Question: An error while using Interval2MAF1 tool on usegalaxy.org
0
gravatar for sap940
5 weeks ago by
sap9400
sap9400 wrote:

Hey, I constently use the "Extract to MAF blocks" tool (Interval2MAF1 ) via usegalaxy.org. For the past 9 days, for some reason this tool produces a very long error message, and fails to perform the analysis. I have previously used the exact same dataset for this exact same analysis and it did work. Also, I tried to "report this error" via galaxy, but the "report" button would'nt press. The bug I get is written to the bottom of my post.

Does anyone know how can I solve it / how can I report this error ? Or maybe - does anyone know of another galaxy adress that its "Interval2MAF1 " does work? Sapir

The error is too long to be posted fully, so I only post about a half of it:

Dataset Error An error occured while running the tool Interval2Maf1.

Tool execution generated the following messages:

Traceback (most recent call last): File "/cvmfs/main.galaxyproject.org/galaxy/tools/maf/interval2maf.py", line 145, in <module> __main__() File "/cvmfs/main.galaxyproject.org/galaxy/tools/maf/interval2maf.py", line 112, in __main__ for num_regions, region in enumerate(bx.intervals.io.NiceReaderWrapper(open(interval_file, 'r'), chrom_col=chromCol, start_col=startCol, end_col=endCol, strand_col=strandCol, fix_strand=True, return_header=False, return_comments=False)): 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__ 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__ 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__ 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__ 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__ 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__ 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__ 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__ 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",

ADD COMMENTlink modified 5 weeks ago • written 5 weeks ago by sap9400

I have been getting the same error with Stitch MAF Blocks on Galaxy main. However, I am currently using usegalaxy.eu and Stitch MAF Blocks is working for me, so I suspect Interval2MAF1 would work there as well.

ADD REPLYlink written 5 weeks ago by mlwright30
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