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Turns out the reason behind issue #783 was a VCF file without any headers. This is how that particular VCF file looks like:
$ head -10 $SOMEPATH/work-Mutect-PT189-PT189_6_13-merged.SureSelect.vcf
chr1 69511 rs75062661 A G . REJECT DB GT:AD:BQ:DP:FA 0/1:0,196:33:196:1.00 0:0,75:.:66:1.00
chr1 69557 . C T . REJECT . GT:AD:BQ:DP:FA 0/1:255,3:34:258:0.012 0:92,0:.:92:0.00
chr1 762273 rs3115849 G A . REJECT DB GT:AD:BQ:DP:FA 0/1:209,195:34:404:0.483 0:24,12:.:34:0.333
chr1 762472 rs145493205 C T . REJECT DB GT:AD:BQ:DP:FA 0/1:54,22:32:76:0.289 0:42,13:.:49:0.236
chr1 762485 rs148989274 C A . REJECT DB GT:AD:BQ:DP:FA 0/1:54,15:33:69:0.217 0:40,18:.:50:0.310
chr1 876499 rs4372192 A G . REJECT DB GT:AD:BQ:DP:FA 0/1:0,55:34:55:1.00 0:0,11:.:11:1.00
chr1 877715 rs6605066 C G . REJECT DB GT:AD:BQ:DP:FA 0/1:0,20:31:20:1.00 0:0,4:.:4:1.00
chr1 877831 rs6672356 T C . REJECT DB GT:AD:BQ:DP:FA 0/1:0,23:33:23:1.00 0:0,3:.:3:1.00
chr1 878314 rs142558220 G C . REJECT DB GT:AD:BQ:DP:FA 0/1:134,88:36:222:0.396 0:4,12:.:16:0.750
chr1 880238 rs3748592 A G . REJECT DB GT:AD:BQ:DP:FA 0/1:0,227:36:227:1.00 0:0,15:.:15:1.00
Submitting VCFs without any headers triggers an Internal Server Error, yet the Run is still created. See this example, which was a re-submission of the same VCF file that was causing #783: http://cycledash.demeter.hpc.mssm.edu/runs/352/examine
and the error on the server side is as follows:
[ERROR] 2015-08-28 17:16:32,790 - cycledash
/home/cycledash/cycledash/venv/lib/python2.7/site-packages/flask_restful/__init__.py:299
Internal Error
Traceback (most recent call last):
File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/flask/app.py", line 1475, in full_dispatch_request
rv = self.dispatch_request()
File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/flask/app.py", line 1461, in dispatch_request
return self.view_functions[rule.endpoint](**req.view_args)
File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/flask_restful/__init__.py", line 462, in wrapper
resp = resource(*args, **kwargs)
File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/flask/views.py", line 84, in view
return self.dispatch_request(*args, **kwargs)
File "/home/cycledash/cycledash/cycledash/api/__init__.py", line 37, in dispatch_request
return super(Resource, self).dispatch_request(*args, **kwargs)
File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/flask_restful/__init__.py", line 572, in dispatch_request
resp = meth(*args, **kwargs)
File "/home/cycledash/cycledash/cycledash/api/__init__.py", line 100, in wrapper
return f(*args, **kwargs)
File "/home/cycledash/cycledash/cycledash/api/__init__.py", line 74, in wrapper
content = marshal(resp[0], schema, envelope=envelope)
File "/home/cycledash/cycledash/cycledash/api/__init__.py", line 56, in marshal
items = schema(data)
File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/voluptuous.py", line 333, in __call__
return self._compiled([], data)
File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/voluptuous.py", line 631, in validate_dict
return base_validate(path, iteritems(data), out)
File "/home/cycledash/cycledash/venv/lib/python2.7/site-packages/voluptuous.py", line 467, in validate_mapping
raise MultipleInvalid(errors)
MultipleInvalid: extra keys not allowed @ data['normal']
We should not allow these problematic files to be submitted in the first place.
The text was updated successfully, but these errors were encountered:
Turns out the reason behind issue #783 was a VCF file without any headers. This is how that particular VCF file looks like:
Submitting VCFs without any headers triggers an Internal Server Error, yet the Run is still created. See this example, which was a re-submission of the same VCF file that was causing #783:
http://cycledash.demeter.hpc.mssm.edu/runs/352/examine
and the error on the server side is as follows:
We should not allow these problematic files to be submitted in the first place.
The text was updated successfully, but these errors were encountered: