The node 55019216 is not in the graph. #57
Comments
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Although it has been working like a charm for preparing multiplex primers for amplifying regions more than 500 bp, I encountered the error mentioned above recently when running it for specifically a set of 15 defined variants in the regions file for amplification of 150bp products. |
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@Vickymj93 Did you use the latest version of the NGS-PrimerPlex? 150 bp was not problem for the program. There may be other issues... |
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As I see in your issue description, line numbers do not correspond to the latest version. Please, try download the latest one, and try it again. Please, give me feedback about the result. |
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Facing the same error with a new line number when I tried to run it with the updated NGS-Primerplex1.3.4 Joining primer pairs to amplified blocks... During handling of the above exception, another exception occurred: Traceback (most recent call last): The above exception was the direct cause of the following exception: Traceback (most recent call last): |
Great program. Thank you very much. I have also recently run into this problem. I don't see why amplicon length would matter but mine was aimed at 160. It still comes up with a list of draft primers after checking for specificity but seems to have problems when attempting to assemble different pools. Log below if it helps.Traceback (most recent call last): During handling of the above exception, another exception occurred: Traceback (most recent call last): The above exception was the direct cause of the following exception: Traceback (most recent call last): |
Joining primer pairs to amplified blocks...
0.0%multiprocessing.pool.RemoteTraceback:
"""
Traceback (most recent call last):
File "/usr/local/lib/python3.5/dist-packages/networkx/classes/graph.py", line 1082, in neighbors_iter
return iter(self.adj[n])
KeyError: 55019216
During handling of the above exception, another exception occurred:
Traceback (most recent call last):
File "/usr/lib/python3.5/multiprocessing/pool.py", line 119, in worker
result = (True, func(*args, **kwds))
File "NGS_primerplex.py", line 1892, in joinAmpliconsToBlocks
path=tuple(nx.algorithms.shortest_paths.generic.shortest_path(blockGraph,firstNodes[i],lastNodes[i]))
File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/generic.py", line 136, in shortest_path
paths=nx.bidirectional_shortest_path(G,source,target)
File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/unweighted.py", line 136, in bidirectional_shortest_path
results=_bidirectional_pred_succ(G,source,target)
File "/usr/local/lib/python3.5/dist-packages/networkx/algorithms/shortest_paths/unweighted.py", line 186, in _bidirectional_pred_succ
for w in Gsucc(v):
File "/usr/local/lib/python3.5/dist-packages/networkx/classes/graph.py", line 1084, in neighbors_iter
raise NetworkXError("The node %s is not in the graph." % (n,))
networkx.exception.NetworkXError: The node 55019216 is not in the graph.
"""
The above exception was the direct cause of the following exception:
Traceback (most recent call last):
File "NGS_primerplex.py", line 3378, in
poolArgs):#results:
File "/usr/lib/python3.5/multiprocessing/pool.py", line 695, in next
raise value
networkx.exception.NetworkXError: The node 55019216 is not in the graph.
I have been facing a similar error, to the one which user @avialee was facing, when trying to run for a handful of SNVs (10-15). Trying to design short ampicons of size ~150bp. Any help would be appreciated.
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