Question: Error when trying to stitch MAF blocks
0
gravatar for mlwright
4 months ago by
mlwright30
mlwright30 wrote:

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

alignment software error • 226 views
ADD COMMENTlink modified 4 months ago by Jennifer Hillman Jackson25k • written 4 months ago by mlwright30
1
gravatar for Jennifer Hillman Jackson
4 months ago by
United States
Jennifer Hillman Jackson25k wrote:

Hello,

There are some known problems with these tools at Galaxy Main https://usegalaxy.org right now. Ticket with details: https://github.com/galaxyproject/usegalaxy-playbook/issues/130

I am not sure if other Galaxy servers are presenting the problem or not, so you could try this at https://usegalaxy.eu instead to test that out. Please feel free to comment with your test case at the Github ticket above. I'll also ask the developers about it again, our updates will post back to the same ticket.

Thanks for reporting the problem! Jen, Galaxy team

ADD COMMENTlink written 4 months ago by Jennifer Hillman Jackson25k

It seemed like Stitch MAF Blocks had been working fine for the past several weeks, but I am experiencing this issue again. Same "maximum recursion depth exceeded" error in Stitch MAF Blocks. I submitted a bug report for it about a week ago, but wanted to bring it to your attention again.

ADD REPLYlink written 9 weeks ago by mlwright30
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