Hi,
I am trying to stitch multiple alignments from about 25 species in the 100-way multiZ MAF on usegalaxy.org. I am using an interval file with hg19 coordinates, lifted over from hg38 coordinates. I can successfully extract genomic coordinates with the same data, so I don't know if this is a problem with the input or something internally. I already submitted a bug report, I'm just wondering if I can do anything on my end to resolve it.
The error it returns is really long, but this is the gist of it:
Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/galaxy/tools/maf/interval_maf_to_merged_fasta.py", line 204, in <module> __main__() File "/cvmfs/main.galaxyproject.org/galaxy/tools/maf/interval_maf_to_merged_fasta.py", line 132, in __main__ for line_count, line in region_enumerator: File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/six.py", line 564, in next return type(self).__next__(self) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__ nextitem = GenomicIntervalReader.next( self ) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/six.py", line 564, in next return type(self).__next__(self) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__ nextitem = GenomicIntervalReader.next( self ) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/six.py", line 564, in next return type(self).__next__(self) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__ nextitem = GenomicIntervalReader.next( self ) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/six.py", line 564, in next return type(self).__next__(self) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__ nextitem = GenomicIntervalReader.next( self ) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/six.py", line 564, in next return type(self).__next__(self) File "/cvmfs/main.galaxyproject.org/venv/lib/python2.7/site-packages/bx/intervals/io.py", line 190, in __next__
...
line 190 , in __next__ nextitem = GenomicIntervalReader.next( self ) RuntimeError: maximum recursion depth exceeded while calling a Python object
