annotation error in 1.6.9

[calchoo]

MAVIS version: 1.6.9

Python version: 3.6

OS: centos06

A bunch of annotation jobs have died due to this index error:

[2018-02-27 17:46:11.421346] (22 of 38) current annotation ZV7do3tXi5AADpQqgdGwWW-v1-a1 PreTranscript(ENSG00000144642:29322803-30051886, name=ENST00000396583) PreTranscript(ENSG00000144642:29322803-30051886, name=ENST00000396583) duplication
                             drawing attempt: 1 1000px 
[2018-02-27 17:46:11.948482] closing: /projects/trans_scratch/mavis_validation/6_pairing_analysis/POG217/v1.6.9/P00637_normal_genome/annotate/batch-GpJraczAd2efbUpAvToauT-1/annotations.tab
[2018-02-27 17:46:11.951993] closing: /projects/trans_scratch/mavis_validation/6_pairing_analysis/POG217/v1.6.9/P00637_normal_genome/annotate/batch-GpJraczAd2efbUpAvToauT-1/annotations.fusion-cdna.fa
Traceback (most recent call last):
  File "/gsc/pipelines/mavis/v1.6.9/venv/bin/mavis", line 11, in <module>
    load_entry_point('mavis==1.6.9', 'console_scripts', 'mavis')()
  File "/gsc/pipelines/mavis/v1.6.9/venv/lib/python3.6/site-packages/mavis-1.6.9-py3.6.egg/mavis/main.py", line 634, in main
  File "/gsc/pipelines/mavis/v1.6.9/venv/lib/python3.6/site-packages/mavis-1.6.9-py3.6.egg/mavis/annotate/main.py", line 245, in main
  File "/gsc/pipelines/mavis/v1.6.9/venv/lib/python3.6/site-packages/mavis-1.6.9-py3.6.egg/mavis/annotate/main.py", line 51, in draw
  File "/gsc/pipelines/mavis/v1.6.9/venv/lib/python3.6/site-packages/mavis-1.6.9-py3.6.egg/mavis/illustrate/diagram.py", line 292, in draw_sv_summary_diagram
  File "/gsc/pipelines/mavis/v1.6.9/venv/lib/python3.6/site-packages/mavis-1.6.9-py3.6.egg/mavis/illustrate/elements.py", line 395, in draw_ustranscript
  File "/gsc/pipelines/mavis/v1.6.9/venv/lib/python3.6/site-packages/mavis-1.6.9-py3.6.egg/mavis/illustrate/elements.py", line 146, in draw_transcript_with_translation
  File "/gsc/pipelines/mavis/v1.6.9/venv/lib/python3.6/site-packages/mavis-1.6.9-py3.6.egg/mavis/illustrate/elements.py", line 78, in draw_exon_track
  File "/gsc/pipelines/mavis/v1.6.9/venv/lib/python3.6/site-packages/mavis-1.6.9-py3.6.egg/mavis/interval.py", line 353, in convert_ratioed_pos
IndexError: (1, 'is outside mapped range', {Interval(8, 446): Interval(0.0, 45.035099575560835, type=<class 'float'>), Interval(447, 153432): Interval(45.035099575560835, 59.06732425775306, type=<class 'float'>), Interval(153433, 153605): Interval(59.06732425775306, 91.35914951759821, type=<class 'float'>), Interval(153606, 207130): Interval(91.35914951759821, 102.76989838425489, type=<class 'float'>), Interval(207131, 207189): Interval(102.76989838425489, 129.60032036593617, type=<class 'float'>), Interval(207190, 305803): Interval(129.60032036593617, 142.19947195372657, type=<class 'float'>), Interval(305804, 305895): Interval(142.19947195372657, 170.6108264632974, type=<class 'float'>), Interval(305896, 458409): Interval(170.6108264632974, 184.63061072577804, type=<class 'float'>), Interval(458410, 458567): Interval(184.63061072577804, 216.20383029112796, type=<class 'float'>), Interval(458568, 481599): Interval(216.20383029112796, 226.81088060213844, type=<class 'float'>), Interval(481600, 481679): Interval(226.81088060213844, 254.64735055611308, type=<class 'float'>), Interval(481680, 587547): Interval(254.64735055611308, 267.4376945265047, type=<class 'float'>), Interval(587548, 587654): Interval(267.4376945265047, 296.5676547305708, type=<class 'float'>), Interval(587655, 599468): Interval(296.5676547305708, 306.87903421886006, type=<class 'float'>), Interval(599469, 599507): Interval(306.87903421886006, 332.7513152745477, type=<class 'float'>), Interval(599508, 602851): Interval(332.7513152745477, 342.83945248538566, type=<class 'float'>), Interval(602852, 602898): Interval(342.83945248538566, 369.09498991147075, type=<class 'float'>), Interval(602899, 616068): Interval(369.09498991147075, 379.44210924960936, type=<class 'float'>), Interval(616069, 616165): Interval(379.44210924960936, 408.0929989906786, type=<class 'float'>), Interval(616166, 618394): Interval(408.0929989906786, 418.1517483456301, type=<class 'float'>), Interval(618395, 618445): Interval(418.1517483456301, 444.5989139569139, type=<class 'float'>), Interval(618446, 654775): Interval(444.5989139569139, 455.5564572792051, type=<class 'float'>), Interval(654776, 654886): Interval(455.5564572792051, 484.87804566846995, type=<class 'float'>), Interval(654887, 706832): Interval(484.87804566846995, 496.2471771141, type=<class 'float'>), Interval(706833, 706913): Interval(496.2471771141, 524.1315541143742, type=<class 'float'>), Interval(706914, 709771): Interval(524.1315541143742, 534.2068819100007, type=<class 'float'>), Interval(709772, 709899): Interval(534.2068819100007, 564.3428900863601, type=<class 'float'>), Interval(709900, 722545): Interval(564.3428900863601, 574.6761984500731, type=<class 'float'>), Interval(722546, 729085): Interval(574.6761984500731, 911.9921875, type=<class 'float'>)})

An example log is here: /projects/trans_scratch/mavis_validation/6_pairing_analysis/POG217/v1.6.9/P00637_normal_genome/annotate/batch-GpJraczAd2efbUpAvToauT-1/slurm-MA_P00637_batch-GpJraczAd2efbUpAvToauT-1-823770.log

[creisle]

looks like this is happening when there is a duplication in the first exon that makes the exon smaller than the minimum focus size. This is a problem b/c I don't throw the small exons into the mapping so that they don't get mapped too large. I can circumvent this by setting a start/end when I generate the mapping which is already built in functionality and just requires a parameter