandline.py", line 348, in index | |
| index.execute() | |
| File "/Users/olga/workspace-git/outrigger/outrigger/commandline.py", line 755, in execute | |
| metadata, db) | |
| File "/Users/olga/workspace-git/outrigger/outrigger/commandline.py", line 619, in make_exon_junction_adjacencies | |
| exon_junction_adjacencies.detect_exons_from_junctions() | |
| File "/Users/olga/workspace-git/outrigger/outrigger/index/adjacencies.py", line 221, in detect_exons_from_junctions | |
| transform=transform) | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/interface.py", line 853, in update | |
| db._update_relations() | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py", line 993, in _update_relations | |
| fixed, final_strategy = self._do_merge(f, 'merge') | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py", line 288, in _do_merge | |
| self._add_duplicate(orig_id, uniqued_feature.id) | |
| File "/Users/olga/anaconda3/envs/outrigger/lib/python3.5/site-packages/gffutils/create.py", line 360, in _add_duplicate | |
| (idspecid, newid)) | |
| sqlite3.IntegrityError: UNIQUE constraint failed: duplicates.newid |
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