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CONVERTER_interval_to_bed_0 is crashing with latest bx-python version #6379

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bgruening opened this issue Jun 22, 2018 · 6 comments
Closed

CONVERTER_interval_to_bed_0 is crashing with latest bx-python version #6379

bgruening opened this issue Jun 22, 2018 · 6 comments

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@bgruening
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It seems that the bx-python version 0.8.x is crashing this tool (and others). Downgrading it to 0.7.3 solves it for usegalaxy.eu. UseGalaxy.org is still affected.

pip install --extra-index-url http://wheels.galaxyproject.org/ bx-python==0.7.3 -U

ping @natefoo @Slugger70

Tool ID	CONVERTER_interval_to_bed_0
Tool Version	1.0.0
Job PID or DRM id	5022819
Job Tool Version	


      Job Execution and Failure Information


        Command Line

python '/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_bed_converter.py' '/data/dnb01/galaxy_db/files/006/982/dataset_6982801.dat' '/data/dnb01/galaxy_db/files/006/982/dataset_6982694.dat' 1 2 3 0 0


        stderr

Traceback (most recent call last):
   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_bed_converter.py", line 65, in <module>
     __main__()
   File "/usr/local/galaxy/galaxy-dist/lib/galaxy/datatypes/converters/interval_to_bed_converter.py", line 44, in __main__
     for count, region in enumerate(bx.intervals.io.NiceReaderWrapper(fh, chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False)):
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/i
..

     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/six.py", line 564, in next
     return type(self).__next__(self)
   File "/usr/local/galaxy/galaxy-dist/.venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
     nextitem = GenomicIntervalReader.next( self )
RuntimeError: maximum recursion depth exceeded while calling a Python object


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@natefoo
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natefoo commented Jun 25, 2018

I've just downgraded it for usegalaxy.org as well.

@nsoranzo
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The bx-python bug has been fixed in bxlab/bx-python#35 , we now need a new bx-python release and bioconda package, and update the requirement in the affected Galaxy tools.

Similar issue in different tool has been reported in #6598 .

@nsoranzo
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nsoranzo commented Aug 24, 2018 •
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Update: we now have a new 0.8.2 release of bx-python on GitHub, PyPI and bioconda, but both CONVERTER_interval_to_bed_0 and Interval2Maf1 tools use it from the Galaxy virtualenv, so we also need new Starforge wheels and to update lib/galaxy/dependencies/pinned-requirements.txt .

@jennaj
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jennaj commented Aug 28, 2018

Would be good to get this on the public servers. Org is failing for certain datatypes when CONVERTER_interval_to_bed_0 is used (bedgraph datatype is specifically set). Right now, users need to use autodetect, which sets the datatype as bed (?? odd), then change the datatype to bedgraph and reset the columns so "name" is assigned to column 4. Bit of a long winded solution for what ideally would be automatic.

There are probably other cases like that one and the tool bug above.

@jennaj
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jennaj commented Aug 30, 2018

Another workaround for end users:

The Concatenate function, when given interval inputs, is impacted by this bug.

Workaround: Try reassigning the datatypes of both inputs to the tabular datatype (direct assignment) then use Concatenate. You can reassign the interval datatype to the result. FAQ: https://galaxyproject.org/support/metadata/

@jennaj
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jennaj commented Aug 30, 2018

And another:

The Convert Genomic Intervals To BED function is impacted by this bug.

Workaround: Use the Cut function to rearrange the columns of your interval dataset to be a match for the bed datatype. You can then directly assign the BED datatype to the result. FAQs: https://galaxyproject.org/support/metadata/ && https://galaxyproject.org/learn/datatypes/#bed

nsoranzo added a commit to nsoranzo/galaxy that referenced this issue Sep 5, 2018
@nsoranzo
Update bx-python to 0.8.2
85cab90 
to include bxlab/bx-python#35 .

Fix galaxyproject#6379 and galaxyproject#6598 .
@nsoranzo nsoranzo mentioned this issue Sep 5, 2018
Merged
jmchilton pushed a commit that referenced this issue Sep 5, 2018
@nsoranzo @jmchilton
Update bx-python to 0.8.2
d645d80 
to include bxlab/bx-python#35 .

Fix #6379 and #6598 .
@jennaj jennaj mentioned this issue Sep 6, 2018
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@natefoo @bgruening @nsoranzo @jennaj