l337x911
commented
7 years ago It looks like there aren't any off-target alignments, which is why the error is being thrown. Check the blat parameters to make sure you are getting enough off-target hits.
Or, check out the zero-cross-align branch ( https://github.com/l337x911/AmBre/tree/zero-cross-aligm) . I haven't tested it, but that may solve your problem.
On Tue, Mar 7, 2017 at 4:41 AM, Ilamdri notifications@github.com wrote:
Hello, I tried to run AmBre with the supported example files and afterwards for my own sequences, but I already received an error message for 'workflow.py' which I could not solve by myself after running 'ambre_test':
ilamdri@watson:~$ ambre_test testBlatInstallation (ambre.test.install_unit.TestInstallationValid) ... ok testMultiPlxInstallation (ambre.test.install_unit.TestInstallationValid) ... ok testPrimer3Installation (ambre.test.install_unit.TestInstallationValid) ... ok testTmpDir (ambre.test.install_unit.TestInstallationValid) ... ok test_workflow (ambre.test.design_unit.TestDesignWorkflow) ... [-1.0, -0.1, -0.01, -0.001] [10000.0, 100000.0, 1000000.0] #Stage1 Primer3Time: 0.0000 #Number of Primers after Blat: 0 #Stage2 AlignTime: 0.0001 #Stage2 MultiPlxTime: 0.0044 /home/ilamdri/.local/lib/python2.7/site-packages/AmBre-1.0release-py2.7.egg/ambre/examples/regions_ex/design_ex.align.out /home/ilamdri/.local/lib/python2.7/site-packages/AmBre-1.0release-py2.7.egg/ambre/examples/regions_ex/design_ex.multiplx /home/ilamdri/.local/lib/python2.7/site-packages/AmBre-1.0release-py2.7.egg/ambre/examples/regions_ex/design_ex.multiplx.out ERROR test_workflow (ambre.test.analyze_unit.TestAnalyze) ... #Stage1 Filtering: 0.0000 #Stage2 Clustering: 0.0000 #Stage3 Templating: 0.0063 ok ====================================================================== ERROR: test_workflow (ambre.test.design_unit.TestDesignWorkflow) ---------------------------------------------------------------------- Traceback (most recent call last): File "/home/ilamdri/.local/lib/python2.7/site-packages/AmBre-1.0release-py2.7.egg/ambre/test/design_unit.py", line 68, in test_workflow pamp_t_bs=(10**4,)) File "/home/ilamdri/.local/lib/python2.7/site-packages/AmBre-1.0release-py2.7.egg/ambre/design/workflow.py", line 344, in run self.check_cross_amplification(max_dist=max_cross_amp_dist) File "/home/ilamdri/.local/lib/python2.7/site-packages/AmBre-1.0release-py2.7.egg/ambre/design/workflow.py", line 130, in check_cross_amplification chrs, pos, orient, primer_pos = zip(*alignments) ValueError: need more than 0 values to unpack ---------------------------------------------------------------------- Ran 6 tests in 0.013s FAILED (errors=1)Is there anything I could do to solve this error?
Sincerely, Ilamdri
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Ilamdri
Hello, I tried to run AmBre with the supported example files and afterwards for my own sequences, but I already received an error message for 'workflow.py' which I could not solve by myself after running 'ambre_test':
Is there anything I could do to solve this error?
Sincerely, Ilamdri